Comments (19)
mikejiang
commented on July 25, 2024
4
the bundled boost source code is out of sync, I will push the fix shortly
from cytolib.
FMKerckhof
commented on July 25, 2024
2
Hi @LuisaFJimenez I don't know enough about the C++ internals of cytolib, but are you sure you have latest BioConductor? I had to update to 3.16 for things to work BiocManager::install(version = "3.16"). If that doesn't work, maybe you can try to install cytolib from the development version (devtools::install_github("RGLab/cytolib"))?
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mikejiang
commented on July 25, 2024
1
@FMKerckhof Thank you for reporting, patch is pushed
from cytolib.
FMKerckhof
commented on July 25, 2024
1
@fbenedett : with the latest BH (CRAN) and cytolib (bioconductor) I was able to build on Ubuntu 22.04, 20.04, 18.04 and amazon linux 2 latest without any problems. Try to make sure you have the latest R, bioconductor (3.16) and it should work. My session on 22.04:
R version 4.2.2 (2022-10-31)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 22.04.1 LTS
Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.20.so
locale:
[1] LC_CTYPE=C.UTF-8 LC_NUMERIC=C LC_TIME=C.UTF-8 LC_COLLATE=C.UTF-8 LC_MONETARY=C.UTF-8
[6] LC_MESSAGES=C.UTF-8 LC_PAPER=C.UTF-8 LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=C.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] splines stats graphics grDevices utils datasets methods base
other attached packages:
[1] ggcyto_1.26.4 flowWorkspace_4.10.1 ncdfFlow_2.44.0
[4] BH_1.81.0-1 ClusterR_1.3.0 tictoc_1.1
[7] forcats_0.5.2 stringr_1.5.0 purrr_1.0.1
[10] readr_2.1.3 tidyr_1.3.0 tibble_3.1.8
[13] tidyverse_1.3.2 patchwork_1.1.2 GGally_2.1.2
[16] lubridate_1.9.1 gam_1.22 plotly_4.10.1
[19] parsedate_1.3.1 scales_1.2.1 ggplot2_3.4.0.9000
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bgbrink
commented on July 25, 2024
I am having the same issue with installing cytolib in the bioconductor/bioconductor_docker.
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mikejiang
commented on July 25, 2024
turned out the process of bundling the latest boost file system library is not straightforward as used to be, here is how I did it:
extraction file system module from boost:
download boost_1_78
./bootstrap.sh
./b2 tools/bcp
mkdir foo
./dist/bin/bcp boost/filesystem foo/
Use foo/* to replace the existing old version of bundled file system library in cytolib, i.e.cytolib/src/boost/libs
then re-compile cytolib but running into errors
g++ -std=gnu++11 -I"/usr/local/lib/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/usr/local/lib/R/site-library/Rcpp/include' -I'/usr/local/lib/R/site-library/BH/include' -I'/usr/local/lib/R/site-library/RProtoBufLib/include' -I'/usr/local/lib/R/site-library/Rhdf5lib/include' -I'/usr/local/lib/R/site-library/RcppArmadillo/include' -I'/usr/local/lib/R/site-library/RcppParallel/include' -I/usr/local/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
In file included from boost/libs/filesystem/src/path.cpp:39:
boost/libs/filesystem/src/atomic_tools.hpp: In function ‘T boost::filesystem::detail::atomic_load_relaxed(T&)’:
boost/libs/filesystem/src/atomic_tools.hpp:29:23: error: ‘atomic_ref’ is not a member of ‘atomic_ns’; did you mean ‘atomic_int’?
29 | return atomic_ns::atomic_ref< T >(a).load(atomic_ns::memory_order_relaxed);
| ^~~~~~~~~~
| atomic_int
boost/libs/filesystem/src/atomic_tools.hpp:29:37: error: expected primary-expression before ‘>’ token
29 | return atomic_ns::atomic_ref< T >(a).load(atomic_ns::memory_order_relaxed);
|
I will give it another try tomorrow
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jacobpwagner
commented on July 25, 2024
Hey @mikejiang. I know you've been investigating this, but I was looking at it as well and tracing the atomic_ref issue. It looks like it may just come down to figuring out how to make configuration use boost::atomic instead of std::atomic, which may not allow support for atomic_ref even with C++20 specified. I think config should catch that. Anyway, as a workaround to test, I simply updated the filesystem and system subdirs in cytolib/src/boost/libs to the 1.78.0 versions (without any other bootstrapping or configuration) and just commented out lines to force this else block. With just those changes, cytolib compiles and flowWorkspace clean rebuilds and tests successfully in my hands (clang 13.0.0).
