Describe the bug Installation from GitHub failed. <div class=

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Hello, I'm here to report that I had a similar error from <a class="

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Installation error in macOS,about rglab/cytolib

Comments (16)

Rhodnius commented on July 25, 2024 1

Hi @jacobpwagner,

Thanks for your help. It worked!!!

Have a nice day :)

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mikejiang commented on July 25, 2024 1

@danxfreeman , your issue is addressed in #46

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jacobpwagner commented on July 25, 2024

Can you give me the output of packageVersion("RProtoBufLib")? Also, for long terminal output, would you please put three backticks before and after the pasted output so it doesn't apply formatting. Like this:

Some stuff from the terminal
* Now this won't start a markdown list for example

For further reference: https://docs.github.com/en/github/writing-on-github/basic-writing-and-formatting-syntax#quoting-code

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masato-ogishi commented on July 25, 2024

Thanks for your guidance!
Here's the thing.
packageVersion("RProtoBufLib")
[1] ‘2.1.0’

By the way when I tried to update packages in RStudio, there were only two packages to be updated from CRAN, indicating that most packages are up-to-date.

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jacobpwagner commented on July 25, 2024

So it looks like the issue is that the compilation is not linking appropriately to the protobuf library. I think this could be due to the intervention of homebrew based on the relevant linking flags in the compilation line:

-L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/Cellar/gcc@8/8.4.0_1/lib -o cytolib.so

Can you give me the output of whereis libprotobuf?

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masato-ogishi commented on July 25, 2024

There's no output by this command. So the lack of this library is perhaps the reason. Could you tell me how to install them?? I googled and I found a script like this but I'm not so familiar with the grammar.

$wget https://github.com/google/protobuf/releases/download/v2.5.0/protobuf-2.5.0.tar.bz2
$tar xvf protobuf-2.5.0.tar.bz2
$cd protobuf-2.5.0
$./configure CC=clang CXX=clang++ CXXFLAGS='-std=c++11 -stdlib=libc++ -O3 -g' LDFLAGS='-stdlib=libc++' LIBS="-lc++ -lc++abi"
$make -j 4
$sudo make install
$protoc --version

Thanks a lot!

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Rhodnius commented on July 25, 2024

Hello,

I'm here to report that I had a similar error from @masato-ogishi.

The only difference is that I probably don't have problems with RProtoBufLib, when I type > packageVersion("RProtoBufLib") I got [1] ‘2.1.0’

>install_github("RGLab/cytolib")
Using github PAT from envvar GITHUB_PAT
Downloading GitHub repo RGLab/cytolib@HEAD
✓  checking for file ‘/private/var/folders/2w/156qfrbn4tg52hxt7pmq38qr0000gn/T/Rtmp2DbJPZ/remotes414a767703ae/RGLab-cytolib-5afbec8/DESCRIPTION’ (376ms)
─  preparing ‘cytolib’: (462ms)
✓  checking DESCRIPTION meta-information ...
─  cleaning src
─  running ‘cleanup’
─  checking for LF line-endings in source and make files and shell scripts (627ms)
─  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... 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
clang++ -mmacosx-version-min=10.13 -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
clang++ -mmacosx-version-min=10.13 -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
clang++ -mmacosx-version-min=10.13 -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 CytoVFS.cpp:8:
../inst/include/cytolib/CytoVFS.hpp:31:7: warning: private field 'num_threads_' is not used [-Wunused-private-field]
                int num_threads_;
                    ^
1 warning generated.
clang++ -mmacosx-version-min=10.13 -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
clang++ -mmacosx-version-min=10.13 -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
clang++ -mmacosx-version-min=10.13 -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
clang++ -mmacosx-version-min=10.13 -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
clang++ -mmacosx-version-min=10.13 -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
clang++ -mmacosx-version-min=10.13 -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
clang++ -mmacosx-version-min=10.13 -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
clang++ -mmacosx-version-min=10.13 -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
clang++ -mmacosx-version-min=10.13 -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
clang++ -mmacosx-version-min=10.13 -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
clang++ -mmacosx-version-min=10.13 -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
clang++ -mmacosx-version-min=10.13 -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
clang++ -mmacosx-version-min=10.13 -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
clang++ -mmacosx-version-min=10.13 -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
clang++ -mmacosx-version-min=10.13 -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
clang++ -mmacosx-version-min=10.13 -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
clang++ -mmacosx-version-min=10.13 -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
clang++ -mmacosx-version-min=10.13 -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
clang++ -mmacosx-version-min=10.13 -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
clang++ -mmacosx-version-min=10.13 -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
clang++ -mmacosx-version-min=10.13 -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
clang++ -mmacosx-version-min=10.13 -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
clang++ -mmacosx-version-min=10.13 -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
clang++ -mmacosx-version-min=10.13 -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
clang++ -mmacosx-version-min=10.13 -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
clang++ -mmacosx-version-min=10.13 -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
clang++ -mmacosx-version-min=10.13 -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
clang++ -mmacosx-version-min=10.13 -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
clang++ -mmacosx-version-min=10.13 -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/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 /Users/juancamilosanchezarcila/gfortran/usr/local/lib /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
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: __ZN6google8protobuf16RepeatedPtrFieldINSt3__112basic_stringIcNS2_11char_traitsIcEENS2_9allocatorIcEEEEE3AddEv
  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/2w/156qfrbn4tg52hxt7pmq38qr0000gn/T//Rtmp2DbJPZ/file414a7f92d144/cytolib_2.1.18.tar.gz’ had non-zero exit status

