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View Code? Open in Web Editor NEWc++ library for representing and interacting the gated cytometry data structure
License: GNU Affero General Public License v3.0
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shelnutt2 zbjornson matthieurouland jacobpwagner user123123123123123 dillonhammill mattjtodd k-motwani almahmoud davidroadcytolib's Issues
Installation error on Ubuntu 16.04
Describe the bug
This may be related to a comment someone left in #41. I'm installing cytolib on Ubuntu 16.04 for Travis testing and I get the following traceback happens when I run Rscript -e 'BiocManager::install("cytolib", lib=Sys.getenv("R_LIBS_USER"))'. I get very similar tracebacks when I install a library (ex. FlowSOM) that has a cytolib dependency:
Bioconductor version 3.12 (BiocManager 1.30.10), R 4.0.3 (2020-10-10)
Installing package(s) 'BiocVersion', 'cytolib'
also installing the dependencies ‘RcppParallel’, ‘RProtoBufLib’, ‘Rcpp’, ‘BH’, ‘Rhdf5lib’, ‘RcppArmadillo’
trying URL 'https://cloud.r-project.org/src/contrib/RcppParallel_5.0.2.tar.gz'
Content type 'application/x-gzip' length 1341240 bytes (1.3 MB)
==================================================
downloaded 1.3 MB
trying URL 'https://bioconductor.org/packages/3.12/bioc/src/contrib/RProtoBufLib_2.2.0.tar.gz'
Content type 'application/x-gzip' length 2534325 bytes (2.4 MB)
==================================================
downloaded 2.4 MB
trying URL 'https://cloud.r-project.org/src/contrib/Rcpp_1.0.6.tar.gz'
Content type 'application/x-gzip' length 2952876 bytes (2.8 MB)
==================================================
downloaded 2.8 MB
trying URL 'https://cloud.r-project.org/src/contrib/BH_1.75.0-0.tar.gz'
Content type 'application/x-gzip' length 12801696 bytes (12.2 MB)
==================================================
downloaded 12.2 MB
trying URL 'https://bioconductor.org/packages/3.12/bioc/src/contrib/Rhdf5lib_1.12.0.tar.gz'
Content type 'application/x-gzip' length 14440702 bytes (13.8 MB)
==================================================
downloaded 13.8 MB
trying URL 'https://cloud.r-project.org/src/contrib/RcppArmadillo_0.10.1.2.2.tar.gz'
Content type 'application/x-gzip' length 1647570 bytes (1.6 MB)
==================================================
downloaded 1.6 MB
trying URL 'https://bioconductor.org/packages/3.12/bioc/src/contrib/BiocVersion_3.12.0.tar.gz'
Content type 'application/x-gzip' length 981 bytes
==================================================
downloaded 981 bytes
trying URL 'https://bioconductor.org/packages/3.12/bioc/src/contrib/cytolib_2.2.0.tar.gz'
Content type 'application/x-gzip' length 7916389 bytes (7.5 MB)
==================================================
downloaded 7.5 MB
* installing *source* package ‘RcppParallel’ ...
** package ‘RcppParallel’ successfully unpacked and MD5 sums checked
** using staged installation
** preparing to configure package 'RcppParallel' ...
*** configured file: 'src/Makevars.in' => 'src/Makevars'
** finished configure for package 'RcppParallel'
** libs
Created ../build/lib_release directory
../../build/Makefile.tbb:32: CONFIG: cfg=release arch=intel64 compiler=gcc target=linux runtime=cc5.4.0_libc2.23_kernel4.15.0
g++ -std=gnu++11 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o RcppParallel.so init.o options.o -L/usr/lib/R/lib -lR
installing to /home/travis/R/x86_64-pc-linux-gnu-library/4.0/00LOCK-RcppParallel/00new/RcppParallel/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (RcppParallel)
* installing *source* package ‘RProtoBufLib’ ...
** using staged installation
checking for gcc... gcc -std=gnu99
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc -std=gnu99 accepts -g... yes
checking for gcc -std=gnu99 option to accept ISO C89... none needed
checking whether we are using the GNU C++ compiler... yes
checking whether g++ -std=gnu++11 accepts -g... yes
untarring protobuf ...
building protobuf...
checking whether to enable maintainer-specific portions of Makefiles... yes
checking build system type... x86_64-pc-linux-gnu
checking host system type... x86_64-pc-linux-gnu
checking target system type... x86_64-pc-linux-gnu
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /bin/mkdir -p
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking whether make supports nested variables... yes
checking whether UID '2000' is supported by ustar format... yes
checking whether GID '2000' is supported by ustar format... yes
checking how to create a ustar tar archive... gnutar
checking whether make supports nested variables... (cached) yes
checking for gcc... gcc -std=gnu99
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc -std=gnu99 accepts -g... yes
checking for gcc -std=gnu99 option to accept ISO C89... none needed
checking whether gcc -std=gnu99 understands -c and -o together... yes
checking for style of include used by make... GNU
checking dependency style of gcc -std=gnu99... gcc3
checking whether we are using the GNU C++ compiler... yes
checking whether g++ -std=gnu++11 accepts -g... yes
checking dependency style of g++ -std=gnu++11... gcc3
checking how to run the C preprocessor... gcc -std=gnu99 -E
checking for gcc... gcc
checking whether we are using the GNU C compiler... (cached) yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... (cached) none needed
checking whether gcc understands -c and -o together... (cached) yes
checking dependency style of gcc... (cached) gcc3
checking how to run the C preprocessor... gcc -E
checking how to run the C++ preprocessor... g++ -std=gnu++11 -E
checking for g++... g++
checking whether we are using the GNU C++ compiler... (cached) yes
checking whether g++ accepts -g... yes
checking dependency style of g++... (cached) gcc3
checking how to run the C++ preprocessor... g++ -E
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking minix/config.h usability... no
checking minix/config.h presence... no
checking for minix/config.h... no
checking whether it is safe to define __EXTENSIONS__... yes
checking for ar... ar
checking the archiver (ar) interface... ar
checking for gcc... gcc
checking whether we are using the GNU Objective C compiler... no
checking whether gcc accepts -g... no
checking dependency style of gcc... gcc3
checking C++ compiler flags...... use user-supplied: -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g
checking whether __SUNPRO_CC is declared... no
checking how to print strings... printf
checking for a sed that does not truncate output... /bin/sed
checking for fgrep... /bin/grep -F
checking for ld used by gcc -std=gnu99... /usr/bin/ld
checking if the linker (/usr/bin/ld) is GNU ld... yes
checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B
checking the name lister (/usr/bin/nm -B) interface... BSD nm
checking whether ln -s works... yes
checking the maximum length of command line arguments... 1572864
checking how to convert x86_64-pc-linux-gnu file names to x86_64-pc-linux-gnu format... func_convert_file_noop
checking how to convert x86_64-pc-linux-gnu file names to toolchain format... func_convert_file_noop
checking for /usr/bin/ld option to reload object files... -r
checking for objdump... objdump
checking how to recognize dependent libraries... pass_all
checking for dlltool... no
checking how to associate runtime and link libraries... printf %s\n
checking for archiver @FILE support... @
checking for strip... strip
checking for ranlib... ranlib
checking command to parse /usr/bin/nm -B output from gcc -std=gnu99 object... ok
checking for sysroot... no
checking for a working dd... /bin/dd
checking how to truncate binary pipes... /bin/dd bs=4096 count=1
checking for mt... mt
checking if mt is a manifest tool... no
checking for dlfcn.h... yes
checking for objdir... .libs
checking if gcc -std=gnu99 supports -fno-rtti -fno-exceptions... no
checking for gcc -std=gnu99 option to produce PIC... -fPIC -DPIC
checking if gcc -std=gnu99 PIC flag -fPIC -DPIC works... yes
checking if gcc -std=gnu99 static flag -static works... yes
checking if gcc -std=gnu99 supports -c -o file.o... yes
checking if gcc -std=gnu99 supports -c -o file.o... (cached) yes
checking whether the gcc -std=gnu99 linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes
checking whether -lc should be explicitly linked in... no
checking dynamic linker characteristics... GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking whether stripping libraries is possible... yes
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... yes
checking whether to build static libraries... no
checking how to run the C++ preprocessor... g++ -std=gnu++11 -E
checking for ld used by g++ -std=gnu++11... /usr/bin/ld -m elf_x86_64
checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld... yes
checking whether the g++ -std=gnu++11 linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes
checking for g++ -std=gnu++11 option to produce PIC... -fPIC -DPIC
checking if g++ -std=gnu++11 PIC flag -fPIC -DPIC works... yes
checking if g++ -std=gnu++11 static flag -static works... yes
checking if g++ -std=gnu++11 supports -c -o file.o... yes
checking if g++ -std=gnu++11 supports -c -o file.o... (cached) yes
checking whether the g++ -std=gnu++11 linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes
checking dynamic linker characteristics... (cached) GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking whether the linker supports version scripts... yes
checking for ANSI C header files... (cached) yes
checking fcntl.h usability... yes
checking fcntl.h presence... yes
checking for fcntl.h... yes
checking for inttypes.h... (cached) yes
checking limits.h usability... yes
checking limits.h presence... yes
checking for limits.h... yes
checking for stdlib.h... (cached) yes
checking for unistd.h... (cached) yes
checking for working memcmp... yes
checking for working strtod... yes
checking for ftruncate... yes
checking for memset... yes
checking for mkdir... yes
checking for strchr... yes
checking for strerror... yes
checking for strtol... yes
checking zlib version... ok (1.2.0.4 or later)
checking for library containing zlibVersion... -lz
checking whether g++ -std=gnu++11 supports C++11 features by default... yes
checking whether -latomic is needed... no
checking whether gcc -std=gnu99 is Clang... no
checking whether pthreads work with -pthread... yes
checking for joinable pthread attribute... PTHREAD_CREATE_JOINABLE
checking whether more special flags are required for pthreads... no
checking for PTHREAD_PRIO_INHERIT... yes
checking the location of hash_map... <unordered_map>
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating Makefile
config.status: creating src/Makefile
config.status: creating protobuf-lite.pc
config.status: creating config.h
config.status: executing depfiles commands
config.status: executing libtool commands
=== configuring in third_party/googletest (/tmp/Rtmp4QGP59/R.INSTALL1f6214d5d536/RProtoBufLib/src/protobuf-3.10.0/third_party/googletest)
configure: WARNING: no configuration information is in third_party/googletest
Making install in .
make[1]: Entering directory '/tmp/Rtmp4QGP59/R.INSTALL1f6214d5d536/RProtoBufLib/src/protobuf-3.10.0'
make[2]: Entering directory '/tmp/Rtmp4QGP59/R.INSTALL1f6214d5d536/RProtoBufLib/src/protobuf-3.10.0'
make[2]: Nothing to be done for 'install-exec-am'.
/bin/mkdir -p '/tmp/Rtmp4QGP59/R.INSTALL1f6214d5d536/RProtoBufLib/src/pb_build/lib/pkgconfig'
/usr/bin/install -c -m 644 protobuf-lite.pc '/tmp/Rtmp4QGP59/R.INSTALL1f6214d5d536/RProtoBufLib/src/pb_build/lib/pkgconfig'
make[2]: Leaving directory '/tmp/Rtmp4QGP59/R.INSTALL1f6214d5d536/RProtoBufLib/src/protobuf-3.10.0'
make[1]: Leaving directory '/tmp/Rtmp4QGP59/R.INSTALL1f6214d5d536/RProtoBufLib/src/protobuf-3.10.0'
Making install in src
make[1]: Entering directory '/tmp/Rtmp4QGP59/R.INSTALL1f6214d5d536/RProtoBufLib/src/protobuf-3.10.0/src'
CXX google/protobuf/stubs/bytestream.lo
CXX google/protobuf/stubs/common.lo
CXX google/protobuf/stubs/int128.lo
CXX google/protobuf/io/io_win32.lo
CXX google/protobuf/stubs/status.lo
CXX google/protobuf/stubs/statusor.lo
CXX google/protobuf/stubs/stringpiece.lo
CXX google/protobuf/stubs/stringprintf.lo
CXX google/protobuf/stubs/structurally_valid.lo
CXX google/protobuf/stubs/strutil.lo
CXX google/protobuf/stubs/time.lo
CXX google/protobuf/any_lite.lo
CXX google/protobuf/arena.lo
CXX google/protobuf/extension_set.lo
CXX google/protobuf/generated_enum_util.lo
CXX google/protobuf/generated_message_util.lo
CXX google/protobuf/generated_message_table_driven_lite.lo
CXX google/protobuf/implicit_weak_message.lo
CXX google/protobuf/message_lite.lo
CXX google/protobuf/parse_context.lo
CXX google/protobuf/repeated_field.lo
CXX google/protobuf/wire_format_lite.lo
CXX google/protobuf/io/coded_stream.lo
CXX google/protobuf/io/strtod.lo
CXX google/protobuf/io/zero_copy_stream.lo
CXX google/protobuf/io/zero_copy_stream_impl.lo
CXX google/protobuf/io/zero_copy_stream_impl_lite.lo
CXXLD libprotobuf-lite.la
make[2]: Entering directory '/tmp/Rtmp4QGP59/R.INSTALL1f6214d5d536/RProtoBufLib/src/protobuf-3.10.0/src'
/bin/mkdir -p '/tmp/Rtmp4QGP59/R.INSTALL1f6214d5d536/RProtoBufLib/src/pb_build/lib'
/bin/bash ../libtool --mode=install /usr/bin/install -c libprotobuf-lite.la '/tmp/Rtmp4QGP59/R.INSTALL1f6214d5d536/RProtoBufLib/src/pb_build/lib'
libtool: install: /usr/bin/install -c .libs/libprotobuf-lite.so.21.0.0 /tmp/Rtmp4QGP59/R.INSTALL1f6214d5d536/RProtoBufLib/src/pb_build/lib/libprotobuf-lite.so.21.0.0
libtool: install: (cd /tmp/Rtmp4QGP59/R.INSTALL1f6214d5d536/RProtoBufLib/src/pb_build/lib && { ln -s -f libprotobuf-lite.so.21.0.0 libprotobuf-lite.so.21 || { rm -f libprotobuf-lite.so.21 && ln -s libprotobuf-lite.so.21.0.0 libprotobuf-lite.so.21; }; })
libtool: install: (cd /tmp/Rtmp4QGP59/R.INSTALL1f6214d5d536/RProtoBufLib/src/pb_build/lib && { ln -s -f libprotobuf-lite.so.21.0.0 libprotobuf-lite.so || { rm -f libprotobuf-lite.so && ln -s libprotobuf-lite.so.21.0.0 libprotobuf-lite.so; }; })
libtool: install: /usr/bin/install -c .libs/libprotobuf-lite.lai /tmp/Rtmp4QGP59/R.INSTALL1f6214d5d536/RProtoBufLib/src/pb_build/lib/libprotobuf-lite.la
libtool: finish: PATH="/home/travis/.rvm/gems/ruby-2.5.3/bin:/home/travis/.rvm/gems/ruby-2.5.3@global/bin:/home/travis/.rvm/rubies/ruby-2.5.3/bin:/home/travis/.rvm/bin:/home/travis/virtualenv/python3.6.7/bin:/home/travis/bin:/home/travis/.local/bin:/usr/local/lib/jvm/openjdk11/bin:/opt/pyenv/shims:/home/travis/.phpenv/shims:/home/travis/perl5/perlbrew/bin:/home/travis/.nvm/versions/node/v8.12.0/bin:/home/travis/gopath/bin:/home/travis/.gimme/versions/go1.11.1.linux.amd64/bin:/usr/local/maven-3.6.3/bin:/usr/local/cmake-3.12.4/bin:/usr/local/clang-7.0.0/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/snap/bin:/home/travis/.phpenv/bin:/opt/pyenv/bin:/home/travis/.yarn/bin:/sbin" ldconfig -n /tmp/Rtmp4QGP59/R.INSTALL1f6214d5d536/RProtoBufLib/src/pb_build/lib
----------------------------------------------------------------------
Libraries have been installed in:
/tmp/Rtmp4QGP59/R.INSTALL1f6214d5d536/RProtoBufLib/src/pb_build/lib
If you ever happen to want to link against installed libraries
in a given directory, LIBDIR, you must either use libtool, and
specify the full pathname of the library, or use the '-LLIBDIR'
flag during linking and do at least one of the following:
- add LIBDIR to the 'LD_LIBRARY_PATH' environment variable
during execution
- add LIBDIR to the 'LD_RUN_PATH' environment variable
during linking
- use the '-Wl,-rpath -Wl,LIBDIR' linker flag
- have your system administrator add LIBDIR to '/etc/ld.so.conf'
See any operating system documentation about shared libraries for
more information, such as the ld(1) and ld.so(8) manual pages.
----------------------------------------------------------------------
/bin/mkdir -p '/tmp/Rtmp4QGP59/R.INSTALL1f6214d5d536/RProtoBufLib/src/pb_build/include'
/bin/mkdir -p '/tmp/Rtmp4QGP59/R.INSTALL1f6214d5d536/RProtoBufLib/src/pb_build/include/google/protobuf'
/usr/bin/install -c -m 644 google/protobuf/descriptor.proto google/protobuf/any.proto google/protobuf/api.proto google/protobuf/duration.proto google/protobuf/empty.proto google/protobuf/field_mask.proto google/protobuf/source_context.proto google/protobuf/struct.proto google/protobuf/timestamp.proto google/protobuf/type.proto google/protobuf/wrappers.proto '/tmp/Rtmp4QGP59/R.INSTALL1f6214d5d536/RProtoBufLib/src/pb_build/include/google/protobuf'
/bin/mkdir -p '/tmp/Rtmp4QGP59/R.INSTALL1f6214d5d536/RProtoBufLib/src/pb_build/include/google/protobuf/compiler'
/usr/bin/install -c -m 644 google/protobuf/compiler/plugin.proto '/tmp/Rtmp4QGP59/R.INSTALL1f6214d5d536/RProtoBufLib/src/pb_build/include/google/protobuf/compiler'
/bin/mkdir -p '/tmp/Rtmp4QGP59/R.INSTALL1f6214d5d536/RProtoBufLib/src/pb_build/include'
/bin/mkdir -p '/tmp/Rtmp4QGP59/R.INSTALL1f6214d5d536/RProtoBufLib/src/pb_build/include/google/protobuf'
/usr/bin/install -c -m 644 google/protobuf/any.pb.h google/protobuf/api.pb.h google/protobuf/any.h google/protobuf/arena.h google/protobuf/arena_impl.h google/protobuf/arenastring.h google/protobuf/descriptor_database.h google/protobuf/descriptor.h google/protobuf/descriptor.pb.h google/protobuf/duration.pb.h google/protobuf/dynamic_message.h google/protobuf/empty.pb.h google/protobuf/extension_set.h google/protobuf/extension_set_inl.h google/protobuf/field_mask.pb.h google/protobuf/generated_enum_reflection.h google/protobuf/generated_enum_util.h google/protobuf/generated_message_reflection.h google/protobuf/generated_message_table_driven.h google/protobuf/generated_message_util.h google/protobuf/has_bits.h google/protobuf/implicit_weak_message.h google/protobuf/inlined_string_field.h google/protobuf/map_entry.h google/protobuf/map_entry_lite.h google/protobuf/map_field.h google/protobuf/map_field_inl.h google/protobuf/map_field_lite.h google/protobuf/map.h google/protobuf/map_type_handler.h google/protobuf/message.h google/protobuf/message_lite.h google/protobuf/metadata.h google/protobuf/metadata_lite.h google/protobuf/parse_context.h google/protobuf/port.h google/protobuf/port_def.inc google/protobuf/port_undef.inc google/protobuf/reflection.h google/protobuf/reflection_ops.h '/tmp/Rtmp4QGP59/R.INSTALL1f6214d5d536/RProtoBufLib/src/pb_build/include/google/protobuf'
/bin/mkdir -p '/tmp/Rtmp4QGP59/R.INSTALL1f6214d5d536/RProtoBufLib/src/pb_build/include/google/protobuf/compiler/java'
/usr/bin/install -c -m 644 google/protobuf/compiler/java/java_generator.h google/protobuf/compiler/java/java_names.h '/tmp/Rtmp4QGP59/R.INSTALL1f6214d5d536/RProtoBufLib/src/pb_build/include/google/protobuf/compiler/java'
/bin/mkdir -p '/tmp/Rtmp4QGP59/R.INSTALL1f6214d5d536/RProtoBufLib/src/pb_build/include/google/protobuf/compiler/cpp'
/usr/bin/install -c -m 644 google/protobuf/compiler/cpp/cpp_generator.h '/tmp/Rtmp4QGP59/R.INSTALL1f6214d5d536/RProtoBufLib/src/pb_build/include/google/protobuf/compiler/cpp'
/bin/mkdir -p '/tmp/Rtmp4QGP59/R.INSTALL1f6214d5d536/RProtoBufLib/src/pb_build/include/google/protobuf/compiler/python'
/usr/bin/install -c -m 644 google/protobuf/compiler/python/python_generator.h '/tmp/Rtmp4QGP59/R.INSTALL1f6214d5d536/RProtoBufLib/src/pb_build/include/google/protobuf/compiler/python'
/bin/mkdir -p '/tmp/Rtmp4QGP59/R.INSTALL1f6214d5d536/RProtoBufLib/src/pb_build/include/google/protobuf/compiler/js'
/usr/bin/install -c -m 644 google/protobuf/compiler/js/js_generator.h google/protobuf/compiler/js/well_known_types_embed.h '/tmp/Rtmp4QGP59/R.INSTALL1f6214d5d536/RProtoBufLib/src/pb_build/include/google/protobuf/compiler/js'
/bin/mkdir -p '/tmp/Rtmp4QGP59/R.INSTALL1f6214d5d536/RProtoBufLib/src/pb_build/include/google/protobuf'
/usr/bin/install -c -m 644 google/protobuf/repeated_field.h google/protobuf/service.h google/protobuf/source_context.pb.h google/protobuf/struct.pb.h google/protobuf/text_format.h google/protobuf/timestamp.pb.h google/protobuf/type.pb.h google/protobuf/unknown_field_set.h google/protobuf/wire_format.h google/protobuf/wire_format_lite.h google/protobuf/wrappers.pb.h '/tmp/Rtmp4QGP59/R.INSTALL1f6214d5d536/RProtoBufLib/src/pb_build/include/google/protobuf'
/bin/mkdir -p '/tmp/Rtmp4QGP59/R.INSTALL1f6214d5d536/RProtoBufLib/src/pb_build/include/google/protobuf/stubs'
/usr/bin/install -c -m 644 google/protobuf/stubs/callback.h google/protobuf/stubs/bytestream.h google/protobuf/stubs/casts.h google/protobuf/stubs/common.h google/protobuf/stubs/fastmem.h google/protobuf/stubs/hash.h google/protobuf/stubs/logging.h google/protobuf/stubs/macros.h google/protobuf/stubs/map_util.h google/protobuf/stubs/mutex.h google/protobuf/stubs/once.h google/protobuf/stubs/platform_macros.h google/protobuf/stubs/port.h google/protobuf/stubs/status.h google/protobuf/stubs/stl_util.h google/protobuf/stubs/stringpiece.h google/protobuf/stubs/strutil.h google/protobuf/stubs/template_util.h '/tmp/Rtmp4QGP59/R.INSTALL1f6214d5d536/RProtoBufLib/src/pb_build/include/google/protobuf/stubs'
/bin/mkdir -p '/tmp/Rtmp4QGP59/R.INSTALL1f6214d5d536/RProtoBufLib/src/pb_build/include/google/protobuf/util'
/usr/bin/install -c -m 644 google/protobuf/util/type_resolver.h google/protobuf/util/delimited_message_util.h google/protobuf/util/field_comparator.h google/protobuf/util/field_mask_util.h google/protobuf/util/json_util.h google/protobuf/util/time_util.h google/protobuf/util/type_resolver_util.h google/protobuf/util/message_differencer.h '/tmp/Rtmp4QGP59/R.INSTALL1f6214d5d536/RProtoBufLib/src/pb_build/include/google/protobuf/util'
/bin/mkdir -p '/tmp/Rtmp4QGP59/R.INSTALL1f6214d5d536/RProtoBufLib/src/pb_build/include/google/protobuf/compiler/php'
/usr/bin/install -c -m 644 google/protobuf/compiler/php/php_generator.h '/tmp/Rtmp4QGP59/R.INSTALL1f6214d5d536/RProtoBufLib/src/pb_build/include/google/protobuf/compiler/php'
/bin/mkdir -p '/tmp/Rtmp4QGP59/R.INSTALL1f6214d5d536/RProtoBufLib/src/pb_build/include/google/protobuf/compiler'
/usr/bin/install -c -m 644 google/protobuf/compiler/code_generator.h google/protobuf/compiler/command_line_interface.h google/protobuf/compiler/importer.h google/protobuf/compiler/parser.h google/protobuf/compiler/plugin.h google/protobuf/compiler/plugin.pb.h '/tmp/Rtmp4QGP59/R.INSTALL1f6214d5d536/RProtoBufLib/src/pb_build/include/google/protobuf/compiler'
/bin/mkdir -p '/tmp/Rtmp4QGP59/R.INSTALL1f6214d5d536/RProtoBufLib/src/pb_build/include/google/protobuf/compiler/ruby'
/usr/bin/install -c -m 644 google/protobuf/compiler/ruby/ruby_generator.h '/tmp/Rtmp4QGP59/R.INSTALL1f6214d5d536/RProtoBufLib/src/pb_build/include/google/protobuf/compiler/ruby'
/bin/mkdir -p '/tmp/Rtmp4QGP59/R.INSTALL1f6214d5d536/RProtoBufLib/src/pb_build/include/google/protobuf/io'
/usr/bin/install -c -m 644 google/protobuf/io/io_win32.h google/protobuf/io/coded_stream.h google/protobuf/io/gzip_stream.h google/protobuf/io/printer.h google/protobuf/io/strtod.h google/protobuf/io/tokenizer.h google/protobuf/io/zero_copy_stream.h google/protobuf/io/zero_copy_stream_impl.h google/protobuf/io/zero_copy_stream_impl_lite.h '/tmp/Rtmp4QGP59/R.INSTALL1f6214d5d536/RProtoBufLib/src/pb_build/include/google/protobuf/io'
/bin/mkdir -p '/tmp/Rtmp4QGP59/R.INSTALL1f6214d5d536/RProtoBufLib/src/pb_build/include/google/protobuf/compiler/csharp'
/usr/bin/install -c -m 644 google/protobuf/compiler/csharp/csharp_generator.h google/protobuf/compiler/csharp/csharp_names.h '/tmp/Rtmp4QGP59/R.INSTALL1f6214d5d536/RProtoBufLib/src/pb_build/include/google/protobuf/compiler/csharp'
/bin/mkdir -p '/tmp/Rtmp4QGP59/R.INSTALL1f6214d5d536/RProtoBufLib/src/pb_build/include/google/protobuf/compiler/objectivec'
/usr/bin/install -c -m 644 google/protobuf/compiler/objectivec/objectivec_generator.h google/protobuf/compiler/objectivec/objectivec_helpers.h '/tmp/Rtmp4QGP59/R.INSTALL1f6214d5d536/RProtoBufLib/src/pb_build/include/google/protobuf/compiler/objectivec'
make[2]: Leaving directory '/tmp/Rtmp4QGP59/R.INSTALL1f6214d5d536/RProtoBufLib/src/protobuf-3.10.0/src'
make[1]: Leaving directory '/tmp/Rtmp4QGP59/R.INSTALL1f6214d5d536/RProtoBufLib/src/protobuf-3.10.0/src'
configure: creating ./config.status
config.status: creating src/Makevars
** libs
mkdir -p "/home/travis/R/x86_64-pc-linux-gnu-library/4.0/00LOCK-RProtoBufLib/00new/RProtoBufLib/include"
cp -r /tmp/Rtmp4QGP59/R.INSTALL1f6214d5d536/RProtoBufLib/src/pb_build/include/google /home/travis/R/x86_64-pc-linux-gnu-library/4.0/00LOCK-RProtoBufLib/00new/RProtoBufLib/include
mkdir -p "/home/travis/R/x86_64-pc-linux-gnu-library/4.0/00LOCK-RProtoBufLib/00new/RProtoBufLib/lib/"
cp /tmp/Rtmp4QGP59/R.INSTALL1f6214d5d536/RProtoBufLib/src/pb_build/lib/libprotobuf* /home/travis/R/x86_64-pc-linux-gnu-library/4.0/00LOCK-RProtoBufLib/00new/RProtoBufLib/lib/
g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I../inst/include/ -I/tmp/Rtmp4QGP59/R.INSTALL1f6214d5d536/RProtoBufLib/src/pb_build/include/ -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c dummy.cpp -o dummy.o
g++ -std=gnu++11 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o RProtoBufLib.so dummy.o -L/usr/lib/R/lib -lR
installing to /home/travis/R/x86_64-pc-linux-gnu-library/4.0/00LOCK-RProtoBufLib/00new/RProtoBufLib/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (RProtoBufLib)
* installing *source* package ‘Rcpp’ ...
** package ‘Rcpp’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I../inst/include/ -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c api.cpp -o api.o
g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I../inst/include/ -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c attributes.cpp -o attributes.o
g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I../inst/include/ -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c barrier.cpp -o barrier.o
g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I../inst/include/ -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c date.cpp -o date.o
g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I../inst/include/ -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c module.cpp -o module.o
g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I../inst/include/ -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c rcpp_init.cpp -o rcpp_init.o
g++ -std=gnu++11 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o Rcpp.so api.o attributes.o barrier.o date.o module.o rcpp_init.o -L/usr/lib/R/lib -lR
installing to /home/travis/R/x86_64-pc-linux-gnu-library/4.0/00LOCK-Rcpp/00new/Rcpp/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (Rcpp)
* installing *source* package ‘BH’ ...
** package ‘BH’ successfully unpacked and MD5 sums checked
** using staged installation
** inst
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (BH)
* installing *source* package ‘Rhdf5lib’ ...
** using staged installation
checking for gcc... gcc -std=gnu99
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
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checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc -std=gnu99 accepts -g... yes
checking for gcc -std=gnu99 option to accept ISO C89... none needed
checking whether we are using the GNU C++ compiler... yes
checking whether g++ -std=gnu++11 accepts -g... yes
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checking how to run the C++ preprocessor... g++ -std=gnu++11 -E
checking for grep that handles long lines and -e... /bin/grep
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S3_VFD=--enable-ros3-vfd
untarring hdf5small_cxx_hl_1.10.6.tar.gz ...
building the szip library...
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checking for config linux-gnu... found
compiler 'gcc -std=gnu99' is GNU gcc-5.4.0
checking for gcc... gcc -std=gnu99
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
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checking whether gcc -std=gnu99 accepts -g... yes
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checking whether gcc -std=gnu99 understands -c and -o together... yes
checking for style of include used by make... GNU
checking dependency style of gcc -std=gnu99... gcc3
checking how to run the C preprocessor... gcc -std=gnu99 -E
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checking whether ln -s works... yes
checking the maximum length of command line arguments... 1572864
checking how to convert x86_64-unknown-linux-gnu file names to x86_64-unknown-linux-gnu format... func_convert_file_noop
checking how to convert x86_64-unknown-linux-gnu file names to toolchain format... func_convert_file_noop
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checking if gcc -std=gnu99 supports -fno-rtti -fno-exceptions... yes
checking for gcc -std=gnu99 option to produce PIC... -fPIC -DPIC
checking if gcc -std=gnu99 PIC flag -fPIC -DPIC works... yes
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checking if gcc -std=gnu99 supports -c -o file.o... (cached) yes
checking whether the gcc -std=gnu99 linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes
checking dynamic linker characteristics... GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
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checking for build mode... production
checking for math library support... no
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checking fcntl.h presence... yes
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checking for stdlib.h... (cached) yes
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checking if encoding enabled... yes
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating Makefile
config.status: creating src/Makefile
config.status: creating src/SZconfig.h
config.status: executing depfiles commands
config.status: executing libtool commands
Making all in src
make[1]: Entering directory '/tmp/RtmpWuOEky/R.INSTALL30797331353d/Rhdf5lib/src/hdf5/szip/src'
make all-am
make[2]: Entering directory '/tmp/RtmpWuOEky/R.INSTALL30797331353d/Rhdf5lib/src/hdf5/szip/src'
/bin/bash ../libtool --tag=CC --mode=compile gcc -std=gnu99 -DHAVE_CONFIG_H -I. -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -w -fpic -ansi -pedantic -Wall -W -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wcast-qual -Wcast-align -Wwrite-strings -Wconversion -Wsign-compare -Waggregate-return -Wstrict-prototypes -Wmissing-prototypes -Wmissing-declarations -Wredundant-decls -Wnested-externs -Winline -O -fomit-frame-pointer -finline-functions -MT rice.lo -MD -MP -MF .deps/rice.Tpo -c -o rice.lo rice.c
libtool: compile: gcc -std=gnu99 -DHAVE_CONFIG_H -I. -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -w -fpic -ansi -pedantic -Wall -W -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wcast-qual -Wcast-align -Wwrite-strings -Wconversion -Wsign-compare -Waggregate-return -Wstrict-prototypes -Wmissing-prototypes -Wmissing-declarations -Wredundant-decls -Wnested-externs -Winline -O -fomit-frame-pointer -finline-functions -MT rice.lo -MD -MP -MF .deps/rice.Tpo -c rice.c -fPIC -DPIC -o rice.o
mv -f .deps/rice.Tpo .deps/rice.Plo
/bin/bash ../libtool --tag=CC --mode=compile gcc -std=gnu99 -DHAVE_CONFIG_H -I. -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -w -fpic -ansi -pedantic -Wall -W -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wcast-qual -Wcast-align -Wwrite-strings -Wconversion -Wsign-compare -Waggregate-return -Wstrict-prototypes -Wmissing-prototypes -Wmissing-declarations -Wredundant-decls -Wnested-externs -Winline -O -fomit-frame-pointer -finline-functions -MT sz_api.lo -MD -MP -MF .deps/sz_api.Tpo -c -o sz_api.lo sz_api.c
libtool: compile: gcc -std=gnu99 -DHAVE_CONFIG_H -I. -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -w -fpic -ansi -pedantic -Wall -W -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wcast-qual -Wcast-align -Wwrite-strings -Wconversion -Wsign-compare -Waggregate-return -Wstrict-prototypes -Wmissing-prototypes -Wmissing-declarations -Wredundant-decls -Wnested-externs -Winline -O -fomit-frame-pointer -finline-functions -MT sz_api.lo -MD -MP -MF .deps/sz_api.Tpo -c sz_api.c -fPIC -DPIC -o sz_api.o
mv -f .deps/sz_api.Tpo .deps/sz_api.Plo
/bin/bash ../libtool --tag=CC --mode=compile gcc -std=gnu99 -DHAVE_CONFIG_H -I. -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -w -fpic -ansi -pedantic -Wall -W -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wcast-qual -Wcast-align -Wwrite-strings -Wconversion -Wsign-compare -Waggregate-return -Wstrict-prototypes -Wmissing-prototypes -Wmissing-declarations -Wredundant-decls -Wnested-externs -Winline -O -fomit-frame-pointer -finline-functions -MT encoding.lo -MD -MP -MF .deps/encoding.Tpo -c -o encoding.lo encoding.c
libtool: compile: gcc -std=gnu99 -DHAVE_CONFIG_H -I. -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -w -fpic -ansi -pedantic -Wall -W -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wcast-qual -Wcast-align -Wwrite-strings -Wconversion -Wsign-compare -Waggregate-return -Wstrict-prototypes -Wmissing-prototypes -Wmissing-declarations -Wredundant-decls -Wnested-externs -Winline -O -fomit-frame-pointer -finline-functions -MT encoding.lo -MD -MP -MF .deps/encoding.Tpo -c encoding.c -fPIC -DPIC -o encoding.o
mv -f .deps/encoding.Tpo .deps/encoding.Plo
/bin/bash ../libtool --tag=CC --mode=link gcc -std=gnu99 -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -w -fpic -ansi -pedantic -Wall -W -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wcast-qual -Wcast-align -Wwrite-strings -Wconversion -Wsign-compare -Waggregate-return -Wstrict-prototypes -Wmissing-prototypes -Wmissing-declarations -Wredundant-decls -Wnested-externs -Winline -O -fomit-frame-pointer -finline-functions -version-info 2:0:0 -o libsz.la -rpath /tmp/RtmpWuOEky/R.INSTALL30797331353d/Rhdf5lib/src/hdf5/szip/szip/lib rice.lo sz_api.lo encoding.lo -lm
libtool: link: ar cru .libs/libsz.a rice.o sz_api.o encoding.o
ar: `u' modifier ignored since `D' is the default (see `U')
libtool: link: ranlib .libs/libsz.a
libtool: link: ( cd ".libs" && rm -f "libsz.la" && ln -s "../libsz.la" "libsz.la" )
make[2]: Leaving directory '/tmp/RtmpWuOEky/R.INSTALL30797331353d/Rhdf5lib/src/hdf5/szip/src'
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make[1]: Entering directory '/tmp/RtmpWuOEky/R.INSTALL30797331353d/Rhdf5lib/src/hdf5/szip'
make[1]: Nothing to be done for 'all-am'.
make[1]: Leaving directory '/tmp/RtmpWuOEky/R.INSTALL30797331353d/Rhdf5lib/src/hdf5/szip'
Making install in src
make[1]: Entering directory '/tmp/RtmpWuOEky/R.INSTALL30797331353d/Rhdf5lib/src/hdf5/szip/src'
make[2]: Entering directory '/tmp/RtmpWuOEky/R.INSTALL30797331353d/Rhdf5lib/src/hdf5/szip/src'
/bin/mkdir -p '/tmp/RtmpWuOEky/R.INSTALL30797331353d/Rhdf5lib/src/hdf5/szip/szip/lib'
/bin/bash ../libtool --mode=install /usr/bin/install -c libsz.la '/tmp/RtmpWuOEky/R.INSTALL30797331353d/Rhdf5lib/src/hdf5/szip/szip/lib'
libtool: install: /usr/bin/install -c .libs/libsz.lai /tmp/RtmpWuOEky/R.INSTALL30797331353d/Rhdf5lib/src/hdf5/szip/szip/lib/libsz.la
libtool: install: /usr/bin/install -c .libs/libsz.a /tmp/RtmpWuOEky/R.INSTALL30797331353d/Rhdf5lib/src/hdf5/szip/szip/lib/libsz.a
libtool: install: chmod 644 /tmp/RtmpWuOEky/R.INSTALL30797331353d/Rhdf5lib/src/hdf5/szip/szip/lib/libsz.a
libtool: install: ranlib /tmp/RtmpWuOEky/R.INSTALL30797331353d/Rhdf5lib/src/hdf5/szip/szip/lib/libsz.a
libtool: finish: PATH="/home/travis/.rvm/gems/ruby-2.5.3/bin:/home/travis/.rvm/gems/ruby-2.5.3@global/bin:/home/travis/.rvm/rubies/ruby-2.5.3/bin:/home/travis/.rvm/bin:/home/travis/virtualenv/python3.6.7/bin:/home/travis/bin:/home/travis/.local/bin:/usr/local/lib/jvm/openjdk11/bin:/opt/pyenv/shims:/home/travis/.phpenv/shims:/home/travis/perl5/perlbrew/bin:/home/travis/.nvm/versions/node/v8.12.0/bin:/home/travis/gopath/bin:/home/travis/.gimme/versions/go1.11.1.linux.amd64/bin:/usr/local/maven-3.6.3/bin:/usr/local/cmake-3.12.4/bin:/usr/local/clang-7.0.0/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/snap/bin:/home/travis/.phpenv/bin:/opt/pyenv/bin:/home/travis/.yarn/bin:/sbin" ldconfig -n /tmp/RtmpWuOEky/R.INSTALL30797331353d/Rhdf5lib/src/hdf5/szip/szip/lib
----------------------------------------------------------------------
Libraries have been installed in:
/tmp/RtmpWuOEky/R.INSTALL30797331353d/Rhdf5lib/src/hdf5/szip/szip/lib
If you ever happen to want to link against installed libraries
in a given directory, LIBDIR, you must either use libtool, and
specify the full pathname of the library, or use the '-LLIBDIR'
flag during linking and do at least one of the following:
- add LIBDIR to the 'LD_LIBRARY_PATH' environment variable
during execution
- add LIBDIR to the 'LD_RUN_PATH' environment variable
during linking
- use the '-Wl,-rpath -Wl,LIBDIR' linker flag
- have your system administrator add LIBDIR to '/etc/ld.so.conf'
See any operating system documentation about shared libraries for
more information, such as the ld(1) and ld.so(8) manual pages.