Anyway, you probably were already figuring all of that out and are working on a less hacky way to fix it, but just in case it helps at all I thought I'd mention it.
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mikejiang
commented on July 25, 2024
Thanks @jacobpwagner for pointing to the right direction, I ended up doing this
PKG_CPPFLAGS =-DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -DBOOST_FILESYSTEM_NO_CXX20_ATOMIC_REF -DBOOST_FILESYSTEM_SINGLE_THREADED
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mikejiang
commented on July 25, 2024
I have pushed the patch to bioconductor the latest release and development branch
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jacobpwagner
commented on July 25, 2024
Ah yes. Of course. Much better way. Thanks!
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eleniel-mocna
commented on July 25, 2024
Installing into rocker/rstudio still crashes.
A quick workaround is just using image rocker/rstudio:4.0.5, which still uses boost 1.75.0.
(This works, just gives a lot of deprecation warnings about the given headers...)
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wu-yc
commented on July 25, 2024
Any updates on the solutions?
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mikejiang
commented on July 25, 2024
If you are on the latest version of R and all the other packages, it should build
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FMKerckhof
commented on July 25, 2024
@mikejiang with the latest version of BH (1.81.0-1) it appears I have issues to compile the latest version of Cytolib (on Amazon Linux 2), could it be that the bundled boost code is out of sync again?
#8 1204.9 checking whether g++ accepts -g... (cached) yes
#8 1204.9 configure: Parsing cytolib version info ...
#8 1204.9 configure: CYTOLIB_VERSION=2.10.0
#8 1204.9 configure: creating ./config.status
#8 1204.9 config.status: creating inst/include/cytolib/cytolibConfig.h
#8 1204.9 config.status: creating src/Makevars
#8 1204.9 ** libs
#8 1204.9 g++ -std=gnu++11 -I"/opt/R/4.2.2/lib/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -DBOOST_FILESYSTEM_NO_CXX20_ATOMIC_REF -DBOOST_FILESYSTEM_SINGLE_THREADED -I'/opt/R/4.2.2/lib/R/library/.renv/1/BH/include' -I'/opt/R/4.2.2/lib/R/library/.renv/1/RProtoBufLib/include' -I'/opt/R/4.2.2/lib/R/library/.renv/1/Rhdf5lib/include' -I/usr/local/include
-fpic -g -O2 -c dummy.cpp -o dummy.o
#8 1204.9 g++ -std=gnu++11 -I"/opt/R/4.2.2/lib/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -DBOOST_FILESYSTEM_NO_CXX20_ATOMIC_REF -DBOOST_FILESYSTEM_SINGLE_THREADED -I'/opt/R/4.2.2/lib/R/library/.renv/1/BH/include' -I'/opt/R/4.2.2/lib/R/library/.renv/1/RProtoBufLib/include' -I'/opt/R/4.2.2/lib/R/library/.renv/1/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
#8 1204.9 g++ -std=gnu++11 -I"/opt/R/4.2.2/lib/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -DBOOST_FILESYSTEM_NO_CXX20_ATOMIC_REF -DBOOST_FILESYSTEM_SINGLE_THREADED -I'/opt/R/4.2.2/lib/R/library/.renv/1/BH/include' -I'/opt/R/4.2.2/lib/R/library/.renv/1/RProtoBufLib/include' -I'/opt/R/4.2.2/lib/R/library/.renv/1/Rhdf5lib/include' -I/usr/local/include
-fpic -g -O2 -c boost/libs/filesystem/src/path_traits.cpp -o boost/libs/filesystem/src/path_traits.o
#8 1204.9 g++ -std=gnu++11 -I"/opt/R/4.2.2/lib/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -DBOOST_FILESYSTEM_NO_CXX20_ATOMIC_REF -DBOOST_FILESYSTEM_SINGLE_THREADED -I'/opt/R/4.2.2/lib/R/library/.renv/1/BH/include' -I'/opt/R/4.2.2/lib/R/library/.renv/1/RProtoBufLib/include' -I'/opt/R/4.2.2/lib/R/library/.renv/1/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#8 1204.9 g++ -std=gnu++11 -I"/opt/R/4.2.2/lib/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -DBOOST_FILESYSTEM_NO_CXX20_ATOMIC_REF -DBOOST_FILESYSTEM_SINGLE_THREADED -I'/opt/R/4.2.2/lib/R/library/.renv/1/BH/include' -I'/opt/R/4.2.2/lib/R/library/.renv/1/RProtoBufLib/include' -I'/opt/R/4.2.2/lib/R/library/.renv/1/Rhdf5lib/include' -I/usr/local/include
-fpic -g -O2 -c boost/libs/filesystem/src/utf8_codecvt_facet.cpp -o boost/libs/filesystem/src/utf8_codecvt_facet.o
#8 1204.9 g++ -std=gnu++11 -I"/opt/R/4.2.2/lib/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -DBOOST_FILESYSTEM_NO_CXX20_ATOMIC_REF -DBOOST_FILESYSTEM_SINGLE_THREADED -I'/opt/R/4.2.2/lib/R/library/.renv/1/BH/include' -I'/opt/R/4.2.2/lib/R/library/.renv/1/RProtoBufLib/include' -I'/opt/R/4.2.2/lib/R/library/.renv/1/Rhdf5lib/include' -I/usr/local/include
-fpic -g -O2 -c boost/libs/filesystem/src/windows_file_codecvt.cpp -o boost/libs/filesystem/src/windows_file_codecvt.o
#8 1204.9 g++ -std=gnu++11 -I"/opt/R/4.2.2/lib/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -DBOOST_FILESYSTEM_NO_CXX20_ATOMIC_REF -DBOOST_FILESYSTEM_SINGLE_THREADED -I'/opt/R/4.2.2/lib/R/library/.renv/1/BH/include' -I'/opt/R/4.2.2/lib/R/library/.renv/1/RProtoBufLib/include' -I'/opt/R/4.2.2/lib/R/library/.renv/1/Rhdf5lib/include' -I/usr/local/include
-fpic -g -O2 -c boost/libs/filesystem/src/exception.cpp -o boost/libs/filesystem/src/exception.o
#8 1204.9 g++ -std=gnu++11 -I"/opt/R/4.2.2/lib/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -DBOOST_FILESYSTEM_NO_CXX20_ATOMIC_REF -DBOOST_FILESYSTEM_SINGLE_THREADED -I'/opt/R/4.2.2/lib/R/library/.renv/1/BH/include' -I'/opt/R/4.2.2/lib/R/library/.renv/1/RProtoBufLib/include' -I'/opt/R/4.2.2/lib/R/library/.renv/1/Rhdf5lib/include' -I/usr/local/include
-fpic -g -O2 -c boost/libs/filesystem/src/directory.cpp -o boost/libs/filesystem/src/directory.o
#8 1204.9 boost/libs/filesystem/src/directory.cpp:134:15: error: ‘codecvt_type’ has not been declared
#8 1204.9 codecvt_type const&)
#8 1204.9 ^~~~~~~~~~~~
#8 1204.9 boost/libs/filesystem/src/directory.cpp: In function ‘boost::system::error_code boost::filesystem::detail::{anonymous}::dir_itr_increment(void*&, void*&, std::__cxx11::string&, boost::filesystem::file_status&, boost::filesystem::file_status&)’:
#8 1204.9 boost/libs/filesystem/src/directory.cpp:264:28: error: ‘dir_itr_close’ is not a member of ‘boost::filesystem::detail’
#8 1204.9 return fs::detail::dir_itr_close(handle, buffer);
#8 1204.9 ^~~~~~~~~~~~~
#8 1204.9 boost/libs/filesystem/src/directory.cpp:264:28: note: suggested alternative: ‘dir_itr_imp’
#8 1204.9 return fs::detail::dir_itr_close(handle, buffer);
#8 1204.9 ^~~~~~~~~~~~~
#8 1204.9 dir_itr_imp
#8 1204.9 boost/libs/filesystem/src/directory.cpp: In function ‘void boost::filesystem::detail::directory_iterator_construct(boost::filesystem::directory_iterator&, const boost::filesystem::path&, unsigned int, boost::system::error_code*)’:
#8 1204.9 boost/libs/filesystem/src/directory.cpp:445:39: error: no matching function for call to ‘boost::filesystem::detail::dir_itr_imp::operator new(sizetype)’
#8 1204.9 imp = new detail::dir_itr_imp();
#8 1204.9 ^
#8 1204.9 In file included from boost/libs/filesystem/src/directory.cpp:17:0:
#8 1204.9 /opt/R/4.2.2/lib/R/library/.renv/1/BH/include/boost/filesystem/directory.hpp:317:40: note: candidate: static void*