----------------------------------------------------------------------
/bin/mkdir -p '/tmp/RtmpWuOEky/R.INSTALL30797331353d/Rhdf5lib/src/hdf5/szip/szip/include'
/usr/bin/install -c -m 644 ricehdf.h szip_adpt.h szlib.h '/tmp/RtmpWuOEky/R.INSTALL30797331353d/Rhdf5lib/src/hdf5/szip/szip/include'
make[2]: Leaving directory '/tmp/RtmpWuOEky/R.INSTALL30797331353d/Rhdf5lib/src/hdf5/szip/src'
make[1]: Leaving directory '/tmp/RtmpWuOEky/R.INSTALL30797331353d/Rhdf5lib/src/hdf5/szip/src'
make[1]: Entering directory '/tmp/RtmpWuOEky/R.INSTALL30797331353d/Rhdf5lib/src/hdf5/szip'
make[2]: Entering directory '/tmp/RtmpWuOEky/R.INSTALL30797331353d/Rhdf5lib/src/hdf5/szip'
make[2]: Nothing to be done for 'install-exec-am'.
make[2]: Nothing to be done for 'install-data-am'.
make[2]: Leaving directory '/tmp/RtmpWuOEky/R.INSTALL30797331353d/Rhdf5lib/src/hdf5/szip'
make[1]: Leaving directory '/tmp/RtmpWuOEky/R.INSTALL30797331353d/Rhdf5lib/src/hdf5/szip'
building the hdf5 library...
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /bin/mkdir -p
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking whether make supports nested variables... yes
checking whether make supports nested variables... (cached) yes
checking whether to enable maintainer-specific portions of Makefiles... no
checking build system type... x86_64-unknown-linux-gnu
checking host system type... x86_64-unknown-linux-gnu
checking shell variables initial values... done
checking if basename works... yes
checking if xargs works... yes
checking for cached host... none
checking for config x86_64-unknown-linux-gnu... no
checking for config x86_64-unknown-linux-gnu... no
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checking for config x86_64-linux-gnu... no
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checking for config x86_64-unknown... no
checking for config linux-gnu... found
compiler 'gcc -std=gnu99' is GNU gcc-5.4.0
compiler 'gfortran' is GNU gfortran-5.4.0
compiler 'g++ -std=gnu++11' is GNU g++-5.4.0
checking for config ./config/site-specific/host-travis-job-d1a87031-28af-4f2b-ba22-010443ffef67... no
checking build mode... production
checking for gcc... gcc -std=gnu99
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc -std=gnu99 accepts -g... yes
checking for gcc -std=gnu99 option to accept ISO C89... none needed
checking whether gcc -std=gnu99 understands -c and -o together... yes
checking for style of include used by make... GNU
checking dependency style of gcc -std=gnu99... gcc3
checking if unsupported combinations of configure options are allowed... no
checking how to run the C preprocessor... gcc -std=gnu99 -E
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking for off_t... yes
checking for size_t... yes
checking for ssize_t... yes
checking for ptrdiff_t... yes
checking whether byte ordering is bigendian... no
checking size of char... 1
checking size of short... 2
checking size of int... 4
checking size of unsigned... 4
checking size of long... 8
checking size of long long... 8
checking size of __int64... 0
checking size of float... 4
checking size of double... 8
checking size of long double... 16
checking size of __float128... 16
checking size of _Quad... 0
checking quadmath.h usability... yes
checking quadmath.h presence... yes
checking for quadmath.h... yes
checking maximum decimal precision for C... 33
checking if Fortran interface enabled... no
checking whether we are using the GNU C++ compiler... yes
checking whether g++ -std=gnu++11 accepts -g... yes
checking dependency style of g++ -std=gnu++11... gcc3
checking how to run the C++ preprocessor... g++ -std=gnu++11 -E
checking if c++ interface enabled... yes
checking if g++ -std=gnu++11 needs old style header files in includes... no
checking if g++ -std=gnu++11 can handle namespaces... yes
checking if g++ -std=gnu++11 can handle static cast... yes
checking if g++ -std=gnu++11 has offsetof extension... yes
checking if the high-level library is enabled... yes
checking for ar... ar
checking whether make sets $(MAKE)... (cached) yes
checking for tr... /usr/bin/tr
checking if srcdir= and time commands work together... yes
checking if Java JNI interface enabled... no
checking if building tests is disabled... checking if building tools is disabled... checking how to print strings... printf
checking for a sed that does not truncate output... /bin/sed
checking for fgrep... /bin/grep -F
checking for ld used by gcc -std=gnu99... /usr/bin/ld
checking if the linker (/usr/bin/ld) is GNU ld... yes
checking for BSD- or MS-compatible name lister (nm)... /usr/bin/nm -B
checking the name lister (/usr/bin/nm -B) interface... BSD nm
checking whether ln -s works... yes
checking the maximum length of command line arguments... 1572864
checking how to convert x86_64-unknown-linux-gnu file names to x86_64-unknown-linux-gnu format... func_convert_file_noop
checking how to convert x86_64-unknown-linux-gnu file names to toolchain format... func_convert_file_noop
checking for /usr/bin/ld option to reload object files... -r
checking for objdump... objdump
checking how to recognize dependent libraries... pass_all
checking for dlltool... no
checking how to associate runtime and link libraries... printf %s\n
checking for archiver @FILE support... @
checking for strip... strip
checking for ranlib... ranlib
checking command to parse /usr/bin/nm -B output from gcc -std=gnu99 object... ok
checking for sysroot... no
checking for a working dd... /bin/dd
checking how to truncate binary pipes... /bin/dd bs=4096 count=1
checking for mt... mt
checking if mt is a manifest tool... no
checking for dlfcn.h... yes
checking for objdir... .libs
checking if gcc -std=gnu99 supports -fno-rtti -fno-exceptions... yes
checking for gcc -std=gnu99 option to produce PIC... -fPIC -DPIC
checking if gcc -std=gnu99 PIC flag -fPIC -DPIC works... yes
checking if gcc -std=gnu99 static flag -static works... yes
checking if gcc -std=gnu99 supports -c -o file.o... yes
checking if gcc -std=gnu99 supports -c -o file.o... (cached) yes
checking whether the gcc -std=gnu99 linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes
checking dynamic linker characteristics... GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking for shl_load... no
checking for shl_load in -ldld... no
checking for dlopen... no
checking for dlopen in -ldl... yes
checking whether a program can dlopen itself... yes
checking whether a statically linked program can dlopen itself... no
checking whether stripping libraries is possible... yes
checking if libtool supports shared libraries... yes
checking whether to build shared libraries... no
checking whether to build static libraries... yes
checking how to run the C++ preprocessor... g++ -std=gnu++11 -E
checking for ld used by g++ -std=gnu++11... /usr/bin/ld -m elf_x86_64
checking if the linker (/usr/bin/ld -m elf_x86_64) is GNU ld... yes
checking whether the g++ -std=gnu++11 linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes
checking for g++ -std=gnu++11 option to produce PIC... -fPIC -DPIC
checking if g++ -std=gnu++11 PIC flag -fPIC -DPIC works... yes
checking if g++ -std=gnu++11 static flag -static works... yes
checking if g++ -std=gnu++11 supports -c -o file.o... yes
checking if g++ -std=gnu++11 supports -c -o file.o... (cached) yes
checking whether the g++ -std=gnu++11 linker (/usr/bin/ld -m elf_x86_64) supports shared libraries... yes
checking dynamic linker characteristics... (cached) GNU/Linux ld.so
checking how to hardcode library paths into programs... immediate
checking if we should install only statically linked executables... no
checking if -Wl,-rpath should be used to link shared libs in nondefault directories... yes
checking for ceil in -lm... yes
checking for dlopen in -ldl... (cached) yes
checking for ANSI C header files... (cached) yes
checking whether time.h and sys/time.h may both be included... yes
checking sys/resource.h usability... yes
checking sys/resource.h presence... yes
checking for sys/resource.h... yes
checking sys/time.h usability... yes
checking sys/time.h presence... yes
checking for sys/time.h... yes
checking for unistd.h... (cached) yes
checking sys/ioctl.h usability... yes
checking sys/ioctl.h presence... yes
checking for sys/ioctl.h... yes
checking for sys/stat.h... (cached) yes
checking sys/socket.h usability... yes
checking sys/socket.h presence... yes
checking for sys/socket.h... yes
checking for sys/types.h... (cached) yes
checking sys/file.h usability... yes
checking sys/file.h presence... yes
checking for sys/file.h... yes
checking stddef.h usability... yes
checking stddef.h presence... yes
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checking setjmp.h usability... yes
checking setjmp.h presence... yes
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checking features.h usability... yes
checking features.h presence... yes
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checking dirent.h usability... yes
checking dirent.h presence... yes
checking for dirent.h... yes
checking for stdint.h... (cached) yes
checking stdbool.h usability... yes
checking stdbool.h presence... yes
checking for stdbool.h... yes
checking mach/mach_time.h usability... no
checking mach/mach_time.h presence... no
checking for mach/mach_time.h... no
checking io.h usability... no
checking io.h presence... no
checking for io.h... no
checking winsock2.h usability... no
checking winsock2.h presence... no
checking for winsock2.h... no
checking sys/timeb.h usability... yes
checking sys/timeb.h presence... yes
checking for sys/timeb.h... yes
checking for _FILE_OFFSET_BITS value needed for large files... no
checking size of int8_t... 1
checking size of uint8_t... 1
checking size of int_least8_t... 1
checking size of uint_least8_t... 1
checking size of int_fast8_t... 1
checking size of uint_fast8_t... 1
checking size of int16_t... 2
checking size of uint16_t... 2
checking size of int_least16_t... 2
checking size of uint_least16_t... 2
checking size of int_fast16_t... 8
checking size of uint_fast16_t... 8
checking size of int32_t... 4
checking size of uint32_t... 4
checking size of int_least32_t... 4
checking size of uint_least32_t... 4
checking size of int_fast32_t... 8
checking size of uint_fast32_t... 8
checking size of int64_t... 8
checking size of uint64_t... 8
checking size of int_least64_t... 8
checking size of uint_least64_t... 8
checking size of int_fast64_t... 8
checking size of uint_fast64_t... 8
checking size of size_t... 8
checking size of ssize_t... 8
checking size of ptrdiff_t... 8
checking size of off_t... 8
checking size of bool... 1
checking size of time_t... 8
checking if dev_t is scalar... yes
checking for dmalloc library... suppressed
checking zlib.h usability... yes
checking zlib.h presence... yes
checking for zlib.h... yes
checking for compress2 in -lz... yes
checking for compress2... yes
checking szlib.h usability... yes
checking szlib.h presence... yes
checking for szlib.h... yes
checking for SZ_BufftoBuffCompress in -lsz... yes
checking for szlib encoder... yes
checking for thread safe support... no
checking whether CLOCK_MONOTONIC is declared... yes
checking for tm_gmtoff in struct tm... yes
checking for global timezone variable... yes
checking for st_blocks in struct stat... no
checking for _getvideoconfig... no
checking for gettextinfo... no
checking for GetConsoleScreenBufferInfo... no
checking for getpwuid... yes
checking for _scrsize... no
checking for ioctl... yes
checking for struct videoconfig... no
checking for struct text_info... no
checking for TIOCGWINSZ... yes
checking for TIOCGETD... yes
checking for library containing clock_gettime... none required
checking for alarm... yes
checking for clock_gettime... yes
checking for difftime... yes
checking for fcntl... yes
checking for flock... yes
checking for fork... yes
checking for frexpf... yes
checking for frexpl... yes
checking for gethostname... yes
checking for getrusage... yes
checking for gettimeofday... yes
checking for lstat... yes
checking for rand_r... yes
checking for random... yes
checking for setsysinfo... no
checking for signal... yes
checking for longjmp... yes
checking for setjmp... yes
checking for siglongjmp... yes
checking for sigsetjmp... no
checking for sigprocmask... yes
checking for snprintf... yes
checking for srandom... yes
checking for strdup... yes
checking for symlink... yes
checking for system... yes
checking for strtoll... yes
checking for strtoull... yes
checking for tmpfile... yes
checking for asprintf... yes
checking for vasprintf... yes
checking for vsnprintf... yes
checking for waitpid... yes
checking for roundf... yes
checking for lroundf... yes
checking for llroundf... yes
checking for round... yes
checking for lround... yes
checking for llround... yes
checking for an ANSI C-conforming const... yes
checking if the compiler understands __inline__... yes
checking if the compiler understands __inline... yes
checking if the compiler understands inline... yes
checking for __attribute__ extension... yes
checking for __func__ extension... yes
checking for __FUNCTION__ extension... yes
checking for C99 designated initialization support... yes
checking how to print long long... %ld and %lu
checking enable debugging symbols... no
checking enable asserts... no
checking enable developer warnings... no
checking profiling... no
checking optimization level... high
checking for internal debug output... none
checking whether function stack tracking is enabled... no
checking for API tracing... no
checking whether a memory checking tool will be used... no
checking whether internal memory allocation sanity checking is used... no
checking for parallel support files... skipped
checking whether O_DIRECT is declared... yes
checking for posix_memalign... yes
checking if the direct I/O virtual file driver (VFD) is enabled... no
checking curl/curl.h usability... yes
checking curl/curl.h presence... yes
checking for curl/curl.h... yes
checking openssl/evp.h usability... yes
checking openssl/evp.h presence... yes
checking for openssl/evp.h... yes
checking openssl/hmac.h usability... yes
checking openssl/hmac.h presence... yes
checking for openssl/hmac.h... yes
checking openssl/sha.h usability... yes
checking openssl/sha.h presence... yes
checking for openssl/sha.h... yes
checking for curl_global_init in -lcurl... yes
checking for EVP_sha256 in -lcrypto... yes
checking if the Read-Only S3 virtual file driver (VFD) is enabled... yes
checking for libhdfs... suppressed
checking for custom plugin default path definition... /usr/local/hdf5/lib/plugin
checking whether exception handling functions is checked during data conversions... yes
checking whether data accuracy is guaranteed during data conversions... yes
checking if the machine has window style path name... no
checking if using special algorithm to convert long double to (unsigned) long values... no
checking if using special algorithm to convert (unsigned) long to long double values... no
checking if correctly converting long double to (unsigned) long long values... yes
checking if correctly converting (unsigned) long long to long double values... yes
checking if the system is IBM ppc64le and cannot correctly convert some long double values... no
checking additional programs should be built... no
checking if deprecated public symbols are available... yes
checking which version of public symbols to use by default... v110
checking whether to perform strict file format checks... no
checking for pread... yes
checking for pwrite... yes
checking whether to use pread/pwrite instead of read/write in certain VFDs... yes
checking whether to have library information embedded in the executables... yes
checking if alignment restrictions are strictly enforced... no
configure: creating ./config.lt
config.lt: creating libtool
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating src/libhdf5.settings
config.status: creating Makefile
config.status: creating src/Makefile
config.status: creating bin/h5cc
config.status: creating bin/Makefile
config.status: creating c++/Makefile
config.status: creating c++/src/Makefile
config.status: creating c++/src/h5c++
config.status: creating hl/Makefile
config.status: creating hl/src/Makefile
config.status: creating hl/c++/Makefile
config.status: creating hl/c++/src/Makefile
config.status: creating src/H5config.h
config.status: executing pubconf commands
creating src/H5pubconf.h
Post process src/libhdf5.settings
config.status: executing depfiles commands
config.status: executing libtool commands
config.status: executing .classes commands
SUMMARY OF THE HDF5 CONFIGURATION
=================================
General Information:
-------------------
HDF5 Version: 1.10.6
Configured on: Fri Jan 15 17:05:49 UTC 2021
Configured by: travis@travis-job-d1a87031-28af-4f2b-ba22-010443ffef67
Host system: x86_64-unknown-linux-gnu
Uname information: Linux travis-job-d1a87031-28af-4f2b-ba22-010443ffef67 4.15.0-1077-gcp #87~16.04.1-Ubuntu SMP Sat Jun 6 01:51:20 UTC 2020 x86_64 x86_64 x86_64 GNU/Linux
Byte sex: little-endian
Installation point: /tmp/RtmpWuOEky/R.INSTALL30797331353d/Rhdf5lib/src/hdf5/hdf5
Compiling Options:
------------------
Build Mode: production
Debugging Symbols: no
Asserts: no
Profiling: no
Optimization Level: high
Linking Options:
----------------
Libraries: static
Statically Linked Executables:
LDFLAGS: -Wl,-Bsymbolic-functions -Wl,-z,relro
H5_LDFLAGS:
AM_LDFLAGS: -L/tmp/RtmpWuOEky/R.INSTALL30797331353d/Rhdf5lib/src/hdf5/szip/szip/lib
Extra libraries: -lcrypto -lcurl -lsz -lz -ldl -lm
Archiver: ar
AR_FLAGS: cr
Ranlib: ranlib
Languages:
----------
C: yes
C Compiler: /usr/bin/gcc -std=gnu99
CPPFLAGS:
H5_CPPFLAGS: -D_GNU_SOURCE -D_POSIX_C_SOURCE=200809L -DNDEBUG -UH5_DEBUG_API
AM_CPPFLAGS: -I/tmp/RtmpWuOEky/R.INSTALL30797331353d/Rhdf5lib/src/hdf5/szip/szip/include
C Flags: -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -w -fpic
H5 C Flags: -std=c99 -pedantic -Wall -Wextra -Wbad-function-cast -Wc++-compat -Wcast-align -Wcast-qual -Wconversion -Wdeclaration-after-statement -Wdisabled-optimization -Wfloat-equal -Wformat=2 -Wno-format-nonliteral -Winit-self -Winvalid-pch -Wmissing-declarations -Wmissing-include-dirs -Wmissing-prototypes -Wnested-externs -Wold-style-definition -Wpacked -Wredundant-decls -Wshadow -Wstrict-prototypes -Wswitch-enum -Wswitch-default -Wundef -Wunused-macros -Wunsafe-loop-optimizations -Wwrite-strings -Wlogical-op -Wlarger-than=2560 -Wsync-nand -Wframe-larger-than=16384 -Wpacked-bitfield-compat -Wstrict-overflow=5 -Wjump-misses-init -Wunsuffixed-float-constants -Wdouble-promotion -Wtrampolines -Wstack-usage=8192 -Wvector-operation-performance -Wdate-time -Warray-bounds=2 -Wc99-c11-compat -fstdarg-opt -s -Wno-inline -Wno-aggregate-return -Wno-missing-format-attribute -Wno-missing-noreturn -Wno-suggest-attribute=const -Wno-suggest-attribute=pure -Wno-suggest-attribute=noreturn -Wno-suggest-attribute=format -O3
AM C Flags:
Shared C Library: no
Static C Library: yes
Fortran: no
C++: yes
C++ Compiler: /usr/bin/g++ -std=gnu++11
C++ Flags: -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -w -fpic
H5 C++ Flags: -pedantic -Wall -Wextra -Wundef -Wshadow -Wpointer-arith -Wcast-qual -Wcast-align -Wwrite-strings -Wconversion -Wredundant-decls -Winline -Wsign-promo -Woverloaded-virtual -Wold-style-cast -Weffc++ -Wreorder -Wnon-virtual-dtor -Wctor-dtor-privacy -Wabi -Wfloat-equal -Wmissing-format-attribute -Wmissing-noreturn -Wpacked -Wdisabled-optimization -Wformat=2 -Wendif-labels -Winvalid-pch -Wvariadic-macros -Winit-self -Wmissing-include-dirs -Wswitch-default -Wswitch-enum -Wunused-macros -Wunsafe-loop-optimizations -Wstrict-overflow -Wlogical-op -Wlarger-than=2048 -Wvla -Wsync-nand -Wframe-larger-than=16384 -Wpacked-bitfield-compat -Wstrict-overflow=5 -Wdouble-promotion -Wsuggest-attribute=const -Wtrampolines -Wstack-usage=8192 -Wvector-operation-performance -Wsuggest-attribute=pure -Wsuggest-attribute=noreturn -Wsuggest-attribute=format -Wdate-time -Wopenmp-simd -Warray-bounds=2 -fstdarg-opt -s -O3
AM C++ Flags:
Shared C++ Library: no
Static C++ Library: yes
Java: no
Features:
---------
Parallel HDF5: no
Parallel Filtered Dataset Writes: no
Large Parallel I/O: no
High-level library: yes
Build HDF5 Tests: yes
Build HDF5 Tools: yes
Threadsafety: no
Default API mapping: v110
With deprecated public symbols: yes
I/O filters (external): deflate(zlib),szip(encoder)
MPE: no
Direct VFD: no
(Read-Only) S3 VFD: yes
(Read-Only) HDFS VFD: no
dmalloc: no
Packages w/ extra debug output: none
API tracing: no
Using memory checker: no
Memory allocation sanity checks: no
Function stack tracing: no
Strict file format checks: no
Optimization instrumentation: no
for d in src . c++ hl; do \
if test $d != .; then \
(cd $d && make lib) || exit 1; \
fi; \
done
make[1]: Entering directory '/tmp/RtmpWuOEky/R.INSTALL30797331353d/Rhdf5lib/src/hdf5/src'
make[2]: Entering directory '/tmp/RtmpWuOEky/R.INSTALL30797331353d/Rhdf5lib/src/hdf5/src'
CC H5.lo
CC H5checksum.lo
CC H5dbg.lo
CC H5system.lo
CC H5timer.lo
CC H5trace.lo
CC H5A.lo
CC H5Abtree2.lo
CC H5Adense.lo
CC H5Adeprec.lo
CC H5Aint.lo
CC H5Atest.lo
CC H5AC.lo
CC H5ACdbg.lo
CC H5ACproxy_entry.lo
CC H5B.lo
CC H5Bcache.lo
CC H5Bdbg.lo
CC H5B2.lo
CC H5B2cache.lo
CC H5B2dbg.lo
CC H5B2hdr.lo
CC H5B2int.lo
CC H5B2internal.lo
CC H5B2leaf.lo
CC H5B2stat.lo
CC H5B2test.lo
CC H5C.lo
CC H5Cdbg.lo
CC H5Cepoch.lo
CC H5Cimage.lo
CC H5Clog.lo
CC H5Clog_json.lo
CC H5Clog_trace.lo
CC H5Cprefetched.lo
CC H5Cquery.lo
CC H5Ctag.lo
CC H5Ctest.lo
CC H5CS.lo
CC H5CX.lo
CC H5D.lo
CC H5Dbtree.lo
CC H5Dbtree2.lo
CC H5Dchunk.lo
CC H5Dcompact.lo
CC H5Dcontig.lo
CC H5Ddbg.lo
CC H5Ddeprec.lo
CC H5Dearray.lo
CC H5Defl.lo
CC H5Dfarray.lo
CC H5Dfill.lo
CC H5Dint.lo
CC H5Dio.lo
CC H5Dlayout.lo
CC H5Dnone.lo
CC H5Doh.lo
CC H5Dscatgath.lo
CC H5Dselect.lo
CC H5Dsingle.lo
CC H5Dtest.lo
CC H5Dvirtual.lo
CC H5E.lo
CC H5Edeprec.lo
CC H5Eint.lo
CC H5EA.lo
CC H5EAcache.lo
CC H5EAdbg.lo
CC H5EAdblkpage.lo
CC H5EAdblock.lo
CC H5EAhdr.lo
CC H5EAiblock.lo
CC H5EAint.lo
CC H5EAsblock.lo
CC H5EAstat.lo
CC H5EAtest.lo
CC H5F.lo
CC H5Faccum.lo
CC H5Fcwfs.lo
CC H5Fdbg.lo
CC H5Fdeprec.lo
CC H5Fefc.lo
CC H5Ffake.lo
CC H5Fint.lo
CC H5Fio.lo
CC H5Fmount.lo
CC H5Fquery.lo
CC H5Fsfile.lo
CC H5Fspace.lo
CC H5Fsuper.lo
CC H5Fsuper_cache.lo
CC H5Ftest.lo
CC H5FA.lo
CC H5FAcache.lo
CC H5FAdbg.lo
CC H5FAdblock.lo
CC H5FAdblkpage.lo
CC H5FAhdr.lo
CC H5FAint.lo
CC H5FAstat.lo
CC H5FAtest.lo
CC H5FD.lo
CC H5FDcore.lo
CC H5FDfamily.lo
CC H5FDhdfs.lo
CC H5FDint.lo
CC H5FDlog.lo
CC H5FDmulti.lo
CC H5FDsec2.lo
CC H5FDspace.lo
CC H5FDstdio.lo
CC H5FDtest.lo
CC H5FL.lo
CC H5FO.lo
CC H5FS.lo
CC H5FScache.lo
CC H5FSdbg.lo
CC H5FSint.lo
CC H5FSsection.lo
CC H5FSstat.lo
CC H5FStest.lo
CC H5G.lo
CC H5Gbtree2.lo
CC H5Gcache.lo
CC H5Gcompact.lo
CC H5Gdense.lo
CC H5Gdeprec.lo
CC H5Gent.lo
CC H5Gint.lo
CC H5Glink.lo
CC H5Gloc.lo
CC H5Gname.lo
CC H5Gnode.lo
CC H5Gobj.lo
CC H5Goh.lo
CC H5Groot.lo
CC H5Gstab.lo
CC H5Gtest.lo
CC H5Gtraverse.lo
CC H5HF.lo
CC H5HFbtree2.lo
CC H5HFcache.lo
CC H5HFdbg.lo
CC H5HFdblock.lo
CC H5HFdtable.lo
CC H5HFhdr.lo
CC H5HFhuge.lo
CC H5HFiblock.lo
CC H5HFiter.lo
CC H5HFman.lo
CC H5HFsection.lo
CC H5HFspace.lo
CC H5HFstat.lo
CC H5HFtest.lo
CC H5HFtiny.lo
CC H5HG.lo
CC H5HGcache.lo
CC H5HGdbg.lo
CC H5HGquery.lo
CC H5HL.lo
CC H5HLcache.lo
CC H5HLdbg.lo
CC H5HLint.lo
CC H5HLprfx.lo
CC H5HLdblk.lo
CC H5HP.lo
CC H5I.lo
CC H5Itest.lo
CC H5L.lo
CC H5Lexternal.lo
CC H5make_libsettings.o
CCLD H5make_libsettings
LD_LIBRARY_PATH="$LD_LIBRARY_PATH`echo -Wl,-Bsymbolic-functions -Wl,-z,relro | \
sed -e 's/-L/:/g' -e 's/ //g'`" \
./H5make_libsettings > H5lib_settings.c || \
(test $HDF5_Make_Ignore && echo "*** Error ignored") || \
(rm -f H5lib_settings.c ; exit 1)
CC H5lib_settings.lo
CC H5MF.lo
CC H5MFaggr.lo
CC H5MFdbg.lo
CC H5MFsection.lo
CC H5MM.lo
CC H5MP.lo
CC H5MPtest.lo
CC H5O.lo
CC H5Odeprec.lo
CC H5Oainfo.lo
CC H5Oalloc.lo
CC H5Oattr.lo
CC H5Oattribute.lo
CC H5Obogus.lo
CC H5Obtreek.lo
CC H5Ocache.lo
CC H5Ocache_image.lo
CC H5Ochunk.lo
CC H5Ocont.lo
CC H5Ocopy.lo
CC H5Odbg.lo
CC H5Odrvinfo.lo
CC H5Odtype.lo
CC H5Oefl.lo
CC H5Ofill.lo
CC H5Oflush.lo
CC H5Ofsinfo.lo
CC H5Oginfo.lo
CC H5Oint.lo
CC H5Olayout.lo
CC H5Olinfo.lo
CC H5Olink.lo
CC H5Omessage.lo
CC H5Omtime.lo
CC H5Oname.lo
CC H5Onull.lo
CC H5Opline.lo
CC H5Orefcount.lo
CC H5Osdspace.lo
CC H5Oshared.lo
CC H5Oshmesg.lo
CC H5Ostab.lo
CC H5Otest.lo
CC H5Ounknown.lo
CC H5P.lo
CC H5Pacpl.lo
CC H5Pdapl.lo
CC H5Pdcpl.lo
CC H5Pdeprec.lo
CC H5Pdxpl.lo
CC H5Pencdec.lo
CC H5Pfapl.lo
CC H5Pfcpl.lo
CC H5Pfmpl.lo
CC H5Pgcpl.lo
CC H5Pint.lo
CC H5Plapl.lo
CC H5Plcpl.lo
CC H5Pocpl.lo
CC H5Pocpypl.lo
CC H5Pstrcpl.lo
CC H5Ptest.lo
CC H5PB.lo
CC H5PL.lo
CC H5PLint.lo
CC H5PLpath.lo
CC H5PLplugin_cache.lo
CC H5R.lo
CC H5Rint.lo
CC H5Rdeprec.lo
CC H5UC.lo
CC H5RS.lo
CC H5S.lo
CC H5Sall.lo
CC H5Sdbg.lo
CC H5Shyper.lo
CC H5Snone.lo
CC H5Spoint.lo
CC H5Sselect.lo
CC H5Stest.lo
CC H5SL.lo
CC H5SM.lo
CC H5SMbtree2.lo
CC H5SMcache.lo
CC H5SMmessage.lo
CC H5SMtest.lo
CC H5ST.lo
CC H5T.lo
CC H5Tarray.lo
CC H5Tbit.lo
CC H5Tcommit.lo
CC H5Tcompound.lo
CC H5Tconv.lo
CC H5Tcset.lo
CC H5Tdbg.lo
CC H5Tdeprec.lo
CC H5Tenum.lo
CC H5Tfields.lo
CC H5Tfixed.lo
CC H5Tfloat.lo
CC H5detect.o
CCLD H5detect
LD_LIBRARY_PATH="$LD_LIBRARY_PATH`echo -Wl,-Bsymbolic-functions -Wl,-z,relro | \
sed -e 's/-L/:/g' -e 's/ //g'`" \
./H5detect > H5Tinit.c || \
(test $HDF5_Make_Ignore && echo "*** Error ignored") || \
(rm -f H5Tinit.c ; exit 1)
CC H5Tinit.lo
CC H5Tnative.lo
CC H5Toffset.lo
CC H5Toh.lo
CC H5Topaque.lo
CC H5Torder.lo
CC H5Tpad.lo
CC H5Tprecis.lo
CC H5Tstrpad.lo
CC H5Tvisit.lo
CC H5Tvlen.lo
CC H5TS.lo
CC H5VM.lo
CC H5WB.lo
CC H5Z.lo
CC H5Zdeflate.lo
CC H5Zfletcher32.lo
CC H5Znbit.lo
CC H5Zshuffle.lo
CC H5Zscaleoffset.lo
CC H5Zszip.lo
CC H5Ztrans.lo
CC H5FDros3.lo
CC H5FDs3comms.lo
CCLD libhdf5.la
make[2]: Leaving directory '/tmp/RtmpWuOEky/R.INSTALL30797331353d/Rhdf5lib/src/hdf5/src'
make[1]: Leaving directory '/tmp/RtmpWuOEky/R.INSTALL30797331353d/Rhdf5lib/src/hdf5/src'
make[1]: Entering directory '/tmp/RtmpWuOEky/R.INSTALL30797331353d/Rhdf5lib/src/hdf5/c++'
make[2]: Entering directory '/tmp/RtmpWuOEky/R.INSTALL30797331353d/Rhdf5lib/src/hdf5/c++'
make[2]: Nothing to be done for 'build-lib'.
make[2]: Leaving directory '/tmp/RtmpWuOEky/R.INSTALL30797331353d/Rhdf5lib/src/hdf5/c++'
+ cd src
+ make lib
make[2]: Entering directory '/tmp/RtmpWuOEky/R.INSTALL30797331353d/Rhdf5lib/src/hdf5/c++/src'
make[3]: Entering directory '/tmp/RtmpWuOEky/R.INSTALL30797331353d/Rhdf5lib/src/hdf5/c++/src'
CXX H5Exception.lo
CXX H5IdComponent.lo
CXX H5DataSpace.lo
CXX H5PropList.lo
CXX H5Library.lo
CXX H5FaccProp.lo
CXX H5FcreatProp.lo
CXX H5LcreatProp.lo
CXX H5LaccProp.lo
CXX H5DaccProp.lo
CXX H5DxferProp.lo
CXX H5DcreatProp.lo
CXX H5Location.lo
CXX H5AbstractDs.lo
CXX H5Attribute.lo
CXX H5Object.lo
CXX H5OcreatProp.lo
CXX H5DataType.lo
CXX H5AtomType.lo
CXX H5PredType.lo
CXX H5EnumType.lo
CXX H5IntType.lo
CXX H5FloatType.lo
CXX H5StrType.lo
CXX H5ArrayType.lo
CXX H5VarLenType.lo
CXX H5CompType.lo
CXX H5DataSet.lo
CXX H5CommonFG.lo
CXX H5Group.lo
CXX H5File.lo
CXXLD libhdf5_cpp.la
make[3]: Leaving directory '/tmp/RtmpWuOEky/R.INSTALL30797331353d/Rhdf5lib/src/hdf5/c++/src'
make[2]: Leaving directory '/tmp/RtmpWuOEky/R.INSTALL30797331353d/Rhdf5lib/src/hdf5/c++/src'
make[1]: Leaving directory '/tmp/RtmpWuOEky/R.INSTALL30797331353d/Rhdf5lib/src/hdf5/c++'
make[1]: Entering directory '/tmp/RtmpWuOEky/R.INSTALL30797331353d/Rhdf5lib/src/hdf5/hl'
make[2]: Entering directory '/tmp/RtmpWuOEky/R.INSTALL30797331353d/Rhdf5lib/src/hdf5/hl'
make[2]: Nothing to be done for 'build-lib'.
make[2]: Leaving directory '/tmp/RtmpWuOEky/R.INSTALL30797331353d/Rhdf5lib/src/hdf5/hl'
+ cd src
+ make lib
make[2]: Entering directory '/tmp/RtmpWuOEky/R.INSTALL30797331353d/Rhdf5lib/src/hdf5/hl/src'
make[3]: Entering directory '/tmp/RtmpWuOEky/R.INSTALL30797331353d/Rhdf5lib/src/hdf5/hl/src'
CC H5DO.lo
CC H5DS.lo
CC H5IM.lo
CC H5LT.lo
CC H5LTanalyze.lo
CC H5LTparse.lo
CC H5PT.lo
CC H5TB.lo
CC H5LD.lo
CCLD libhdf5_hl.la
make[3]: Leaving directory '/tmp/RtmpWuOEky/R.INSTALL30797331353d/Rhdf5lib/src/hdf5/hl/src'
make[2]: Leaving directory '/tmp/RtmpWuOEky/R.INSTALL30797331353d/Rhdf5lib/src/hdf5/hl/src'
+ cd c++
+ make lib
make[2]: Entering directory '/tmp/RtmpWuOEky/R.INSTALL30797331353d/Rhdf5lib/src/hdf5/hl/c++'
make[3]: Entering directory '/tmp/RtmpWuOEky/R.INSTALL30797331353d/Rhdf5lib/src/hdf5/hl/c++'
make[3]: Nothing to be done for 'build-lib'.
make[3]: Leaving directory '/tmp/RtmpWuOEky/R.INSTALL30797331353d/Rhdf5lib/src/hdf5/hl/c++'
+ cd src
+ make lib
make[3]: Entering directory '/tmp/RtmpWuOEky/R.INSTALL30797331353d/Rhdf5lib/src/hdf5/hl/c++/src'
make[4]: Entering directory '/tmp/RtmpWuOEky/R.INSTALL30797331353d/Rhdf5lib/src/hdf5/hl/c++/src'
CXX H5PacketTable.lo
CXXLD libhdf5_hl_cpp.la
libtool: warning: '/usr/lib/gcc/x86_64-linux-gnu/5/../../../x86_64-linux-gnu/libcurl.la' seems to be moved
make[4]: Leaving directory '/tmp/RtmpWuOEky/R.INSTALL30797331353d/Rhdf5lib/src/hdf5/hl/c++/src'
make[3]: Leaving directory '/tmp/RtmpWuOEky/R.INSTALL30797331353d/Rhdf5lib/src/hdf5/hl/c++/src'
make[2]: Leaving directory '/tmp/RtmpWuOEky/R.INSTALL30797331353d/Rhdf5lib/src/hdf5/hl/c++'
make[1]: Leaving directory '/tmp/RtmpWuOEky/R.INSTALL30797331353d/Rhdf5lib/src/hdf5/hl'
configure: HDF5_INCLUDE=hdf5/src
configure: HDF5_CXX_INCLUDE=hdf5/c++/src
configure: HDF5_HL_INCLUDE=hdf5/hl/src
configure: HDF5_HL_CXX_INCLUDE=hdf5/hl/c++/src
configure: HDF5_LIB=hdf5/src/.libs/libhdf5.a
configure: HDF5_CXX_LIB=hdf5/c++/src/.libs/libhdf5_cpp.a
configure: HDF5_HL_LIB=hdf5/hl/src/.libs/libhdf5_hl.a
configure: HDF5_HL_CXX_LIB=hdf5/hl/c++/src/.libs/libhdf5_hl_cpp.a
configure: SZIP_LIB=hdf5/szip/src/.libs/libsz.a
configure: creating ./config.status
config.status: creating src/Makevars
** libs
mkdir -p "/home/travis/R/x86_64-pc-linux-gnu-library/4.0/00LOCK-Rhdf5lib/00new/Rhdf5lib/include"
cp "hdf5/src/"*.h "/home/travis/R/x86_64-pc-linux-gnu-library/4.0/00LOCK-Rhdf5lib/00new/Rhdf5lib/include"
cp "hdf5/c++/src/"*.h "/home/travis/R/x86_64-pc-linux-gnu-library/4.0/00LOCK-Rhdf5lib/00new/Rhdf5lib/include"
cp "hdf5/hl/src/"*.h "/home/travis/R/x86_64-pc-linux-gnu-library/4.0/00LOCK-Rhdf5lib/00new/Rhdf5lib/include"
cp "hdf5/hl/c++/src/"*.h "/home/travis/R/x86_64-pc-linux-gnu-library/4.0/00LOCK-Rhdf5lib/00new/Rhdf5lib/include"
cp "hdf5/src/"libhdf5.settings "/home/travis/R/x86_64-pc-linux-gnu-library/4.0/00LOCK-Rhdf5lib/00new/Rhdf5lib/include"
mkdir -p "/home/travis/R/x86_64-pc-linux-gnu-library/4.0/00LOCK-Rhdf5lib/00new/Rhdf5lib/lib/"
cp "hdf5/src/.libs/libhdf5.a" "/home/travis/R/x86_64-pc-linux-gnu-library/4.0/00LOCK-Rhdf5lib/00new/Rhdf5lib/lib/"
cp "hdf5/c++/src/.libs/libhdf5_cpp.a" "/home/travis/R/x86_64-pc-linux-gnu-library/4.0/00LOCK-Rhdf5lib/00new/Rhdf5lib/lib/"
cp "hdf5/hl/src/.libs/libhdf5_hl.a" "/home/travis/R/x86_64-pc-linux-gnu-library/4.0/00LOCK-Rhdf5lib/00new/Rhdf5lib/lib/"
cp "hdf5/hl/c++/src/.libs/libhdf5_hl_cpp.a" "/home/travis/R/x86_64-pc-linux-gnu-library/4.0/00LOCK-Rhdf5lib/00new/Rhdf5lib/lib/"
cp "hdf5/szip/src/.libs/libsz.a" "/home/travis/R/x86_64-pc-linux-gnu-library/4.0/00LOCK-Rhdf5lib/00new/Rhdf5lib/lib/"
gcc -std=gnu99 -I"/usr/share/R/include" -DNDEBUG -Ihdf5/src -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c Rhdf5lib.c -o Rhdf5lib.o
gcc -std=gnu99 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o Rhdf5lib.so Rhdf5lib.o /home/travis/R/x86_64-pc-linux-gnu-library/4.0/00LOCK-Rhdf5lib/00new/Rhdf5lib/lib/libhdf5.a /home/travis/R/x86_64-pc-linux-gnu-library/4.0/00LOCK-Rhdf5lib/00new/Rhdf5lib/lib/libsz.a -lz -L/usr/lib/R/lib -lR
installing to /home/travis/R/x86_64-pc-linux-gnu-library/4.0/00LOCK-Rhdf5lib/00new/Rhdf5lib/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (Rhdf5lib)
* installing *source* package ‘BiocVersion’ ...
** using staged installation
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (BiocVersion)
* installing *source* package ‘RcppArmadillo’ ...