boost::filesystem::detail::dir_itr_imp::operator new(std::size_t, std::size_t)
#8 1204.9 BOOST_FILESYSTEM_DECL static void* operator new(std::size_t class_size, std::size_t extra_size) BOOST_NOEXCEPT;
#8 1204.9 ^~~~~~~~
#8 1204.9 /opt/R/4.2.2/lib/R/library/.renv/1/BH/include/boost/filesystem/directory.hpp:317:40: note: candidate expects 2 arguments, 1 provided
#8 1204.9 boost/libs/filesystem/src/directory.cpp:449:54: error: no matching function for call to ‘boost::filesystem::detail::dir_itr_imp::operator new(sizetype, const std::nothrow_t&)’
#8 1204.9 imp = new (std::nothrow) detail::dir_itr_imp();
#8 1204.9 ^
#8 1204.9 In file included from boost/libs/filesystem/src/directory.cpp:17:0:
#8 1204.9 /opt/R/4.2.2/lib/R/library/.renv/1/BH/include/boost/filesystem/directory.hpp:317:40: note: candidate: static void*
boost::filesystem::detail::dir_itr_imp::operator new(std::size_t, std::size_t)
#8 1204.9 BOOST_FILESYSTEM_DECL static void* operator new(std::size_t class_size, std::size_t extra_size) BOOST_NOEXCEPT;
#8 1204.9 ^~~~~~~~
#8 1204.9 /opt/R/4.2.2/lib/R/library/.renv/1/BH/include/boost/filesystem/directory.hpp:317:40: note: no known conversion for argument 2 from ‘const std::nothrow_t’ to ‘std::size_t {aka long unsigned int}’
#8 1204.9 boost/libs/filesystem/src/directory.cpp:463:48: error: ‘struct boost::filesystem::detail::dir_itr_imp’ has no member named ‘buffer’
#8 1204.9 imp->buffer,
#8 1204.9 ^~~~~~
#8 1204.9 boost/libs/filesystem/src/directory.cpp:481:16: error: ‘boost::intrusive_ptr<boost::filesystem::detail::dir_itr_imp> boost::filesystem::directory_iterator::m_imp’ is private within this context
#8 1204.9 it.m_imp.swap(imp);
#8 1204.9 ^~~~~
#8 1204.9 In file included from boost/libs/filesystem/src/directory.cpp:17:0:
#8 1204.9 /opt/R/4.2.2/lib/R/library/.renv/1/BH/include/boost/filesystem/directory.hpp:417:49: note: declared private here
#8 1204.9 boost::intrusive_ptr< detail::dir_itr_imp > m_imp;
#8 1204.9 ^~~~~
#8 1204.9 boost/libs/filesystem/src/directory.cpp:482:16: error: ‘boost::intrusive_ptr<boost::filesystem::detail::dir_itr_imp> boost::filesystem::directory_iterator::m_imp’ is private within this context
#8 1204.9 it.m_imp->dir_entry.assign(p / filename, file_stat, symlink_file_stat);
#8 1204.9 ^~~~~
#8 1204.9 In file included from boost/libs/filesystem/src/directory.cpp:17:0:
#8 1204.9 /opt/R/4.2.2/lib/R/library/.renv/1/BH/include/boost/filesystem/directory.hpp:417:49: note: declared private here
#8 1204.9 boost::intrusive_ptr< detail::dir_itr_imp > m_imp;
#8 1204.9 ^~~~~
#8 1204.9 boost/libs/filesystem/src/directory.cpp:498:12: error: ‘boost::intrusive_ptr<boost::filesystem::detail::dir_itr_imp> boost::filesystem::directory_iterator::m_imp’ is private within this context
#8 1204.9 it.m_imp.reset();
#8 1204.9 ^~~~~
#8 1204.9 In file included from boost/libs/filesystem/src/directory.cpp:17:0:
#8 1204.9 /opt/R/4.2.2/lib/R/library/.renv/1/BH/include/boost/filesystem/directory.hpp:417:49: note: declared private here
#8 1204.9 boost::intrusive_ptr< detail::dir_itr_imp > m_imp;
#8 1204.9 ^~~~~
#8 1204.9 boost/libs/filesystem/src/directory.cpp: In function ‘void boost::filesystem::detail::directory_iterator_increment(boost::filesystem::directory_iterator&, boost::system::error_code*)’:
#8 1204.9 boost/libs/filesystem/src/directory.cpp:520:56: error: ‘struct boost::filesystem::detail::dir_itr_imp’ has no member named ‘buffer’
#8 1204.9 it.m_imp->buffer,
#8 1204.9 ^~~~~~
#8 1204.9 make: *** [boost/libs/filesystem/src/directory.o] Error 1
#8 1204.9 ERROR: compilation failed for package ‘cytolib’
#8 1204.9 * removing ‘/opt/R/4.2.2/lib/R/library/.renv/1/cytolib’
#8 1204.9 Traceback (most recent calls last):
#8 1204.9 12: renv::restore()
#8 1204.9 11: renv_restore_run_actions(project, diff, current, lockfile, rebuild)
#8 1204.9 10: renv_install_impl(records)
#8 1204.9 9: renv_install_staged(records)
#8 1204.9 8: renv_install_default(records)
#8 1204.9 7: handler(package, renv_install_package(record))
#8 1204.9 6: renv_install_package(record)
#8 1204.9 5: withCallingHandlers(renv_install_package_impl(record), error = function(e) {
#8 1204.9 vwritef("\tFAILED")
#8 1204.9 writef(e$output)
#8 1204.9 })
#8 1204.9 4: renv_install_package_impl(record)
#8 1204.9 3: r_cmd_install(package, path)
#8 1204.9 2: r_exec_error(package, output, "install", status)
#8 1204.9 1: stop(error)
#8 1205.6 Execution halted
from cytolib.
fbenedett
commented on July 25, 2024
I have the same error.
Currently I am on ubuntu 22.04.
Session info:
R version 4.1.2 (2021-11-01)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 22.04.1 LTS
Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.10.0
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.10.0
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=de_CH.UTF-8 LC_COLLATE=en_US.UTF-8 LC_MONETARY=de_CH.UTF-8 LC_MESSAGES=en_US.UTF-8 LC_PAPER=de_CH.UTF-8
[8] LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=de_CH.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] Rcpp_1.0.10 rstudioapi_0.14 magrittr_2.0.3 tidyselect_1.2.0 R6_2.5.1 rlang_1.0.6 fansi_1.0.4 stringr_1.5.0 plyr_1.8.8 dplyr_1.1.0
[11] tools_4.1.2 utf8_1.2.3 cli_3.6.0 readxl_1.4.1 tibble_3.1.8 lifecycle_1.0.3 BiocManager_1.30.19 purrr_1.0.1 reshape2_1.4.4 tidyr_1.3.0
[21] vctrs_0.5.2 glue_1.6.2 stringi_1.7.12 compiler_4.1.2 pillar_1.8.1 cellranger_1.1.0 generics_0.1.3 pkgconfig_2.0.3
```How can I solve it?
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LuisaFJimenez
commented on July 25, 2024
Dear All,
I am really struggling to install the flowCell because if the cytolib. Help! Warning: Not too much experience with R. I have updated the Bioconductor, and my R is 4.2.2. Update: Using Linux Mint 20.
Here is the last command for the g++ and the following errors and messages:
g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -DBOOST_FILESYSTEM_NO_CXX20_ATOMIC_REF -DBOOST_FILESYSTEM_SINGLE_THREADED -I'/home/luisa/R/x86_64-pc-linux-gnu-library/4.2/Rcpp/include' -I'/home/luisa/R/x86_64-pc-linux-gnu-library/4.2/BH/include' -I'/home/luisa/R/x86_64-pc-linux-gnu-library/4.2/RProtoBufLib/include' -I'/home/luisa/R/x86_64-pc-linux-gnu-library/4.2/Rhdf5lib/include' -I'/home/luisa/R/x86_64-pc-linux-gnu-library/4.2/RcppArmadillo/include' -I'/home/luisa/R/x86_64-pc-linux-gnu-library/4.2/RcppParallel/include' -fpic -g -O2 -fdebug-prefix-map=/build/r-base-a3XuZ5/r-base-4.2.2.20221110=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c boost/libs/filesystem/src/directory.cpp -o boost/libs/filesystem/src/directory.o
boost/libs/filesystem/src/directory.cpp:134:15: error: ‘codecvt_type’ has not been declared
134 | codecvt_type const&)
| ^~~~~~~~~~~~
boost/libs/filesystem/src/directory.cpp: In function ‘boost::system::error_code boost::filesystem::detail::{anonymous}::dir_itr_increment(void*&, void*&, std::string&, boost::filesystem::file_status&, boost::filesystem::file_status&)’:
boost/libs/filesystem/src/directory.cpp:264:28: error: ‘dir_itr_close’ is not a member of ‘boost::filesystem::detail’; did you mean ‘dir_itr_imp’?