** package ‘RcppArmadillo’ successfully unpacked and MD5 sums checked
** using staged installation
checking whether the C++ compiler works... yes
checking for C++ compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C++ compiler... yes
checking whether g++ -std=gnu++11 accepts -g... yes
checking how to run the C++ preprocessor... g++ -std=gnu++11 -E
checking whether we are using the GNU C++ compiler... (cached) yes
checking whether g++ -std=gnu++11 accepts -g... (cached) yes
checking whether we have a suitable tempdir... /tmp
checking whether R CMD SHLIB can already compile programs using OpenMP... yes
checking LAPACK_LIBS... system LAPACK found
configure: creating ./config.status
config.status: creating inst/include/RcppArmadilloConfigGenerated.h
config.status: creating src/Makevars
** libs
g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I'/home/travis/R/x86_64-pc-linux-gnu-library/4.0/Rcpp/include' -I../inst/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c RcppArmadillo.cpp -o RcppArmadillo.o
g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I'/home/travis/R/x86_64-pc-linux-gnu-library/4.0/Rcpp/include' -I../inst/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I'/home/travis/R/x86_64-pc-linux-gnu-library/4.0/Rcpp/include' -I../inst/include -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c fastLm.cpp -o fastLm.o
g++ -std=gnu++11 -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -Wl,-z,relro -o RcppArmadillo.so RcppArmadillo.o RcppExports.o fastLm.o -llapack -lblas -lgfortran -lm -lquadmath -L/usr/lib/R/lib -lR
installing to /home/travis/R/x86_64-pc-linux-gnu-library/4.0/00LOCK-RcppArmadillo/00new/RcppArmadillo/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (RcppArmadillo)
* installing *source* package ‘cytolib’ ...
** using staged installation
checking for a sed that does not truncate output... /bin/sed
checking for g++... g++
checking whether the C++ compiler works... yes
checking for C++ compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C++ compiler... yes
checking whether g++ accepts -g... yes
checking how to run the C++ preprocessor... g++ -E
checking whether we are using the GNU C++ compiler... (cached) yes
checking whether g++ accepts -g... (cached) yes
checking for pkg-config... /usr/bin/pkg-config
checking pkg-config knows TileDB... no
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for ANSI C header files... no
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking tiledb/tiledb.h usability... no
checking tiledb/tiledb.h presence... no
checking for tiledb/tiledb.h... no
configure: No tiledb is found, build without tiledb...
configure: Parsing cytolib version info ...
configure: CYTOLIB_VERSION=2.2.0
configure: creating ./config.status
config.status: creating inst/include/cytolib/cytolibConfig.h
config.status: creating src/Makevars
** libs
g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/home/travis/R/x86_64-pc-linux-gnu-library/4.0/Rcpp/include' -I'/home/travis/R/x86_64-pc-linux-gnu-library/4.0/BH/include' -I'/home/travis/R/x86_64-pc-linux-gnu-library/4.0/RProtoBufLib/include' -I'/home/travis/R/x86_64-pc-linux-gnu-library/4.0/Rhdf5lib/include' -I'/home/travis/R/x86_64-pc-linux-gnu-library/4.0/RcppArmadillo/include' -I'/home/travis/R/x86_64-pc-linux-gnu-library/4.0/RcppParallel/include' -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c CytoFrame.cpp -o CytoFrame.o
g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/home/travis/R/x86_64-pc-linux-gnu-library/4.0/Rcpp/include' -I'/home/travis/R/x86_64-pc-linux-gnu-library/4.0/BH/include' -I'/home/travis/R/x86_64-pc-linux-gnu-library/4.0/RProtoBufLib/include' -I'/home/travis/R/x86_64-pc-linux-gnu-library/4.0/Rhdf5lib/include' -I'/home/travis/R/x86_64-pc-linux-gnu-library/4.0/RcppArmadillo/include' -I'/home/travis/R/x86_64-pc-linux-gnu-library/4.0/RcppParallel/include' -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c CytoFrameView.cpp -o CytoFrameView.o
g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/home/travis/R/x86_64-pc-linux-gnu-library/4.0/Rcpp/include' -I'/home/travis/R/x86_64-pc-linux-gnu-library/4.0/BH/include' -I'/home/travis/R/x86_64-pc-linux-gnu-library/4.0/RProtoBufLib/include' -I'/home/travis/R/x86_64-pc-linux-gnu-library/4.0/Rhdf5lib/include' -I'/home/travis/R/x86_64-pc-linux-gnu-library/4.0/RcppArmadillo/include' -I'/home/travis/R/x86_64-pc-linux-gnu-library/4.0/RcppParallel/include' -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c CytoVFS.cpp -o CytoVFS.o
g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/home/travis/R/x86_64-pc-linux-gnu-library/4.0/Rcpp/include' -I'/home/travis/R/x86_64-pc-linux-gnu-library/4.0/BH/include' -I'/home/travis/R/x86_64-pc-linux-gnu-library/4.0/RProtoBufLib/include' -I'/home/travis/R/x86_64-pc-linux-gnu-library/4.0/Rhdf5lib/include' -I'/home/travis/R/x86_64-pc-linux-gnu-library/4.0/RcppArmadillo/include' -I'/home/travis/R/x86_64-pc-linux-gnu-library/4.0/RcppParallel/include' -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c GatingHierarchy.cpp -o GatingHierarchy.o
In file included from /home/travis/R/x86_64-pc-linux-gnu-library/4.0/BH/include/boost/graph/adjacency_iterator.hpp:13:0,
from /home/travis/R/x86_64-pc-linux-gnu-library/4.0/BH/include/boost/graph/detail/adjacency_list.hpp:37,
from /home/travis/R/x86_64-pc-linux-gnu-library/4.0/BH/include/boost/graph/adjacency_list.hpp:255,
from ../inst/include/cytolib/populationTree.hpp:14,
from ../inst/include/cytolib/GatingHierarchy.hpp:17,
from GatingHierarchy.cpp:3:
/home/travis/R/x86_64-pc-linux-gnu-library/4.0/BH/include/boost/detail/iterator.hpp:13:67: note: #pragma message: This header is deprecated. Use <iterator> instead.
g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/home/travis/R/x86_64-pc-linux-gnu-library/4.0/Rcpp/include' -I'/home/travis/R/x86_64-pc-linux-gnu-library/4.0/BH/include' -I'/home/travis/R/x86_64-pc-linux-gnu-library/4.0/RProtoBufLib/include' -I'/home/travis/R/x86_64-pc-linux-gnu-library/4.0/Rhdf5lib/include' -I'/home/travis/R/x86_64-pc-linux-gnu-library/4.0/RcppArmadillo/include' -I'/home/travis/R/x86_64-pc-linux-gnu-library/4.0/RcppParallel/include' -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c GatingSet.cpp -o GatingSet.o
In file included from /home/travis/R/x86_64-pc-linux-gnu-library/4.0/BH/include/boost/graph/adjacency_iterator.hpp:13:0,
from /home/travis/R/x86_64-pc-linux-gnu-library/4.0/BH/include/boost/graph/detail/adjacency_list.hpp:37,
from /home/travis/R/x86_64-pc-linux-gnu-library/4.0/BH/include/boost/graph/adjacency_list.hpp:255,
from ../inst/include/cytolib/populationTree.hpp:14,
from ../inst/include/cytolib/GatingHierarchy.hpp:17,
from ../inst/include/cytolib/GatingSet.hpp:14,
from GatingSet.cpp:3:
/home/travis/R/x86_64-pc-linux-gnu-library/4.0/BH/include/boost/detail/iterator.hpp:13:67: note: #pragma message: This header is deprecated. Use <iterator> instead.
g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/home/travis/R/x86_64-pc-linux-gnu-library/4.0/Rcpp/include' -I'/home/travis/R/x86_64-pc-linux-gnu-library/4.0/BH/include' -I'/home/travis/R/x86_64-pc-linux-gnu-library/4.0/RProtoBufLib/include' -I'/home/travis/R/x86_64-pc-linux-gnu-library/4.0/Rhdf5lib/include' -I'/home/travis/R/x86_64-pc-linux-gnu-library/4.0/RcppArmadillo/include' -I'/home/travis/R/x86_64-pc-linux-gnu-library/4.0/RcppParallel/include' -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c GatingSet.pb.cc -o GatingSet.pb.o
g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/home/travis/R/x86_64-pc-linux-gnu-library/4.0/Rcpp/include' -I'/home/travis/R/x86_64-pc-linux-gnu-library/4.0/BH/include' -I'/home/travis/R/x86_64-pc-linux-gnu-library/4.0/RProtoBufLib/include' -I'/home/travis/R/x86_64-pc-linux-gnu-library/4.0/Rhdf5lib/include' -I'/home/travis/R/x86_64-pc-linux-gnu-library/4.0/RcppArmadillo/include' -I'/home/travis/R/x86_64-pc-linux-gnu-library/4.0/RcppParallel/include' -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c H5CytoFrame.cpp -o H5CytoFrame.o
g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/home/travis/R/x86_64-pc-linux-gnu-library/4.0/Rcpp/include' -I'/home/travis/R/x86_64-pc-linux-gnu-library/4.0/BH/include' -I'/home/travis/R/x86_64-pc-linux-gnu-library/4.0/RProtoBufLib/include' -I'/home/travis/R/x86_64-pc-linux-gnu-library/4.0/Rhdf5lib/include' -I'/home/travis/R/x86_64-pc-linux-gnu-library/4.0/RcppArmadillo/include' -I'/home/travis/R/x86_64-pc-linux-gnu-library/4.0/RcppParallel/include' -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c MemCytoFrame.cpp -o MemCytoFrame.o
g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/home/travis/R/x86_64-pc-linux-gnu-library/4.0/Rcpp/include' -I'/home/travis/R/x86_64-pc-linux-gnu-library/4.0/BH/include' -I'/home/travis/R/x86_64-pc-linux-gnu-library/4.0/RProtoBufLib/include' -I'/home/travis/R/x86_64-pc-linux-gnu-library/4.0/Rhdf5lib/include' -I'/home/travis/R/x86_64-pc-linux-gnu-library/4.0/RcppArmadillo/include' -I'/home/travis/R/x86_64-pc-linux-gnu-library/4.0/RcppParallel/include' -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c POPINDICES.cpp -o POPINDICES.o
g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/home/travis/R/x86_64-pc-linux-gnu-library/4.0/Rcpp/include' -I'/home/travis/R/x86_64-pc-linux-gnu-library/4.0/BH/include' -I'/home/travis/R/x86_64-pc-linux-gnu-library/4.0/RProtoBufLib/include' -I'/home/travis/R/x86_64-pc-linux-gnu-library/4.0/Rhdf5lib/include' -I'/home/travis/R/x86_64-pc-linux-gnu-library/4.0/RcppArmadillo/include' -I'/home/travis/R/x86_64-pc-linux-gnu-library/4.0/RcppParallel/include' -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c calibrationTable.cpp -o calibrationTable.o
g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/home/travis/R/x86_64-pc-linux-gnu-library/4.0/Rcpp/include' -I'/home/travis/R/x86_64-pc-linux-gnu-library/4.0/BH/include' -I'/home/travis/R/x86_64-pc-linux-gnu-library/4.0/RProtoBufLib/include' -I'/home/travis/R/x86_64-pc-linux-gnu-library/4.0/Rhdf5lib/include' -I'/home/travis/R/x86_64-pc-linux-gnu-library/4.0/RcppArmadillo/include' -I'/home/travis/R/x86_64-pc-linux-gnu-library/4.0/RcppParallel/include' -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c compensation.cpp -o compensation.o
g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/home/travis/R/x86_64-pc-linux-gnu-library/4.0/Rcpp/include' -I'/home/travis/R/x86_64-pc-linux-gnu-library/4.0/BH/include' -I'/home/travis/R/x86_64-pc-linux-gnu-library/4.0/RProtoBufLib/include' -I'/home/travis/R/x86_64-pc-linux-gnu-library/4.0/Rhdf5lib/include' -I'/home/travis/R/x86_64-pc-linux-gnu-library/4.0/RcppArmadillo/include' -I'/home/travis/R/x86_64-pc-linux-gnu-library/4.0/RcppParallel/include' -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c dummy.cpp -o dummy.o
g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/home/travis/R/x86_64-pc-linux-gnu-library/4.0/Rcpp/include' -I'/home/travis/R/x86_64-pc-linux-gnu-library/4.0/BH/include' -I'/home/travis/R/x86_64-pc-linux-gnu-library/4.0/RProtoBufLib/include' -I'/home/travis/R/x86_64-pc-linux-gnu-library/4.0/Rhdf5lib/include' -I'/home/travis/R/x86_64-pc-linux-gnu-library/4.0/RcppArmadillo/include' -I'/home/travis/R/x86_64-pc-linux-gnu-library/4.0/RcppParallel/include' -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c ellipse2points.cpp -o ellipse2points.o
g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/home/travis/R/x86_64-pc-linux-gnu-library/4.0/Rcpp/include' -I'/home/travis/R/x86_64-pc-linux-gnu-library/4.0/BH/include' -I'/home/travis/R/x86_64-pc-linux-gnu-library/4.0/RProtoBufLib/include' -I'/home/travis/R/x86_64-pc-linux-gnu-library/4.0/Rhdf5lib/include' -I'/home/travis/R/x86_64-pc-linux-gnu-library/4.0/RcppArmadillo/include' -I'/home/travis/R/x86_64-pc-linux-gnu-library/4.0/RcppParallel/include' -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c gate.cpp -o gate.o
g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/home/travis/R/x86_64-pc-linux-gnu-library/4.0/Rcpp/include' -I'/home/travis/R/x86_64-pc-linux-gnu-library/4.0/BH/include' -I'/home/travis/R/x86_64-pc-linux-gnu-library/4.0/RProtoBufLib/include' -I'/home/travis/R/x86_64-pc-linux-gnu-library/4.0/Rhdf5lib/include' -I'/home/travis/R/x86_64-pc-linux-gnu-library/4.0/RcppArmadillo/include' -I'/home/travis/R/x86_64-pc-linux-gnu-library/4.0/RcppParallel/include' -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c global.cpp -o global.o
g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/home/travis/R/x86_64-pc-linux-gnu-library/4.0/Rcpp/include' -I'/home/travis/R/x86_64-pc-linux-gnu-library/4.0/BH/include' -I'/home/travis/R/x86_64-pc-linux-gnu-library/4.0/RProtoBufLib/include' -I'/home/travis/R/x86_64-pc-linux-gnu-library/4.0/Rhdf5lib/include' -I'/home/travis/R/x86_64-pc-linux-gnu-library/4.0/RcppArmadillo/include' -I'/home/travis/R/x86_64-pc-linux-gnu-library/4.0/RcppParallel/include' -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c in_polygon.cpp -o in_polygon.o
g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/home/travis/R/x86_64-pc-linux-gnu-library/4.0/Rcpp/include' -I'/home/travis/R/x86_64-pc-linux-gnu-library/4.0/BH/include' -I'/home/travis/R/x86_64-pc-linux-gnu-library/4.0/RProtoBufLib/include' -I'/home/travis/R/x86_64-pc-linux-gnu-library/4.0/Rhdf5lib/include' -I'/home/travis/R/x86_64-pc-linux-gnu-library/4.0/RcppArmadillo/include' -I'/home/travis/R/x86_64-pc-linux-gnu-library/4.0/RcppParallel/include' -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c nodeProperties.cpp -o nodeProperties.o
g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/home/travis/R/x86_64-pc-linux-gnu-library/4.0/Rcpp/include' -I'/home/travis/R/x86_64-pc-linux-gnu-library/4.0/BH/include' -I'/home/travis/R/x86_64-pc-linux-gnu-library/4.0/RProtoBufLib/include' -I'/home/travis/R/x86_64-pc-linux-gnu-library/4.0/Rhdf5lib/include' -I'/home/travis/R/x86_64-pc-linux-gnu-library/4.0/RcppArmadillo/include' -I'/home/travis/R/x86_64-pc-linux-gnu-library/4.0/RcppParallel/include' -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c spline.cpp -o spline.o
g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/home/travis/R/x86_64-pc-linux-gnu-library/4.0/Rcpp/include' -I'/home/travis/R/x86_64-pc-linux-gnu-library/4.0/BH/include' -I'/home/travis/R/x86_64-pc-linux-gnu-library/4.0/RProtoBufLib/include' -I'/home/travis/R/x86_64-pc-linux-gnu-library/4.0/Rhdf5lib/include' -I'/home/travis/R/x86_64-pc-linux-gnu-library/4.0/RcppArmadillo/include' -I'/home/travis/R/x86_64-pc-linux-gnu-library/4.0/RcppParallel/include' -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c trans_group.cpp -o trans_group.o
g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/home/travis/R/x86_64-pc-linux-gnu-library/4.0/Rcpp/include' -I'/home/travis/R/x86_64-pc-linux-gnu-library/4.0/BH/include' -I'/home/travis/R/x86_64-pc-linux-gnu-library/4.0/RProtoBufLib/include' -I'/home/travis/R/x86_64-pc-linux-gnu-library/4.0/Rhdf5lib/include' -I'/home/travis/R/x86_64-pc-linux-gnu-library/4.0/RcppArmadillo/include' -I'/home/travis/R/x86_64-pc-linux-gnu-library/4.0/RcppParallel/include' -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c transformation.cpp -o transformation.o
g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/home/travis/R/x86_64-pc-linux-gnu-library/4.0/Rcpp/include' -I'/home/travis/R/x86_64-pc-linux-gnu-library/4.0/BH/include' -I'/home/travis/R/x86_64-pc-linux-gnu-library/4.0/RProtoBufLib/include' -I'/home/travis/R/x86_64-pc-linux-gnu-library/4.0/Rhdf5lib/include' -I'/home/travis/R/x86_64-pc-linux-gnu-library/4.0/RcppArmadillo/include' -I'/home/travis/R/x86_64-pc-linux-gnu-library/4.0/RcppParallel/include' -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c boost/libs/system/src/error_code.cpp -o boost/libs/system/src/error_code.o
g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/home/travis/R/x86_64-pc-linux-gnu-library/4.0/Rcpp/include' -I'/home/travis/R/x86_64-pc-linux-gnu-library/4.0/BH/include' -I'/home/travis/R/x86_64-pc-linux-gnu-library/4.0/RProtoBufLib/include' -I'/home/travis/R/x86_64-pc-linux-gnu-library/4.0/Rhdf5lib/include' -I'/home/travis/R/x86_64-pc-linux-gnu-library/4.0/RcppArmadillo/include' -I'/home/travis/R/x86_64-pc-linux-gnu-library/4.0/RcppParallel/include' -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c boost/libs/filesystem/src/path_traits.cpp -o boost/libs/filesystem/src/path_traits.o
g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/home/travis/R/x86_64-pc-linux-gnu-library/4.0/Rcpp/include' -I'/home/travis/R/x86_64-pc-linux-gnu-library/4.0/BH/include' -I'/home/travis/R/x86_64-pc-linux-gnu-library/4.0/RProtoBufLib/include' -I'/home/travis/R/x86_64-pc-linux-gnu-library/4.0/Rhdf5lib/include' -I'/home/travis/R/x86_64-pc-linux-gnu-library/4.0/RcppArmadillo/include' -I'/home/travis/R/x86_64-pc-linux-gnu-library/4.0/RcppParallel/include' -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c boost/libs/filesystem/src/codecvt_error_category.cpp -o boost/libs/filesystem/src/codecvt_error_category.o
g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/home/travis/R/x86_64-pc-linux-gnu-library/4.0/Rcpp/include' -I'/home/travis/R/x86_64-pc-linux-gnu-library/4.0/BH/include' -I'/home/travis/R/x86_64-pc-linux-gnu-library/4.0/RProtoBufLib/include' -I'/home/travis/R/x86_64-pc-linux-gnu-library/4.0/Rhdf5lib/include' -I'/home/travis/R/x86_64-pc-linux-gnu-library/4.0/RcppArmadillo/include' -I'/home/travis/R/x86_64-pc-linux-gnu-library/4.0/RcppParallel/include' -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c boost/libs/filesystem/src/utf8_codecvt_facet.cpp -o boost/libs/filesystem/src/utf8_codecvt_facet.o
g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/home/travis/R/x86_64-pc-linux-gnu-library/4.0/Rcpp/include' -I'/home/travis/R/x86_64-pc-linux-gnu-library/4.0/BH/include' -I'/home/travis/R/x86_64-pc-linux-gnu-library/4.0/RProtoBufLib/include' -I'/home/travis/R/x86_64-pc-linux-gnu-library/4.0/Rhdf5lib/include' -I'/home/travis/R/x86_64-pc-linux-gnu-library/4.0/RcppArmadillo/include' -I'/home/travis/R/x86_64-pc-linux-gnu-library/4.0/RcppParallel/include' -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c boost/libs/filesystem/src/windows_file_codecvt.cpp -o boost/libs/filesystem/src/windows_file_codecvt.o
g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/home/travis/R/x86_64-pc-linux-gnu-library/4.0/Rcpp/include' -I'/home/travis/R/x86_64-pc-linux-gnu-library/4.0/BH/include' -I'/home/travis/R/x86_64-pc-linux-gnu-library/4.0/RProtoBufLib/include' -I'/home/travis/R/x86_64-pc-linux-gnu-library/4.0/Rhdf5lib/include' -I'/home/travis/R/x86_64-pc-linux-gnu-library/4.0/RcppArmadillo/include' -I'/home/travis/R/x86_64-pc-linux-gnu-library/4.0/RcppParallel/include' -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c boost/libs/filesystem/src/exception.cpp -o boost/libs/filesystem/src/exception.o
g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/home/travis/R/x86_64-pc-linux-gnu-library/4.0/Rcpp/include' -I'/home/travis/R/x86_64-pc-linux-gnu-library/4.0/BH/include' -I'/home/travis/R/x86_64-pc-linux-gnu-library/4.0/RProtoBufLib/include' -I'/home/travis/R/x86_64-pc-linux-gnu-library/4.0/Rhdf5lib/include' -I'/home/travis/R/x86_64-pc-linux-gnu-library/4.0/RcppArmadillo/include' -I'/home/travis/R/x86_64-pc-linux-gnu-library/4.0/RcppParallel/include' -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c boost/libs/filesystem/src/directory.cpp -o boost/libs/filesystem/src/directory.o
g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/home/travis/R/x86_64-pc-linux-gnu-library/4.0/Rcpp/include' -I'/home/travis/R/x86_64-pc-linux-gnu-library/4.0/BH/include' -I'/home/travis/R/x86_64-pc-linux-gnu-library/4.0/RProtoBufLib/include' -I'/home/travis/R/x86_64-pc-linux-gnu-library/4.0/Rhdf5lib/include' -I'/home/travis/R/x86_64-pc-linux-gnu-library/4.0/RcppArmadillo/include' -I'/home/travis/R/x86_64-pc-linux-gnu-library/4.0/RcppParallel/include' -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c boost/libs/filesystem/src/path.cpp -o boost/libs/filesystem/src/path.o
g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/home/travis/R/x86_64-pc-linux-gnu-library/4.0/Rcpp/include' -I'/home/travis/R/x86_64-pc-linux-gnu-library/4.0/BH/include' -I'/home/travis/R/x86_64-pc-linux-gnu-library/4.0/RProtoBufLib/include' -I'/home/travis/R/x86_64-pc-linux-gnu-library/4.0/Rhdf5lib/include' -I'/home/travis/R/x86_64-pc-linux-gnu-library/4.0/RcppArmadillo/include' -I'/home/travis/R/x86_64-pc-linux-gnu-library/4.0/RcppParallel/include' -fpic -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c boost/libs/filesystem/src/operations.cpp -o boost/libs/filesystem/src/operations.o
boost/libs/filesystem/src/operations.cpp: In function ‘boost::filesystem::path boost::filesystem::absolute(const boost::filesystem::path&, const boost::filesystem::path&)’:
boost/libs/filesystem/src/operations.cpp:680:6: error: redefinition of ‘boost::filesystem::path boost::filesystem::absolute(const boost::filesystem::path&, const boost::filesystem::path&)’
path absolute(const path& p, const path& base)
^
In file included from boost/libs/filesystem/src/operations.cpp:71:0:
/home/travis/R/x86_64-pc-linux-gnu-library/4.0/BH/include/boost/filesystem/operations.hpp:258:6: note: ‘boost::filesystem::path boost::filesystem::absolute(const boost::filesystem::path&, const boost::filesystem::path&)’ previously defined here
path absolute(const path& p, const path& base=current_path()) {return detail::absolute(p, base);}
^
boost/libs/filesystem/src/operations.cpp: In function ‘boost::filesystem::path boost::filesystem::detail::canonical(const boost::filesystem::path&, const boost::filesystem::path&, boost::system::error_code*)’:
boost/libs/filesystem/src/operations.cpp:747:54: error: call of overloaded ‘absolute(const boost::filesystem::path&, const boost::filesystem::path&)’ is ambiguous
path source (p.is_absolute() ? p : absolute(p, base));
^
In file included from boost/libs/filesystem/src/operations.cpp:71:0:
/home/travis/R/x86_64-pc-linux-gnu-library/4.0/BH/include/boost/filesystem/operations.hpp:96:6: note: candidate: boost::filesystem::path boost::filesystem::detail::absolute(const boost::filesystem::path&, const boost::filesystem::path&, boost::system::error_code*)
path absolute(const path& p, const path& base, system::error_code* ec=0);
^
/home/travis/R/x86_64-pc-linux-gnu-library/4.0/BH/include/boost/filesystem/operations.hpp:258:6: note: candidate: boost::filesystem::path boost::filesystem::absolute(const boost::filesystem::path&, const boost::filesystem::path&)
path absolute(const path& p, const path& base=current_path()) {return detail::absolute(p, base);}
^
boost/libs/filesystem/src/operations.cpp: In function ‘void boost::filesystem::detail::copy(const boost::filesystem::path&, const boost::filesystem::path&, boost::system::error_code*)’:
boost/libs/filesystem/src/operations.cpp:842:33: error: ‘fail_if_exists’ is not a member of ‘boost::filesystem::detail’
detail::copy_file(from, to, detail::fail_if_exists, ec);
^
boost/libs/filesystem/src/operations.cpp: In function ‘void boost::filesystem::detail::copy_file(const boost::filesystem::path&, const boost::filesystem::path&, boost::filesystem::copy_option, boost::system::error_code*)’:
boost/libs/filesystem/src/operations.cpp:867:15: error: ‘fail_if_exists’ was not declared in this scope
option == fail_if_exists) ? BOOST_ERRNO : 0,
^
boost/libs/filesystem/src/operations.cpp:232:69: note: in definition of macro ‘BOOST_COPY_FILE’
# define BOOST_COPY_FILE(F,T,FailIfExistsBool)copy_file_api(F, T, FailIfExistsBool)
^
boost/libs/filesystem/src/operations.cpp: In function ‘bool boost::filesystem::detail::create_directories(const boost::filesystem::path&, boost::system::error_code*)’:
boost/libs/filesystem/src/operations.cpp:938:32: error: no matching function for call to ‘create_directory(const boost::filesystem::path&, boost::system::error_code*&)’
return create_directory(p, ec);
^
In file included from boost/libs/filesystem/src/operations.cpp:71:0:
/home/travis/R/x86_64-pc-linux-gnu-library/4.0/BH/include/boost/filesystem/operations.hpp:121:6: note: candidate: bool boost::filesystem::detail::create_directory(const boost::filesystem::path&, const boost::filesystem::path*, boost::system::error_code*)
bool create_directory(const path& p, const path* existing, system::error_code* ec=0);
^
/home/travis/R/x86_64-pc-linux-gnu-library/4.0/BH/include/boost/filesystem/operations.hpp:121:6: note: no known conversion for argument 2 from ‘boost::system::error_code*’ to ‘const boost::filesystem::path*’
/home/travis/R/x86_64-pc-linux-gnu-library/4.0/BH/include/boost/filesystem/operations.hpp:388:6: note: candidate: bool boost::filesystem::create_directory(const boost::filesystem::path&, const boost::filesystem::path&, boost::system::error_code&)
bool create_directory(const path& p, const path& existing, system::error_code& ec) BOOST_NOEXCEPT
^
/home/travis/R/x86_64-pc-linux-gnu-library/4.0/BH/include/boost/filesystem/operations.hpp:388:6: note: candidate expects 3 arguments, 2 provided
/home/travis/R/x86_64-pc-linux-gnu-library/4.0/BH/include/boost/filesystem/operations.hpp:385:6: note: candidate: bool boost::filesystem::create_directory(const boost::filesystem::path&, const boost::filesystem::path&)
bool create_directory(const path& p, const path& existing)
^
/home/travis/R/x86_64-pc-linux-gnu-library/4.0/BH/include/boost/filesystem/operations.hpp:385:6: note: no known conversion for argument 2 from ‘boost::system::error_code*’ to ‘const boost::filesystem::path&’
/home/travis/R/x86_64-pc-linux-gnu-library/4.0/BH/include/boost/filesystem/operations.hpp:382:6: note: candidate: bool boost::filesystem::create_directory(const boost::filesystem::path&, boost::system::error_code&)
bool create_directory(const path& p, system::error_code& ec) BOOST_NOEXCEPT
^
/home/travis/R/x86_64-pc-linux-gnu-library/4.0/BH/include/boost/filesystem/operations.hpp:382:6: note: no known conversion for argument 2 from ‘boost::system::error_code*’ to ‘boost::system::error_code&’
/home/travis/R/x86_64-pc-linux-gnu-library/4.0/BH/include/boost/filesystem/operations.hpp:379:6: note: candidate: bool boost::filesystem::create_directory(const boost::filesystem::path&)
bool create_directory(const path& p) {return detail::create_directory(p, 0);}
^
/home/travis/R/x86_64-pc-linux-gnu-library/4.0/BH/include/boost/filesystem/operations.hpp:379:6: note: candidate expects 1 argument, 2 provided
/usr/lib/R/etc/Makeconf:181: recipe for target 'boost/libs/filesystem/src/operations.o' failed
make: *** [boost/libs/filesystem/src/operations.o] Error 1
ERROR: compilation failed for package ‘cytolib’
* removing ‘/home/travis/R/x86_64-pc-linux-gnu-library/4.0/cytolib’
add libver log file to archive folder
When GatingSet is archived, we will also try to save the versions of protobuf,h5 used by cytolib. The txt file won't be used by program but can provide some troubleshooting information to users when something goes wrong with loading/reading archive.
replace valarray with simple C array to avoid the memory reallocation overhead
here during the gating, the flow data as a wholematrix is at least copied 4 times (not mention the channel wise subsetting during the actual hierarchical gating)
- R matrix converted to flowData object (valarray)
- flowData object loaded to GatingHierarchy
- retrieve the transformed flowData from GatingHierarchy
- sync back to R matrix
Even though, we may eliminate the copy during 2nd, 3rd stage by storing the pointer of flowData, it will be still worth to simply use C array in cytolib so that R matrix can be passed as it is and updated in place with zero-copy overhead. (and this will not impact the existing GaitngSet archive since flow data is currently not serialized)
I chose valarray originally for its claimed good performance on the vectorized arithmetic operations (close to fortran), how ever I found that in practice cytolib does element-wise operation most of time (e.g. polygon gating and biexp transforming), thus the disadvantage of using it seems to outweigh the advantage.
Cytolib install fails on github actions CI/CD for Ubuntu 22.04 (C++11?)
Describe the bug
I am using github actions for CI/CD of a package that depends on cytolib. I am specifically specifying to use the github version (remotes::github::RGLab/cytolib) as a dependency in the DESCRIPTION file.
Windows and MacOS binary R CMD check succeed, but on Ubuntu 22.04 with R 4.3.3 I am observing a build error listed below.
2024-04-13T12:58:29.5751920Z * installing *source* package ‘cytolib’ ...
2024-04-13T12:58:29.5754222Z ** using staged installation
2024-04-13T12:58:29.9185594Z checking for a sed that does not truncate output... /usr/bin/sed
2024-04-13T12:58:30.0286921Z checking whether the C++ compiler works... yes
2024-04-13T12:58:30.0288306Z checking for C++ compiler default output file name... a.out
2024-04-13T12:58:30.0681681Z checking for suffix of executables...
2024-04-13T12:58:30.1183968Z checking whether we are cross compiling... no
2024-04-13T12:58:30.1373322Z checking for suffix of object files... o
2024-04-13T12:58:30.1540567Z checking whether we are using the GNU C++ compiler... yes
2024-04-13T12:58:30.1699950Z checking whether g++ -std=gnu++17 accepts -g... yes
2024-04-13T12:58:30.1929642Z checking how to run the C++ preprocessor... g++ -std=gnu++17 -E
2024-04-13T12:58:30.2354774Z checking whether we are using the GNU C++ compiler... (cached) yes
2024-04-13T12:58:30.2356448Z checking whether g++ -std=gnu++17 accepts -g... (cached) yes
2024-04-13T12:58:30.2357726Z configure: Parsing cytolib version info ...
2024-04-13T12:58:30.2389767Z configure: CYTOLIB_VERSION=2.12.1
2024-04-13T12:58:30.2562950Z configure: creating ./config.status
2024-04-13T12:58:30.3317539Z config.status: creating inst/include/cytolib/cytolibConfig.h
2024-04-13T12:58:30.3487525Z config.status: creating src/Makevars
2024-04-13T12:58:30.3909806Z ** libs
2024-04-13T12:58:30.4041392Z using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
2024-04-13T12:58:30.4042575Z using C++11
2024-04-13T12:58:30.4071008Z g++ -std=gnu++11 -I"/opt/R/4.3.3/lib/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -DBOOST_FILESYSTEM_NO_CXX20_ATOMIC_REF -DBOOST_FILESYSTEM_SINGLE_THREADED -I'/home/runner/work/_temp/Library/BH/include' -I'/home/runner/work/_temp/Library/RProtoBufLib/include' -I'/home/runner/work/_temp/Library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -c dummy.cpp -o dummy.o
2024-04-13T12:58:30.4227164Z g++ -std=gnu++11 -I"/opt/R/4.3.3/lib/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -DBOOST_FILESYSTEM_NO_CXX20_ATOMIC_REF -DBOOST_FILESYSTEM_SINGLE_THREADED -I'/home/runner/work/_temp/Library/BH/include' -I'/home/runner/work/_temp/Library/RProtoBufLib/include' -I'/home/runner/work/_temp/Library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -c boost/libs/system/src/error_code.cpp -o boost/libs/system/src/error_code.o
2024-04-13T12:58:30.4566480Z g++ -std=gnu++11 -I"/opt/R/4.3.3/lib/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -DBOOST_FILESYSTEM_NO_CXX20_ATOMIC_REF -DBOOST_FILESYSTEM_SINGLE_THREADED -I'/home/runner/work/_temp/Library/BH/include' -I'/home/runner/work/_temp/Library/RProtoBufLib/include' -I'/home/runner/work/_temp/Library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -c boost/libs/filesystem/src/codecvt_error_category.cpp -o boost/libs/filesystem/src/codecvt_error_category.o
2024-04-13T12:58:30.8613720Z g++ -std=gnu++11 -I"/opt/R/4.3.3/lib/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -DBOOST_FILESYSTEM_NO_CXX20_ATOMIC_REF -DBOOST_FILESYSTEM_SINGLE_THREADED -I'/home/runner/work/_temp/Library/BH/include' -I'/home/runner/work/_temp/Library/RProtoBufLib/include' -I'/home/runner/work/_temp/Library/Rhdf5lib/include' -I/usr/local/include -fpic -g -O2 -c boost/libs/filesystem/src/directory.cpp -o boost/libs/filesystem/src/directory.o
2024-04-13T12:58:31.2679279Z boost/libs/filesystem/src/directory.cpp:100:13: error: no declaration matches ‘boost::filesystem::file_status boost::filesystem::directory_entry::get_status(boost::system::error_code*) const’
2024-04-13T12:58:31.2682355Z 100 | file_status directory_entry::get_status(system::error_code* ec) const
2024-04-13T12:58:31.2683488Z | ^~~~~~~~~~~~~~~
2024-04-13T12:58:31.2737103Z boost/libs/filesystem/src/directory.cpp:100:13: note: no functions named ‘boost::filesystem::file_status boost::filesystem::directory_entry::get_status(boost::system::error_code*) const’
2024-04-13T12:58:31.2739262Z In file included from boost/libs/filesystem/src/directory.cpp:18:
2024-04-13T12:58:31.2741706Z /home/runner/work/_temp/Library/BH/include/boost/filesystem/directory.hpp:65:7: note: ‘class boost::filesystem::directory_entry’ defined here
2024-04-13T12:58:31.2743369Z 65 | class directory_entry
2024-04-13T12:58:31.2743961Z | ^~~~~~~~~~~~~~~
2024-04-13T12:58:31.2746720Z boost/libs/filesystem/src/directory.cpp:127:13: error: no declaration matches ‘boost::filesystem::file_status boost::filesystem::directory_entry::get_symlink_status(boost::system::error_code*) const’
2024-04-13T12:58:31.2749194Z 127 | file_status directory_entry::get_symlink_status(system::error_code* ec) const
2024-04-13T12:58:31.2750206Z | ^~~~~~~~~~~~~~~
2024-04-13T12:58:31.2752728Z boost/libs/filesystem/src/directory.cpp:127:13: note: no functions named ‘boost::filesystem::file_status boost::filesystem::directory_entry::get_symlink_status(boost::system::error_code*) const’
2024-04-13T12:58:31.2754930Z In file included from boost/libs/filesystem/src/directory.cpp:18:
2024-04-13T12:58:31.2757342Z /home/runner/work/_temp/Library/BH/include/boost/filesystem/directory.hpp:65:7: note: ‘class boost::filesystem::directory_entry’ defined here
2024-04-13T12:58:31.2759011Z 65 | class directory_entry
2024-04-13T12:58:31.2759592Z | ^~~~~~~~~~~~~~~
2024-04-13T12:58:31.3245881Z make: *** [/opt/R/4.3.3/lib/R/etc/Makeconf:200: boost/libs/filesystem/src/directory.o] Error 1
2024-04-13T12:58:31.3252062Z ERROR: compilation failed for package ‘cytolib’
It appears that the error is the interface with boost (there are related issues, e.g. #49) Boost (BH) which is installed in by the github actions runner is 1.84.0-0, which should be compatible (887b8d8)
To Reproduce
I would assume any package depending on cytolib (like flowWorkspace etc.) should get a similar error with the same workflow?
Expected behavior
The build to pass on ubuntu 22.04, as it is LTS and I am using BH 1.84.0-0, which is also latest on CRAN?
SessionInfo:
cf. supra - as this is a github action I don't have an interactive session to run sessionInfo, but the necessary versions etc. should be provided
fail to save big gs
Here is the reproducible example
library(flowCore)
library(flowWorkspace)
fr <- flowFrame(matrix(rnorm(1e6), ncol = 2, dimnames = list(NULL, letters[1:2])))
fs <- as(list(s1 = fr), "flowSet")
fs
gs <- GatingSet(fs)
#create big tree with dummy gates
for(i in seq_len(1e3))
{
g <- rectangleGate(a = c(-Inf, Inf))
gs_pop_add(gs, g, name = as.character(i))
}
recompute(gs)
length(gs_get_pop_paths(gs))
#replace the data with smaller version to avoid writing too big h5
fs <- as(list(s1 = flowFrame(matrix(rnorm(2), ncol = 2, dimnames = list(NULL, letters[1:2])))), "flowSet")
gs_cyto_data(gs) <- flowSet_to_cytoset(fs)
#copy gs to mimic large data set
ptrlist <- sampleList <- list()
for(i in seq_len(100))
{
sn <- paste0("s",i)
gs1 <- gs_copy_tree_only(gs)
sampleNames(gs1) <- sn
ptrlist <- c(ptrlist, gs1@pointer)
sampleList <- c(sampleList, sn)
}
#combine to a big gs (a hack to bypass validity check)
gs_big <- new("GatingSet", pointer = flowWorkspace:::.cpp_combineGatingSet(ptrlist, sampleList))
tmp <- tempfile()
save_gs(gs_big, tmp)
[libprotobuf ERROR google/protobuf/io/zero_copy_stream_impl_lite.cc:155] Cannot allocate buffer larger than kint32max for StringOutputStream.
Error in save_gs(gs_big, tmp) : fix the quadgate issue
Currently quadGate is represented as 4 independent rectGate in cytolib, which has issue with the cell events that happen to be on the intersection lines of quadrants. See RGLab/openCyto#199 (comment) for details
In order to assign these cells exclusively to one of the quadrant, we will need to add a new class quadGate in order to achieve the non-overlapping quadrants.
cytolib fails to build with clang9
From: Prof Brian Ripley [email protected]
To: Jiang, Mike [email protected]
Subject: flowWorkspace etc in BioC 3.11 on macOS
Finally this installs on Linux (it is needed for CRAN package flowDiv).But not on macOS (with clang 9, the likely preferred compiler for R
4.0.0, if not clang 10):Error: package or namespace load failed for ‘cytolib’:
.onLoad failed in loadNamespace() for 'cytolib', details:
call: dyn.load(cytolib, local = FALSE, now = TRUE)
error: unable to load shared object
'/Users/ripley/R/test-3.7/00LOCK-cytolib/00new/cytolib/libs/cytolib.so':dlopen(/Users/ripley/R/test-3.7/00LOCK-cytolib/00new/cytolib/libs/cytolib.so,
10): Symbol not found: _ZN5boost10filesystem4pathdVERKS1
Referenced from:
/Users/ripley/R/test-3.7/00LOCK-cytolib/00new/cytolib/libs/cytolib.so
Expected in: flat namespace
in
/Users/ripley/R/test-3.7/00LOCK-cytolib/00new/cytolib/libs/cytolib.sowhich demangles to
boost::filesystem::path::operator/=(boost::filesystem::path const&)
cytolib installation failed under OSX 10.14
Installation of cytolib failed under OSX 10.14 with a following command;
R CMD INSTALL cytolib-trunk.zip
Output is as follows;
Bioconductor version 3.7 (BiocInstaller 1.30.0), ?biocLite for help
Successfully loaded .Rprofile at Wed Oct 10 20:01:39 2018
Error in rawToChar(block[seq_len(ns)]) : embedded nul in string: 'PK\003\004\n\0\0\0\0\0\xd8k\034M\0\0\0\0\0\0\0\0\0\0\0\0\016\0\t\0cytolib-trunk/UT\005\0\001\xf8\xb0\x85[PK\003\004\n\0\0\0\b\0\xd8k\034M\002\xee(5\x9a\001\0\0w\002\0\0\031\0\t\0cytolib-trunk/DES`
Installation error in macOS
Describe the bug
Installation from GitHub failed.