264 | return fs::detail::dir_itr_close(handle, buffer);
| ^~~~~~~~~~~~~
| dir_itr_imp
boost/libs/filesystem/src/directory.cpp: In function ‘void boost::filesystem::detail::directory_iterator_construct(boost::filesystem::directory_iterator&, const boost::filesystem::path&, unsigned int, boost::system::error_code*)’:
boost/libs/filesystem/src/directory.cpp:445:39: error: no matching function for call to ‘boost::filesystem::detail::dir_itr_imp::operator new(sizetype)’
445 | imp = new detail::dir_itr_imp();
| ^
In file included from boost/libs/filesystem/src/directory.cpp:17:
/home/luisa/R/x86_64-pc-linux-gnu-library/4.2/BH/include/boost/filesystem/directory.hpp:317:40: note: candidate: ‘static void* boost::filesystem::detail::dir_itr_imp::operator new(std::size_t, std::size_t)’
317 | BOOST_FILESYSTEM_DECL static void* operator new(std::size_t class_size, std::size_t extra_size) BOOST_NOEXCEPT;
| ^~~~~~~~
/home/luisa/R/x86_64-pc-linux-gnu-library/4.2/BH/include/boost/filesystem/directory.hpp:317:40: note: candidate expects 2 arguments, 1 provided
boost/libs/filesystem/src/directory.cpp:449:25: error: cannot convert ‘const std::nothrow_t’ to ‘std::size_t’ {aka ‘long unsigned int’}
449 | imp = new (std::nothrow) detail::dir_itr_imp();
| ~~~~~^~~~~~~
| |
| const std::nothrow_t
In file included from boost/libs/filesystem/src/directory.cpp:17:
/home/luisa/R/x86_64-pc-linux-gnu-library/4.2/BH/include/boost/filesystem/directory.hpp:317:89: note: initializing argument 2 of ‘static void* boost::filesystem::detail::dir_itr_imp::operator new(std::size_t, std::size_t)’
317 | BOOST_FILESYSTEM_DECL static void* operator new(std::size_t class_size, std::size_t extra_size) BOOST_NOEXCEPT;
| ~~~~~~~~~~~~^~~~~~~~~~
boost/libs/filesystem/src/directory.cpp:463:48: error: ‘struct boost::filesystem::detail::dir_itr_imp’ has no member named ‘buffer’
463 | imp->buffer,
| ^~~~~~
boost/libs/filesystem/src/directory.cpp:481:16: error: ‘boost::intrusive_ptr<boost::filesystem::detail::dir_itr_imp> boost::filesystem::directory_iterator::m_imp’ is private within this context
481 | it.m_imp.swap(imp);
| ^~~~~
In file included from boost/libs/filesystem/src/directory.cpp:17:
/home/luisa/R/x86_64-pc-linux-gnu-library/4.2/BH/include/boost/filesystem/directory.hpp:417:49: note: declared private here
417 | boost::intrusive_ptr< detail::dir_itr_imp > m_imp;
| ^~~~~
boost/libs/filesystem/src/directory.cpp:482:16: error: ‘boost::intrusive_ptr<boost::filesystem::detail::dir_itr_imp> boost::filesystem::directory_iterator::m_imp’ is private within this context
482 | it.m_imp->dir_entry.assign(p / filename, file_stat, symlink_file_stat);
| ^~~~~
In file included from boost/libs/filesystem/src/directory.cpp:17:
/home/luisa/R/x86_64-pc-linux-gnu-library/4.2/BH/include/boost/filesystem/directory.hpp:417:49: note: declared private here
417 | boost::intrusive_ptr< detail::dir_itr_imp > m_imp;
| ^~~~~
boost/libs/filesystem/src/directory.cpp:498:12: error: ‘boost::intrusive_ptr<boost::filesystem::detail::dir_itr_imp> boost::filesystem::directory_iterator::m_imp’ is private within this context
498 | it.m_imp.reset();
| ^~~~~
In file included from boost/libs/filesystem/src/directory.cpp:17:
/home/luisa/R/x86_64-pc-linux-gnu-library/4.2/BH/include/boost/filesystem/directory.hpp:417:49: note: declared private here
417 | boost::intrusive_ptr< detail::dir_itr_imp > m_imp;
| ^~~~~
boost/libs/filesystem/src/directory.cpp: In function ‘void boost::filesystem::detail::directory_iterator_increment(boost::filesystem::directory_iterator&, boost::system::error_code*)’:
boost/libs/filesystem/src/directory.cpp:520:56: error: ‘struct boost::filesystem::detail::dir_itr_imp’ has no member named ‘buffer’
520 | it.m_imp->buffer,
| ^~~~~~
make: *** [/usr/lib/R/etc/Makeconf:178: boost/libs/filesystem/src/directory.o] Error 1
ERROR: compilation failed for package ‘cytolib’
* removing ‘/home/luisa/R/x86_64-pc-linux-gnu-library/4.2/cytolib’
The downloaded source packages are in
‘/tmp/RtmpEUeMrr/downloaded_packages’
Installation paths not writeable, unable to update packages
path: /usr/lib/R/library
packages:
boot, foreign, Matrix, spatial
Warning message:
In install.packages(...) :
installation of package ‘cytolib’ had non-zero exit status
We really need to get it up and running soon. I do not want to buy the flowjo 😢
Thanks for any help!
Luisa
from cytolib.
LuisaFJimenez
commented on July 25, 2024
More details in case they are needed:
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Linux Mint 20.1
Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.9.0
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.9.0
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=de_DE.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=de_DE.UTF-8 LC_NAME=C LC_ADDRESS=C
[10] LC_TELEPHONE=C LC_MEASUREMENT=de_DE.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] lubridate_1.9.2 forcats_1.0.0 stringr_1.5.0 dplyr_1.1.0
[5] purrr_1.0.1 readr_2.1.4 tidyr_1.3.0 tibble_3.1.8
[9] ggplot2_3.4.1 tidyverse_2.0.0 BH_1.81.0-1 BiocManager_1.30.20
loaded via a namespace (and not attached):
[1] compiler_4.2.2 pillar_1.8.1 tools_4.2.2 digest_0.6.31 timechange_0.2.0
[6] evaluate_0.20 lifecycle_1.0.3 gtable_0.3.1 pkgconfig_2.0.3 rlang_1.0.6
[11] cli_3.6.0 rstudioapi_0.14 yaml_2.3.7 xfun_0.37 fastmap_1.1.1
[16] withr_2.5.0 knitr_1.42 generics_0.1.3 vctrs_0.5.2 hms_1.1.2
[21] grid_4.2.2 tidyselect_1.2.0 glue_1.6.2 R6_2.5.1 fansi_1.0.4
[26] rmarkdown_2.20 tzdb_0.3.0 magrittr_2.0.3 scales_1.2.1 htmltools_0.5.4
[31] ellipsis_0.3.2 colorspace_2.1-0 utf8_1.2.3 stringi_1.7.12 munsell_0.5.0 ```from cytolib.
LuisaFJimenez
commented on July 25, 2024
Hi @FMKerckhof ... I checked again... that was the trick. For some reason I had in my mind that if I had the latest BiocManager updated, that was equivalent to having the latest Bioconductor... it was not. As soon as I added the command you wrote, it installed 40 new updates/packages. The flowCore and the cytolib are running smoothly. Thanks a lot!
from cytolib.
jamesboot
commented on July 25, 2024
Hello, I'm also having issues installing, I'm running latest version of R (4.2.3) and Bioconductor (3.16). My session info is below. Any suggestions would be much appreciated.