> remotes::install_github("RGLab/cytolib")
Downloading GitHub repo RGLab/cytolib@HEAD
Skipping 2 packages ahead of CRAN: Rhdf5lib, RProtoBufLib
✓ checking for file ‘/private/var/folders/0l/27166dcs57z48cjmt6y57r540000gp/T/Rtmpx27kuL/remotes1867d162102bb/RGLab-cytolib-b3931f3/DESCRIPTION’ ...
─ preparing ‘cytolib’: (363ms)
✓ checking DESCRIPTION meta-information
─ cleaning src
─ running ‘cleanup’
─ checking for LF line-endings in source and make files and shell scripts (495ms)
─ checking for empty or unneeded directories
─ building ‘cytolib_2.1.18.tar.gz’
Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, :
storing paths of more than 100 bytes is not portable:
‘cytolib/thirdparty/protobuf/win/include/google/protobuf/stubs/atomicops_internals_atomicword_compat.h’
* installing *source* package ‘cytolib’ ...
** using staged installation
checking for a sed that does not truncate output... /usr/bin/sed
checking for g++... g++
checking whether the C++ compiler works... yes
checking for C++ compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C++ compiler... yes
checking whether g++ accepts -g... yes
checking how to run the C++ preprocessor... g++ -E
checking whether we are using the GNU C++ compiler... (cached) yes
checking whether g++ accepts -g... (cached) yes
checking for pkg-config... /usr/local/bin/pkg-config
checking pkg-config knows TileDB... no
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for ANSI C header files... rm: conftest.dSYM: is a directory
rm: conftest.dSYM: is a directory
no
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking tiledb/tiledb.h usability... no
checking tiledb/tiledb.h presence... no
checking for tiledb/tiledb.h... no
configure: No tiledb is found, build without tiledb...
configure: Parsing cytolib version info ...
configure: CYTOLIB_VERSION=2.1.18
configure: creating ./config.status
config.status: creating inst/include/cytolib/cytolibConfig.h
config.status: creating src/Makevars
** libs
/usr/local/Cellar/gcc@8/8.4.0_1/bin/g++-8 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RProtoBufLib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhdf5lib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppParallel/include' -I/usr/local/include -fPIC -Wall -g -O2 -c CytoFrame.cpp -o CytoFrame.o
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/arg.hpp:25,
from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/placeholders.hpp:24,
from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/iterator/iterator_categories.hpp:16,
from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/iterator/iterator_facade.hpp:13,
from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/range/iterator_range_core.hpp:27,
from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/range/iterator_range.hpp:13,
from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/range/as_literal.hpp:22,
from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/algorithm/string/trim.hpp:19,
from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/algorithm/string.hpp:19,
from ../inst/include/cytolib/transformation.hpp:18,
from ../inst/include/cytolib/compensation.hpp:15,
from ../inst/include/cytolib/CytoFrame.hpp:16,
from CytoFrame.cpp:3:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
failed ************ (Pred::************
^
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
failed ************ (boost::mpl::not_<Pred>::************
^
In file included from ../inst/include/cytolib/CytoFrame.hpp:16,
from CytoFrame.cpp:3:
../inst/include/cytolib/compensation.hpp: In constructor 'cytolib::compensation::compensation(const string&)':
../inst/include/cytolib/compensation.hpp:50:20: warning: comparison of integer expressions of different signedness: 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare]
if(valVec.size() != 1+n+n*n){
~~~~~~~~~~~~~~^~~~~~~~~~
../inst/include/cytolib/compensation.hpp:54:21: warning: comparison of integer expressions of different signedness: 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare]
if(valVec.size() == 1+n+2*n*n){
~~~~~~~~~~~~~~^~~~~~~~~~~~
../inst/include/cytolib/compensation.hpp:60:33: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'long unsigned int'} [-Wsign-compare]
for(int i = 1+n, j = 1+n; i < valVec_fixed.size(); i++, j+=2)
~~^~~~~~~~~~~~~~~~~~~~~
/usr/local/Cellar/gcc@8/8.4.0_1/bin/g++-8 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RProtoBufLib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhdf5lib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppParallel/include' -I/usr/local/include -fPIC -Wall -g -O2 -c CytoFrameView.cpp -o CytoFrameView.o
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/arg.hpp:25,
from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/placeholders.hpp:24,
from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/iterator/iterator_categories.hpp:16,
from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/iterator/iterator_facade.hpp:13,
from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/range/iterator_range_core.hpp:27,
from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/range/iterator_range.hpp:13,
from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/range/as_literal.hpp:22,
from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/algorithm/string/trim.hpp:19,
from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/algorithm/string.hpp:19,
from ../inst/include/cytolib/transformation.hpp:18,
from ../inst/include/cytolib/compensation.hpp:15,
from ../inst/include/cytolib/CytoFrame.hpp:16,
from ../inst/include/cytolib/MemCytoFrame.hpp:12,
from ../inst/include/cytolib/CytoFrameView.hpp:12,
from CytoFrameView.cpp:3:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
failed ************ (Pred::************
^
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
failed ************ (boost::mpl::not_<Pred>::************
^
In file included from ../inst/include/cytolib/CytoFrame.hpp:16,
from ../inst/include/cytolib/MemCytoFrame.hpp:12,
from ../inst/include/cytolib/CytoFrameView.hpp:12,
from CytoFrameView.cpp:3:
../inst/include/cytolib/compensation.hpp: In constructor 'cytolib::compensation::compensation(const string&)':
../inst/include/cytolib/compensation.hpp:50:20: warning: comparison of integer expressions of different signedness: 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare]
if(valVec.size() != 1+n+n*n){
~~~~~~~~~~~~~~^~~~~~~~~~
../inst/include/cytolib/compensation.hpp:54:21: warning: comparison of integer expressions of different signedness: 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare]
if(valVec.size() == 1+n+2*n*n){
~~~~~~~~~~~~~~^~~~~~~~~~~~
../inst/include/cytolib/compensation.hpp:60:33: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'long unsigned int'} [-Wsign-compare]
for(int i = 1+n, j = 1+n; i < valVec_fixed.size(); i++, j+=2)
~~^~~~~~~~~~~~~~~~~~~~~
/usr/local/Cellar/gcc@8/8.4.0_1/bin/g++-8 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RProtoBufLib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhdf5lib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppParallel/include' -I/usr/local/include -fPIC -Wall -g -O2 -c CytoVFS.cpp -o CytoVFS.o
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/arg.hpp:25,
from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/placeholders.hpp:24,
from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/iterator/iterator_categories.hpp:16,
from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/iterator/iterator_facade.hpp:13,
from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/filesystem/path.hpp:29,
from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/filesystem.hpp:16,
from ../inst/include/cytolib/CytoVFS.hpp:16,
from CytoVFS.cpp:8:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
failed ************ (Pred::************
^
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
failed ************ (boost::mpl::not_<Pred>::************
^
/usr/local/Cellar/gcc@8/8.4.0_1/bin/g++-8 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RProtoBufLib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhdf5lib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppParallel/include' -I/usr/local/include -fPIC -Wall -g -O2 -c GatingHierarchy.cpp -o GatingHierarchy.o
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/arg.hpp:25,
from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/placeholders.hpp:24,
from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/iterator/iterator_categories.hpp:16,
from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/iterator/iterator_facade.hpp:13,
from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/range/iterator_range_core.hpp:27,
from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/range/iterator_range.hpp:13,
from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/range/as_literal.hpp:22,
from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/algorithm/string/trim.hpp:19,
from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/algorithm/string.hpp:19,
from ../inst/include/cytolib/transformation.hpp:18,
from ../inst/include/cytolib/compensation.hpp:15,
from ../inst/include/cytolib/CytoFrame.hpp:16,
from ../inst/include/cytolib/MemCytoFrame.hpp:12,
from ../inst/include/cytolib/gate.hpp:12,
from ../inst/include/cytolib/POPINDICES.hpp:14,
from ../inst/include/cytolib/nodeProperties.hpp:13,
from ../inst/include/cytolib/populationTree.hpp:13,
from ../inst/include/cytolib/GatingHierarchy.hpp:17,
from GatingHierarchy.cpp:3:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
failed ************ (Pred::************
^
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
failed ************ (boost::mpl::not_<Pred>::************
^
In file included from ../inst/include/cytolib/CytoFrame.hpp:16,
from ../inst/include/cytolib/MemCytoFrame.hpp:12,
from ../inst/include/cytolib/gate.hpp:12,
from ../inst/include/cytolib/POPINDICES.hpp:14,
from ../inst/include/cytolib/nodeProperties.hpp:13,
from ../inst/include/cytolib/populationTree.hpp:13,
from ../inst/include/cytolib/GatingHierarchy.hpp:17,
from GatingHierarchy.cpp:3:
../inst/include/cytolib/compensation.hpp: In constructor 'cytolib::compensation::compensation(const string&)':
../inst/include/cytolib/compensation.hpp:50:20: warning: comparison of integer expressions of different signedness: 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare]
if(valVec.size() != 1+n+n*n){
~~~~~~~~~~~~~~^~~~~~~~~~
../inst/include/cytolib/compensation.hpp:54:21: warning: comparison of integer expressions of different signedness: 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare]
if(valVec.size() == 1+n+2*n*n){
~~~~~~~~~~~~~~^~~~~~~~~~~~
../inst/include/cytolib/compensation.hpp:60:33: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'long unsigned int'} [-Wsign-compare]
for(int i = 1+n, j = 1+n; i < valVec_fixed.size(); i++, j+=2)
~~^~~~~~~~~~~~~~~~~~~~~
/usr/local/Cellar/gcc@8/8.4.0_1/bin/g++-8 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RProtoBufLib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhdf5lib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppParallel/include' -I/usr/local/include -fPIC -Wall -g -O2 -c GatingSet.cpp -o GatingSet.o
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/arg.hpp:25,
from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/placeholders.hpp:24,
from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/iterator/iterator_categories.hpp:16,
from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/iterator/iterator_facade.hpp:13,
from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/range/iterator_range_core.hpp:27,
from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/range/iterator_range.hpp:13,
from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/range/as_literal.hpp:22,
from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/algorithm/string/trim.hpp:19,
from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/algorithm/string.hpp:19,
from ../inst/include/cytolib/transformation.hpp:18,
from ../inst/include/cytolib/compensation.hpp:15,
from ../inst/include/cytolib/CytoFrame.hpp:16,
from ../inst/include/cytolib/MemCytoFrame.hpp:12,
from ../inst/include/cytolib/gate.hpp:12,
from ../inst/include/cytolib/POPINDICES.hpp:14,
from ../inst/include/cytolib/nodeProperties.hpp:13,
from ../inst/include/cytolib/populationTree.hpp:13,
from ../inst/include/cytolib/GatingHierarchy.hpp:17,
from ../inst/include/cytolib/GatingSet.hpp:14,
from GatingSet.cpp:3:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
failed ************ (Pred::************
^
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
failed ************ (boost::mpl::not_<Pred>::************
^
In file included from ../inst/include/cytolib/CytoFrame.hpp:16,
from ../inst/include/cytolib/MemCytoFrame.hpp:12,
from ../inst/include/cytolib/gate.hpp:12,
from ../inst/include/cytolib/POPINDICES.hpp:14,
from ../inst/include/cytolib/nodeProperties.hpp:13,
from ../inst/include/cytolib/populationTree.hpp:13,
from ../inst/include/cytolib/GatingHierarchy.hpp:17,
from ../inst/include/cytolib/GatingSet.hpp:14,
from GatingSet.cpp:3:
../inst/include/cytolib/compensation.hpp: In constructor 'cytolib::compensation::compensation(const string&)':
../inst/include/cytolib/compensation.hpp:50:20: warning: comparison of integer expressions of different signedness: 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare]
if(valVec.size() != 1+n+n*n){
~~~~~~~~~~~~~~^~~~~~~~~~
../inst/include/cytolib/compensation.hpp:54:21: warning: comparison of integer expressions of different signedness: 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare]
if(valVec.size() == 1+n+2*n*n){
~~~~~~~~~~~~~~^~~~~~~~~~~~
../inst/include/cytolib/compensation.hpp:60:33: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'long unsigned int'} [-Wsign-compare]
for(int i = 1+n, j = 1+n; i < valVec_fixed.size(); i++, j+=2)
~~^~~~~~~~~~~~~~~~~~~~~
In file included from ../inst/include/cytolib/compensation.hpp:19,
from ../inst/include/cytolib/CytoFrame.hpp:16,
from ../inst/include/cytolib/MemCytoFrame.hpp:12,
from ../inst/include/cytolib/gate.hpp:12,
from ../inst/include/cytolib/POPINDICES.hpp:14,
from ../inst/include/cytolib/nodeProperties.hpp:13,
from ../inst/include/cytolib/populationTree.hpp:13,
from ../inst/include/cytolib/GatingHierarchy.hpp:17,
from ../inst/include/cytolib/GatingSet.hpp:14,
from GatingSet.cpp:3:
../inst/include/cytolib/global.hpp: In constructor 'cytolib::GatingSet::GatingSet(std::__cxx11::string, bool, bool, std::vector<std::__cxx11::basic_string<char> >, bool, cytolib::CytoCtx)':
../inst/include/cytolib/global.hpp:29:3: warning: 'fmt' may be used uninitialized in this function [-Wmaybe-uninitialized]
switch(fmt)
^~~~~~
GatingSet.cpp:30:14: note: 'fmt' was declared here
FileFormat fmt;
^~~
/usr/local/Cellar/gcc@8/8.4.0_1/bin/g++-8 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RProtoBufLib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhdf5lib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppParallel/include' -I/usr/local/include -fPIC -Wall -g -O2 -c GatingSet.pb.cc -o GatingSet.pb.o
/usr/local/Cellar/gcc@8/8.4.0_1/bin/g++-8 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RProtoBufLib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhdf5lib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppParallel/include' -I/usr/local/include -fPIC -Wall -g -O2 -c H5CytoFrame.cpp -o H5CytoFrame.o
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/arg.hpp:25,
from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/placeholders.hpp:24,
from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/iterator/iterator_categories.hpp:16,
from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/iterator/iterator_facade.hpp:13,
from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/range/iterator_range_core.hpp:27,
from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/range/iterator_range.hpp:13,
from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/range/as_literal.hpp:22,
from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/algorithm/string/trim.hpp:19,
from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/algorithm/string.hpp:19,
from ../inst/include/cytolib/transformation.hpp:18,
from ../inst/include/cytolib/compensation.hpp:15,
from ../inst/include/cytolib/CytoFrame.hpp:16,
from ../inst/include/cytolib/MemCytoFrame.hpp:12,
from ../inst/include/cytolib/H5CytoFrame.hpp:12,
from H5CytoFrame.cpp:3:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
failed ************ (Pred::************
^
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
failed ************ (boost::mpl::not_<Pred>::************
^
In file included from ../inst/include/cytolib/CytoFrame.hpp:16,
from ../inst/include/cytolib/MemCytoFrame.hpp:12,
from ../inst/include/cytolib/H5CytoFrame.hpp:12,
from H5CytoFrame.cpp:3:
../inst/include/cytolib/compensation.hpp: In constructor 'cytolib::compensation::compensation(const string&)':
../inst/include/cytolib/compensation.hpp:50:20: warning: comparison of integer expressions of different signedness: 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare]
if(valVec.size() != 1+n+n*n){
~~~~~~~~~~~~~~^~~~~~~~~~
../inst/include/cytolib/compensation.hpp:54:21: warning: comparison of integer expressions of different signedness: 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare]
if(valVec.size() == 1+n+2*n*n){
~~~~~~~~~~~~~~^~~~~~~~~~~~
../inst/include/cytolib/compensation.hpp:60:33: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'long unsigned int'} [-Wsign-compare]
for(int i = 1+n, j = 1+n; i < valVec_fixed.size(); i++, j+=2)
~~^~~~~~~~~~~~~~~~~~~~~
/usr/local/Cellar/gcc@8/8.4.0_1/bin/g++-8 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RProtoBufLib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhdf5lib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppParallel/include' -I/usr/local/include -fPIC -Wall -g -O2 -c MemCytoFrame.cpp -o MemCytoFrame.o
MemCytoFrame.cpp:551: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
#pragma omp parallel for
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/arg.hpp:25,
from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/placeholders.hpp:24,
from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/iterator/iterator_categories.hpp:16,
from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/iterator/iterator_facade.hpp:13,
from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/range/iterator_range_core.hpp:27,
from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/range/iterator_range.hpp:13,
from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/range/as_literal.hpp:22,
from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/algorithm/string/trim.hpp:19,
from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/algorithm/string.hpp:19,
from ../inst/include/cytolib/transformation.hpp:18,
from ../inst/include/cytolib/compensation.hpp:15,
from ../inst/include/cytolib/CytoFrame.hpp:16,
from ../inst/include/cytolib/MemCytoFrame.hpp:12,
from MemCytoFrame.cpp:3:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
failed ************ (Pred::************
^
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
failed ************ (boost::mpl::not_<Pred>::************
^
In file included from ../inst/include/cytolib/CytoFrame.hpp:16,
from ../inst/include/cytolib/MemCytoFrame.hpp:12,
from MemCytoFrame.cpp:3:
../inst/include/cytolib/compensation.hpp: In constructor 'cytolib::compensation::compensation(const string&)':
../inst/include/cytolib/compensation.hpp:50:20: warning: comparison of integer expressions of different signedness: 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare]
if(valVec.size() != 1+n+n*n){
~~~~~~~~~~~~~~^~~~~~~~~~
../inst/include/cytolib/compensation.hpp:54:21: warning: comparison of integer expressions of different signedness: 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare]
if(valVec.size() == 1+n+2*n*n){
~~~~~~~~~~~~~~^~~~~~~~~~~~
../inst/include/cytolib/compensation.hpp:60:33: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'long unsigned int'} [-Wsign-compare]
for(int i = 1+n, j = 1+n; i < valVec_fixed.size(); i++, j+=2)
~~^~~~~~~~~~~~~~~~~~~~~
/usr/local/Cellar/gcc@8/8.4.0_1/bin/g++-8 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RProtoBufLib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhdf5lib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppParallel/include' -I/usr/local/include -fPIC -Wall -g -O2 -c POPINDICES.cpp -o POPINDICES.o
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/arg.hpp:25,
from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/placeholders.hpp:24,
from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/iterator/iterator_categories.hpp:16,
from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/iterator/iterator_facade.hpp:13,
from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/range/iterator_range_core.hpp:27,
from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/range/iterator_range.hpp:13,
from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/range/as_literal.hpp:22,
from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/algorithm/string/trim.hpp:19,
from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/algorithm/string.hpp:19,
from ../inst/include/cytolib/transformation.hpp:18,
from ../inst/include/cytolib/compensation.hpp:15,
from ../inst/include/cytolib/CytoFrame.hpp:16,
from ../inst/include/cytolib/MemCytoFrame.hpp:12,
from ../inst/include/cytolib/gate.hpp:12,
from ../inst/include/cytolib/POPINDICES.hpp:14,
from POPINDICES.cpp:3:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
failed ************ (Pred::************
^
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
failed ************ (boost::mpl::not_<Pred>::************
^
In file included from ../inst/include/cytolib/CytoFrame.hpp:16,
from ../inst/include/cytolib/MemCytoFrame.hpp:12,
from ../inst/include/cytolib/gate.hpp:12,
from ../inst/include/cytolib/POPINDICES.hpp:14,
from POPINDICES.cpp:3:
../inst/include/cytolib/compensation.hpp: In constructor 'cytolib::compensation::compensation(const string&)':
../inst/include/cytolib/compensation.hpp:50:20: warning: comparison of integer expressions of different signedness: 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare]
if(valVec.size() != 1+n+n*n){
~~~~~~~~~~~~~~^~~~~~~~~~
../inst/include/cytolib/compensation.hpp:54:21: warning: comparison of integer expressions of different signedness: 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare]
if(valVec.size() == 1+n+2*n*n){
~~~~~~~~~~~~~~^~~~~~~~~~~~
../inst/include/cytolib/compensation.hpp:60:33: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'long unsigned int'} [-Wsign-compare]
for(int i = 1+n, j = 1+n; i < valVec_fixed.size(); i++, j+=2)
~~^~~~~~~~~~~~~~~~~~~~~
/usr/local/Cellar/gcc@8/8.4.0_1/bin/g++-8 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RProtoBufLib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhdf5lib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppParallel/include' -I/usr/local/include -fPIC -Wall -g -O2 -c calibrationTable.cpp -o calibrationTable.o
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/foreach.hpp:76,
from calibrationTable.cpp:5:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
failed ************ (Pred::************
^
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
failed ************ (boost::mpl::not_<Pred>::************
^
/usr/local/Cellar/gcc@8/8.4.0_1/bin/g++-8 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RProtoBufLib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhdf5lib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppParallel/include' -I/usr/local/include -fPIC -Wall -g -O2 -c compensation.cpp -o compensation.o
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/arg.hpp:25,
from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/placeholders.hpp:24,
from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/iterator/iterator_categories.hpp:16,
from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/iterator/iterator_facade.hpp:13,
from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/range/iterator_range_core.hpp:27,
from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/range/iterator_range.hpp:13,
from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/range/as_literal.hpp:22,
from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/algorithm/string/trim.hpp:19,
from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/algorithm/string.hpp:19,
from ../inst/include/cytolib/transformation.hpp:18,
from ../inst/include/cytolib/compensation.hpp:15,
from compensation.cpp:3:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
failed ************ (Pred::************
^
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
failed ************ (boost::mpl::not_<Pred>::************
^
In file included from compensation.cpp:3:
../inst/include/cytolib/compensation.hpp: In constructor 'cytolib::compensation::compensation(const string&)':
../inst/include/cytolib/compensation.hpp:50:20: warning: comparison of integer expressions of different signedness: 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare]
if(valVec.size() != 1+n+n*n){
~~~~~~~~~~~~~~^~~~~~~~~~
../inst/include/cytolib/compensation.hpp:54:21: warning: comparison of integer expressions of different signedness: 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare]
if(valVec.size() == 1+n+2*n*n){
~~~~~~~~~~~~~~^~~~~~~~~~~~
../inst/include/cytolib/compensation.hpp:60:33: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'long unsigned int'} [-Wsign-compare]
for(int i = 1+n, j = 1+n; i < valVec_fixed.size(); i++, j+=2)
~~^~~~~~~~~~~~~~~~~~~~~
/usr/local/Cellar/gcc@8/8.4.0_1/bin/g++-8 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RProtoBufLib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhdf5lib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppParallel/include' -I/usr/local/include -fPIC -Wall -g -O2 -c dummy.cpp -o dummy.o
/usr/local/Cellar/gcc@8/8.4.0_1/bin/g++-8 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RProtoBufLib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhdf5lib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppParallel/include' -I/usr/local/include -fPIC -Wall -g -O2 -c ellipse2points.cpp -o ellipse2points.o
/usr/local/Cellar/gcc@8/8.4.0_1/bin/g++-8 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RProtoBufLib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhdf5lib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppParallel/include' -I/usr/local/include -fPIC -Wall -g -O2 -c gate.cpp -o gate.o
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/arg.hpp:25,
from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/placeholders.hpp:24,
from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/iterator/iterator_categories.hpp:16,
from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/iterator/iterator_facade.hpp:13,
from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/range/iterator_range_core.hpp:27,
from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/range/iterator_range.hpp:13,
from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/range/as_literal.hpp:22,
from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/algorithm/string/trim.hpp:19,
from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/algorithm/string.hpp:19,
from ../inst/include/cytolib/transformation.hpp:18,
from ../inst/include/cytolib/compensation.hpp:15,
from ../inst/include/cytolib/CytoFrame.hpp:16,
from ../inst/include/cytolib/MemCytoFrame.hpp:12,
from ../inst/include/cytolib/gate.hpp:12,
from gate.cpp:3:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
failed ************ (Pred::************
^
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
failed ************ (boost::mpl::not_<Pred>::************
^
In file included from ../inst/include/cytolib/CytoFrame.hpp:16,
from ../inst/include/cytolib/MemCytoFrame.hpp:12,
from ../inst/include/cytolib/gate.hpp:12,
from gate.cpp:3:
../inst/include/cytolib/compensation.hpp: In constructor 'cytolib::compensation::compensation(const string&)':
../inst/include/cytolib/compensation.hpp:50:20: warning: comparison of integer expressions of different signedness: 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare]
if(valVec.size() != 1+n+n*n){
~~~~~~~~~~~~~~^~~~~~~~~~
../inst/include/cytolib/compensation.hpp:54:21: warning: comparison of integer expressions of different signedness: 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare]
if(valVec.size() == 1+n+2*n*n){
~~~~~~~~~~~~~~^~~~~~~~~~~~
../inst/include/cytolib/compensation.hpp:60:33: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'long unsigned int'} [-Wsign-compare]
for(int i = 1+n, j = 1+n; i < valVec_fixed.size(); i++, j+=2)
~~^~~~~~~~~~~~~~~~~~~~~
/usr/local/Cellar/gcc@8/8.4.0_1/bin/g++-8 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RProtoBufLib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhdf5lib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppParallel/include' -I/usr/local/include -fPIC -Wall -g -O2 -c global.cpp -o global.o
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/arg.hpp:25,
from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/placeholders.hpp:24,
from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/iterator/iterator_categories.hpp:16,
from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/iterator/iterator_facade.hpp:13,
from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/filesystem/path.hpp:29,
from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/filesystem.hpp:16,
from ../inst/include/cytolib/CytoVFS.hpp:16,
from ../inst/include/cytolib/global.hpp:21,
from global.cpp:3:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
failed ************ (Pred::************
^
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
failed ************ (boost::mpl::not_<Pred>::************
^
global.cpp: In function 'std::__cxx11::string cytolib::s3_to_http(std::__cxx11::string)':
global.cpp:46:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'long unsigned int'} [-Wsign-compare]
for(int i = 1; i < tokens.size(); i++)
~~^~~~~~~~~~~~~~~
/usr/local/Cellar/gcc@8/8.4.0_1/bin/g++-8 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RProtoBufLib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhdf5lib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppParallel/include' -I/usr/local/include -fPIC -Wall -g -O2 -c in_polygon.cpp -o in_polygon.o
/usr/local/Cellar/gcc@8/8.4.0_1/bin/g++-8 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RProtoBufLib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhdf5lib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppParallel/include' -I/usr/local/include -fPIC -Wall -g -O2 -c nodeProperties.cpp -o nodeProperties.o
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/arg.hpp:25,
from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/placeholders.hpp:24,
from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/iterator/iterator_categories.hpp:16,
from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/iterator/iterator_facade.hpp:13,
from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/range/iterator_range_core.hpp:27,
from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/range/iterator_range.hpp:13,
from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/range/as_literal.hpp:22,
from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/algorithm/string/trim.hpp:19,
from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/algorithm/string.hpp:19,
from ../inst/include/cytolib/transformation.hpp:18,
from ../inst/include/cytolib/compensation.hpp:15,
from ../inst/include/cytolib/CytoFrame.hpp:16,
from ../inst/include/cytolib/MemCytoFrame.hpp:12,
from ../inst/include/cytolib/gate.hpp:12,
from ../inst/include/cytolib/POPINDICES.hpp:14,
from ../inst/include/cytolib/nodeProperties.hpp:13,
from nodeProperties.cpp:3:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
failed ************ (Pred::************
^
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
failed ************ (boost::mpl::not_<Pred>::************
^
In file included from ../inst/include/cytolib/CytoFrame.hpp:16,
from ../inst/include/cytolib/MemCytoFrame.hpp:12,
from ../inst/include/cytolib/gate.hpp:12,
from ../inst/include/cytolib/POPINDICES.hpp:14,
from ../inst/include/cytolib/nodeProperties.hpp:13,
from nodeProperties.cpp:3:
../inst/include/cytolib/compensation.hpp: In constructor 'cytolib::compensation::compensation(const string&)':
../inst/include/cytolib/compensation.hpp:50:20: warning: comparison of integer expressions of different signedness: 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare]
if(valVec.size() != 1+n+n*n){
~~~~~~~~~~~~~~^~~~~~~~~~
../inst/include/cytolib/compensation.hpp:54:21: warning: comparison of integer expressions of different signedness: 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'long unsigned int'} and 'int' [-Wsign-compare]
if(valVec.size() == 1+n+2*n*n){
~~~~~~~~~~~~~~^~~~~~~~~~~~
../inst/include/cytolib/compensation.hpp:60:33: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'long unsigned int'} [-Wsign-compare]
for(int i = 1+n, j = 1+n; i < valVec_fixed.size(); i++, j+=2)
~~^~~~~~~~~~~~~~~~~~~~~
/usr/local/Cellar/gcc@8/8.4.0_1/bin/g++-8 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RProtoBufLib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhdf5lib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppParallel/include' -I/usr/local/include -fPIC -Wall -g -O2 -c spline.cpp -o spline.o
/usr/local/Cellar/gcc@8/8.4.0_1/bin/g++-8 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RProtoBufLib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhdf5lib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppParallel/include' -I/usr/local/include -fPIC -Wall -g -O2 -c trans_group.cpp -o trans_group.o
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/arg.hpp:25,
from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/placeholders.hpp:24,
from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/iterator/iterator_categories.hpp:16,
from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/iterator/iterator_facade.hpp:13,
from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/range/iterator_range_core.hpp:27,
from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/range/iterator_range.hpp:13,
from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/range/as_literal.hpp:22,
from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/algorithm/string/trim.hpp:19,
from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/algorithm/string.hpp:19,
from ../inst/include/cytolib/transformation.hpp:18,
from ../inst/include/cytolib/trans_group.hpp:13,
from trans_group.cpp:3:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
failed ************ (Pred::************
^
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
failed ************ (boost::mpl::not_<Pred>::************
^
/usr/local/Cellar/gcc@8/8.4.0_1/bin/g++-8 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RProtoBufLib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhdf5lib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppParallel/include' -I/usr/local/include -fPIC -Wall -g -O2 -c transformation.cpp -o transformation.o
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/arg.hpp:25,
from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/placeholders.hpp:24,
from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/iterator/iterator_categories.hpp:16,
from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/iterator/iterator_facade.hpp:13,
from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/range/iterator_range_core.hpp:27,
from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/range/iterator_range.hpp:13,
from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/range/as_literal.hpp:22,
from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/algorithm/string/trim.hpp:19,
from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/algorithm/string.hpp:19,
from ../inst/include/cytolib/transformation.hpp:18,
from transformation.cpp:3:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
failed ************ (Pred::************
^
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
failed ************ (boost::mpl::not_<Pred>::************
^
/usr/local/Cellar/gcc@8/8.4.0_1/bin/g++-8 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RProtoBufLib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhdf5lib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppParallel/include' -I/usr/local/include -fPIC -Wall -g -O2 -c boost/libs/system/src/error_code.cpp -o boost/libs/system/src/error_code.o
/usr/local/Cellar/gcc@8/8.4.0_1/bin/g++-8 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RProtoBufLib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhdf5lib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppParallel/include' -I/usr/local/include -fPIC -Wall -g -O2 -c boost/libs/filesystem/src/codecvt_error_category.cpp -o boost/libs/filesystem/src/codecvt_error_category.o
/usr/local/Cellar/gcc@8/8.4.0_1/bin/g++-8 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RProtoBufLib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhdf5lib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppParallel/include' -I/usr/local/include -fPIC -Wall -g -O2 -c boost/libs/filesystem/src/directory.cpp -o boost/libs/filesystem/src/directory.o
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/arg.hpp:25,
from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/placeholders.hpp:24,
from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/iterator/iterator_categories.hpp:16,
from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/iterator/iterator_facade.hpp:13,
from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/filesystem/path.hpp:29,
from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/filesystem/directory.hpp:26,
from boost/libs/filesystem/src/directory.cpp:28:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
failed ************ (Pred::************
^
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
failed ************ (boost::mpl::not_<Pred>::************
^
/usr/local/Cellar/gcc@8/8.4.0_1/bin/g++-8 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RProtoBufLib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhdf5lib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppParallel/include' -I/usr/local/include -fPIC -Wall -g -O2 -c boost/libs/filesystem/src/exception.cpp -o boost/libs/filesystem/src/exception.o
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/arg.hpp:25,
from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/placeholders.hpp:24,
from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/iterator/iterator_categories.hpp:16,
from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/iterator/iterator_facade.hpp:13,
from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/filesystem/path.hpp:29,
from boost/libs/filesystem/src/exception.cpp:13:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
failed ************ (Pred::************
^
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
failed ************ (boost::mpl::not_<Pred>::************
^
/usr/local/Cellar/gcc@8/8.4.0_1/bin/g++-8 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RProtoBufLib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhdf5lib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppParallel/include' -I/usr/local/include -fPIC -Wall -g -O2 -c boost/libs/filesystem/src/operations.cpp -o boost/libs/filesystem/src/operations.o
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/arg.hpp:25,
from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/placeholders.hpp:24,
from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/iterator/iterator_categories.hpp:16,
from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/iterator/iterator_facade.hpp:13,
from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/filesystem/path.hpp:29,
from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/filesystem/operations.hpp:25,
from boost/libs/filesystem/src/operations.cpp:71:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
failed ************ (Pred::************
^
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
failed ************ (boost::mpl::not_<Pred>::************
^
/usr/local/Cellar/gcc@8/8.4.0_1/bin/g++-8 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RProtoBufLib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhdf5lib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppParallel/include' -I/usr/local/include -fPIC -Wall -g -O2 -c boost/libs/filesystem/src/path.cpp -o boost/libs/filesystem/src/path.o
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/arg.hpp:25,
from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/placeholders.hpp:24,
from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/iterator/iterator_categories.hpp:16,
from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/iterator/iterator_facade.hpp:13,
from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/filesystem/path.hpp:29,
from boost/libs/filesystem/src/path.cpp:28:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
failed ************ (Pred::************
^
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
failed ************ (boost::mpl::not_<Pred>::************
^
/usr/local/Cellar/gcc@8/8.4.0_1/bin/g++-8 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RProtoBufLib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhdf5lib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppParallel/include' -I/usr/local/include -fPIC -Wall -g -O2 -c boost/libs/filesystem/src/path_traits.cpp -o boost/libs/filesystem/src/path_traits.o
/usr/local/Cellar/gcc@8/8.4.0_1/bin/g++-8 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RProtoBufLib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhdf5lib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppParallel/include' -I/usr/local/include -fPIC -Wall -g -O2 -c boost/libs/filesystem/src/portability.cpp -o boost/libs/filesystem/src/portability.o
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/arg.hpp:25,
from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/placeholders.hpp:24,
from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/iterator/iterator_categories.hpp:16,
from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/iterator/iterator_facade.hpp:13,
from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/filesystem/path.hpp:29,
from boost/libs/filesystem/src/portability.cpp:17:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
failed ************ (Pred::************
^
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
failed ************ (boost::mpl::not_<Pred>::************
^
/usr/local/Cellar/gcc@8/8.4.0_1/bin/g++-8 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RProtoBufLib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhdf5lib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppParallel/include' -I/usr/local/include -fPIC -Wall -g -O2 -c boost/libs/filesystem/src/unique_path.cpp -o boost/libs/filesystem/src/unique_path.o
In file included from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/arg.hpp:25,
from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/placeholders.hpp:24,
from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/iterator/iterator_categories.hpp:16,
from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/iterator/iterator_facade.hpp:13,
from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/filesystem/path.hpp:29,
from /Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/filesystem/operations.hpp:25,
from boost/libs/filesystem/src/unique_path.cpp:16:
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
failed ************ (Pred::************
^
/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
failed ************ (boost::mpl::not_<Pred>::************
^
/usr/local/Cellar/gcc@8/8.4.0_1/bin/g++-8 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RProtoBufLib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhdf5lib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppParallel/include' -I/usr/local/include -fPIC -Wall -g -O2 -c boost/libs/filesystem/src/utf8_codecvt_facet.cpp -o boost/libs/filesystem/src/utf8_codecvt_facet.o
/usr/local/Cellar/gcc@8/8.4.0_1/bin/g++-8 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RProtoBufLib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhdf5lib/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppArmadillo/include' -I'/Library/Frameworks/R.framework/Versions/4.0/Resources/library/RcppParallel/include' -I/usr/local/include -fPIC -Wall -g -O2 -c boost/libs/filesystem/src/windows_file_codecvt.cpp -o boost/libs/filesystem/src/windows_file_codecvt.o
/usr/local/Cellar/gcc@8/8.4.0_1/bin/g++-8 -std=gnu++11 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/Cellar/gcc@8/8.4.0_1/lib -o cytolib.so CytoFrame.o CytoFrameView.o CytoVFS.o GatingHierarchy.o GatingSet.o GatingSet.pb.o H5CytoFrame.o MemCytoFrame.o POPINDICES.o calibrationTable.o compensation.o dummy.o ellipse2points.o gate.o global.o in_polygon.o nodeProperties.o spline.o trans_group.o transformation.o boost/libs/filesystem/src/codecvt_error_category.o boost/libs/filesystem/src/directory.o boost/libs/filesystem/src/exception.o boost/libs/filesystem/src/operations.o boost/libs/filesystem/src/path.o boost/libs/filesystem/src/path_traits.o boost/libs/filesystem/src/portability.o boost/libs/filesystem/src/unique_path.o boost/libs/filesystem/src/utf8_codecvt_facet.o boost/libs/filesystem/src/windows_file_codecvt.o boost/libs/system/src/error_code.o -L/Library/Frameworks/R.framework/Resources/lib -lRlapack -L/Library/Frameworks/R.framework/Resources/lib -lRblas -L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin18/8.2.0 -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm /Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhdf5lib/lib/libhdf5_cpp.a /Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhdf5lib/lib/libhdf5.a /Library/Frameworks/R.framework/Versions/4.0/Resources/library/Rhdf5lib/lib/libsz.a -lz -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
ld: warning: directory not found for option '-L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin18/8.2.0'
ld: warning: directory not found for option '-L/usr/local/gfortran/lib'
ld: warning: text-based stub file /System/Library/Frameworks//CoreFoundation.framework/CoreFoundation.tbd and library file /System/Library/Frameworks//CoreFoundation.framework/CoreFoundation are out of sync. Falling back to library file for linking.
installing to /Library/Frameworks/R.framework/Versions/4.0/Resources/library/00LOCK-cytolib/00new/cytolib/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Error: package or namespace load failed for ‘cytolib’:
.onLoad failed in loadNamespace() for 'cytolib', details:
call: dyn.load(cytolib, local = FALSE, now = TRUE)
error: unable to load shared object '/Library/Frameworks/R.framework/Versions/4.0/Resources/library/00LOCK-cytolib/00new/cytolib/libs/cytolib.so':
dlopen(/Library/Frameworks/R.framework/Versions/4.0/Resources/library/00LOCK-cytolib/00new/cytolib/libs/cytolib.so, 10): Symbol not found: __ZN6google8protobuf8internal26fixed_address_empty_stringB5cxx11E
Referenced from: /Library/Frameworks/R.framework/Versions/4.0/Resources/library/00LOCK-cytolib/00new/cytolib/libs/cytolib.so
Expected in: flat namespace
in /Library/Frameworks/R.framework/Versions/4.0/Resources/library/00LOCK-cytolib/00new/cytolib/libs/cytolib.so
Error: loading failed
Execution halted
ERROR: loading failed
* removing ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library/cytolib’
* restoring previous ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library/cytolib’
Error: Failed to install 'cytolib' from GitHub:
(converted from warning) installation of package ‘/var/folders/0l/27166dcs57z48cjmt6y57r540000gp/T//Rtmpx27kuL/file1867d3e878b3/cytolib_2.1.18.tar.gz’ had non-zero exit status
**To Reproduce**
sessionInfo
R version 4.0.2 (2020-06-22)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS High Sierra 10.13.6
Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] prettyunits_1.1.1 ps_1.3.4 fansi_0.4.1 withr_2.2.0 rprojroot_1.3-2 crayon_1.3.4 assertthat_0.2.1
[8] R6_2.4.1 backports_1.1.9 cli_2.0.2 curl_4.3 remotes_2.2.0 rstudioapi_0.11 callr_3.4.3
[15] tools_4.0.2 glue_1.4.2 tinytex_0.25 xfun_0.16 compiler_4.0.2 processx_3.4.3 pkgbuild_1.1.0
support cloud storage for cytoframe
This requires the abstraction/or redesign some existing APIs that involves the POSIX local file system IO operations (e.g. GatingSet::generate_h5_folder, save_gs/load_gs .etc...).
Once GatingSet/GatingHierarchy/CytoFrame classes are agnostic about file system types, the rest generic IO can be automatically taken care of by H5CytoFrame(or TileDBCytoFrame) classes through the VFD(virtual file driver) mechanism provided by hdf5 and tiledb
eliminate global variables
There are currently two global variables used by cytolib (mainly for troubleshooting purpose)
https://github.com/RGLab/cytolib/blob/trunk/inst/include/cytolib/global.hpp#L30-L31
extern keyword indicates they are only the variable declaration instead of definition. Because due to the nature of header-only, cytolib can't define them in any header in order to avoid multi-definition compiling errors (when header is included multiple times).
Therefore it implicitly requires the cytolib users to define it somewhere in the user code in order for cytolib function, even if they don't necessarily need to care about this log feature.
We shouldn't force user to do this (besides it is not best practice to use global variable). Instead, we can move them into GatingSet class and initialize/change their values either through parseWorkspace call or through setter methods once GatingSet is created.
cytolib.dylib vs .so extension on macOS with R 4
The cytolibLibPath function returns the path to the shared library, and commit 3ca3d46 (October 2019) changed it from cytolib.dylib to cytolib.so on macOS.
In building Bioconda's bioconductor-cytolib package for R 4.0.3 / Bioconductor 3.12, I found that the library was built as cytolib.dylib and I needed to revert this change to make packages that use cytolib work correctly. Without this change back to .dylib any attempt to use the bioconda-built cytolib produced:
> library(cytolib)
Warning message:
In fun(libname, pkgname) : cytolib library not found.
and dlopen() errors complaining that various function symbols supplied by the library could not be resolved. (Notice the double space in library … not indicating that the string returned was the empty string.)
See bioconda/bioconda-recipes#25292, in particular @dpryan79's comment hinting that .so may have been needed on macOS for R 3.6 but is no longer correct for R 4.
test and work on the compatibility between COMPASS and cytolib 2.0
Install fails with BH 1.78.0-0
Describe the bug
Install proceeds fully with BH 1.75.0-0 (installed from source), but with 1.78.0-0 I get the following error traceback. Appears to be an issue with boost/libs/filesystem/src/path.o?
Bioconductor version 3.14 (BiocManager 1.30.16), R 4.1.1 (2021-08-10)
Installing package(s) 'cytolib'
trying URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/cytolib_2.6.0.tar.gz'
Content type 'application/x-gzip' length 5463300 bytes (5.2 MB)
==================================================
downloaded 5.2 MB
* installing *source* package ‘cytolib’ ...
** using staged installation
checking for a sed that does not truncate output... /usr/bin/sed
checking whether the C++ compiler works... yes
checking for C++ compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C++ compiler... yes
checking whether /software/gcc/11.2.0/bin/g++ accepts -g... yes
checking how to run the C++ preprocessor... /software/gcc/11.2.0/bin/g++ -E
checking whether we are using the GNU C++ compiler... (cached) yes
checking whether /software/gcc/11.2.0/bin/g++ accepts -g... (cached) yes
configure: Parsing cytolib version info ...
configure: CYTOLIB_VERSION=2.6.0
configure: creating ./config.status
config.status: creating inst/include/cytolib/cytolibConfig.h
config.status: creating src/Makevars
** libs
g++ -std=gnu++11 -I"/software/R/4.1.1/lib64/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/home/rag0151/aging_microglia_flu/renv/library/R-4.1/x86_64-pc-linux-gnu/Rcpp/include' -I'/home/rag0151/aging_microglia_flu/renv/library/R-4.1/x86_64-pc-linux-gnu/BH/include' -I'/home/rag0151/aging_microglia_flu/renv/library/R-4.1/x86_64-pc-linux-gnu/RProtoBufLib/include' -I'/home/rag0151/aging_microglia_flu/renv/library/R-4.1/x86_64-pc-linux-gnu/Rhdf5lib/include' -I'/home/rag0151/aging_microglia_flu/renv/library/R-4.1/x86_64-pc-linux-gnu/RcppArmadillo/include' -I'/home/rag0151/aging_microglia_flu/renv/library/R-4.1/x86_64-pc-linux-gnu/RcppParallel/include' -I/software/supplemental/zlib/1.2.8/include -I/software/pcre/8.44/include -I/software/curl/7.73.0/include -I/software/cairo/1.16/include -I/software/supplemental/bzip2/1.0.8/include -std=c++11 -fpic -g -O2 -c dummy.cpp -o dummy.o
g++ -std=gnu++11 -I"/software/R/4.1.1/lib64/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/home/rag0151/aging_microglia_flu/renv/library/R-4.1/x86_64-pc-linux-gnu/Rcpp/include' -I'/home/rag0151/aging_microglia_flu/renv/library/R-4.1/x86_64-pc-linux-gnu/BH/include' -I'/home/rag0151/aging_microglia_flu/renv/library/R-4.1/x86_64-pc-linux-gnu/RProtoBufLib/include' -I'/home/rag0151/aging_microglia_flu/renv/library/R-4.1/x86_64-pc-linux-gnu/Rhdf5lib/include' -I'/home/rag0151/aging_microglia_flu/renv/library/R-4.1/x86_64-pc-linux-gnu/RcppArmadillo/include' -I'/home/rag0151/aging_microglia_flu/renv/library/R-4.1/x86_64-pc-linux-gnu/RcppParallel/include' -I/software/supplemental/zlib/1.2.8/include -I/software/pcre/8.44/include -I/software/curl/7.73.0/include -I/software/cairo/1.16/include -I/software/supplemental/bzip2/1.0.8/include -std=c++11 -fpic -g -O2 -c boost/libs/system/src/error_code.cpp -o boost/libs/system/src/error_code.o
g++ -std=gnu++11 -I"/software/R/4.1.1/lib64/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/home/rag0151/aging_microglia_flu/renv/library/R-4.1/x86_64-pc-linux-gnu/Rcpp/include' -I'/home/rag0151/aging_microglia_flu/renv/library/R-4.1/x86_64-pc-linux-gnu/BH/include' -I'/home/rag0151/aging_microglia_flu/renv/library/R-4.1/x86_64-pc-linux-gnu/RProtoBufLib/include' -I'/home/rag0151/aging_microglia_flu/renv/library/R-4.1/x86_64-pc-linux-gnu/Rhdf5lib/include' -I'/home/rag0151/aging_microglia_flu/renv/library/R-4.1/x86_64-pc-linux-gnu/RcppArmadillo/include' -I'/home/rag0151/aging_microglia_flu/renv/library/R-4.1/x86_64-pc-linux-gnu/RcppParallel/include' -I/software/supplemental/zlib/1.2.8/include -I/software/pcre/8.44/include -I/software/curl/7.73.0/include -I/software/cairo/1.16/include -I/software/supplemental/bzip2/1.0.8/include -std=c++11 -fpic -g -O2 -c boost/libs/filesystem/src/path_traits.cpp -o boost/libs/filesystem/src/path_traits.o
g++ -std=gnu++11 -I"/software/R/4.1.1/lib64/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/home/rag0151/aging_microglia_flu/renv/library/R-4.1/x86_64-pc-linux-gnu/Rcpp/include' -I'/home/rag0151/aging_microglia_flu/renv/library/R-4.1/x86_64-pc-linux-gnu/BH/include' -I'/home/rag0151/aging_microglia_flu/renv/library/R-4.1/x86_64-pc-linux-gnu/RProtoBufLib/include' -I'/home/rag0151/aging_microglia_flu/renv/library/R-4.1/x86_64-pc-linux-gnu/Rhdf5lib/include' -I'/home/rag0151/aging_microglia_flu/renv/library/R-4.1/x86_64-pc-linux-gnu/RcppArmadillo/include' -I'/home/rag0151/aging_microglia_flu/renv/library/R-4.1/x86_64-pc-linux-gnu/RcppParallel/include' -I/software/supplemental/zlib/1.2.8/include -I/software/pcre/8.44/include -I/software/curl/7.73.0/include -I/software/cairo/1.16/include -I/software/supplemental/bzip2/1.0.8/include -std=c++11 -fpic -g -O2 -c boost/libs/filesystem/src/codecvt_error_category.cpp -o boost/libs/filesystem/src/codecvt_error_category.o
g++ -std=gnu++11 -I"/software/R/4.1.1/lib64/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/home/rag0151/aging_microglia_flu/renv/library/R-4.1/x86_64-pc-linux-gnu/Rcpp/include' -I'/home/rag0151/aging_microglia_flu/renv/library/R-4.1/x86_64-pc-linux-gnu/BH/include' -I'/home/rag0151/aging_microglia_flu/renv/library/R-4.1/x86_64-pc-linux-gnu/RProtoBufLib/include' -I'/home/rag0151/aging_microglia_flu/renv/library/R-4.1/x86_64-pc-linux-gnu/Rhdf5lib/include' -I'/home/rag0151/aging_microglia_flu/renv/library/R-4.1/x86_64-pc-linux-gnu/RcppArmadillo/include' -I'/home/rag0151/aging_microglia_flu/renv/library/R-4.1/x86_64-pc-linux-gnu/RcppParallel/include' -I/software/supplemental/zlib/1.2.8/include -I/software/pcre/8.44/include -I/software/curl/7.73.0/include -I/software/cairo/1.16/include -I/software/supplemental/bzip2/1.0.8/include -std=c++11 -fpic -g -O2 -c boost/libs/filesystem/src/utf8_codecvt_facet.cpp -o boost/libs/filesystem/src/utf8_codecvt_facet.o
g++ -std=gnu++11 -I"/software/R/4.1.1/lib64/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/home/rag0151/aging_microglia_flu/renv/library/R-4.1/x86_64-pc-linux-gnu/Rcpp/include' -I'/home/rag0151/aging_microglia_flu/renv/library/R-4.1/x86_64-pc-linux-gnu/BH/include' -I'/home/rag0151/aging_microglia_flu/renv/library/R-4.1/x86_64-pc-linux-gnu/RProtoBufLib/include' -I'/home/rag0151/aging_microglia_flu/renv/library/R-4.1/x86_64-pc-linux-gnu/Rhdf5lib/include' -I'/home/rag0151/aging_microglia_flu/renv/library/R-4.1/x86_64-pc-linux-gnu/RcppArmadillo/include' -I'/home/rag0151/aging_microglia_flu/renv/library/R-4.1/x86_64-pc-linux-gnu/RcppParallel/include' -I/software/supplemental/zlib/1.2.8/include -I/software/pcre/8.44/include -I/software/curl/7.73.0/include -I/software/cairo/1.16/include -I/software/supplemental/bzip2/1.0.8/include -std=c++11 -fpic -g -O2 -c boost/libs/filesystem/src/windows_file_codecvt.cpp -o boost/libs/filesystem/src/windows_file_codecvt.o
g++ -std=gnu++11 -I"/software/R/4.1.1/lib64/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/home/rag0151/aging_microglia_flu/renv/library/R-4.1/x86_64-pc-linux-gnu/Rcpp/include' -I'/home/rag0151/aging_microglia_flu/renv/library/R-4.1/x86_64-pc-linux-gnu/BH/include' -I'/home/rag0151/aging_microglia_flu/renv/library/R-4.1/x86_64-pc-linux-gnu/RProtoBufLib/include' -I'/home/rag0151/aging_microglia_flu/renv/library/R-4.1/x86_64-pc-linux-gnu/Rhdf5lib/include' -I'/home/rag0151/aging_microglia_flu/renv/library/R-4.1/x86_64-pc-linux-gnu/RcppArmadillo/include' -I'/home/rag0151/aging_microglia_flu/renv/library/R-4.1/x86_64-pc-linux-gnu/RcppParallel/include' -I/software/supplemental/zlib/1.2.8/include -I/software/pcre/8.44/include -I/software/curl/7.73.0/include -I/software/cairo/1.16/include -I/software/supplemental/bzip2/1.0.8/include -std=c++11 -fpic -g -O2 -c boost/libs/filesystem/src/exception.cpp -o boost/libs/filesystem/src/exception.o
g++ -std=gnu++11 -I"/software/R/4.1.1/lib64/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/home/rag0151/aging_microglia_flu/renv/library/R-4.1/x86_64-pc-linux-gnu/Rcpp/include' -I'/home/rag0151/aging_microglia_flu/renv/library/R-4.1/x86_64-pc-linux-gnu/BH/include' -I'/home/rag0151/aging_microglia_flu/renv/library/R-4.1/x86_64-pc-linux-gnu/RProtoBufLib/include' -I'/home/rag0151/aging_microglia_flu/renv/library/R-4.1/x86_64-pc-linux-gnu/Rhdf5lib/include' -I'/home/rag0151/aging_microglia_flu/renv/library/R-4.1/x86_64-pc-linux-gnu/RcppArmadillo/include' -I'/home/rag0151/aging_microglia_flu/renv/library/R-4.1/x86_64-pc-linux-gnu/RcppParallel/include' -I/software/supplemental/zlib/1.2.8/include -I/software/pcre/8.44/include -I/software/curl/7.73.0/include -I/software/cairo/1.16/include -I/software/supplemental/bzip2/1.0.8/include -std=c++11 -fpic -g -O2 -c boost/libs/filesystem/src/directory.cpp -o boost/libs/filesystem/src/directory.o
g++ -std=gnu++11 -I"/software/R/4.1.1/lib64/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/home/rag0151/aging_microglia_flu/renv/library/R-4.1/x86_64-pc-linux-gnu/Rcpp/include' -I'/home/rag0151/aging_microglia_flu/renv/library/R-4.1/x86_64-pc-linux-gnu/BH/include' -I'/home/rag0151/aging_microglia_flu/renv/library/R-4.1/x86_64-pc-linux-gnu/RProtoBufLib/include' -I'/home/rag0151/aging_microglia_flu/renv/library/R-4.1/x86_64-pc-linux-gnu/Rhdf5lib/include' -I'/home/rag0151/aging_microglia_flu/renv/library/R-4.1/x86_64-pc-linux-gnu/RcppArmadillo/include' -I'/home/rag0151/aging_microglia_flu/renv/library/R-4.1/x86_64-pc-linux-gnu/RcppParallel/include' -I/software/supplemental/zlib/1.2.8/include -I/software/pcre/8.44/include -I/software/curl/7.73.0/include -I/software/cairo/1.16/include -I/software/supplemental/bzip2/1.0.8/include -std=c++11 -fpic -g -O2 -c boost/libs/filesystem/src/path.cpp -o boost/libs/filesystem/src/path.o
boost/libs/filesystem/src/path.cpp:124:31: error: no declaration matches ‘boost::filesystem::path& boost::filesystem::path::operator/=(const boost::filesystem::path&)’
124 | BOOST_FILESYSTEM_DECL path& path::operator/=(const path& p)
| ^~~~
In file included from boost/libs/filesystem/src/path.cpp:19:
/home/rag0151/aging_microglia_flu/renv/library/R-4.1/x86_64-pc-linux-gnu/BH/include/boost/filesystem/path.hpp:559:13: note: candidate is: ‘template<class Source> typename boost::enable_if_c<(boost::filesystem::path_traits::is_pathable<typename boost::decay<Source>::type>::value || boost::filesystem::path_detail::is_native_pathable<T>::value), boost::filesystem::path&>::type boost::filesystem::path::operator/=(const Source&)’
559 | >::type operator/=(Source const& source)
| ^~~~~~~~
/home/rag0151/aging_microglia_flu/renv/library/R-4.1/x86_64-pc-linux-gnu/BH/include/boost/filesystem/path.hpp:132:7: note: ‘class boost::filesystem::path’ defined here
132 | class path :
| ^~~~
boost/libs/filesystem/src/path.cpp:144:31: error: no declaration matches ‘boost::filesystem::path& boost::filesystem::path::operator/=(const value_type*)’
144 | BOOST_FILESYSTEM_DECL path& path::operator/=(const value_type* ptr)
| ^~~~
In file included from boost/libs/filesystem/src/path.cpp:19:
/home/rag0151/aging_microglia_flu/renv/library/R-4.1/x86_64-pc-linux-gnu/BH/include/boost/filesystem/path.hpp:559:13: note: candidate is: ‘template<class Source> typename boost::enable_if_c<(boost::filesystem::path_traits::is_pathable<typename boost::decay<Source>::type>::value || boost::filesystem::path_detail::is_native_pathable<T>::value), boost::filesystem::path&>::type boost::filesystem::path::operator/=(const Source&)’
559 | >::type operator/=(Source const& source)
| ^~~~~~~~
/home/rag0151/aging_microglia_flu/renv/library/R-4.1/x86_64-pc-linux-gnu/BH/include/boost/filesystem/path.hpp:132:7: note: ‘class boost::filesystem::path’ defined here
132 | class path :
| ^~~~
boost/libs/filesystem/src/path.cpp:176:29: error: redefinition of ‘int boost::filesystem::path::compare(const boost::filesystem::path&) const’
176 | BOOST_FILESYSTEM_DECL int path::compare(const path& p) const BOOST_NOEXCEPT
| ^~~~
In file included from boost/libs/filesystem/src/path.cpp:19:
/home/rag0151/aging_microglia_flu/renv/library/R-4.1/x86_64-pc-linux-gnu/BH/include/boost/filesystem/path.hpp:780:27: note: ‘int boost::filesystem::path::compare(const boost::filesystem::path&) const’ previously defined here
780 | BOOST_FORCEINLINE int compare(path const& p) const BOOST_NOEXCEPT // generic, lexicographical
| ^~~~~~~
boost/libs/filesystem/src/path.cpp:183:54: error: no declaration matches ‘std::__cxx11::basic_string<char>::size_type boost::filesystem::path::m_append_separator_if_needed()’
183 | BOOST_FILESYSTEM_DECL path::string_type::size_type path::m_append_separator_if_needed()
| ^~~~
boost/libs/filesystem/src/path.cpp:183:54: note: no functions named ‘std::__cxx11::basic_string<char>::size_type boost::filesystem::path::m_append_separator_if_needed()’
In file included from boost/libs/filesystem/src/path.cpp:19:
/home/rag0151/aging_microglia_flu/renv/library/R-4.1/x86_64-pc-linux-gnu/BH/include/boost/filesystem/path.hpp:132:7: note: ‘class boost::filesystem::path’ defined here
132 | class path :
| ^~~~
boost/libs/filesystem/src/path.cpp:200:30: error: no declaration matches ‘void boost::filesystem::path::m_erase_redundant_separator(std::__cxx11::basic_string<char>::size_type)’
200 | BOOST_FILESYSTEM_DECL void path::m_erase_redundant_separator(string_type::size_type sep_pos)
| ^~~~
boost/libs/filesystem/src/path.cpp:200:30: note: no functions named ‘void boost::filesystem::path::m_erase_redundant_separator(std::__cxx11::basic_string<char>::size_type)’
In file included from boost/libs/filesystem/src/path.cpp:19:
/home/rag0151/aging_microglia_flu/renv/library/R-4.1/x86_64-pc-linux-gnu/BH/include/boost/filesystem/path.hpp:132:7: note: ‘class boost::filesystem::path’ defined here
132 | class path :
| ^~~~
boost/libs/filesystem/src/path.cpp: In member function ‘boost::filesystem::path& boost::filesystem::path::remove_filename()’:
boost/libs/filesystem/src/path.cpp:223:22: error: ‘m_parent_path_end’ was not declared in this scope; did you mean ‘parent_path’?
223 | m_pathname.erase(m_parent_path_end());
| ^~~~~~~~~~~~~~~~~
| parent_path
boost/libs/filesystem/src/path.cpp: At global scope:
boost/libs/filesystem/src/path.cpp:253:30: error: redefinition of ‘boost::filesystem::path boost::filesystem::path::root_path() const’
253 | BOOST_FILESYSTEM_DECL path path::root_path() const
| ^~~~
In file included from boost/libs/filesystem/src/path.cpp:19:
/home/rag0151/aging_microglia_flu/renv/library/R-4.1/x86_64-pc-linux-gnu/BH/include/boost/filesystem/path.hpp:789:10: note: ‘boost::filesystem::path boost::filesystem::path::root_path() const’ previously defined here
789 | path root_path() const { return path(m_pathname.c_str(), m_pathname.c_str() + find_root_path_size()); }
| ^~~~~~~~~
boost/libs/filesystem/src/path.cpp:260:30: error: redefinition of ‘boost::filesystem::path boost::filesystem::path::root_name() const’
260 | BOOST_FILESYSTEM_DECL path path::root_name() const
| ^~~~
In file included from boost/libs/filesystem/src/path.cpp:19:
/home/rag0151/aging_microglia_flu/renv/library/R-4.1/x86_64-pc-linux-gnu/BH/include/boost/filesystem/path.hpp:791:10: note: ‘boost::filesystem::path boost::filesystem::path::root_name() const’ previously defined here
791 | path root_name() const { return path(m_pathname.c_str(), m_pathname.c_str() + find_root_name_size()); }
| ^~~~~~~~~
boost/libs/filesystem/src/path.cpp:277:30: error: redefinition of ‘boost::filesystem::path boost::filesystem::path::root_directory() const’
277 | BOOST_FILESYSTEM_DECL path path::root_directory() const
| ^~~~
In file included from boost/libs/filesystem/src/path.cpp:19:
/home/rag0151/aging_microglia_flu/renv/library/R-4.1/x86_64-pc-linux-gnu/BH/include/boost/filesystem/path.hpp:794:10: note: ‘boost::filesystem::path boost::filesystem::path::root_directory() const’ previously defined here
794 | path root_directory() const
| ^~~~~~~~~~~~~~
boost/libs/filesystem/src/path.cpp:286:30: error: redefinition of ‘boost::filesystem::path boost::filesystem::path::relative_path() const’
286 | BOOST_FILESYSTEM_DECL path path::relative_path() const
| ^~~~
In file included from boost/libs/filesystem/src/path.cpp:19:
/home/rag0151/aging_microglia_flu/renv/library/R-4.1/x86_64-pc-linux-gnu/BH/include/boost/filesystem/path.hpp:801:10: note: ‘boost::filesystem::path boost::filesystem::path::relative_path() const’ previously defined here
801 | path relative_path() const
| ^~~~~~~~~~~~~
boost/libs/filesystem/src/path.cpp:300:48: error: no declaration matches ‘std::__cxx11::basic_string<char>::size_type boost::filesystem::path::m_parent_path_end() const’
300 | BOOST_FILESYSTEM_DECL string_type::size_type path::m_parent_path_end() const
| ^~~~
boost/libs/filesystem/src/path.cpp:300:48: note: no functions named ‘std::__cxx11::basic_string<char>::size_type boost::filesystem::path::m_parent_path_end() const’
In file included from boost/libs/filesystem/src/path.cpp:19:
/home/rag0151/aging_microglia_flu/renv/library/R-4.1/x86_64-pc-linux-gnu/BH/include/boost/filesystem/path.hpp:132:7: note: ‘class boost::filesystem::path’ defined here
132 | class path :
| ^~~~
boost/libs/filesystem/src/path.cpp:321:30: error: redefinition of ‘boost::filesystem::path boost::filesystem::path::parent_path() const’
321 | BOOST_FILESYSTEM_DECL path path::parent_path() const
| ^~~~
In file included from boost/libs/filesystem/src/path.cpp:19:
/home/rag0151/aging_microglia_flu/renv/library/R-4.1/x86_64-pc-linux-gnu/BH/include/boost/filesystem/path.hpp:808:10: note: ‘boost::filesystem::path boost::filesystem::path::parent_path() const’ previously defined here
808 | path parent_path() const { return path(m_pathname.c_str(), m_pathname.c_str() + find_parent_path_size()); }
| ^~~~~~~~~~~
boost/libs/filesystem/src/path.cpp:329:30: error: redefinition of ‘boost::filesystem::path boost::filesystem::path::filename() const’
329 | BOOST_FILESYSTEM_DECL path path::filename() const
| ^~~~
In file included from boost/libs/filesystem/src/path.cpp:19:
/home/rag0151/aging_microglia_flu/renv/library/R-4.1/x86_64-pc-linux-gnu/BH/include/boost/filesystem/path.hpp:810:28: note: ‘boost::filesystem::path boost::filesystem::path::filename() const’ previously defined here
810 | BOOST_FORCEINLINE path filename() const { return BOOST_FILESYSTEM_VERSIONED_SYM(filename)(); } // returns 0 or 1 element path
| ^~~~~~~~
boost/libs/filesystem/src/path.cpp:340:30: error: redefinition of ‘boost::filesystem::path boost::filesystem::path::stem() const’
340 | BOOST_FILESYSTEM_DECL path path::stem() const
| ^~~~
In file included from boost/libs/filesystem/src/path.cpp:19:
/home/rag0151/aging_microglia_flu/renv/library/R-4.1/x86_64-pc-linux-gnu/BH/include/boost/filesystem/path.hpp:811:28: note: ‘boost::filesystem::path boost::filesystem::path::stem() const’ previously defined here
811 | BOOST_FORCEINLINE path stem() const { return BOOST_FILESYSTEM_VERSIONED_SYM(stem)(); } // returns 0 or 1 element path
| ^~~~
boost/libs/filesystem/src/path.cpp:350:30: error: redefinition of ‘boost::filesystem::path boost::filesystem::path::extension() const’
350 | BOOST_FILESYSTEM_DECL path path::extension() const
| ^~~~
In file included from boost/libs/filesystem/src/path.cpp:19:
/home/rag0151/aging_microglia_flu/renv/library/R-4.1/x86_64-pc-linux-gnu/BH/include/boost/filesystem/path.hpp:812:28: note: ‘boost::filesystem::path boost::filesystem::path::extension() const’ previously defined here
812 | BOOST_FORCEINLINE path extension() const { return BOOST_FILESYSTEM_VERSIONED_SYM(extension)(); } // returns 0 or 1 element path
| ^~~~~~~~~
boost/libs/filesystem/src/path.cpp:412:30: error: redefinition of ‘boost::filesystem::path boost::filesystem::path::lexically_normal() const’
412 | BOOST_FILESYSTEM_DECL path path::lexically_normal() const
| ^~~~
In file included from boost/libs/filesystem/src/path.cpp:19:
/home/rag0151/aging_microglia_flu/renv/library/R-4.1/x86_64-pc-linux-gnu/BH/include/boost/filesystem/path.hpp:840:28: note: ‘boost::filesystem::path boost::filesystem::path::lexically_normal() const’ previously defined here
840 | BOOST_FORCEINLINE path lexically_normal() const { return BOOST_FILESYSTEM_VERSIONED_SYM(lexically_normal)(); }
| ^~~~~~~~~~~~~~~~
boost/libs/filesystem/src/path.cpp:741:30: error: no declaration matches ‘void boost::filesystem::path::m_path_iterator_increment(boost::filesystem::path::iterator&)’
741 | BOOST_FILESYSTEM_DECL void path::m_path_iterator_increment(path::iterator & it)
| ^~~~
boost/libs/filesystem/src/path.cpp:741:30: note: no functions named ‘void boost::filesystem::path::m_path_iterator_increment(boost::filesystem::path::iterator&)’
In file included from boost/libs/filesystem/src/path.cpp:19:
/home/rag0151/aging_microglia_flu/renv/library/R-4.1/x86_64-pc-linux-gnu/BH/include/boost/filesystem/path.hpp:132:7: note: ‘class boost::filesystem::path’ defined here
132 | class path :
| ^~~~
boost/libs/filesystem/src/path.cpp:800:30: error: no declaration matches ‘void boost::filesystem::path::m_path_iterator_decrement(boost::filesystem::path::iterator&)’
800 | BOOST_FILESYSTEM_DECL void path::m_path_iterator_decrement(path::iterator & it)
| ^~~~
boost/libs/filesystem/src/path.cpp:800:30: note: no functions named ‘void boost::filesystem::path::m_path_iterator_decrement(boost::filesystem::path::iterator&)’
In file included from boost/libs/filesystem/src/path.cpp:19:
/home/rag0151/aging_microglia_flu/renv/library/R-4.1/x86_64-pc-linux-gnu/BH/include/boost/filesystem/path.hpp:132:7: note: ‘class boost::filesystem::path’ defined here
132 | class path :
| ^~~~
make: *** [boost/libs/filesystem/src/path.o] Error 1
SessionInfo:
R version 4.1.1 (2021-08-10)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Red Hat Enterprise Linux Server 7.5 (Maipo)
Matrix products: default
BLAS: /hpc/software/R/4.1.1/lib64/R/lib/libRblas.so
LAPACK: /hpc/software/R/4.1.1/lib64/R/lib/libRlapack.so
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8
[4] LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C LC_ADDRESS=C
[10] LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices datasets utils methods base
loaded via a namespace (and not attached):
[1] BiocManager_1.30.16 compiler_4.1.1 tools_4.1.1 renv_0.14.0
Complete documentation and build doc website
It would be helpful to have a website with a doc/API reference page for cytolib similar to the other cytoverse packages. For example, see the flowWorkspace site. This will require:
- Completing the documentation in the form of Doxygen-compliant docstrings to enable easy building of corresponding HTML.
- Weaving the generated documentation HTML in to a nicely formatted website. Again, Doxygen will make this much easier, but if we would like a similar format to the other doc websites we may be able to leverage
pkgdownafter the the doc HTML files are generated.
The first point is by far the more time consuming, but will pay off in the long run in terms of maintenance of the code base.