R version 4.2.3 (2023-03-15)
Platform: aarch64-apple-darwin20 (64-bit)
Running under: macOS Monterey 12.6
Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.2-arm64/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
other attached packages:
[1] flowCore_2.10.0 pROC_1.18.0 caret_6.0-94 lattice_0.21-8 RColorBrewer_1.1-3
[6] data.table_1.14.8 factoextra_1.0.7 cluster_2.1.4 corrplot_0.92 lubridate_1.9.2
[11] forcats_1.0.0 purrr_1.0.1 readr_2.1.4 tidyr_1.3.0 tibble_3.2.1
[16] tidyverse_2.0.0 reshape2_1.4.4 limma_3.54.2 dplyr_1.1.1 ggplot2_3.4.2
[21] stringr_1.5.0
loaded via a namespace (and not attached):
[1] nlme_3.1-162 matrixStats_0.63.0 fs_1.6.1 usethis_2.1.6 devtools_2.4.5
[6] rprojroot_2.0.3 profvis_0.3.7 tools_4.2.3 utf8_1.2.3 R6_2.5.1
[11] rpart_4.1.19 BiocGenerics_0.44.0 colorspace_2.1-0 nnet_7.3-18 urlchecker_1.0.1
[16] withr_2.5.0 prettyunits_1.1.1 processx_3.8.0 tidyselect_1.2.0 curl_5.0.0
[21] compiler_4.2.3 cli_3.6.1 Biobase_2.58.0 desc_1.4.2 scales_1.2.1
[26] callr_3.7.3 digest_0.6.31 pkgconfig_2.0.3 htmltools_0.5.5 sessioninfo_1.2.2
[31] parallelly_1.35.0 fastmap_1.1.1 htmlwidgets_1.6.2 rlang_1.1.0 rstudioapi_0.14
[36] shiny_1.7.4 generics_0.1.3 ModelMetrics_1.2.2.2 magrittr_2.0.3 RProtoBufLib_2.10.0
[41] Matrix_1.5-4 Rcpp_1.0.10 munsell_0.5.0 S4Vectors_0.36.2 fansi_1.0.4
[46] lifecycle_1.0.3 stringi_1.7.12 MASS_7.3-58.3 pkgbuild_1.4.0 plyr_1.8.8
[51] recipes_1.0.5 grid_4.2.3 parallel_4.2.3 listenv_0.9.0 promises_1.2.0.1
[56] ggrepel_0.9.3 crayon_1.5.2 miniUI_0.1.1.1 splines_4.2.3 hms_1.1.3
[61] ps_1.7.4 pillar_1.9.0 pkgload_1.3.2 future.apply_1.10.0 codetools_0.2-19
[66] stats4_4.2.3 glue_1.6.2 remotes_2.4.2 BiocManager_1.30.20 vctrs_0.6.1
[71] tzdb_0.3.0 httpuv_1.6.9 foreach_1.5.2 gtable_0.3.3 future_1.32.0
[76] cachem_1.0.7 gower_1.0.1 mime_0.12 prodlim_2023.03.31 xtable_1.8-4
[81] later_1.3.0 class_7.3-21 survival_3.5-5 timeDate_4022.108 iterators_1.0.14
[86] cytolib_2.10.0 memoise_2.0.1 hardhat_1.3.0 lava_1.7.2.1 timechange_0.2.0
[91] globals_0.16.2 ellipsis_0.3.2 ipred_0.9-14
from cytolib.
Related Issues (20)
- Complete documentation and build doc website
- move readonly lock from cytoframe to h5cytoframe
- cytolib installation error with Rtools 4.0 + R-testing HOT 2
- fail to save big gs HOT 5
- Rework time channel scaling HOT 1
- deal with redundant channels from some individual samples HOT 4
- Revert to Artistic lisence - The Fred Hutchinson software license makes CRAN packages impossible HOT 1
- load_gs requires write permissions, even with h5_readonly = TRUE HOT 2
- library(cytolib); library(mzR) crashes R 4.0.0 alpha on Linux HOT 6
- library(cytolib) crashes Rfast::rowMaxs() HOT 4
- Installation error in macOS HOT 16
- cytolib.dylib vs .so extension on macOS with R 4 HOT 7
- Loading cytolib crashes mbkmeans HOT 6
- Installation error on Ubuntu 16.04 HOT 15
- Installation failed HOT 2
- cytolib install R4.1.2 on ubuntu18 failed HOT 1
- failed cytolib installation with 'no matching function for call to 'weakly_canonical'' HOT 11
- General question about H5 backed gating HOT 4
- Cytolib install fails on github actions CI/CD for Ubuntu 22.04 (C++11?) HOT 1
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from cytolib.