library(cytolib) crashes Rfast::rowMaxs()
Hi,
The following code crashes my session if I load cytolib before running it:
library(Rfast)
x <- matrix(runif(40), nrow=8)
Rfast::rowMaxs(x)
For example in a fresh R session on my laptop:
> library(cytolib)
> library(Rfast)
Loading required package: Rcpp
Loading required package: RcppZiggurat
> x <- matrix(runif(40), nrow=8)
> Rfast::rowMaxs(x)
*** Error in `/home/hpages/R/R-4.0.r78037/bin/exec/R': double free or corruption (out): 0x00007f6f1bc38270 ***
======= Backtrace: =========
/lib/x86_64-linux-gnu/libc.so.6(+0x777e5)[0x7f6f1b0307e5]
/lib/x86_64-linux-gnu/libc.so.6(+0x8037a)[0x7f6f1b03937a]
/lib/x86_64-linux-gnu/libc.so.6(cfree+0x4c)[0x7f6f1b03d53c]
/home/hpages/R/R-4.0.r78037/library/Rfast/libs/Rfast.so(_Z15row_min_indicesN4Rcpp6MatrixILi14ENS_15PreserveStorageEEE+0x11a)[0x7f6f12439cba]
/home/hpages/R/R-4.0.r78037/library/Rfast/libs/Rfast.so(Rfast_row_min_indices+0x68)[0x7f6f1243f7f8]
/home/hpages/R/R-4.0.r78037/lib/libR.so(+0xfcaa0)[0x7f6f1b69caa0]
/home/hpages/R/R-4.0.r78037/lib/libR.so(+0x13a55e)[0x7f6f1b6da55e]
/home/hpages/R/R-4.0.r78037/lib/libR.so(Rf_eval+0x1a0)[0x7f6f1b6e3fd0]
/home/hpages/R/R-4.0.r78037/lib/libR.so(+0x145d91)[0x7f6f1b6e5d91]
/home/hpages/R/R-4.0.r78037/lib/libR.so(Rf_applyClosure+0x1b4)[0x7f6f1b6e6b34]
/home/hpages/R/R-4.0.r78037/lib/libR.so(Rf_eval+0x2ce)[0x7f6f1b6e40fe]
/home/hpages/R/R-4.0.r78037/lib/libR.so(Rf_ReplIteration+0x242)[0x7f6f1b717662]
/home/hpages/R/R-4.0.r78037/lib/libR.so(+0x1779f1)[0x7f6f1b7179f1]
/home/hpages/R/R-4.0.r78037/lib/libR.so(run_Rmainloop+0x48)[0x7f6f1b717aa8]
/home/hpages/R/R-4.0.r78037/bin/exec/R(main+0x1b)[0x4007cb]
/lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf0)[0x7f6f1afd9830]
/home/hpages/R/R-4.0.r78037/bin/exec/R(_start+0x29)[0x400809]
======= Memory map: ========
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00600000-00601000 r--p 00000000 00:32 23419198 /home/hpages/R/R-4.0.r78037/bin/exec/R
00601000-00602000 rw-p 00001000 00:32 23419198 /home/hpages/R/R-4.0.r78037/bin/exec/R
01dac000-04f29000 rw-p 00000000 00:00 0 [heap]
7f6f0c000000-7f6f0c021000 rw-p 00000000 00:00 0
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7f6f128b3000-7f6f12ab2000 ---p 0003d000 103:02 9963668 /usr/lib/x86_64-linux-gnu/libgslcblas.so.0.0.0
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7f6f12ab4000-7f6f12ce2000 r-xp 00000000 103:02 9963666 /usr/lib/x86_64-linux-gnu/libgsl.so.19.0.0
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7f6f12ef2000-7f6f12ef3000 rw-p 00000000 00:00 0
7f6f12ef3000-7f6f12f1a000 r-xp 00000000 00:32 23517352 /home/hpages/R/R-4.0.r78037/library/RcppZiggurat/libs/RcppZiggurat.so
7f6f12f1a000-7f6f1311a000 ---p 00027000 00:32 23517352 /home/hpages/R/R-4.0.r78037/library/RcppZiggurat/libs/RcppZiggurat.so
7f6f1311a000-7f6f1311b000 r--p 00027000 00:32 23517352 /home/hpages/R/R-4.0.r78037/library/RcppZiggurat/libs/RcppZiggurat.so
7f6f1311b000-7f6f1311c000 rw-p 00028000 00:32 23517352 /home/hpages/R/R-4.0.r78037/library/RcppZiggurat/libs/RcppZiggurat.so
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7f6f147f0000-7f6f147f1000 rw-p 0000b000 103:02 394748 /lib/x86_64-linux-gnu/libnss_files-2.23.so
7f6f147f1000-7f6f147f7000 rw-p 00000000 00:00 0
7f6f147f7000-7f6f14802000 r-xp 00000000 103:02 394741 /lib/x86_64-linux-gnu/libnss_nis-2.23.so
7f6f14802000-7f6f14a01000 ---p 0000b000 103:02 394741 /lib/x86_64-linux-gnu/libnss_nis-2.23.so
7f6f14a01000-7f6f14a02000 r--p 0000a000 103:02 394741 /lib/x86_64-linux-gnu/libnss_nis-2.23.so
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7f6f14a03000-7f6f14a19000 r-xp 00000000 103:02 394746 /lib/x86_64-linux-gnu/libnsl-2.23.so
7f6f14a19000-7f6f14c18000 ---p 00016000 103:02 394746 /lib/x86_64-linux-gnu/libnsl-2.23.so
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7f6f14c19000-7f6f14c1a000 rw-p 00016000 103:02 394746 /lib/x86_64-linux-gnu/libnsl-2.23.so
7f6f14c1a000-7f6f14c1c000 rw-p 00000000 00:00 0
7f6f14c1c000-7f6f14c24000 r-xp 00000000 103:02 394771 /lib/x86_64-linux-gnu/libnss_compat-2.23.so
7f6f14c24000-7f6f14e23000 ---p 00008000 103:02 394771 /lib/x86_64-linux-gnu/libnss_compat-2.23.so
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7f6f14e25000-7f6f14e63000 r-xp 00000000 103:02 9966876 /usr/lib/x86_64-linux-gnu/libquadmath.so.0.0.0
7f6f14e63000-7f6f15062000 ---p 0003e000 103:02 9966876 /usr/lib/x86_64-linux-gnu/libquadmath.so.0.0.0
7f6f15062000-7f6f15063000 r--p 0003d000 103:02 9966876 /usr/lib/x86_64-linux-gnu/libquadmath.so.0.0.0
7f6f15063000-7f6f15064000 rw-p 0003e000 103:02 9966876 /usr/lib/x86_64-linux-gnu/libquadmath.so.0.0.0
7f6f15064000-7f6f1518d000 r-xp 00000000 103:02 9961885 /usr/lib/x86_64-linux-gnu/libgfortran.so.3.0.0
7f6f1518d000-7f6f1538c000 ---p 00129000 103:02 9961885 /usr/lib/x86_64-linux-gnu/libgfortran.so.3.0.0
7f6f1538c000-7f6f1538d000 r--p 00128000 103:02 9961885 /usr/lib/x86_64-linux-gnu/libgfortran.so.3.0.0
7f6f1538d000-7f6f1538f000 rw-p 00129000 103:02 9961885 /usr/lib/x86_64-linux-gnu/libgfortran.so.3.0.0
7f6f1538f000-7f6f15571000 r-xp 00000000 00:32 23419236 /home/hpages/R/R-4.0.r78037/lib/libRlapack.so
7f6f15571000-7f6f15770000 ---p 001e2000 00:32 23419236 /home/hpages/R/R-4.0.r78037/lib/libRlapack.so
7f6f15770000-7f6f15771000 r--p 001e1000 00:32 23419236 /home/hpages/R/R-4.0.r78037/lib/libRlapack.so
7f6f15771000-7f6f15772000 rw-p 001e2000 00:32 23419236 /home/hpages/R/R-4.0.r78037/lib/libRlapack.so
7f6f15772000-7f6f1578c000 rw-p 00000000 00:00 0
7f6f1578c000-7f6f1582f000 r-xp 00000000 00:32 23419929 /home/hpages/R/R-4.0.r78037/library/stats/libs/stats.so
7f6f1582f000-7f6f15a2e000 ---p 000a3000 00:32 23419929 /home/hpages/R/R-4.0.r78037/library/stats/libs/stats.so
7f6f15a2e000-7f6f15a30000 r--p 000a2000 00:32 23419929 /home/hpages/R/R-4.0.r78037/library/stats/libs/stats.so
7f6f15a30000-7f6f15a32000 rw-p 000a4000 00:32 23419929 /home/hpages/R/R-4.0.r78037/library/stats/libs/stats.so
7f6f15a32000-7f6f15a7d000 r-xp 00000000 00:32 23419788 /home/hpages/R/R-4.0.r78037/library/graphics/libs/graphics.so
7f6f15a7d000-7f6f15c7d000 ---p 0004b000 00:32 23419788 /home/hpages/R/R-4.0.r78037/library/graphics/libs/graphics.so
7f6f15c7d000-7f6f15c7e000 r--p 0004b000 00:32 23419788 /home/hpages/R/R-4.0.r78037/library/graphics/libs/graphics.so
7f6f15c7e000-7f6f15c7f000 rw-p 0004c000 00:32 23419788 /home/hpages/R/R-4.0.r78037/library/graphics/libs/graphics.so
7f6f15c7f000-7f6f15cb5000 r-xp 00000000 00:32 23419746 /home/hpages/R/R-4.0.r78037/library/grDevices/libs/grDevices.so
7f6f15cb5000-7f6f15eb5000 ---p 00036000 00:32 23419746 /home/hpages/R/R-4.0.r78037/library/grDevices/libs/grDevices.so
7f6f15eb5000-7f6f15eba000 r--p 00036000 00:32 23419746 /home/hpages/R/R-4.0.r78037/library/grDevices/libs/grDevices.so
7f6f15eba000-7f6f15ebc000 rw-p 0003b000 00:32 23419746 /home/hpages/R/R-4.0.r78037/library/grDevices/libs/grDevices.so
7f6f15ebc000-7f6f15ebd000 rw-p 00000000 00:00 0
7f6f15ebd000-7f6f15ec9000 r-xp 00000000 00:32 23419597 /home/hpages/R/R-4.0.r78037/library/utils/libs/utils.so
7f6f15ec9000-7f6f160c8000 ---p 0000c000 00:32 23419597 /home/hpages/R/R-4.0.r78037/library/utils/libs/utils.so
7f6f160c8000-7f6f160c9000 r--p 0000b000 00:32 23419597 /home/hpages/R/R-4.0.r78037/library/utils/libs/utils.so
7f6f160c9000-7f6f160ca000 rw-p 0000c000 00:32 23419597 /home/hpages/R/R-4.0.r78037/library/utils/libs/utils.so
7f6f160ca000-7f6f161af000 rw-p 00000000 00:00 0
7f6f161af000-7f6f161b1000 r-xp 00000000 103:02 10235424 /usr/lib/x86_64-linux-gnu/gconv/ISO8859-1.so
7f6f161b1000-7f6f163b0000 ---p 00002000 103:02 10235424 /usr/lib/x86_64-linux-gnu/gconv/ISO8859-1.so
7f6f163b0000-7f6f163b1000 r--p 00001000 103:02 10235424 /usr/lib/x86_64-linux-gnu/gconv/ISO8859-1.so
7f6f163b1000-7f6f163b2000 rw-p 00002000 103:02 10235424 /usr/lib/x86_64-linux-gnu/gconv/ISO8859-1.so
7f6f1647e000-7f6f165bf000 rw-p 00000000 00:00 0
7f6f165bf000-7f6f165c7000 r-xp 00000000 00:32 23419959 /home/hpages/R/R-4.0.r78037/library/methods/libs/methods.so
7f6f165c7000-7f6f167c7000 ---p 00008000 00:32 23419959 /home/hpages/R/R-4.0.r78037/library/methods/libs/methods.so
7f6f167c7000-7f6f167c8000 r--p 00008000 00:32 23419959 /home/hpages/R/R-4.0.r78037/library/methods/libs/methods.so
7f6f167c8000-7f6f167c9000 rw-p 00009000 00:32 23419959 /home/hpages/R/R-4.0.r78037/library/methods/libs/methods.so
7f6f167f8000-7f6f16c04000 rw-p 00000000 00:00 0
7f6f16c04000-7f6f16edc000 r--p 00000000 103:02 9965611 /usr/lib/locale/locale-archive
7f6f16edc000-7f6f16ef2000 r-xp 00000000 103:02 397791 /lib/x86_64-linux-gnu/libgcc_s.so.1
7f6f16ef2000-7f6f170f1000 ---p 00016000 103:02 397791 /lib/x86_64-linux-gnu/libgcc_s.so.1
7f6f170f1000-7f6f170f2000 rw-p 00015000 103:02 397791 /lib/x86_64-linux-gnu/libgcc_s.so.1
7f6f170f2000-7f6f17264000 r-xp 00000000 103:02 9961864 /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.21
7f6f17264000-7f6f17464000 ---p 00172000 103:02 9961864 /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.21
7f6f17464000-7f6f1746e000 r--p 00172000 103:02 9961864 /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.21
7f6f1746e000-7f6f17470000 rw-p 0017c000 103:02 9961864 /usr/lib/x86_64-linux-gnu/libstdc++.so.6.0.21
7f6f17470000-7f6f17474000 rw-p 00000000 00:00 0
7f6f17474000-7f6f18d2a000 r-xp 00000000 103:02 9965696 /usr/lib/x86_64-linux-gnu/libicudata.so.55.1
7f6f18d2a000-7f6f18f29000 ---p 018b6000 103:02 9965696 /usr/lib/x86_64-linux-gnu/libicudata.so.55.1
7f6f18f29000-7f6f18f2a000 r--p 018b5000 103:02 9965696 /usr/lib/x86_64-linux-gnu/libicudata.so.55.1
7f6f18f2a000-7f6f18f2b000 rw-p 018b6000 103:02 9965696 /usr/lib/x86_64-linux-gnu/libicudata.so.55.1
7f6f18f2b000-7f6f18f50000 r-xp 00000000 103:02 397925 /lib/x86_64-linux-gnu/libtinfo.so.5.9
7f6f18f50000-7f6f1914f000 ---p 00025000 103:02 397925 /lib/x86_64-linux-gnu/libtinfo.so.5.9
7f6f1914f000-7f6f19153000 r--p 00024000 103:02 397925 /lib/x86_64-linux-gnu/libtinfo.so.5.9
7f6f19153000-7f6f19154000 rw-p 00028000 103:02 397925 /lib/x86_64-linux-gnu/libtinfo.so.5.9
7f6f19154000-7f6f19175000 r-xp 00000000 103:02 9969010 /usr/lib/x86_64-linux-gnu/libgomp.so.1.0.0
7f6f19175000-7f6f19374000 ---p 00021000 103:02 9969010 /usr/lib/x86_64-linux-gnu/libgomp.so.1.0.0
7f6f19374000-7f6f19375000 r--p 00020000 103:02 9969010 /usr/lib/x86_64-linux-gnu/libgomp.so.1.0.0
7f6f19375000-7f6f19376000 rw-p 00021000 103:02 9969010 /usr/lib/x86_64-linux-gnu/libgomp.so.1.0.0
7f6f19376000-7f6f195c8000 r-xp 00000000 103:02 9965694 /usr/lib/x86_64-linux-gnu/libicui18n.so.55.1
7f6f195c8000-7f6f197c8000 ---p 00252000 103:02 9965694 /usr/lib/x86_64-linux-gnu/libicui18n.so.55.1
7f6f197c8000-7f6f197d7000 r--p 00252000 103:02 9965694 /usr/lib/x86_64-linux-gnu/libicui18n.so.55.1
7f6f197d7000-7f6f197d8000 rw-p 00261000 103:02 9965694 /usr/lib/x86_64-linux-gnu/libicui18n.so.55.1
7f6f197d8000-7f6f19957000 r-xp 00000000 103:02 9965692 /usr/lib/x86_64-linux-gnu/libicuuc.so.55.1
7f6f19957000-7f6f19b57000 ---p 0017f000 103:02 9965692 /usr/lib/x86_64-linux-gnu/libicuuc.so.55.1
7f6f19b57000-7f6f19b67000 r--p 0017f000 103:02 9965692 /usr/lib/x86_64-linux-gnu/libicuuc.so.55.1
7f6f19b67000-7f6f19b68000 rw-p 0018f000 103:02 9965692 /usr/lib/x86_64-linux-gnu/libicuuc.so.55.1
7f6f19b68000-7f6f19b6c000 rw-p 00000000 00:00 0
7f6f19b6c000-7f6f19b6f000 r-xp 00000000 103:02 394736 /lib/x86_64-linux-gnu/libdl-2.23.so
7f6f19b6f000-7f6f19d6e000 ---p 00003000 103:02 394736 /lib/x86_64-linux-gnu/libdl-2.23.so
7f6f19d6e000-7f6f19d6f000 r--p 00002000 103:02 394736 /lib/x86_64-linux-gnu/libdl-2.23.so
7f6f19d6f000-7f6f19d70000 rw-p 00003000 103:02 394736 /lib/x86_64-linux-gnu/libdl-2.23.so
7f6f19d70000-7f6f19d77000 r-xp 00000000 103:02 394731 /lib/x86_64-linux-gnu/librt-2.23.so
7f6f19d77000-7f6f19f76000 ---p 00007000 103:02 394731 /lib/x86_64-linux-gnu/librt-2.23.so
7f6f19f76000-7f6f19f77000 r--p 00006000 103:02 394731 /lib/x86_64-linux-gnu/librt-2.23.so
7f6f19f77000-7f6f19f78000 rw-p 00007000 103:02 394731 /lib/x86_64-linux-gnu/librt-2.23.so
7f6f19f78000-7f6f19f91000 r-xp 00000000 103:02 393404 /lib/x86_64-linux-gnu/libz.so.1.2.8
7f6f19f91000-7f6f1a190000 ---p 00019000 103:02 393404 /lib/x86_64-linux-gnu/libz.so.1.2.8
7f6f1a190000-7f6f1a191000 r--p 00018000 103:02 393404 /lib/x86_64-linux-gnu/libz.so.1.2.8
7f6f1a191000-7f6f1a192000 rw-p 00019000 103:02 393404 /lib/x86_64-linux-gnu/libz.so.1.2.8
7f6f1a192000-7f6f1a1a1000 r-xp 00000000 103:02 393588 /lib/x86_64-linux-gnu/libbz2.so.1.0.4
7f6f1a1a1000-7f6f1a3a0000 ---p 0000f000 103:02 393588 /lib/x86_64-linux-gnu/libbz2.so.1.0.4
7f6f1a3a0000-7f6f1a3a1000 r--p 0000e000 103:02 393588 /lib/x86_64-linux-gnu/libbz2.so.1.0.4
7f6f1a3a1000-7f6f1a3a2000 rw-p 0000f000 103:02 393588 /lib/x86_64-linux-gnu/libbz2.so.1.0.4
7f6f1a3a2000-7f6f1a3c3000 r-xp 00000000 103:02 397820 /lib/x86_64-linux-gnu/liblzma.so.5.0.0
7f6f1a3c3000-7f6f1a5c2000 ---p 00021000 103:02 397820 /lib/x86_64-linux-gnu/liblzma.so.5.0.0
7f6f1a5c2000-7f6f1a5c3000 r--p 00020000 103:02 397820 /lib/x86_64-linux-gnu/liblzma.so.5.0.0
7f6f1a5c3000-7f6f1a5c4000 rw-p 00021000 103:02 397820 /lib/x86_64-linux-gnu/liblzma.so.5.0.0
7f6f1a5c4000-7f6f1a63c000 r-xp 00000000 103:02 9971004 /usr/lib/x86_64-linux-gnu/libpcre2-8.so.0.3.0
7f6f1a63c000-7f6f1a83b000 ---p 00078000 103:02 9971004 /usr/lib/x86_64-linux-gnu/libpcre2-8.so.0.3.0
7f6f1a83b000-7f6f1a83c000 r--p 00077000 103:02 9971004 /usr/lib/x86_64-linux-gnu/libpcre2-8.so.0.3.0
7f6f1a83c000-7f6f1a83d000 rw-p 00078000 103:02 9971004 /usr/lib/x86_64-linux-gnu/libpcre2-8.so.0.3.0
7f6f1a83d000-7f6f1a87a000 r-xp 00000000 103:02 397904 /lib/x86_64-linux-gnu/libreadline.so.6.3
7f6f1a87a000-7f6f1aa7a000 ---p 0003d000 103:02 397904 /lib/x86_64-linux-gnu/libreadline.so.6.3
7f6f1aa7a000-7f6f1aa7c000 r--p 0003d000 103:02 397904 /lib/x86_64-linux-gnu/libreadline.so.6.3
7f6f1aa7c000-7f6f1aa82000 rw-p 0003f000 103:02 397904 /lib/x86_64-linux-gnu/libreadline.so.6.3
7f6f1aa82000-7f6f1aa83000 rw-p 00000000 00:00 0
7f6f1aa83000-7f6f1ab8b000 r-xp 00000000 103:02 394777 /lib/x86_64-linux-gnu/libm-2.23.so
7f6f1ab8b000-7f6f1ad8a000 ---p 00108000 103:02 394777 /lib/x86_64-linux-gnu/libm-2.23.so
7f6f1ad8a000-7f6f1ad8b000 r--p 00107000 103:02 394777 /lib/x86_64-linux-gnu/libm-2.23.so
7f6f1ad8b000-7f6f1ad8c000 rw-p 00108000 103:02 394777 /lib/x86_64-linux-gnu/libm-2.23.so
7f6f1ad8c000-7f6f1adb8000 r-xp 00000000 00:32 23418713 /home/hpages/R/R-4.0.r78037/lib/libRblas.so
7f6f1adb8000-7f6f1afb7000 ---p 0002c000 00:32 23418713 /home/hpages/R/R-4.0.r78037/lib/libRblas.so
7f6f1afb7000-7f6f1afb8000 r--p 0002b000 00:32 23418713 /home/hpages/R/R-4.0.r78037/lib/libRblas.so
7f6f1afb8000-7f6f1afb9000 rw-p 0002c000 00:32 23418713 /home/hpages/R/R-4.0.r78037/lib/libRblas.so
7f6f1afb9000-7f6f1b179000 r-xp 00000000 103:02 394763 /lib/x86_64-linux-gnu/libc-2.23.so
7f6f1b179000-7f6f1b379000 ---p 001c0000 103:02 394763 /lib/x86_64-linux-gnu/libc-2.23.so
7f6f1b379000-7f6f1b37d000 r--p 001c0000 103:02 394763 /lib/x86_64-linux-gnu/libc-2.23.so
7f6f1b37d000-7f6f1b37f000 rw-p 001c4000 103:02 394763 /lib/x86_64-linux-gnu/libc-2.23.so
7f6f1b37f000-7f6f1b383000 rw-p 00000000 00:00 0
7f6f1b383000-7f6f1b39b000 r-xp 00000000 103:02 394738 /lib/x86_64-linux-gnu/libpthread-2.23.so
7f6f1b39b000-7f6f1b59a000 ---p 00018000 103:02 394738 /lib/x86_64-linux-gnu/libpthread-2.23.so
7f6f1b59a000-7f6f1b59b000 r--p 00017000 103:02 394738 /lib/x86_64-linux-gnu/libpthread-2.23.so
7f6f1b59b000-7f6f1b59c000 rw-p 00018000 103:02 394738 /lib/x86_64-linux-gnu/libpthread-2.23.so
7f6f1b59c000-7f6f1b5a0000 rw-p 00000000 00:00 0
7f6f1b5a0000-7f6f1b8bd000 r-xp 00000000 00:32 23419195 /home/hpages/R/R-4.0.r78037/lib/libR.so
7f6f1b8bd000-7f6f1babd000 ---p 0031d000 00:32 23419195 /home/hpages/R/R-4.0.r78037/lib/libR.so
7f6f1babd000-7f6f1badb000 r--p 0031d000 00:32 23419195 /home/hpages/R/R-4.0.r78037/lib/libR.so
7f6f1badb000-7f6f1bae9000 rw-p 0033b000 00:32 23419195 /home/hpages/R/R-4.0.r78037/lib/libR.so
7f6f1bae9000-7f6f1bc39000 rw-p 00000000 00:00 0
7f6f1bc39000-7f6f1bc5f000 r-xp 00000000 103:02 394737 /lib/x86_64-linux-gnu/ld-2.23.so
7f6f1bce6000-7f6f1be38000 rw-p 00000000 00:00 0
7f6f1be54000-7f6f1be55000 rw-p 00000000 00:00 0
7f6f1be55000-7f6f1be56000 r--p 00000000 00:32 23419290 /home/hpages/R/R-4.0.r78037/library/translations/en/LC_MESSAGES/R.mo
7f6f1be56000-7f6f1be5d000 r--s 00000000 103:02 10235479 /usr/lib/x86_64-linux-gnu/gconv/gconv-modules.cache
7f6f1be5d000-7f6f1be5e000 rw-p 00000000 00:00 0
7f6f1be5e000-7f6f1be5f000 r--p 00025000 103:02 394737 /lib/x86_64-linux-gnu/ld-2.23.so
7f6f1be5f000-7f6f1be60000 rw-p 00026000 103:02 394737 /lib/x86_64-linux-gnu/ld-2.23.so
7f6f1be60000-7f6f1be61000 rw-p 00000000 00:00 0
7fff065cc000-7fff065fd000 rw-p 00000000 00:00 0 [stack]
7fff06638000-7fff0663b000 r--p 00000000 00:00 0 [vvar]
7fff0663b000-7fff0663d000 r-xp 00000000 00:00 0 [vdso]
ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0 [vsyscall]
Aborted (core dumped)
sessionInfo():
R Under development (unstable) (2020-03-23 r78037)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.6 LTS
Matrix products: default
BLAS: /home/hpages/R/R-4.0.r78037/lib/libRblas.so
LAPACK: /home/hpages/R/R-4.0.r78037/lib/libRlapack.so
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] Rfast_1.9.9 RcppZiggurat_0.1.5 Rcpp_1.0.4.6 cytolib_1.99.28
loaded via a namespace (and not attached):
[1] compiler_4.0.0 RProtoBufLib_1.99.8 parallel_4.0.0
[4] RcppParallel_5.0.0
FWIW I also get a crash on other Linux machines e.g. on Bioconductor build machine malbec2 where I get:
> library(cytolib)
> library(Rfast)
Loading required package: Rcpp
Loading required package: RcppZiggurat
> x <- matrix(runif(40), nrow=8)
> Rfast::rowMaxs(x)
double free or corruption (out)
Aborted (core dumped)
Note that on this machine I get the crash most of the time but not every time (e.g. 6-8 times out of 10).
sessionInfo():
R version 4.0.0 RC (2020-04-19 r78255)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 18.04.4 LTS
Matrix products: default
BLAS: /home/biocbuild/bbs-3.11-bioc/R/lib/libRblas.so
LAPACK: /home/biocbuild/bbs-3.11-bioc/R/lib/libRlapack.so
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] Rfast_1.9.9 RcppZiggurat_0.1.5 Rcpp_1.0.4.6 cytolib_1.99.28
loaded via a namespace (and not attached):
[1] compiler_4.0.0 RProtoBufLib_1.99.8 parallel_4.0.0
[4] RcppParallel_5.0.0
Finally it's worth noting that I don't get a crash with R 3.6.0 and the RELEASE_3_10 branch of cytolib:
library(cytolib)
library(Rfast)
x <- matrix(runif(40), nrow=8)
Rfast::rowMaxs(x)
# [1] 1 2 3 3 4 4 5 4
sessionInfo():
R version 3.6.0 Patched (2019-05-02 r76454)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.6 LTS
Matrix products: default
BLAS: /home/hpages/R/R-3.6.r76454/lib/libRblas.so
LAPACK: /home/hpages/R/R-3.6.r76454/lib/libRlapack.so
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] Rfast_1.9.9 RcppZiggurat_0.1.5 Rcpp_1.0.4.6 cytolib_1.8.0
loaded via a namespace (and not attached):
[1] compiler_3.6.0 parallel_3.6.0
Thanks,
H.
conflict definition of 'POINT' with windows API
C:/Users/wjiang2/Documents/R/win-library/4.0/cytolib/include/cytolib/in_polygon.hpp:22:8: note: struct cytolib::POINT
struct POINT
^
In file included from C:/Rtools/mingw_32/i686-w64-mingw32/include/windows.h:130:0,
from C:/Users/wjiang2/Documents/R/win-library/4.0/RcppParallel/include/tbb/machine/windows_api.h:26,
from C:/Users/wjiang2/Documents/R/win-library/4.0/RcppParallel/include/tbb/tbb_thread.h:27,
from C:/Users/wjiang2/Documents/R/win-library/4.0/RcppParallel/include/tbb/enumerable_thread_specific.h:26,
from C:/Users/wjiang2/Documents/R/win-library/4.0/RcppParallel/include/tbb/combinable.h:24,
from C:/Users/wjiang2/Documents/R/win-library/4.0/RcppParallel/include/tbb/tbb.h:41,
from ../inst/include/CytoML/flowJoWorkspace.hpp:19,
from ../inst/include/CytoML/macFlowJoWorkspace.hpp:10,
from ../inst/include/CytoML/openWorkspace.hpp:11,
from ../inst/include/CytoML.h:5,
from RcppExports.cpp:4:
C:/Rtools/mingw_32/i686-w64-mingw32/include/imm.h:29:5: error: 'POINT' does not name a type
POINT ptCurrentPos;
^
C:/Rtools/mingw_32/i686-w64-mingw32/include/imm.h:36:5: error: reference to 'POINT' is ambiguous
POINT ptCurrentPos;The easy fix would be referring to POINT explicitly through namespace prefix cytolib::
write portable configure scripts for windows
We are currently using the configure script auto-generated through autoconf for writing package version info into the c++ header file. However this script doesn't seem to be portable for windows
cytolib>R CMD INSTALL .
* installing to library 'C:/Users/wjiang2/Documents/R/win-library/3.6'
* installing *source* package 'cytolib' ...
** using staged installation
chmod: not found
configure.win: error: cannot create configure.win.lineno; rerun with a POSIX shell
ERROR: configuration failed for package 'cytolib'Unless we can find the tool that can generate mingw version of configure.win file , we may consider to use R to perform such pre-installation configuring process
https://github.com/kevinushey/configure
implement and benchmark C++11 std::thread vs openMP
Since openMP has some portability issue with older clang.
test and work on the compatibility between openCyto and cytolib 2.0
library(cytolib); library(mzR) crashes R 4.0.0 alpha on Linux
Hi,
I don't know if I should fill an issue here or under mzR so I'm doing both, sorry for that.
So on Linux, with R 4.0.0 alpha and current devel versions of cytolib and mzR, trying to load the 2 packages in this order crashes my session:
> library(cytolib)
> library(mzR)
Loading required package: Rcpp
terminate called after throwing an instance of 'H5::DataSpaceIException'
Aborted (core dumped)
No problem if I load them in the reverse order:
> library(mzR)
Loading required package: Rcpp
> library(cytolib)
> sessionInfo()
R version 4.0.0 alpha (2020-03-31 r78116)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 18.04.4 LTS
Matrix products: default
BLAS: /home/biocbuild/bbs-3.11-bioc/R/lib/libRblas.so
LAPACK: /home/biocbuild/bbs-3.11-bioc/R/lib/libRlapack.so
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] cytolib_1.99.24 mzR_2.21.1 Rcpp_1.0.4
loaded via a namespace (and not attached):
[1] compiler_4.0.0 RProtoBufLib_1.99.7 ProtGenerics_1.19.3
[4] parallel_4.0.0 Biobase_2.47.3 codetools_0.2-16
[7] ncdf4_1.17 BiocGenerics_0.33.3 RcppParallel_5.0.0
Thanks,
H.
move readonly lock from cytoframe to h5cytoframe
To achieve the temporary/experimental modifications(e.g, rename channels/markers/keywords) on GatingSet object (particularly the underlying cytoset/cytoframe), we now relax the locking mechanism so that all the changes(except exprs data) are permitted even when readonly = TRUE.
The changes remain in cache until
flush_metais explicitly invoked by usersave_gsgs_clone(since the new copy is writable by default)
Currently we intentionally disable the auto-flushing at destructor (i.e. when gs is out of scope) to prevent the accidental changes unexpectedly become permanent, which means users have to do one of the three actions above in order to save the changes.
regarding multiple opens of the same h5 file
In ncdfFlow, we simply close h5 file handler immediately after each read/write operation. Thus we never experienced any issues. Now cytolib keeps the h5 file handler open during the life cycle of H5CytoFrame object to maintain the h5 cache for speeding up the subsequent IO.
This worked fine for multi-opens within the same process(e.g. the same R session) even if the file are opened with write flag
library(rhdf5)
file <- "/tmp/RtmpArlTHw/test.h5"
f1 <- H5Fopen(file, "H5F_ACC_RDWR")
f2 <- H5Fopen(file, "H5F_ACC_RDWR")
> f1
HDF5 FILE
name /
filename
name otype dclass dim
0 data H5I_DATASET FLOAT 3002125 x 14
1 keywords H5I_DATASET COMPOUND 219
2 params H5I_DATASET COMPOUND 14
3 pdata H5I_DATASET COMPOUND 1However when a separate process (e.g. another R session or command line tool) tries open the same file , it will fail on either H5F_ACC_RDONLY or H5F_ACC_RDWR flag since the file was locked by another h5 lib instance.
> f <- H5Fopen(file, "H5F_ACC_RDONLY")
Error in H5Fopen(file, "H5F_ACC_RDONLY") :
HDF5. File accessibilty. Unable to open file.If the initial open was H5F_ACC_RDONLY, then it seems to succeed for both process. So I guess the inter-process lock was only applied when the file was opened with write permission.
Even though it makes sense for such locking mechanism, the behavior of allowing multi-opens within the same process is somewhat misleading. It could be that h5 lib inherently is designed for single-process application and thus no concurrent IOs are expected within the same process.
Yet the same assumption can't be hold when it comes to multi-process scenario, which is why h5 prohibits it.
Given the statement from H5 API specs
It is generally recommended that applications avoid multiple opens of the same file.
and also in our use cases, we can't guarantee the data (i.e. GatingSet) is always initially opened as read-only, the best we can do is follow ncdfFlow's practice by not maintaining the state of H5File handler.
misterious rstudio crash issue due to the inline member function
The headeronly branch works fine for all the test cases at R console, but crashes R session within rstudio for several workspaces. e.g. the test case below will fail in rstudio
library(flowWorkspace)
path <- "~/rglab/workspace/flowWorkspace/wsTestSuite"
setLoglevel("Gate")
thisPath <- file.path(path, "combineNode/OrNode")
wsFile <- file.path(thisPath, "Test_EW.wsp")
ws <- openWorkspace(wsFile)
gs <- parseWorkspace(ws, name = 1, path = file.path(path))I've spend the past two days trying to pinpoint the source of problem without success. Not sure if it has something to do with rstudio ( I am using Version 1.0.153).
To test it, the flowWorkspace/headeronly branch is required as well as RProtoBufLib/headeronly
Installation problems
Hi guys,
I'm having trouble installing the cytolib package. I have successfully installed the most recent RProtoBufLib but end up with the error belowand would appreciate advice as to what else I can try.
Cheers,
Claudia
> install_github("RGLab/cytolib",
+ ref = "trunk",
+ lib="C:/Program Files/R/R-3.6.1/library")
Downloading GitHub repo RGLab/cytolib@trunk
Skipping 1 packages ahead of CRAN: Rhdf5lib
√ checking for file 'C:\Users\u5746262\AppData\Local\Temp\RtmpwR9qJh\remotes218422756d3\RGLab-cytolib-168cd50/DESCRIPTION' (810ms)
- preparing 'cytolib': (2.5s)
√ checking DESCRIPTION meta-information ...
- cleaning src
- running 'cleanup.win'
- checking for LF line-endings in source and make files and shell scripts (978ms)
- checking for empty or unneeded directories (345ms)
- building 'cytolib_1.9.5.tar.gz'
Warning: file 'cytolib/cleanup' did not have execute permissions: corrected
Warning: file 'cytolib/configure' did not have execute permissions: corrected
Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, :
storing paths of more than 100 bytes is not portable:
'cytolib/thirdparty/protobuf/win/include/google/protobuf/stubs/atomicops_internals_atomicword_compat.h'
* installing *source* package 'cytolib' ...
** using staged installation
** preparing to configure package 'cytolib' ...
*** configured file: 'cytolibConfig.h.in' => 'inst/include/cytolib/cytolibConfig.h'
** finished configure for package 'cytolib'
** libs
*** arch - i386
c:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/PROGRA~1/R/R-36~1.1/include" -DNDEBUG -DROUT -I../inst/include -DRCPP_PARALLEL_USE_TBB=1 -fpermissive -Wno-deprecated-declarations -DBOOST_NO_AUTO_PTR -Wno-unknown-pragmas -Wno-comment -I"C:/Program Files/R/R-3.6.1/library/Rcpp/include" -I"\\mhsdata.anu.edu.au/mydocsu5746262/My Documents/R/win-library/3.6/BH/include" -I"C:/Program Files/R/R-3.6.1/library/RProtoBufLib/include" -I"C:/Program Files/R/R-3.6.1/library/Rhdf5lib/include" -I"C:/Program Files/R/R-3.6.1/library/RcppArmadillo/include" -I"C:/Program Files/R/R-3.6.1/library/RcppParallel/include" -O2 -Wall -mtune=generic -c boost/libs/system/src/error_code.cpp -o boost/libs/system/src/error_code.o
cytolib install R4.1.2 on ubuntu18 failed
I cannot install cytolib due to some compiling problem:
Bioconductor 3.14 (BiocManager 1.30.16) R4.1.2
The message is:
......
/opt/R/4.1.2/lib/R/etc/Makeconf:177: recipe for target 'boost/libs/filesystem/src/path.o' failed
make: *** [boost/libs/filesystem/src/paht.o] Error 1
ERROR: compilation failed for package 'cytolib'
......
Thank you!
Loading cytolib crashes mbkmeans
In the same vein as #37 and #38, I get:
library(cytolib)
library(mbkmeans)
set.seed(1000)
x <- matrix(runif(10000), ncol=10)
out <- mbkmeans(t(x), 20)
## error: arma::memory::acquire(): out of memory
## Error in mini_batch(data = t(x), clusters = clusters, batch_size = batch_size, :
## std::bad_allocThis fails 100% of the time on my system. I am confident that mbkmeans is not doing any particularly unusual. The more obvious culprit is the local=FALSE in cytolib's dyn.load statement; setting it back to TRUE avoids this error.
Session information
R Under development (unstable) (2021-01-01 r79759)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 18.04.5 LTS
Matrix products: default
BLAS: /home/luna/Software/R/trunk/lib/libRblas.so
LAPACK: /home/luna/Software/R/trunk/lib/libRlapack.so
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] mbkmeans_1.7.1 cytolib_2.3.0
loaded via a namespace (and not attached):
[1] gmp_0.6-2 Rcpp_1.0.5
[3] benchmarkmeData_1.0.4 bluster_1.1.2
[5] XVector_0.31.1 GenomeInfoDb_1.27.3
[7] pillar_1.4.7 compiler_4.1.0
[9] BiocNeighbors_1.9.4 iterators_1.0.13
[11] zlibbioc_1.37.0 bitops_1.0-6
[13] tools_4.1.0 MatrixGenerics_1.3.0
[15] SingleCellExperiment_1.13.3 lifecycle_0.2.0
[17] tibble_3.0.4 gtable_0.3.0
[19] lattice_0.20-41 pkgconfig_2.0.3
[21] rlang_0.4.10 igraph_1.2.6
[23] foreach_1.5.1 Matrix_1.3-2
[25] DelayedArray_0.17.7 parallel_4.1.0
[27] GenomeInfoDbData_1.2.4 httr_1.4.2
[29] dplyr_1.0.2 generics_0.1.0
[31] vctrs_0.3.6 S4Vectors_0.29.6
[33] gtools_3.8.2 IRanges_2.25.6
[35] stats4_4.1.0 grid_4.1.0
[37] tidyselect_1.1.0 Biobase_2.51.0
[39] glue_1.4.2 R6_2.5.0
[41] BiocParallel_1.25.2 RProtoBufLib_2.3.0
[43] ggplot2_3.3.3 purrr_0.3.4
[45] ClusterR_1.2.2 magrittr_2.0.1
[47] codetools_0.2-18 GenomicRanges_1.43.1
[49] scales_1.1.1 ellipsis_0.3.1
[51] matrixStats_0.57.0 BiocGenerics_0.37.0
[53] SummarizedExperiment_1.21.1 benchmarkme_1.0.4
[55] colorspace_2.0-0 doParallel_1.0.16
[57] RCurl_1.98-1.2 RcppParallel_5.0.2
[59] munsell_0.5.0 crayon_1.3.4
load_gs requires write permissions, even with h5_readonly = TRUE
This was discovered by internal tests that were failing due to symlinking to test file directories for which I did not have write permissions (even though that shouldn't be necessary), but it was fortunate as it exposed the underlying problem that load_gs requires write permissions for the H5 files of the archive, even when h5_readonly is set to TRUE.
To reproduce, block write permissions for the H5 file of a GatingSet archive directory to the user owning the R session. I used gs_manual from flowWorkspaceData and blocked write permissions.
$ sudo chmod -R 555 gs_manual/
$ ls -l gs_manual
total 5892
-r-xr-xr-x 1 jpwagner g_jpwagner 89 Apr 5 12:23 63c60e66-779b-4712-ad6e-b9349b965401.gs
-r-xr-xr-x 1 jpwagner g_jpwagner 5778880 Apr 5 12:23 CytoTrol_CytoTrol_1.fcs.h5
-r-xr-xr-x 1 jpwagner g_jpwagner 247118 Apr 5 12:23 CytoTrol_CytoTrol_1.fcs.pb
Then, in R:
# h5_readonly = TRUE is default anyway
> load_gs("gs_manual", h5_readonly = TRUE)
error #000: in H5Fopen(): line 509
major: File accessibilty
minor: Unable to open file
error #001: in H5F_open(): line 1498
major: File accessibilty
minor: Unable to open file
error #002: in H5FD_open(): line 734
major: Virtual File Layer
minor: Unable to initialize object
error #003: in H5FD_sec2_open(): line 346
major: File accessibilty
minor: Unable to open file
Error in .cpp_loadGatingSet(normalizePath(path), h5_readonly, select.sn, :
hdf Error
A rough stack trace:
load_gs --> .cpp_loadGatingSet --> load_gatingset
https://github.com/RGLab/flowWorkspace/blob/4b30a5baeacf62ad902d08c832d3a149912a5dd1/src/R_GatingSet.cpp#L224
-->add_GatingHierarchy
cytolib/inst/include/cytolib/GatingSet.hpp
Line 251 in a009aa8
-->
H5CytoFrame constructorcytolib/src/GatingHierarchy.cpp
Line 344 in a009aa8
Which, although it initializes the
readonly_ flag appropriately for the new H5CytoFrame, still has the issue of opening the file with the default file access flag,Lines 130 to 133 in d270e92
which is read/write:
This may be as simple as temporarily overriding the default_flag for H5File with H5F_ACC_RDONLY if the readonly flag passed down is TRUE, but that likely has wider implications.
Rework time channel scaling
This is sort of a post-mortem issue to wrangle related commits to cytolib, flowWorkspace, and CytoML to address the following and provide some rationale to our future selves:
Before these commits, flowWorkspace::gh_apply_to_new_fcs was calling flowWorkspace:::.cpp_NewGatingSet, which in turn was automatically scaling the time channel by the factor in the $TIMESTEP keyword from the sample FCS:
Line 354 in 4a03d99
This makes sense if the source for the template GatingHierarchy for gh_apply_to_new_fcs originated in FlowJo where this scaling is standard. But otherwise, this results in a perhaps unexpected scaling of the time channel for the new samples relative to the template GatingHierarchy. Furthermore, there would be no intrinsic history of whether this transformation had already been applied, meaning using a result itself as a template would result in further rescaling.
For these reasons, it made sense to instead add the time channel transformation back as a separate transformation object during FlowJo parsing in CytoML. This in turn required some changes to cytolib::scaleTrans to handle a scale transformation based on a single floating point factor (as opposed to two ints). That in turn required some changes to the protocol buffers.
Create CytoFramePersistent class
as the middle layer between CytoFrame and H5CytoFrame
goals to achieve:
- abstract out the
h5operations so thatGatingSetis agnostic abouth5operations - easy extension to other backend format
test and work on the compatibility between CytoML and cytolib 2.0
add c++ class for flowCore::logtGml2
Due to edeb097, flowCore::logtGml2 is no longer convertible to the existing logTrans class (which is flowjo implementation).
We need to add a separate logtGml2 class to be able to store this type of transformation that was applied in R. (e.g. store the gs parsed from cytobank where logtGml2 is still pretty commonly used.
use more recent `H5CPP` lib for h5 IO
The existing official h5c++ wrapper is outdated and incomplete. E.g. it doesn't support std::string and seamless conversion between user defined struct and h5 compound type. Thus requires somewhat tedious boilerplate code on user end.
https://github.com/steven-varga/h5cpp11 seems to tackle all those as well as armadillo data structure support
Determine whether to keep MemCytoFrame class
While @jacobpwagner is investigating H5FD_CORE (in memory H5 for faster IO, which potentially can replace the existing MemCytoFrame to simplify/unify the code base for CytoFrame), he discovered there is no significant performance advantage by keeping data in memory based on the benchmarking at R level
tmp <- tempfile()
fr <- matrix(rnorm(16*3e6), ncol = 16, dimnames = list(NULL, letters[1:16]))
fr <- flowFrame(fr)
write.FCS(fr, tmp)
utils:::format.object_size(file.size(tmp), "auto")
[1] "183.1 Mb"
cf1 <- load_cytoframe_from_fcs(tmp, is_h5 = F)
cf2 <- load_cytoframe_from_fcs(tmp, is_h5 = T)
> microbenchmark( a<- exprs(cf1[,1]), b <- exprs(cf2[,1]), times = 4)
Unit: milliseconds
expr min lq mean median uq max neval
a <- exprs(cf1[, 1]) 15.40628 16.32062 20.41917 20.63623 24.51772 24.99796 4
b <- exprs(cf2[, 1]) 12.84491 15.25784 16.78892 17.90347 18.32001 18.50385 4
> microbenchmark( a<- exprs(cf1), b <- exprs(cf2), times = 4)
Unit: milliseconds
expr min lq mean median uq max neval
a <- exprs(cf1) 361.6466 362.8688 415.8592 383.3787 468.8496 535.0328 4
b <- exprs(cf2) 386.0428 388.0514 472.7467 472.1052 557.4420 560.7336 4It shows very minor speedup for in-memory version of cytoframe when reading the whole dataset. For the partial IO, on-disk version is even better.
We will have to further profile code to see where exactly slows down in-memory cytoframe, otherwise we have no reason to keep it.
failed cytolib installation with 'no matching function for call to 'weakly_canonical''
I'm trying to install flowCore package using BiocManager, but this fails due to errors in cytolib installation:
Installing package(s) 'flowCore'
also installing the dependency ‘cytolib’
trying URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/cytolib_2.6.0.tar.gz'
Content type 'application/x-gzip' length 5463300 bytes (5.2 MB)
==================================================
downloaded 5.2 MB
trying URL 'https://bioconductor.org/packages/3.14/bioc/src/contrib/flowCore_2.6.0.tar.gz'
Content type 'application/x-gzip' length 7356052 bytes (7.0 MB)
==================================================
downloaded 7.0 MB
* installing *source* package ‘cytolib’ ...
** using staged installation
checking for a sed that does not truncate output... /usr/bin/sed
checking for g++... g++
checking whether the C++ compiler works... yes
checking for C++ compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C++ compiler... yes
checking whether g++ accepts -g... yes
checking how to run the C++ preprocessor... g++ -E
checking whether we are using the GNU C++ compiler... (cached) yes
checking whether g++ accepts -g... (cached) yes
configure: Parsing cytolib version info ...
configure: CYTOLIB_VERSION=2.6.0
configure: creating ./config.status
config.status: creating inst/include/cytolib/cytolibConfig.h
config.status: creating src/Makevars
** libs
clang++ -std=gnu++11 -I"/usr/local/Cellar/r/4.1.2/lib/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/usr/local/lib/R/4.1/site-library/Rcpp/include' -I'/usr/local/lib/R/4.1/site-library/BH/include' -I'/usr/local/lib/R/4.1/site-library/RProtoBufLib/include' -I'/usr/local/lib/R/4.1/site-library/Rhdf5lib/include' -I'/usr/local/lib/R/4.1/site-library/RcppArmadillo/include' -I'/usr/local/lib/R/4.1/site-library/RcppParallel/include' -I/usr/local/opt/gettext/include -I/usr/local/opt/readline/include -I/usr/local/opt/xz/include -I/usr/local/include -fPIC -g -O2 -c dummy.cpp -o dummy.o
clang++ -std=gnu++11 -I"/usr/local/Cellar/r/4.1.2/lib/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/usr/local/lib/R/4.1/site-library/Rcpp/include' -I'/usr/local/lib/R/4.1/site-library/BH/include' -I'/usr/local/lib/R/4.1/site-library/RProtoBufLib/include' -I'/usr/local/lib/R/4.1/site-library/Rhdf5lib/include' -I'/usr/local/lib/R/4.1/site-library/RcppArmadillo/include' -I'/usr/local/lib/R/4.1/site-library/RcppParallel/include' -I/usr/local/opt/gettext/include -I/usr/local/opt/readline/include -I/usr/local/opt/xz/include -I/usr/local/include -fPIC -g -O2 -c boost/libs/system/src/error_code.cpp -o boost/libs/system/src/error_code.o
clang++ -std=gnu++11 -I"/usr/local/Cellar/r/4.1.2/lib/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/usr/local/lib/R/4.1/site-library/Rcpp/include' -I'/usr/local/lib/R/4.1/site-library/BH/include' -I'/usr/local/lib/R/4.1/site-library/RProtoBufLib/include' -I'/usr/local/lib/R/4.1/site-library/Rhdf5lib/include' -I'/usr/local/lib/R/4.1/site-library/RcppArmadillo/include' -I'/usr/local/lib/R/4.1/site-library/RcppParallel/include' -I/usr/local/opt/gettext/include -I/usr/local/opt/readline/include -I/usr/local/opt/xz/include -I/usr/local/include -fPIC -g -O2 -c boost/libs/filesystem/src/codecvt_error_category.cpp -o boost/libs/filesystem/src/codecvt_error_category.o
clang++ -std=gnu++11 -I"/usr/local/Cellar/r/4.1.2/lib/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/usr/local/lib/R/4.1/site-library/Rcpp/include' -I'/usr/local/lib/R/4.1/site-library/BH/include' -I'/usr/local/lib/R/4.1/site-library/RProtoBufLib/include' -I'/usr/local/lib/R/4.1/site-library/Rhdf5lib/include' -I'/usr/local/lib/R/4.1/site-library/RcppArmadillo/include' -I'/usr/local/lib/R/4.1/site-library/RcppParallel/include' -I/usr/local/opt/gettext/include -I/usr/local/opt/readline/include -I/usr/local/opt/xz/include -I/usr/local/include -fPIC -g -O2 -c boost/libs/filesystem/src/directory.cpp -o boost/libs/filesystem/src/directory.o
clang++ -std=gnu++11 -I"/usr/local/Cellar/r/4.1.2/lib/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/usr/local/lib/R/4.1/site-library/Rcpp/include' -I'/usr/local/lib/R/4.1/site-library/BH/include' -I'/usr/local/lib/R/4.1/site-library/RProtoBufLib/include' -I'/usr/local/lib/R/4.1/site-library/Rhdf5lib/include' -I'/usr/local/lib/R/4.1/site-library/RcppArmadillo/include' -I'/usr/local/lib/R/4.1/site-library/RcppParallel/include' -I/usr/local/opt/gettext/include -I/usr/local/opt/readline/include -I/usr/local/opt/xz/include -I/usr/local/include -fPIC -g -O2 -c boost/libs/filesystem/src/exception.cpp -o boost/libs/filesystem/src/exception.o
clang++ -std=gnu++11 -I"/usr/local/Cellar/r/4.1.2/lib/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/usr/local/lib/R/4.1/site-library/Rcpp/include' -I'/usr/local/lib/R/4.1/site-library/BH/include' -I'/usr/local/lib/R/4.1/site-library/RProtoBufLib/include' -I'/usr/local/lib/R/4.1/site-library/Rhdf5lib/include' -I'/usr/local/lib/R/4.1/site-library/RcppArmadillo/include' -I'/usr/local/lib/R/4.1/site-library/RcppParallel/include' -I/usr/local/opt/gettext/include -I/usr/local/opt/readline/include -I/usr/local/opt/xz/include -I/usr/local/include -fPIC -g -O2 -c boost/libs/filesystem/src/operations.cpp -o boost/libs/filesystem/src/operations.o
boost/libs/filesystem/src/operations.cpp:2421:16: error:
no matching function for call to 'weakly_canonical'
path wc_base(weakly_canonical(base, &tmp_ec));
^~~~~~~~~~~~~~~~
/usr/local/lib/R/4.1/site-library/BH/include/boost/filesystem/operations.hpp:689:13: note:
candidate function not viable: no known conversion from
'boost::system::error_code *' to 'system::error_code &' for 2nd argument;
remove &
inline path weakly_canonical(path const& p, system::error_code& ec)
^
/usr/local/lib/R/4.1/site-library/BH/include/boost/filesystem/operations.hpp:163:6: note:
candidate function not viable: no known conversion from
'boost::system::error_code *' to 'const boost::filesystem::path' for 2nd
argument
path weakly_canonical(path const& p, path const& base, system::error_cod...
^
/usr/local/lib/R/4.1/site-library/BH/include/boost/filesystem/operations.hpp:684:13: note:
candidate function not viable: no known conversion from
'boost::system::error_code *' to 'const boost::filesystem::path' for 2nd
argument
inline path weakly_canonical(path const& p, path const& base = current_path())
^
/usr/local/lib/R/4.1/site-library/BH/include/boost/filesystem/operations.hpp:697:13: note:
candidate function not viable: requires 3 arguments, but 2 were provided
inline path weakly_canonical(path const& p, path const& base, system::er...
^
boost/libs/filesystem/src/operations.cpp:2424:13: error:
no matching function for call to 'weakly_canonical'
path wc_p(weakly_canonical(p, &tmp_ec));
^~~~~~~~~~~~~~~~
/usr/local/lib/R/4.1/site-library/BH/include/boost/filesystem/operations.hpp:689:13: note:
candidate function not viable: no known conversion from
'boost::system::error_code *' to 'system::error_code &' for 2nd argument;
remove &
inline path weakly_canonical(path const& p, system::error_code& ec)
^
/usr/local/lib/R/4.1/site-library/BH/include/boost/filesystem/operations.hpp:163:6: note:
candidate function not viable: no known conversion from
'boost::system::error_code *' to 'const boost::filesystem::path' for 2nd
argument
path weakly_canonical(path const& p, path const& base, system::error_cod...
^
/usr/local/lib/R/4.1/site-library/BH/include/boost/filesystem/operations.hpp:684:13: note:
candidate function not viable: no known conversion from
'boost::system::error_code *' to 'const boost::filesystem::path' for 2nd
argument
inline path weakly_canonical(path const& p, path const& base = current_path())
^
/usr/local/lib/R/4.1/site-library/BH/include/boost/filesystem/operations.hpp:697:13: note:
candidate function not viable: requires 3 arguments, but 2 were provided
inline path weakly_canonical(path const& p, path const& base, system::er...
^
2 errors generated.
make: *** [boost/libs/filesystem/src/operations.o] Error 1
ERROR: compilation failed for package ‘cytolib’
* removing ‘/usr/local/lib/R/4.1/site-library/cytolib’
ERROR: dependency ‘cytolib’ is not available for package ‘flowCore’
* removing ‘/usr/local/lib/R/4.1/site-library/flowCore’
The downloaded source packages are in
‘/private/var/folders/qx/vhg6t8_j0fq3bht256ppwffr0000gp/T/RtmpgIfErn/downloaded_packages’
Warning messages:
1: In .inet_warning(msg) :
installation of package ‘cytolib’ had non-zero exit status
2: In .inet_warning(msg) :
installation of package ‘flowCore’ had non-zero exit status
SessionInfo:
Platform: x86_64-apple-darwin21.1.0 (64-bit)
Running under: macOS Monterey 12.0.1
Matrix products: default
BLAS: /usr/local/Cellar/openblas/0.3.18/lib/libopenblasp-r0.3.18.dylib
LAPACK: /usr/local/Cellar/r/4.1.2/lib/R/lib/libRlapack.dylib
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] reprex_2.0.1
loaded via a namespace (and not attached):
[1] ps_1.6.0 digest_0.6.29 withr_2.4.3
[4] R6_2.5.1 evaluate_0.14 highr_0.9
[7] rlang_0.4.12 cli_3.1.0 rstudioapi_0.13
[10] fs_1.5.2 callr_3.7.0 rmarkdown_2.11
[13] tools_4.1.2 glue_1.6.0 processx_3.5.2
[16] yaml_2.2.1 fastmap_1.1.0 xfun_0.29
[19] compiler_4.1.2 BiocManager_1.30.16 clipr_0.7.1
[22] htmltools_0.5.2 knitr_1.37 Create the separate view class for subsetting operations on CytoFrame
Currently row_idx and col_idx are stored within CytoFrame class and it seems to be incorrect design since we can't do the efficient subsetting without impacting the original object.
The solution is to detach these idx and have a separate proxy class CytoFrameView to store them along with the shared_ptr of CytoFrame
Error Gating Empty Populations
Hi @mikejiang & @jacobpwagner ,
Not sure if this is the best place to post this issue. It looks like there are issues gating empty populations with the latest cytolib, flowWorkspace and openCyto.
> gt_gating(gt, gs)
Preprocessing for 'Cells'
Gating for 'Cells'
done!
done.
Preprocessing for 'Single Cells'
Gating for 'Single Cells'
done!
done.
Preprocessing for 'Dead Cells'
Gating for 'Dead Cells'
done!
done.
Live Cells gating...
done!
done.
Preprocessing for 'T Cells'
Gating for 'T Cells'
done!
done.
Preprocessing for 'CD8 T Cells'
error: Mat::max(): object has no elements
Error in get_cytoset_from_node(obj@pointer, y) :
Mat::max(): object has no elements
Thanks for your help.
Dillon
BH 1.69->1.72 breaks installation due to bundled boost::filesystem lib src
It looks like some internal reorganization in the boost classes means that the bundled 1.69 source won't work with the boost headers from BH now that it has moved to 1.72. @mikejiang , the solution is probably just to update the bundled boost::filesystem source to 1.72, but I thought I'd get your take on it as you recently dealt with this in d364026 and related commits.
The errors can be seen by updating BH to version 1.72 and then attempting to re-install cytolib or just by checking out the Bioconductor build errors: http://bioconductor.org/checkResults/devel/bioc-LATEST/cytolib/malbec2-install.html
Revert to Artistic lisence - The Fred Hutchinson software license makes CRAN packages impossible
I maintain the R package beadplexr, which evaluates bead assays (like LegendPLex or CBA) acquired on a flow cytometer. For reading the fcs files, I rely on flowCore which imports cytolib in the coming version.
The restrictions in the Fred Hutchinson software license used by cytolib:
Derviative works must be free, open source, and non-commercial, academic, research only. Commercial and internal business use is not permitted.
makes packages such as mine unacceptable to CRAN.
Would it be possible to revert to the previous Artistic license?
General question about H5 backed gating
Thanks for putting together this framework. We are currently trying to adopt flowWorkspace for image based gating.
Let me know if the following is technically not possible or a stupid idea.
At the moment we are converting an Anndata H5 file to a CytoFrame and then use a GatingSet to create populations.
In theory, would it be possible to use gating directly on the H5 backed Anndata file? I was thinking to adopt the CytoFrame class to make something compatible to working with Anndata.
If that was in theory possible, would you have a suggestion where to start?
remove cols and rows API
Currently we have two sets of subsetting c++ APIs for CytoSet/CytoFrame
cols()androws()--> returns a copycols_()androws_()--> subset in place
It starts causing confusion down the road and against the common c++ operation idiom i.e. always doing things by reference or in place(as @gfinak mentioned,)
Also we don't the deep copy happen toH5CytoFrameanyway due to the cost of disk IO. Therefore I am going to only keep the second group of APIs and let it up to user to explicitly making a copy of the original object before subsetting (which should be pretty straightforward by theircopy()member function.)
cytolib installation error with Rtools 4.0 + R-testing
Hi Mike,
In addition to the usual devel builds, we've started to build a small subset of Bioconductor packages using Rtools40 and R-testing:
https://bioconductor.org/checkResults/3.11/bioc-testing-LATEST/
We're hoping that having these experimental builds will help us get ready for when R core decides to officially make the switch to Rtools40.
This is a heads-up that cytolib fails to install with Rtools40 + R-testing.
Best,
H.
deal with redundant channels from some individual samples
With the channel_consistency_check introduced lately, The identical channel settings are guaranteed at the time when GatingSet is constructed or modified. We impose this strict rule based on the decision of eliminating the possibility of surprising/or misleading error in downstream analysis caused by discrepancy of channel name and order (e.g. getSingleCellExpression).
However, I just ran into a problem when parsing a lyoplate workspace ,which used to succeed with the old toolchains.
gs <- flowjo_to_gatingset(ws, name = groupNames[groupID], path = this_fcs_path, extend_val = -10)
Error in get_cytoset(x@pointer) :
Found channel inconsistency across samples. T_CELL_12828_002_P1.fcs_169845 has the channel 'FSC-H' that is not found in other samples!In the ncdfFlowSet -based GatingSet, we did the prescanning of all FCS files and found the common channel set across samples and then only load that subset, which automatically removed the redundant channels.
And new cytoset-based gs (before this strict rule was imposed), each FCS/sample was independently loaded and parsed , then loosely collected into GatingSet without any prior or post validity checks.
None of the previous approaches are flawless and risk-free. The first one has the danger of losing important channel that could be used or referred by flowjo workspace, which will lead to the parsing error. The second one will cause the discrepancy within GatingSet, which is the very reason we added this new check.
The most straightforward way is to require cytoqc to be used to clean up FCS files before proceeding parsing if such error is reported.
But we will have to take care the legacy(cytoset-based) gs that was archived before channel_consistency_check was added. Because apparently load_gs will fail for the same reason
Error in .cpp_loadGatingSet(normalizePath(path), h5_readonly, select.sn, :
Found channel inconsistency across samples. T_CELL_12828_002_P1.fcs_169845 has the channel 'FSC-H' that is not found in other samples!Whether this backward-compatibility efforts is worth depends on how many such legacy archives exists.
time string parsing API 'strptime' not portable on windows
global.cpp: In function 'cytolib::TM_ext cytolib::parse_time_with_fractional_seconds(std::string)':
global.cpp:123:57: error: 'strptime' was not declared in this scopeThe c++ version std::get_time is only for GCC 5 above. And unfortunately (and almost cerntainly) not present in the current bioc win/ming32 settings (gcc 4.9.3)
Installation failed
Hello,
I'm having trouble installing the cytolib package. I have successfully installed the most recent RProtoBufLib but end up with the error below. I saw a similar issue closed in 2019, but it seems a different issue in my case. I'd appreciate any advice.
Thanks!
Shannon
install_github("RGLab/cytolib")
Downloading GitHub repo RGLab/cytolib@HEAD
√ checking for file 'C:\Users\lingfeir\AppData\Local\Temp\RtmpEB48K6\remotes3ae841782c3b\RGLab-cytolib-ed1f895/DESCRIPTION' (443ms)
- preparing 'cytolib': (12.2s)
√ checking DESCRIPTION meta-information ... - cleaning src
- running 'cleanup.win'
- checking for LF line-endings in source and make files and shell scripts (838ms)
- checking for empty or unneeded directories (620ms)
- building 'cytolib_2.3.8.tar.gz'
Warning: file 'cytolib/cleanup' did not have execute permissions: corrected
Warning: file 'cytolib/configure' did not have execute permissions: corrected
- installing source package 'cytolib' ...
** using staged installation
** preparing to configure package 'cytolib' ...
*** configured file: 'cytolibConfig.h.in' => 'inst/include/cytolib/cytolibConfig.h'
*** configured file: 'src/Makevars.in' => 'src/Makevars'
** finished configure for package 'cytolib'
** libs
"C:/ProgramFiles/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/ProgramFiles/R/R-401.0/include" -DNDEBUG -DROUT -I../inst/include -DRCPP_PARALLEL_USE_TBB=1 -fpermissive -DBOOST_NO_AUTO_PTR -I'C:/ProgramFiles/R/R-4.0.0/library/Rcpp/include' -I'C:/ProgramFiles/R/R-4.0.0/library/BH/include' -I'C:/ProgramFiles/R/R-4.0.0/library/RProtoBufLib/include' -I'C:/ProgramFiles/R/R-4.0.0/library/Rhdf5lib/include' -I'C:/ProgramFiles/R/R-4.0.0/library/RcppArmadillo/include' -I'C:/ProgramFiles/R/R-4.0.0/library/RcppParallel/include' -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c dummy.cpp -o dummy.o1.0/include" -DNDEBUG -DROUT -I../inst/include -DRCPP_PARALLEL_USE_TBB=1 -fpermissive -DBOOST_NO_AUTO_PTR -I'C:/ProgramFiles/R/R-4.0.0/library/Rcpp/include' -I'C:/ProgramFiles/R/R-4.0.0/library/BH/include' -I'C:/ProgramFiles/R/R-4.0.0/library/RProtoBufLib/include' -I'C:/ProgramFiles/R/R-4.0.0/library/Rhdf5lib/include' -I'C:/ProgramFiles/R/R-4.0.0/library/RcppArmadillo/include' -I'C:/ProgramFiles/R/R-4.0.0/library/RcppParallel/include' -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c boost/libs/system/src/error_code.cpp -o boost/libs/system/src/error_code.o
"C:/ProgramFiles/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/ProgramFiles/R/R-40
"C:/ProgramFiles/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/ProgramFiles/R/R-401.0/include" -DNDEBUG -DROUT -I../inst/include -DRCPP_PARALLEL_USE_TBB=1 -fpermissive -DBOOST_NO_AUTO_PTR -I'C:/ProgramFiles/R/R-4.0.0/library/Rcpp/include' -I'C:/ProgramFiles/R/R-4.0.0/library/BH/include' -I'C:/ProgramFiles/R/R-4.0.0/library/RProtoBufLib/include' -I'C:/ProgramFiles/R/R-4.0.0/library/Rhdf5lib/include' -I'C:/ProgramFiles/R/R-4.0.0/library/RcppArmadillo/include' -I'C:/ProgramFiles/R/R-4.0.0/library/RcppParallel/include' -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c boost/libs/filesystem/src/portability.cpp -o boost/libs/filesystem/src/portability.o1.0/include" -DNDEBUG -DROUT -I../inst/include -DRCPP_PARALLEL_USE_TBB=1 -fpermissive -DBOOST_NO_AUTO_PTR -I'C:/ProgramFiles/R/R-4.0.0/library/Rcpp/include' -I'C:/ProgramFiles/R/R-4.0.0/library/BH/include' -I'C:/ProgramFiles/R/R-4.0.0/library/RProtoBufLib/include' -I'C:/ProgramFiles/R/R-4.0.0/library/Rhdf5lib/include' -I'C:/ProgramFiles/R/R-4.0.0/library/RcppArmadillo/include' -I'C:/ProgramFiles/R/R-4.0.0/library/RcppParallel/include' -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c boost/libs/filesystem/src/unique_path.cpp -o boost/libs/filesystem/src/unique_path.o
In file included from C:/ProgramFiles/R/R-4.0.0/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
from C:/ProgramFiles/R/R-4.0.0/library/BH/include/boost/mpl/arg.hpp:25,
from C:/ProgramFiles/R/R-4.0.0/library/BH/include/boost/mpl/placeholders.hpp:24,
from C:/ProgramFiles/R/R-4.0.0/library/BH/include/boost/iterator/iterator_categories.hpp:16,
from C:/ProgramFiles/R/R-4.0.0/library/BH/include/boost/iterator/iterator_facade.hpp:13,
from C:/ProgramFiles/R/R-4.0.0/library/BH/include/boost/filesystem/path.hpp:29,
from boost/libs/filesystem/src/portability.cpp:14:
C:/ProgramFiles/R/R-4.0.0/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
failed ************ (Pred::************
^
C:/ProgramFiles/R/R-4.0.0/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
failed ************ (boost::mpl::not_::************
^
"C:/ProgramFiles/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/ProgramFiles/R/R-40
In file included from C:/ProgramFiles/R/R-4.0.0/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
from C:/ProgramFiles/R/R-4.0.0/library/BH/include/boost/mpl/arg.hpp:25,
from C:/ProgramFiles/R/R-4.0.0/library/BH/include/boost/mpl/placeholders.hpp:24,
from C:/ProgramFiles/R/R-4.0.0/library/BH/include/boost/iterator/iterator_categories.hpp:16,
from C:/ProgramFiles/R/R-4.0.0/library/BH/include/boost/iterator/iterator_facade.hpp:13,
from C:/ProgramFiles/R/R-4.0.0/library/BH/include/boost/filesystem/path.hpp:29,
from C:/ProgramFiles/R/R-4.0.0/library/BH/include/boost/filesystem/operations.hpp:26,
from boost/libs/filesystem/src/unique_path.cpp:76:
C:/ProgramFiles/R/R-4.0.0/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
failed ************ (Pred::************
^
C:/ProgramFiles/R/R-4.0.0/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
failed ************ (boost::mpl::not_::************
^
"C:/ProgramFiles/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/ProgramFiles/R/R-401.0/include" -DNDEBUG -DROUT -I../inst/include -DRCPP_PARALLEL_USE_TBB=1 -fpermissive -DBOOST_NO_AUTO_PTR -I'C:/ProgramFiles/R/R-4.0.0/library/Rcpp/include' -I'C:/ProgramFiles/R/R-4.0.0/library/BH/include' -I'C:/ProgramFiles/R/R-4.0.0/library/RProtoBufLib/include' -I'C:/ProgramFiles/R/R-4.0.0/library/Rhdf5lib/include' -I'C:/ProgramFiles/R/R-4.0.0/library/RcppArmadillo/include' -I'C:/ProgramFiles/R/R-4.0.0/library/RcppParallel/include' -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c boost/libs/filesystem/src/operations.cpp -o boost/libs/filesystem/src/operations.o1.0/include" -DNDEBUG -DROUT -I../inst/include -DRCPP_PARALLEL_USE_TBB=1 -fpermissive -DBOOST_NO_AUTO_PTR -I'C:/ProgramFiles/R/R-4.0.0/library/Rcpp/include' -I'C:/ProgramFiles/R/R-4.0.0/library/BH/include' -I'C:/ProgramFiles/R/R-4.0.0/library/RProtoBufLib/include' -I'C:/ProgramFiles/R/R-4.0.0/library/Rhdf5lib/include' -I'C:/ProgramFiles/R/R-4.0.0/library/RcppArmadillo/include' -I'C:/ProgramFiles/R/R-4.0.0/library/RcppParallel/include' -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c boost/libs/filesystem/src/path.cpp -o boost/libs/filesystem/src/path.o
In file included from C:/ProgramFiles/R/R-4.0.0/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
from C:/ProgramFiles/R/R-4.0.0/library/BH/include/boost/mpl/arg.hpp:25,
from C:/ProgramFiles/R/R-4.0.0/library/BH/include/boost/mpl/placeholders.hpp:24,
from C:/ProgramFiles/R/R-4.0.0/library/BH/include/boost/iterator/iterator_categories.hpp:16,
from C:/ProgramFiles/R/R-4.0.0/library/BH/include/boost/iterator/iterator_facade.hpp:13,
from C:/ProgramFiles/R/R-4.0.0/library/BH/include/boost/filesystem/path.hpp:29,
from C:/ProgramFiles/R/R-4.0.0/library/BH/include/boost/filesystem/operations.hpp:26,
from boost/libs/filesystem/src/operations.cpp:17:
C:/ProgramFiles/R/R-4.0.0/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
failed ************ (Pred::************
^
C:/ProgramFiles/R/R-4.0.0/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
failed ************ (boost::mpl::not_::************
^
"C:/ProgramFiles/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/ProgramFiles/R/R-40
In file included from C:/ProgramFiles/R/R-4.0.0/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
from C:/ProgramFiles/R/R-4.0.0/library/BH/include/boost/mpl/arg.hpp:25,
from C:/ProgramFiles/R/R-4.0.0/library/BH/include/boost/mpl/placeholders.hpp:24,
from C:/ProgramFiles/R/R-4.0.0/library/BH/include/boost/iterator/iterator_categories.hpp:16,
from C:/ProgramFiles/R/R-4.0.0/library/BH/include/boost/iterator/iterator_facade.hpp:13,
from C:/ProgramFiles/R/R-4.0.0/library/BH/include/boost/filesystem/path.hpp:29,
from boost/libs/filesystem/src/path.cpp:19:
C:/ProgramFiles/R/R-4.0.0/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
failed ************ (Pred::************
^
C:/ProgramFiles/R/R-4.0.0/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
failed ************ (boost::mpl::not_::************
^
"C:/ProgramFiles/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/ProgramFiles/R/R-401.0/include" -DNDEBUG -DROUT -I../inst/include -DRCPP_PARALLEL_USE_TBB=1 -fpermissive -DBOOST_NO_AUTO_PTR -I'C:/ProgramFiles/R/R-4.0.0/library/Rcpp/include' -I'C:/ProgramFiles/R/R-4.0.0/library/BH/include' -I'C:/ProgramFiles/R/R-4.0.0/library/RProtoBufLib/include' -I'C:/ProgramFiles/R/R-4.0.0/library/Rhdf5lib/include' -I'C:/ProgramFiles/R/R-4.0.0/library/RcppArmadillo/include' -I'C:/ProgramFiles/R/R-4.0.0/library/RcppParallel/include' -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c boost/libs/filesystem/src/directory.cpp -o boost/libs/filesystem/src/directory.o1.0/include" -DNDEBUG -DROUT -I../inst/include -DRCPP_PARALLEL_USE_TBB=1 -fpermissive -DBOOST_NO_AUTO_PTR -I'C:/ProgramFiles/R/R-4.0.0/library/Rcpp/include' -I'C:/ProgramFiles/R/R-4.0.0/library/BH/include' -I'C:/ProgramFiles/R/R-4.0.0/library/RProtoBufLib/include' -I'C:/ProgramFiles/R/R-4.0.0/library/Rhdf5lib/include' -I'C:/ProgramFiles/R/R-4.0.0/library/RcppArmadillo/include' -I'C:/ProgramFiles/R/R-4.0.0/library/RcppParallel/include' -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c boost/libs/filesystem/src/exception.cpp -o boost/libs/filesystem/src/exception.o
In file included from C:/ProgramFiles/R/R-4.0.0/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
from C:/ProgramFiles/R/R-4.0.0/library/BH/include/boost/mpl/arg.hpp:25,
from C:/ProgramFiles/R/R-4.0.0/library/BH/include/boost/mpl/placeholders.hpp:24,
from C:/ProgramFiles/R/R-4.0.0/library/BH/include/boost/iterator/iterator_categories.hpp:16,
from C:/ProgramFiles/R/R-4.0.0/library/BH/include/boost/iterator/iterator_facade.hpp:13,
from C:/ProgramFiles/R/R-4.0.0/library/BH/include/boost/filesystem/path.hpp:29,
from C:/ProgramFiles/R/R-4.0.0/library/BH/include/boost/filesystem/directory.hpp:26,
from boost/libs/filesystem/src/directory.cpp:16:
C:/ProgramFiles/R/R-4.0.0/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
failed ************ (Pred::************
^
C:/ProgramFiles/R/R-4.0.0/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
failed ************ (boost::mpl::not_::************
^
"C:/ProgramFiles/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/ProgramFiles/R/R-40
In file included from C:/ProgramFiles/R/R-4.0.0/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
from C:/ProgramFiles/R/R-4.0.0/library/BH/include/boost/mpl/arg.hpp:25,
from C:/ProgramFiles/R/R-4.0.0/library/BH/include/boost/mpl/placeholders.hpp:24,
from C:/ProgramFiles/R/R-4.0.0/library/BH/include/boost/iterator/iterator_categories.hpp:16,
from C:/ProgramFiles/R/R-4.0.0/library/BH/include/boost/iterator/iterator_facade.hpp:13,
from C:/ProgramFiles/R/R-4.0.0/library/BH/include/boost/filesystem/path.hpp:29,
from boost/libs/filesystem/src/exception.cpp:15:
C:/ProgramFiles/R/R-4.0.0/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
failed ************ (Pred::************
^
C:/ProgramFiles/R/R-4.0.0/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
failed ************ (boost::mpl::not_::************
^
"C:/ProgramFiles/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/ProgramFiles/R/R-401.0/include" -DNDEBUG -DROUT -I../inst/include -DRCPP_PARALLEL_USE_TBB=1 -fpermissive -DBOOST_NO_AUTO_PTR -I'C:/ProgramFiles/R/R-4.0.0/library/Rcpp/include' -I'C:/ProgramFiles/R/R-4.0.0/library/BH/include' -I'C:/ProgramFiles/R/R-4.0.0/library/RProtoBufLib/include' -I'C:/ProgramFiles/R/R-4.0.0/library/Rhdf5lib/include' -I'C:/ProgramFiles/R/R-4.0.0/library/RcppArmadillo/include' -I'C:/ProgramFiles/R/R-4.0.0/library/RcppParallel/include' -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c boost/libs/filesystem/src/windows_file_codecvt.cpp -o boost/libs/filesystem/src/windows_file_codecvt.o1.0/include" -DNDEBUG -DROUT -I../inst/include -DRCPP_PARALLEL_USE_TBB=1 -fpermissive -DBOOST_NO_AUTO_PTR -I'C:/ProgramFiles/R/R-4.0.0/library/Rcpp/include' -I'C:/ProgramFiles/R/R-4.0.0/library/BH/include' -I'C:/ProgramFiles/R/R-4.0.0/library/RProtoBufLib/include' -I'C:/ProgramFiles/R/R-4.0.0/library/Rhdf5lib/include' -I'C:/ProgramFiles/R/R-4.0.0/library/RcppArmadillo/include' -I'C:/ProgramFiles/R/R-4.0.0/library/RcppParallel/include' -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c boost/libs/filesystem/src/utf8_codecvt_facet.cpp -o boost/libs/filesystem/src/utf8_codecvt_facet.o
"C:/ProgramFiles/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/ProgramFiles/R/R-40
"C:/ProgramFiles/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/ProgramFiles/R/R-401.0/include" -DNDEBUG -DROUT -I../inst/include -DRCPP_PARALLEL_USE_TBB=1 -fpermissive -DBOOST_NO_AUTO_PTR -I'C:/ProgramFiles/R/R-4.0.0/library/Rcpp/include' -I'C:/ProgramFiles/R/R-4.0.0/library/BH/include' -I'C:/ProgramFiles/R/R-4.0.0/library/RProtoBufLib/include' -I'C:/ProgramFiles/R/R-4.0.0/library/Rhdf5lib/include' -I'C:/ProgramFiles/R/R-4.0.0/library/RcppArmadillo/include' -I'C:/ProgramFiles/R/R-4.0.0/library/RcppParallel/include' -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c boost/libs/filesystem/src/codecvt_error_category.cpp -o boost/libs/filesystem/src/codecvt_error_category.o1.0/include" -DNDEBUG -DROUT -I../inst/include -DRCPP_PARALLEL_USE_TBB=1 -fpermissive -DBOOST_NO_AUTO_PTR -I'C:/ProgramFiles/R/R-4.0.0/library/Rcpp/include' -I'C:/ProgramFiles/R/R-4.0.0/library/BH/include' -I'C:/ProgramFiles/R/R-4.0.0/library/RProtoBufLib/include' -I'C:/ProgramFiles/R/R-4.0.0/library/Rhdf5lib/include' -I'C:/ProgramFiles/R/R-4.0.0/library/RcppArmadillo/include' -I'C:/ProgramFiles/R/R-4.0.0/library/RcppParallel/include' -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c boost/libs/filesystem/src/path_traits.cpp -o boost/libs/filesystem/src/path_traits.o
"C:/ProgramFiles/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/ProgramFiles/R/R-40
"C:/ProgramFiles/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/ProgramFiles/R/R-401.0/include" -DNDEBUG -DROUT -I../inst/include -DRCPP_PARALLEL_USE_TBB=1 -fpermissive -DBOOST_NO_AUTO_PTR -I'C:/ProgramFiles/R/R-4.0.0/library/Rcpp/include' -I'C:/ProgramFiles/R/R-4.0.0/library/BH/include' -I'C:/ProgramFiles/R/R-4.0.0/library/RProtoBufLib/include' -I'C:/ProgramFiles/R/R-4.0.0/library/Rhdf5lib/include' -I'C:/ProgramFiles/R/R-4.0.0/library/RcppArmadillo/include' -I'C:/ProgramFiles/R/R-4.0.0/library/RcppParallel/include' -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c src/compensation.cpp -o src/compensation.o1.0/include" -DNDEBUG -DROUT -I../inst/include -DRCPP_PARALLEL_USE_TBB=1 -fpermissive -DBOOST_NO_AUTO_PTR -I'C:/ProgramFiles/R/R-4.0.0/library/Rcpp/include' -I'C:/ProgramFiles/R/R-4.0.0/library/BH/include' -I'C:/ProgramFiles/R/R-4.0.0/library/RProtoBufLib/include' -I'C:/ProgramFiles/R/R-4.0.0/library/Rhdf5lib/include' -I'C:/ProgramFiles/R/R-4.0.0/library/RcppArmadillo/include' -I'C:/ProgramFiles/R/R-4.0.0/library/RcppParallel/include' -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c src/nodeProperties.cpp -o src/nodeProperties.o
In file included from C:/ProgramFiles/R/R-4.0.0/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
from C:/ProgramFiles/R/R-4.0.0/library/BH/include/boost/mpl/arg.hpp:25,
from C:/ProgramFiles/R/R-4.0.0/library/BH/include/boost/mpl/placeholders.hpp:24,
from C:/ProgramFiles/R/R-4.0.0/library/BH/include/boost/iterator/iterator_categories.hpp:16,
from C:/ProgramFiles/R/R-4.0.0/library/BH/include/boost/iterator/iterator_facade.hpp:13,
from C:/ProgramFiles/R/R-4.0.0/library/BH/include/boost/range/iterator_range_core.hpp:27,
from C:/ProgramFiles/R/R-4.0.0/library/BH/include/boost/range/iterator_range.hpp:13,
from C:/ProgramFiles/R/R-4.0.0/library/BH/include/boost/range/as_literal.hpp:18,
from C:/ProgramFiles/R/R-4.0.0/library/BH/include/boost/algorithm/string/trim.hpp:19,
from C:/ProgramFiles/R/R-4.0.0/library/BH/include/boost/algorithm/string.hpp:19,
from ../inst/include/cytolib/transformation.hpp:18,
from ../inst/include/cytolib/compensation.hpp:15,
from src/compensation.cpp:3:
C:/ProgramFiles/R/R-4.0.0/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
failed ************ (Pred::************
^
C:/ProgramFiles/R/R-4.0.0/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
failed ************ (boost::mpl::not_::************
^
In file included from src/compensation.cpp:3:
../inst/include/cytolib/compensation.hpp: In constructor 'cytolib::compensation::compensation(const string&)':
../inst/include/cytolib/compensation.hpp:58:20: warning: comparison of integer expressions of different signedness: 'std::vector<std::__cxx11::basic_string, std::allocator<std::__cxx11::basic_string > >::size_type' {aka 'long long unsigned int'} and 'int' [-Wsign-compare]
if(valVec.size() != 1+n+nn){
~~~~~~~~~~~~~~^~~~~~~~~~
../inst/include/cytolib/compensation.hpp:62:21: warning: comparison of integer expressions of different signedness: 'std::vector<std::__cxx11::basic_string, std::allocator<std::__cxx11::basic_string > >::size_type' {aka 'long long unsigned int'} and 'int' [-Wsign-compare]
if(valVec.size() == 1+n+2n*n){
~~~~~~~~~~~~~~^~~~~~~~~~~~
../inst/include/cytolib/compensation.hpp:68:33: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::__cxx11::basic_string, std::allocator<std::__cxx11::basic_string > >::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
for(int i = 1+n, j = 1+n; i < valVec_fixed.size(); i++, j+=2)
~~^~~~~~~~~~~~~~~~~~~~~
"C:/ProgramFiles/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/ProgramFiles/R/R-40
In file included from C:/ProgramFiles/R/R-4.0.0/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
from C:/ProgramFiles/R/R-4.0.0/library/BH/include/boost/mpl/arg.hpp:25,
from C:/ProgramFiles/R/R-4.0.0/library/BH/include/boost/mpl/placeholders.hpp:24,
from C:/ProgramFiles/R/R-4.0.0/library/BH/include/boost/iterator/iterator_categories.hpp:16,
from C:/ProgramFiles/R/R-4.0.0/library/BH/include/boost/iterator/iterator_facade.hpp:13,
from C:/ProgramFiles/R/R-4.0.0/library/BH/include/boost/range/iterator_range_core.hpp:27,
from C:/ProgramFiles/R/R-4.0.0/library/BH/include/boost/range/iterator_range.hpp:13,
from C:/ProgramFiles/R/R-4.0.0/library/BH/include/boost/range/as_literal.hpp:18,
from C:/ProgramFiles/R/R-4.0.0/library/BH/include/boost/algorithm/string/trim.hpp:19,
from C:/ProgramFiles/R/R-4.0.0/library/BH/include/boost/algorithm/string.hpp:19,
from ../inst/include/cytolib/transformation.hpp:18,
from ../inst/include/cytolib/compensation.hpp:15,
from ../inst/include/cytolib/CytoFrame.hpp:16,
from ../inst/include/cytolib/MemCytoFrame.hpp:12,
from ../inst/include/cytolib/gate.hpp:12,
from ../inst/include/cytolib/POPINDICES.hpp:14,
from ../inst/include/cytolib/nodeProperties.hpp:13,
from src/nodeProperties.cpp:3:
C:/ProgramFiles/R/R-4.0.0/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
failed ************ (Pred::************
^
C:/ProgramFiles/R/R-4.0.0/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
failed ************ (boost::mpl::not_::************
^
In file included from ../inst/include/cytolib/CytoFrame.hpp:16,
from ../inst/include/cytolib/MemCytoFrame.hpp:12,
from ../inst/include/cytolib/gate.hpp:12,
from ../inst/include/cytolib/POPINDICES.hpp:14,
from ../inst/include/cytolib/nodeProperties.hpp:13,
from src/nodeProperties.cpp:3:
../inst/include/cytolib/compensation.hpp: In constructor 'cytolib::compensation::compensation(const string&)':
../inst/include/cytolib/compensation.hpp:58:20: warning: comparison of integer expressions of different signedness: 'std::vector<std::__cxx11::basic_string, std::allocator<std::_cxx11::basic_string > >::size_type' {aka 'long long unsigned int'} and 'int' [-Wsign-compare]
if(valVec.size() != 1+n+nn){
~~~~~~~~~~~~~~^~~~~~~~~~
../inst/include/cytolib/compensation.hpp:62:21: warning: comparison of integer expressions of different signedness: 'std::vector<std::__cxx11::basic_string, std::allocator<std::__cxx11::basic_string > >::size_type' {aka 'long long unsigned int'} and 'int' [-Wsign-compare]
if(valVec.size() == 1+n+2nn){
~~~~~~~~~~~~~~^~~~~~~~~~~~
../inst/include/cytolib/compensation.hpp:68:33: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::__cxx11::basic_string, std::allocator<std::_cxx11::basic_string > >::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
for(int i = 1+n, j = 1+n; i < valVec_fixed.size(); i++, j+=2)
~~^~~~~~~~~~~~~~~~~~~~~
"C:/ProgramFiles/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/ProgramFiles/R/R-40~1.0/include" -DNDEBUG -DROUT -I../inst/include -DRCPP_PARALLEL_USE_TBB=1 -fpermissive -DBOOST_NO_AUTO_PTR -I'C:/ProgramFiles/R/R-4.0.0/library/Rcpp/include' -I'C:/ProgramFiles/R/R-4.0.0/library/BH/include' -I'C:/ProgramFiles/R/R-4.0.0/library/RProtoBufLib/include' -I'C:/ProgramFiles/R/R-4.0.0/library/Rhdf5lib/include' -I'C:/ProgramFiles/R/R-4.0.0/library/RcppArmadillo/include' -I'C:/ProgramFiles/R/R-4.0.0/library/RcppParallel/include' -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c src/gate.cpp -o src/gate.o
In file included from C:/ProgramFiles/R/R-4.0.0/library/BH/include/boost/mpl/aux/na_assert.hpp:23,
from C:/ProgramFiles/R/R-4.0.0/library/BH/include/boost/mpl/arg.hpp:25,
from C:/ProgramFiles/R/R-4.0.0/library/BH/include/boost/mpl/placeholders.hpp:24,
from C:/ProgramFiles/R/R-4.0.0/library/BH/include/boost/iterator/iterator_categories.hpp:16,
from C:/ProgramFiles/R/R-4.0.0/library/BH/include/boost/iterator/iterator_facade.hpp:13,
from C:/ProgramFiles/R/R-4.0.0/library/BH/include/boost/range/iterator_range_core.hpp:27,
from C:/ProgramFiles/R/R-4.0.0/library/BH/include/boost/range/iterator_range.hpp:13,
from C:/ProgramFiles/R/R-4.0.0/library/BH/include/boost/range/as_literal.hpp:18,
from C:/ProgramFiles/R/R-4.0.0/library/BH/include/boost/algorithm/string/trim.hpp:19,
from C:/ProgramFiles/R/R-4.0.0/library/BH/include/boost/algorithm/string.hpp:19,
from ../inst/include/cytolib/transformation.hpp:18,
from ../inst/include/cytolib/compensation.hpp:15,
from ../inst/include/cytolib/CytoFrame.hpp:16,
from ../inst/include/cytolib/MemCytoFrame.hpp:12,
from ../inst/include/cytolib/gate.hpp:12,
from src/gate.cpp:3:
C:/ProgramFiles/R/R-4.0.0/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
failed ************ (Pred::***********
^
C:/ProgramFiles/R/R-4.0.0/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
failed ************ (boost::mpl::not::************
^
In file included from ../inst/include/cytolib/CytoFrame.hpp:16,
from ../inst/include/cytolib/MemCytoFrame.hpp:12,
from ../inst/include/cytolib/gate.hpp:12,
from src/gate.cpp:3:
../inst/include/cytolib/compensation.hpp: In constructor 'cytolib::compensation::compensation(const string&)':
../inst/include/cytolib/compensation.hpp:58:20: warning: comparison of integer expressions of different signedness: 'std::vector<std::__cxx11::basic_string, std::allocator<std::_cxx11::basic_string > >::size_type' {aka 'long long unsigned int'} and 'int' [-Wsign-compare]
if(valVec.size() != 1+n+nn){
~~~~~~~~~~~~~~^~~~~~~~~~
../inst/include/cytolib/compensation.hpp:62:21: warning: comparison of integer expressions of different signedness: 'std::vector<std::__cxx11::basic_string, std::allocator<std::__cxx11::basic_string > >::size_type' {aka 'long long unsigned int'} and 'int' [-Wsign-compare]
if(valVec.size() == 1+n+2nn){
~~~~~~~~~~~~~~^~~~~~~~~~~~
../inst/include/cytolib/compensation.hpp:68:33: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::__cxx11::basic_string, std::allocator<std::_cxx11::basic_string > >::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
for(int i = 1+n, j = 1+n; i < valVec_fixed.size(); i++, j+=2)
~~^~~~~~~~~~~~~~~~~~~~~
"C:/ProgramFiles/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/ProgramFiles/R/R-401.0/include" -DNDEBUG -DROUT -I../inst/include -DRCPP_PARALLEL_USE_TBB=1 -fpermissive -DBOOST_NO_AUTO_PTR -I'C:/ProgramFiles/R/R-4.0.0/library/Rcpp/include' -I'C:/ProgramFiles/R/R-4.0.0/library/BH/include' -I'C:/ProgramFiles/R/R-4.0.0/library/RProtoBufLib/include' -I'C:/ProgramFiles/R/R-4.0.0/library/Rhdf5lib/include' -I'C:/ProgramFiles/R/R-4.0.0/library/RcppArmadillo/include' -I'C:/ProgramFiles/R/R-4.0.0/library/RcppParallel/include' -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c src/in_polygon.cpp -o src/in_polygon.o1.0/include" -DNDEBUG -DROUT -I../inst/include -DRCPP_PARALLEL_USE_TBB=1 -fpermissive -DBOOST_NO_AUTO_PTR -I'C:/ProgramFiles/R/R-4.0.0/library/Rcpp/include' -I'C:/ProgramFiles/R/R-4.0.0/library/BH/include' -I'C:/ProgramFiles/R/R-4.0.0/library/RProtoBufLib/include' -I'C:/ProgramFiles/R/R-4.0.0/library/Rhdf5lib/include' -I'C:/ProgramFiles/R/R-4.0.0/library/RcppArmadillo/include' -I'C:/ProgramFiles/R/R-4.0.0/library/RcppParallel/include' -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c src/CytoFrame.cpp -o src/CytoFrame.o
"C:/ProgramFiles/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/ProgramFiles/R/R-40
In file included from C:/ProgramFiles/R/R-4.0.0/library/BH/include/boost/mpl/aux/na_assert.hpp:23,
from C:/ProgramFiles/R/R-4.0.0/library/BH/include/boost/mpl/arg.hpp:25,
from C:/ProgramFiles/R/R-4.0.0/library/BH/include/boost/mpl/placeholders.hpp:24,
from C:/ProgramFiles/R/R-4.0.0/library/BH/include/boost/iterator/iterator_categories.hpp:16,
from C:/ProgramFiles/R/R-4.0.0/library/BH/include/boost/iterator/iterator_facade.hpp:13,
from C:/ProgramFiles/R/R-4.0.0/library/BH/include/boost/range/iterator_range_core.hpp:27,
from C:/ProgramFiles/R/R-4.0.0/library/BH/include/boost/range/iterator_range.hpp:13,
from C:/ProgramFiles/R/R-4.0.0/library/BH/include/boost/range/as_literal.hpp:18,
from C:/ProgramFiles/R/R-4.0.0/library/BH/include/boost/algorithm/string/trim.hpp:19,
from C:/ProgramFiles/R/R-4.0.0/library/BH/include/boost/algorithm/string.hpp:19,
from ../inst/include/cytolib/transformation.hpp:18,
from ../inst/include/cytolib/compensation.hpp:15,
from ../inst/include/cytolib/CytoFrame.hpp:16,
from src/CytoFrame.cpp:3:
C:/ProgramFiles/R/R-4.0.0/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
failed ************ (Pred::***********
^
C:/ProgramFiles/R/R-4.0.0/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
failed ************ (boost::mpl::not::************
^
In file included from ../inst/include/cytolib/CytoFrame.hpp:16,
from src/CytoFrame.cpp:3:
../inst/include/cytolib/compensation.hpp: In constructor 'cytolib::compensation::compensation(const string&)':
../inst/include/cytolib/compensation.hpp:58:20: warning: comparison of integer expressions of different signedness: 'std::vector<std::__cxx11::basic_string, std::allocator<std::_cxx11::basic_string > >::size_type' {aka 'long long unsigned int'} and 'int' [-Wsign-compare]
if(valVec.size() != 1+n+nn){
~~~~~~~~~~~~~~^~~~~~~~~~
../inst/include/cytolib/compensation.hpp:62:21: warning: comparison of integer expressions of different signedness: 'std::vector<std::__cxx11::basic_string, std::allocator<std::__cxx11::basic_string > >::size_type' {aka 'long long unsigned int'} and 'int' [-Wsign-compare]
if(valVec.size() == 1+n+2nn){
~~~~~~~~~~~~~~^~~~~~~~~~~~
../inst/include/cytolib/compensation.hpp:68:33: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::__cxx11::basic_string, std::allocator<std::__cxx11::basic_string > >::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
for(int i = 1+n, j = 1+n; i < valVec_fixed.size(); i++, j+=2)
~~^~~~~~~~~~~~~~~~~~~~~
"C:/ProgramFiles/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/ProgramFiles/R/R-40~1.0/include" -DNDEBUG -DROUT -I../inst/include -DRCPP_PARALLEL_USE_TBB=1 -fpermissive -DBOOST_NO_AUTO_PTR -I'C:/ProgramFiles/R/R-4.0.0/library/Rcpp/include' -I'C:/ProgramFiles/R/R-4.0.0/library/BH/include' -I'C:/ProgramFiles/R/R-4.0.0/library/RProtoBufLib/include' -I'C:/ProgramFiles/R/R-4.0.0/library/Rhdf5lib/include' -I'C:/ProgramFiles/R/R-4.0.0/library/RcppArmadillo/include' -I'C:/ProgramFiles/R/R-4.0.0/library/RcppParallel/include' -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c src/calibrationTable.cpp -o src/calibrationTable.o
In file included from C:/ProgramFiles/R/R-4.0.0/library/BH/include/boost/foreach.hpp:76,
from src/calibrationTable.cpp:5:
C:/ProgramFiles/R/R-4.0.0/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
failed ************ (Pred::***********
^
C:/ProgramFiles/R/R-4.0.0/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
failed ************ (boost::mpl::not::************
^
"C:/ProgramFiles/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/ProgramFiles/R/R-40~1.0/include" -DNDEBUG -DROUT -I../inst/include -DRCPP_PARALLEL_USE_TBB=1 -fpermissive -DBOOST_NO_AUTO_PTR -I'C:/ProgramFiles/R/R-4.0.0/library/Rcpp/include' -I'C:/ProgramFiles/R/R-4.0.0/library/BH/include' -I'C:/ProgramFiles/R/R-4.0.0/library/RProtoBufLib/include' -I'C:/ProgramFiles/R/R-4.0.0/library/Rhdf5lib/include' -I'C:/ProgramFiles/R/R-4.0.0/library/RcppArmadillo/include' -I'C:/ProgramFiles/R/R-4.0.0/library/RcppParallel/include' -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c src/MemCytoFrame.cpp -o src/MemCytoFrame.o
src/MemCytoFrame.cpp:538: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
#pragma omp parallel for
In file included from C:/ProgramFiles/R/R-4.0.0/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
from C:/ProgramFiles/R/R-4.0.0/library/BH/include/boost/mpl/arg.hpp:25,
from C:/ProgramFiles/R/R-4.0.0/library/BH/include/boost/mpl/placeholders.hpp:24,
from C:/ProgramFiles/R/R-4.0.0/library/BH/include/boost/iterator/iterator_categories.hpp:16,
from C:/ProgramFiles/R/R-4.0.0/library/BH/include/boost/iterator/iterator_facade.hpp:13,
from C:/ProgramFiles/R/R-4.0.0/library/BH/include/boost/range/iterator_range_core.hpp:27,
from C:/ProgramFiles/R/R-4.0.0/library/BH/include/boost/range/iterator_range.hpp:13,
from C:/ProgramFiles/R/R-4.0.0/library/BH/include/boost/range/as_literal.hpp:18,
from C:/ProgramFiles/R/R-4.0.0/library/BH/include/boost/algorithm/string/trim.hpp:19,
from C:/ProgramFiles/R/R-4.0.0/library/BH/include/boost/algorithm/string.hpp:19,
from ../inst/include/cytolib/transformation.hpp:18,
from ../inst/include/cytolib/compensation.hpp:15,
from ../inst/include/cytolib/CytoFrame.hpp:16,
from ../inst/include/cytolib/MemCytoFrame.hpp:12,
from src/MemCytoFrame.cpp:3:
C:/ProgramFiles/R/R-4.0.0/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
failed ************ (Pred::************
^
C:/ProgramFiles/R/R-4.0.0/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
failed ************ (boost::mpl::not_::************
^
In file included from ../inst/include/cytolib/CytoFrame.hpp:16,
from ../inst/include/cytolib/MemCytoFrame.hpp:12,
from src/MemCytoFrame.cpp:3:
../inst/include/cytolib/compensation.hpp: In constructor 'cytolib::compensation::compensation(const string&)':
../inst/include/cytolib/compensation.hpp:58:20: warning: comparison of integer expressions of different signedness: 'std::vector<std::__cxx11::basic_string, std::allocator<std::_cxx11::basic_string > >::size_type' {aka 'long long unsigned int'} and 'int' [-Wsign-compare]
if(valVec.size() != 1+n+nn){
~~~~~~~~~~~~~~^~~~~~~~~~
../inst/include/cytolib/compensation.hpp:62:21: warning: comparison of integer expressions of different signedness: 'std::vector<std::__cxx11::basic_string, std::allocator<std::__cxx11::basic_string > >::size_type' {aka 'long long unsigned int'} and 'int' [-Wsign-compare]
if(valVec.size() == 1+n+2nn){
~~~~~~~~~~~~~~^~~~~~~~~~~~
../inst/include/cytolib/compensation.hpp:68:33: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::__cxx11::basic_string, std::allocator<std::_cxx11::basic_string > >::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
for(int i = 1+n, j = 1+n; i < valVec_fixed.size(); i++, j+=2)
~~^~~~~~~~~~~~~~~~~~~~~
"C:/ProgramFiles/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/ProgramFiles/R/R-40~1.0/include" -DNDEBUG -DROUT -I../inst/include -DRCPP_PARALLEL_USE_TBB=1 -fpermissive -DBOOST_NO_AUTO_PTR -I'C:/ProgramFiles/R/R-4.0.0/library/Rcpp/include' -I'C:/ProgramFiles/R/R-4.0.0/library/BH/include' -I'C:/ProgramFiles/R/R-4.0.0/library/RProtoBufLib/include' -I'C:/ProgramFiles/R/R-4.0.0/library/Rhdf5lib/include' -I'C:/ProgramFiles/R/R-4.0.0/library/RcppArmadillo/include' -I'C:/ProgramFiles/R/R-4.0.0/library/RcppParallel/include' -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c src/POPINDICES.cpp -o src/POPINDICES.o
In file included from C:/ProgramFiles/R/R-4.0.0/library/BH/include/boost/mpl/aux/na_assert.hpp:23,
from C:/ProgramFiles/R/R-4.0.0/library/BH/include/boost/mpl/arg.hpp:25,
from C:/ProgramFiles/R/R-4.0.0/library/BH/include/boost/mpl/placeholders.hpp:24,
from C:/ProgramFiles/R/R-4.0.0/library/BH/include/boost/iterator/iterator_categories.hpp:16,
from C:/ProgramFiles/R/R-4.0.0/library/BH/include/boost/iterator/iterator_facade.hpp:13,
from C:/ProgramFiles/R/R-4.0.0/library/BH/include/boost/range/iterator_range_core.hpp:27,
from C:/ProgramFiles/R/R-4.0.0/library/BH/include/boost/range/iterator_range.hpp:13,
from C:/ProgramFiles/R/R-4.0.0/library/BH/include/boost/range/as_literal.hpp:18,
from C:/ProgramFiles/R/R-4.0.0/library/BH/include/boost/algorithm/string/trim.hpp:19,
from C:/ProgramFiles/R/R-4.0.0/library/BH/include/boost/algorithm/string.hpp:19,
from ../inst/include/cytolib/transformation.hpp:18,
from ../inst/include/cytolib/compensation.hpp:15,
from ../inst/include/cytolib/CytoFrame.hpp:16,
from ../inst/include/cytolib/MemCytoFrame.hpp:12,
from ../inst/include/cytolib/gate.hpp:12,
from ../inst/include/cytolib/POPINDICES.hpp:14,
from src/POPINDICES.cpp:3:
C:/ProgramFiles/R/R-4.0.0/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
failed ************ (Pred::***********
^
C:/ProgramFiles/R/R-4.0.0/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
failed ************ (boost::mpl::not::************
^
In file included from ../inst/include/cytolib/CytoFrame.hpp:16,
from ../inst/include/cytolib/MemCytoFrame.hpp:12,
from ../inst/include/cytolib/gate.hpp:12,
from ../inst/include/cytolib/POPINDICES.hpp:14,
from src/POPINDICES.cpp:3:
../inst/include/cytolib/compensation.hpp: In constructor 'cytolib::compensation::compensation(const string&)':
../inst/include/cytolib/compensation.hpp:58:20: warning: comparison of integer expressions of different signedness: 'std::vector<std::_cxx11::basic_string, std::allocator<std::cxx11::basic_string > >::size_type' {aka 'long long unsigned int'} and 'int' [-Wsign-compare]
if(valVec.size() != 1+n+nn){
~~~~~~~~~~~~~~^~~~~~~~~~
../inst/include/cytolib/compensation.hpp:62:21: warning: comparison of integer expressions of different signedness: 'std::vector<std::__cxx11::basic_string, std::allocator<std::__cxx11::basic_string > >::size_type' {aka 'long long unsigned int'} and 'int' [-Wsign-compare]
if(valVec.size() == 1+n+2nn){
~~~~~~~~~~~~~~^~~~~~~~~~~~
../inst/include/cytolib/compensation.hpp:68:33: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::__cxx11::basic_string, std::allocator<std::_cxx11::basic_string > >::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
for(int i = 1+n, j = 1+n; i < valVec_fixed.size(); i++, j+=2)
~~^~~~~~~~~~~~~~~~~~~~~
"C:/ProgramFiles/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/ProgramFiles/R/R-40~1.0/include" -DNDEBUG -DROUT -I../inst/include -DRCPP_PARALLEL_USE_TBB=1 -fpermissive -DBOOST_NO_AUTO_PTR -I'C:/ProgramFiles/R/R-4.0.0/library/Rcpp/include' -I'C:/ProgramFiles/R/R-4.0.0/library/BH/include' -I'C:/ProgramFiles/R/R-4.0.0/library/RProtoBufLib/include' -I'C:/ProgramFiles/R/R-4.0.0/library/Rhdf5lib/include' -I'C:/ProgramFiles/R/R-4.0.0/library/RcppArmadillo/include' -I'C:/ProgramFiles/R/R-4.0.0/library/RcppParallel/include' -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c src/CytoVFS.cpp -o src/CytoVFS.o
In file included from C:/ProgramFiles/R/R-4.0.0/library/BH/include/boost/mpl/aux/na_assert.hpp:23,
from C:/ProgramFiles/R/R-4.0.0/library/BH/include/boost/mpl/arg.hpp:25,
from C:/ProgramFiles/R/R-4.0.0/library/BH/include/boost/mpl/placeholders.hpp:24,
from C:/ProgramFiles/R/R-4.0.0/library/BH/include/boost/iterator/iterator_categories.hpp:16,
from C:/ProgramFiles/R/R-4.0.0/library/BH/include/boost/iterator/iterator_facade.hpp:13,
from C:/ProgramFiles/R/R-4.0.0/library/BH/include/boost/filesystem/path.hpp:29,
from C:/ProgramFiles/R/R-4.0.0/library/BH/include/boost/filesystem.hpp:16,
from ../inst/include/cytolib/CytoVFS.hpp:17,
from src/CytoVFS.cpp:8:
C:/ProgramFiles/R/R-4.0.0/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
failed ************ (Pred::***********
^
C:/ProgramFiles/R/R-4.0.0/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
failed ************ (boost::mpl::not::************
^
"C:/ProgramFiles/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/ProgramFiles/R/R-40~1.0/include" -DNDEBUG -DROUT -I../inst/include -DRCPP_PARALLEL_USE_TBB=1 -fpermissive -DBOOST_NO_AUTO_PTR -I'C:/ProgramFiles/R/R-4.0.0/library/Rcpp/include' -I'C:/ProgramFiles/R/R-4.0.0/library/BH/include' -I'C:/ProgramFiles/R/R-4.0.0/library/RProtoBufLib/include' -I'C:/ProgramFiles/R/R-4.0.0/library/Rhdf5lib/include' -I'C:/ProgramFiles/R/R-4.0.0/library/RcppArmadillo/include' -I'C:/ProgramFiles/R/R-4.0.0/library/RcppParallel/include' -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c src/GatingSet.cpp -o src/GatingSet.o
In file included from C:/ProgramFiles/R/R-4.0.0/library/BH/include/boost/mpl/aux/na_assert.hpp:23,
from C:/ProgramFiles/R/R-4.0.0/library/BH/include/boost/mpl/arg.hpp:25,
from C:/ProgramFiles/R/R-4.0.0/library/BH/include/boost/mpl/placeholders.hpp:24,
from C:/ProgramFiles/R/R-4.0.0/library/BH/include/boost/iterator/iterator_categories.hpp:16,
from C:/ProgramFiles/R/R-4.0.0/library/BH/include/boost/iterator/iterator_facade.hpp:13,
from C:/ProgramFiles/R/R-4.0.0/library/BH/include/boost/range/iterator_range_core.hpp:27,
from C:/ProgramFiles/R/R-4.0.0/library/BH/include/boost/range/iterator_range.hpp:13,
from C:/ProgramFiles/R/R-4.0.0/library/BH/include/boost/range/as_literal.hpp:18,
from C:/ProgramFiles/R/R-4.0.0/library/BH/include/boost/algorithm/string/trim.hpp:19,
from C:/ProgramFiles/R/R-4.0.0/library/BH/include/boost/algorithm/string.hpp:19,
from ../inst/include/cytolib/transformation.hpp:18,
from ../inst/include/cytolib/compensation.hpp:15,
from ../inst/include/cytolib/CytoFrame.hpp:16,
from ../inst/include/cytolib/MemCytoFrame.hpp:12,
from ../inst/include/cytolib/gate.hpp:12,
from ../inst/include/cytolib/POPINDICES.hpp:14,
from ../inst/include/cytolib/nodeProperties.hpp:13,
from ../inst/include/cytolib/populationTree.hpp:13,
from ../inst/include/cytolib/GatingHierarchy.hpp:17,
from ../inst/include/cytolib/GatingSet.hpp:14,
from src/GatingSet.cpp:3:
C:/ProgramFiles/R/R-4.0.0/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
failed ************ (Pred::************
^
C:/ProgramFiles/R/R-4.0.0/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
failed ************ (boost::mpl::not::************
^
In file included from ../inst/include/cytolib/CytoFrame.hpp:16,
from ../inst/include/cytolib/MemCytoFrame.hpp:12,
from ../inst/include/cytolib/gate.hpp:12,
from ../inst/include/cytolib/POPINDICES.hpp:14,
from ../inst/include/cytolib/nodeProperties.hpp:13,
from ../inst/include/cytolib/populationTree.hpp:13,
from ../inst/include/cytolib/GatingHierarchy.hpp:17,
from ../inst/include/cytolib/GatingSet.hpp:14,
from src/GatingSet.cpp:3:
../inst/include/cytolib/compensation.hpp: In constructor 'cytolib::compensation::compensation(const string&)':
../inst/include/cytolib/compensation.hpp:58:20: warning: comparison of integer expressions of different signedness: 'std::vector<std::_cxx11::basic_string, std::allocator<std::cxx11::basic_string > >::size_type' {aka 'long long unsigned int'} and 'int' [-Wsign-compare]
if(valVec.size() != 1+n+nn){
~~~~~~~~~~~~~~^~~~~~~~~~
../inst/include/cytolib/compensation.hpp:62:21: warning: comparison of integer expressions of different signedness: 'std::vector<std::__cxx11::basic_string, std::allocator<std::__cxx11::basic_string > >::size_type' {aka 'long long unsigned int'} and 'int' [-Wsign-compare]
if(valVec.size() == 1+n+2nn){
~~~~~~~~~~~~~~^~~~~~~~~~~~
../inst/include/cytolib/compensation.hpp:68:33: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::__cxx11::basic_string, std::allocator<std::_cxx11::basic_string > >::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
for(int i = 1+n, j = 1+n; i < valVec_fixed.size(); i++, j+=2)
^~~~~~~~~~~~~~~~~~~~~
In file included from C:/ProgramFiles/R/R-4.0.0/library/BH/include/boost/graph/adjacency_iterator.hpp:13,
from C:/ProgramFiles/R/R-4.0.0/library/BH/include/boost/graph/detail/adjacency_list.hpp:37,
from C:/ProgramFiles/R/R-4.0.0/library/BH/include/boost/graph/adjacency_list.hpp:255,
from ../inst/include/cytolib/populationTree.hpp:14,
from ../inst/include/cytolib/GatingHierarchy.hpp:17,
from ../inst/include/cytolib/GatingSet.hpp:14,
from src/GatingSet.cpp:3:
C:/ProgramFiles/R/R-4.0.0/library/BH/include/boost/detail/iterator.hpp: At global scope:
C:/ProgramFiles/R/R-4.0.0/library/BH/include/boost/detail/iterator.hpp:13:37: note: #pragma message: This header is deprecated. Use instead.
BOOST_HEADER_DEPRECATED("")
^
In file included from ../inst/include/cytolib/compensation.hpp:19,
from ../inst/include/cytolib/CytoFrame.hpp:16,
from ../inst/include/cytolib/MemCytoFrame.hpp:12,
from ../inst/include/cytolib/gate.hpp:12,
from ../inst/include/cytolib/POPINDICES.hpp:14,
from ../inst/include/cytolib/nodeProperties.hpp:13,
from ../inst/include/cytolib/populationTree.hpp:13,
from ../inst/include/cytolib/GatingHierarchy.hpp:17,
from ../inst/include/cytolib/GatingSet.hpp:14,
from src/GatingSet.cpp:3:
../inst/include/cytolib/global.hpp: In constructor 'cytolib::GatingSet::GatingSet(std::__cxx11::string, bool, bool, std::vector<std::__cxx11::basic_string, std::allocator<std::__cxx11::basic_string > >, bool, cytolib::CytoCtx)':
../inst/include/cytolib/global.hpp:29:3: warning: 'fmt' may be used uninitialized in this function [-Wmaybe-uninitialized]
switch(fmt)
^~~~~~
src/GatingSet.cpp:30:14: note: 'fmt' was declared here
FileFormat fmt;
^
"C:/ProgramFiles/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/ProgramFiles/R/R-40~1.0/include" -DNDEBUG -DROUT -I../inst/include -DRCPP_PARALLEL_USE_TBB=1 -fpermissive -DBOOST_NO_AUTO_PTR -I'C:/ProgramFiles/R/R-4.0.0/library/Rcpp/include' -I'C:/ProgramFiles/R/R-4.0.0/library/BH/include' -I'C:/ProgramFiles/R/R-4.0.0/library/RProtoBufLib/include' -I'C:/ProgramFiles/R/R-4.0.0/library/Rhdf5lib/include' -I'C:/ProgramFiles/R/R-4.0.0/library/RcppArmadillo/include' -I'C:/ProgramFiles/R/R-4.0.0/library/RcppParallel/include' -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c src/transformation.cpp -o src/transformation.o
In file included from C:/ProgramFiles/R/R-4.0.0/library/BH/include/boost/mpl/aux/na_assert.hpp:23,
from C:/ProgramFiles/R/R-4.0.0/library/BH/include/boost/mpl/arg.hpp:25,
from C:/ProgramFiles/R/R-4.0.0/library/BH/include/boost/mpl/placeholders.hpp:24,
from C:/ProgramFiles/R/R-4.0.0/library/BH/include/boost/iterator/iterator_categories.hpp:16,
from C:/ProgramFiles/R/R-4.0.0/library/BH/include/boost/iterator/iterator_facade.hpp:13,
from C:/ProgramFiles/R/R-4.0.0/library/BH/include/boost/range/iterator_range_core.hpp:27,
from C:/ProgramFiles/R/R-4.0.0/library/BH/include/boost/range/iterator_range.hpp:13,
from C:/ProgramFiles/R/R-4.0.0/library/BH/include/boost/range/as_literal.hpp:18,
from C:/ProgramFiles/R/R-4.0.0/library/BH/include/boost/algorithm/string/trim.hpp:19,
from C:/ProgramFiles/R/R-4.0.0/library/BH/include/boost/algorithm/string.hpp:19,
from ../inst/include/cytolib/transformation.hpp:18,
from src/transformation.cpp:3:
C:/ProgramFiles/R/R-4.0.0/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
failed ************ (Pred::***********
^
C:/ProgramFiles/R/R-4.0.0/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
failed ************ (boost::mpl::not::************
^
"C:/ProgramFiles/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/ProgramFiles/R/R-401.0/include" -DNDEBUG -DROUT -I../inst/include -DRCPP_PARALLEL_USE_TBB=1 -fpermissive -DBOOST_NO_AUTO_PTR -I'C:/ProgramFiles/R/R-4.0.0/library/Rcpp/include' -I'C:/ProgramFiles/R/R-4.0.0/library/BH/include' -I'C:/ProgramFiles/R/R-4.0.0/library/RProtoBufLib/include' -I'C:/ProgramFiles/R/R-4.0.0/library/Rhdf5lib/include' -I'C:/ProgramFiles/R/R-4.0.0/library/RcppArmadillo/include' -I'C:/ProgramFiles/R/R-4.0.0/library/RcppParallel/include' -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c src/ellipse2points.cpp -o src/ellipse2points.o1.0/include" -DNDEBUG -DROUT -I../inst/include -DRCPP_PARALLEL_USE_TBB=1 -fpermissive -DBOOST_NO_AUTO_PTR -I'C:/ProgramFiles/R/R-4.0.0/library/Rcpp/include' -I'C:/ProgramFiles/R/R-4.0.0/library/BH/include' -I'C:/ProgramFiles/R/R-4.0.0/library/RProtoBufLib/include' -I'C:/ProgramFiles/R/R-4.0.0/library/Rhdf5lib/include' -I'C:/ProgramFiles/R/R-4.0.0/library/RcppArmadillo/include' -I'C:/ProgramFiles/R/R-4.0.0/library/RcppParallel/include' -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c src/H5CytoFrame.cpp -o src/H5CytoFrame.o
"C:/ProgramFiles/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/ProgramFiles/R/R-40
In file included from C:/ProgramFiles/R/R-4.0.0/library/BH/include/boost/mpl/aux/na_assert.hpp:23,
from C:/ProgramFiles/R/R-4.0.0/library/BH/include/boost/mpl/arg.hpp:25,
from C:/ProgramFiles/R/R-4.0.0/library/BH/include/boost/mpl/placeholders.hpp:24,
from C:/ProgramFiles/R/R-4.0.0/library/BH/include/boost/iterator/iterator_categories.hpp:16,
from C:/ProgramFiles/R/R-4.0.0/library/BH/include/boost/iterator/iterator_facade.hpp:13,
from C:/ProgramFiles/R/R-4.0.0/library/BH/include/boost/range/iterator_range_core.hpp:27,
from C:/ProgramFiles/R/R-4.0.0/library/BH/include/boost/range/iterator_range.hpp:13,
from C:/ProgramFiles/R/R-4.0.0/library/BH/include/boost/range/as_literal.hpp:18,
from C:/ProgramFiles/R/R-4.0.0/library/BH/include/boost/algorithm/string/trim.hpp:19,
from C:/ProgramFiles/R/R-4.0.0/library/BH/include/boost/algorithm/string.hpp:19,
from ../inst/include/cytolib/transformation.hpp:18,
from ../inst/include/cytolib/compensation.hpp:15,
from ../inst/include/cytolib/CytoFrame.hpp:16,
from ../inst/include/cytolib/MemCytoFrame.hpp:12,
from ../inst/include/cytolib/H5CytoFrame.hpp:12,
from src/H5CytoFrame.cpp:3:
C:/ProgramFiles/R/R-4.0.0/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
failed ************ (Pred::************
^
C:/ProgramFiles/R/R-4.0.0/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
failed ************ (boost::mpl::not::************
^
In file included from ../inst/include/cytolib/CytoFrame.hpp:16,
from ../inst/include/cytolib/MemCytoFrame.hpp:12,
from ../inst/include/cytolib/H5CytoFrame.hpp:12,
from src/H5CytoFrame.cpp:3:
../inst/include/cytolib/compensation.hpp: In constructor 'cytolib::compensation::compensation(const string&)':
../inst/include/cytolib/compensation.hpp:58:20: warning: comparison of integer expressions of different signedness: 'std::vector<std::_cxx11::basic_string, std::allocator<std::cxx11::basic_string > >::size_type' {aka 'long long unsigned int'} and 'int' [-Wsign-compare]
if(valVec.size() != 1+n+nn){
~~~~~~~~~~~~~~^~~~~~~~~~
../inst/include/cytolib/compensation.hpp:62:21: warning: comparison of integer expressions of different signedness: 'std::vector<std::__cxx11::basic_string, std::allocator<std::__cxx11::basic_string > >::size_type' {aka 'long long unsigned int'} and 'int' [-Wsign-compare]
if(valVec.size() == 1+n+2nn){
~~~~~~~~~~~~~~^~~~~~~~~~~~
../inst/include/cytolib/compensation.hpp:68:33: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::__cxx11::basic_string, std::allocator<std::_cxx11::basic_string > >::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
for(int i = 1+n, j = 1+n; i < valVec_fixed.size(); i++, j+=2)
~~^~~~~~~~~~~~~~~~~~~~~
"C:/ProgramFiles/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/ProgramFiles/R/R-40~1.0/include" -DNDEBUG -DROUT -I../inst/include -DRCPP_PARALLEL_USE_TBB=1 -fpermissive -DBOOST_NO_AUTO_PTR -I'C:/ProgramFiles/R/R-4.0.0/library/Rcpp/include' -I'C:/ProgramFiles/R/R-4.0.0/library/BH/include' -I'C:/ProgramFiles/R/R-4.0.0/library/RProtoBufLib/include' -I'C:/ProgramFiles/R/R-4.0.0/library/Rhdf5lib/include' -I'C:/ProgramFiles/R/R-4.0.0/library/RcppArmadillo/include' -I'C:/ProgramFiles/R/R-4.0.0/library/RcppParallel/include' -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c src/trans_group.cpp -o src/trans_group.o
In file included from C:/ProgramFiles/R/R-4.0.0/library/BH/include/boost/mpl/aux/na_assert.hpp:23,
from C:/ProgramFiles/R/R-4.0.0/library/BH/include/boost/mpl/arg.hpp:25,
from C:/ProgramFiles/R/R-4.0.0/library/BH/include/boost/mpl/placeholders.hpp:24,
from C:/ProgramFiles/R/R-4.0.0/library/BH/include/boost/iterator/iterator_categories.hpp:16,
from C:/ProgramFiles/R/R-4.0.0/library/BH/include/boost/iterator/iterator_facade.hpp:13,
from C:/ProgramFiles/R/R-4.0.0/library/BH/include/boost/range/iterator_range_core.hpp:27,
from C:/ProgramFiles/R/R-4.0.0/library/BH/include/boost/range/iterator_range.hpp:13,
from C:/ProgramFiles/R/R-4.0.0/library/BH/include/boost/range/as_literal.hpp:18,
from C:/ProgramFiles/R/R-4.0.0/library/BH/include/boost/algorithm/string/trim.hpp:19,
from C:/ProgramFiles/R/R-4.0.0/library/BH/include/boost/algorithm/string.hpp:19,
from ../inst/include/cytolib/transformation.hpp:18,
from ../inst/include/cytolib/trans_group.hpp:13,
from src/trans_group.cpp:3:
C:/ProgramFiles/R/R-4.0.0/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
failed ************ (Pred::***********
^
C:/ProgramFiles/R/R-4.0.0/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
failed ************ (boost::mpl::not::************
^
"C:/ProgramFiles/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/ProgramFiles/R/R-401.0/include" -DNDEBUG -DROUT -I../inst/include -DRCPP_PARALLEL_USE_TBB=1 -fpermissive -DBOOST_NO_AUTO_PTR -I'C:/ProgramFiles/R/R-4.0.0/library/Rcpp/include' -I'C:/ProgramFiles/R/R-4.0.0/library/BH/include' -I'C:/ProgramFiles/R/R-4.0.0/library/RProtoBufLib/include' -I'C:/ProgramFiles/R/R-4.0.0/library/Rhdf5lib/include' -I'C:/ProgramFiles/R/R-4.0.0/library/RcppArmadillo/include' -I'C:/ProgramFiles/R/R-4.0.0/library/RcppParallel/include' -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c src/spline.cpp -o src/spline.o1.0/include" -DNDEBUG -DROUT -I../inst/include -DRCPP_PARALLEL_USE_TBB=1 -fpermissive -DBOOST_NO_AUTO_PTR -I'C:/ProgramFiles/R/R-4.0.0/library/Rcpp/include' -I'C:/ProgramFiles/R/R-4.0.0/library/BH/include' -I'C:/ProgramFiles/R/R-4.0.0/library/RProtoBufLib/include' -I'C:/ProgramFiles/R/R-4.0.0/library/Rhdf5lib/include' -I'C:/ProgramFiles/R/R-4.0.0/library/RcppArmadillo/include' -I'C:/ProgramFiles/R/R-4.0.0/library/RcppParallel/include' -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c src/global.cpp -o src/global.o
"C:/ProgramFiles/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/ProgramFiles/R/R-40
In file included from C:/ProgramFiles/R/R-4.0.0/library/BH/include/boost/mpl/aux/na_assert.hpp:23,
from C:/ProgramFiles/R/R-4.0.0/library/BH/include/boost/mpl/arg.hpp:25,
from C:/ProgramFiles/R/R-4.0.0/library/BH/include/boost/mpl/placeholders.hpp:24,
from C:/ProgramFiles/R/R-4.0.0/library/BH/include/boost/iterator/iterator_categories.hpp:16,
from C:/ProgramFiles/R/R-4.0.0/library/BH/include/boost/iterator/iterator_facade.hpp:13,
from C:/ProgramFiles/R/R-4.0.0/library/BH/include/boost/filesystem/path.hpp:29,
from C:/ProgramFiles/R/R-4.0.0/library/BH/include/boost/filesystem.hpp:16,
from ../inst/include/cytolib/CytoVFS.hpp:17,
from ../inst/include/cytolib/global.hpp:21,
from src/global.cpp:3:
C:/ProgramFiles/R/R-4.0.0/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
failed ************ (Pred::************
^
C:/ProgramFiles/R/R-4.0.0/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
failed ************ (boost::mpl::not::************
^
src/global.cpp: In function 'std::__cxx11::string cytolib::s3_to_http(std::__cxx11::string)':
src/global.cpp:46:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::cxx11::basic_string >::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
for(int i = 1; i < tokens.size(); i++)
~~^~~~~~~~~~~~~~~
"C:/ProgramFiles/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/ProgramFiles/R/R-40~1.0/include" -DNDEBUG -DROUT -I../inst/include -DRCPP_PARALLEL_USE_TBB=1 -fpermissive -DBOOST_NO_AUTO_PTR -I'C:/ProgramFiles/R/R-4.0.0/library/Rcpp/include' -I'C:/ProgramFiles/R/R-4.0.0/library/BH/include' -I'C:/ProgramFiles/R/R-4.0.0/library/RProtoBufLib/include' -I'C:/ProgramFiles/R/R-4.0.0/library/Rhdf5lib/include' -I'C:/ProgramFiles/R/R-4.0.0/library/RcppArmadillo/include' -I'C:/ProgramFiles/R/R-4.0.0/library/RcppParallel/include' -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c src/GatingHierarchy.cpp -o src/GatingHierarchy.o
In file included from C:/ProgramFiles/R/R-4.0.0/library/BH/include/boost/mpl/aux/na_assert.hpp:23,
from C:/ProgramFiles/R/R-4.0.0/library/BH/include/boost/mpl/arg.hpp:25,
from C:/ProgramFiles/R/R-4.0.0/library/BH/include/boost/mpl/placeholders.hpp:24,
from C:/ProgramFiles/R/R-4.0.0/library/BH/include/boost/iterator/iterator_categories.hpp:16,
from C:/ProgramFiles/R/R-4.0.0/library/BH/include/boost/iterator/iterator_facade.hpp:13,
from C:/ProgramFiles/R/R-4.0.0/library/BH/include/boost/range/iterator_range_core.hpp:27,
from C:/ProgramFiles/R/R-4.0.0/library/BH/include/boost/range/iterator_range.hpp:13,
from C:/ProgramFiles/R/R-4.0.0/library/BH/include/boost/range/as_literal.hpp:18,
from C:/ProgramFiles/R/R-4.0.0/library/BH/include/boost/algorithm/string/trim.hpp:19,
from C:/ProgramFiles/R/R-4.0.0/library/BH/include/boost/algorithm/string.hpp:19,
from ../inst/include/cytolib/transformation.hpp:18,
from ../inst/include/cytolib/compensation.hpp:15,
from ../inst/include/cytolib/CytoFrame.hpp:16,
from ../inst/include/cytolib/MemCytoFrame.hpp:12,
from ../inst/include/cytolib/gate.hpp:12,
from ../inst/include/cytolib/POPINDICES.hpp:14,
from ../inst/include/cytolib/nodeProperties.hpp:13,
from ../inst/include/cytolib/populationTree.hpp:13,
from ../inst/include/cytolib/GatingHierarchy.hpp:17,
from src/GatingHierarchy.cpp:3:
C:/ProgramFiles/R/R-4.0.0/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
failed ************ (Pred::************
^
C:/ProgramFiles/R/R-4.0.0/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
failed ************ (boost::mpl::not::************
^
In file included from ../inst/include/cytolib/CytoFrame.hpp:16,
from ../inst/include/cytolib/MemCytoFrame.hpp:12,
from ../inst/include/cytolib/gate.hpp:12,
from ../inst/include/cytolib/POPINDICES.hpp:14,
from ../inst/include/cytolib/nodeProperties.hpp:13,
from ../inst/include/cytolib/populationTree.hpp:13,
from ../inst/include/cytolib/GatingHierarchy.hpp:17,
from src/GatingHierarchy.cpp:3:
../inst/include/cytolib/compensation.hpp: In constructor 'cytolib::compensation::compensation(const string&)':
../inst/include/cytolib/compensation.hpp:58:20: warning: comparison of integer expressions of different signedness: 'std::vector<std::__cxx11::basic_string, std::allocator<std::__cxx11::basic_string > >::size_type' {aka 'long long unsigned int'} and 'int' [-Wsign-compare]
if(valVec.size() != 1+n+nn){
~~~~~~~~~~~~~~^~~~~~~~~~
../inst/include/cytolib/compensation.hpp:62:21: warning: comparison of integer expressions of different signedness: 'std::vector<std::__cxx11::basic_string, std::allocator<std::__cxx11::basic_string > >::size_type' {aka 'long long unsigned int'} and 'int' [-Wsign-compare]
if(valVec.size() == 1+n+2n*n){
~~~~~~~~~~~~~~^~~~~~~~~~~~
../inst/include/cytolib/compensation.hpp:68:33: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::__cxx11::basic_string, std::allocator<std::__cxx11::basic_string > >::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
for(int i = 1+n, j = 1+n; i < valVec_fixed.size(); i++, j+=2)
~~^~~~~~~~~~~~~~~~~~~~~
In file included from C:/ProgramFiles/R/R-4.0.0/library/BH/include/boost/graph/adjacency_iterator.hpp:13,
from C:/ProgramFiles/R/R-4.0.0/library/BH/include/boost/graph/detail/adjacency_list.hpp:37,
from C:/ProgramFiles/R/R-4.0.0/library/BH/include/boost/graph/adjacency_list.hpp:255,
from ../inst/include/cytolib/populationTree.hpp:14,
from ../inst/include/cytolib/GatingHierarchy.hpp:17,
from src/GatingHierarchy.cpp:3:
C:/ProgramFiles/R/R-4.0.0/library/BH/include/boost/detail/iterator.hpp: At global scope:
C:/ProgramFiles/R/R-4.0.0/library/BH/include/boost/detail/iterator.hpp:13:37: note: #pragma message: This header is deprecated. Use instead.
BOOST_HEADER_DEPRECATED("")
garbage collection on the h5 folders
The flowJo parser generates temporary h5 folders and h5 files for each run. Right now we set the default h5_dir as /tmp or Rtmp and let os or R session to do the clean up job.
If we ever want to proactively do the garbage collection to avoid flooding the fs by the large number of temporary h5s (given os may not clean /tmp folder as frequent).
We will have to maintain a global counter (at cytolib level) for each GatingSet in order to decide whether to delete the associated h5 folder. It may not always be easy, because GatingSet can be loaded from user-archived folder, which we don't necessarily want to delete them after it is done.
What makes it more complicated is, CytoFrame can potentially live outside of the scope of GatingSet and we then also need to have a counter per frame.
For now, I will leave it as it is. We can revisit this issue as needed later.
Bioc build failure due to missing file system library
fatal error: experimental/filesystem: No such file or directory This indicates that mingw32/gcc from Rtools doesn't ship this lib. We may need to bundle boost version of it for windows
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