##### The sessionInfo ###
─ Session info ──────────────────────────────────────────────────────────────────
 setting  value                       
 version  R version 4.0.2 (2020-06-22)
 os       macOS High Sierra 10.13.6   
 system   x86_64, darwin17.0          
 ui       RStudio                     
 language (EN)                        
 collate  en_US.UTF-8                 
 ctype    en_US.UTF-8                 
 tz       America/Los_Angeles         
 date     2020-09-09                  

─ Packages ──────────────────────────────────────────────────────────────────────
 package     * version date       lib source        
 assertthat    0.2.1   2019-03-21 [1] CRAN (R 4.0.2)
 backports     1.1.9   2020-08-24 [1] CRAN (R 4.0.2)
 bit           4.0.4   2020-08-04 [1] CRAN (R 4.0.2)
 bit64         4.0.5   2020-08-30 [1] CRAN (R 4.0.2)
 callr         3.4.4   2020-09-07 [1] CRAN (R 4.0.2)
 cli           2.0.2   2020-02-28 [1] CRAN (R 4.0.2)
 crayon        1.3.4   2017-09-16 [1] CRAN (R 4.0.2)
 curl          4.3     2019-12-02 [1] CRAN (R 4.0.1)
 desc          1.2.0   2018-05-01 [1] CRAN (R 4.0.2)
 devtools    * 2.3.1   2020-07-21 [1] CRAN (R 4.0.2)
 digest        0.6.25  2020-02-23 [1] CRAN (R 4.0.2)
 ellipsis      0.3.1   2020-05-15 [1] CRAN (R 4.0.2)
 fansi         0.4.1   2020-01-08 [1] CRAN (R 4.0.2)
 fs            1.5.0   2020-07-31 [1] CRAN (R 4.0.2)
 glue          1.4.2   2020-08-27 [1] CRAN (R 4.0.2)
 lattice       0.20-41 2020-04-02 [1] CRAN (R 4.0.2)
 magrittr      1.5     2014-11-22 [1] CRAN (R 4.0.2)
 memoise       1.1.0   2017-04-21 [1] CRAN (R 4.0.2)
 nanotime      0.3.2   2020-09-04 [1] CRAN (R 4.0.2)
 pkgbuild      1.1.0   2020-07-13 [1] CRAN (R 4.0.2)
 pkgload       1.1.0   2020-05-29 [1] CRAN (R 4.0.2)
 prettyunits   1.1.1   2020-01-24 [1] CRAN (R 4.0.2)
 processx      3.4.4   2020-09-03 [1] CRAN (R 4.0.2)
 ps            1.3.4   2020-08-11 [1] CRAN (R 4.0.2)
 R6            2.4.1   2019-11-12 [1] CRAN (R 4.0.2)
 Rcpp          1.0.5   2020-07-06 [1] CRAN (R 4.0.2)
 RcppCCTZ      0.2.9   2020-08-30 [1] CRAN (R 4.0.2)
 remotes       2.2.0   2020-07-21 [1] CRAN (R 4.0.2)
 rlang         0.4.7   2020-07-09 [1] CRAN (R 4.0.2)
 rprojroot     1.3-2   2018-01-03 [1] CRAN (R 4.0.2)
 rstudioapi    0.11    2020-02-07 [1] CRAN (R 4.0.2)
 sessioninfo   1.1.1   2018-11-05 [1] CRAN (R 4.0.2)
 testthat      2.3.2   2020-03-02 [1] CRAN (R 4.0.2)
 tiledb      * 0.8.0   2020-09-03 [1] CRAN (R 4.0.2)
 usethis     * 1.6.1   2020-04-29 [1] CRAN (R 4.0.2)
 withr         2.2.0   2020-04-20 [1] CRAN (R 4.0.2)
 zoo           1.8-8   2020-05-02 [1] CRAN (R 4.0.2)

[1] /Library/Frameworks/R.framework/Versions/4.0/Resources/library

I appreciate any suggestions to solve this issue.

Thanks a lot and have a nice day.

Juan C.

from cytolib.

jacobpwagner commented on July 25, 2024

@masato-ogishi , sorry, ignore my whereis libprotobuf comment before. RProtoBufLib removes the need for a system installation of libprotobuf. I'm still looking in to this linking failure and trying to reproduce it, however.

from cytolib.

jacobpwagner commented on July 25, 2024

@Rhodnius , @masato-ogishi , can you try a fresh installation of RProtoBufLib from GitHub followed by re-attempting installing cytolib.

edit: To be sure you are getting a completely clean installation, could you also remove the existing package directories entirely before re-installing. That is, delete the two directories pointed to by the output of these:

find.package("RProtoBufLib")
find.package("cytolib")

Then re-install

devtools::install_github("RGLab/RProtoBufLib", force = TRUE)
devtools::install_github("RGLab/cytolib", force = TRUE)

Particularly if either of you have recently moved from R 3.6.3 -> R 4.0.2 and not re-installed RProtoBufLib after the upgrade, this could be the case after compiler updates in Rtools.

from cytolib.

masato-ogishi commented on July 25, 2024

I was able to install the RProtoBufLib, but I still didn't have the luck for the cytolib.
Here's my output. Hope you can resolve this mystery. Or, for the time being, could you consider compiling the package and push it to the bioconductor dev branch? (same for the flowWorkspace)? Thank you for your help!


R version 4.0.2 (2020-06-22) -- "Taking Off Again"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

  Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> devtools::install_github("RGLab/cytolib", force = TRUE)
Downloading GitHub repo RGLab/cytolib@HEAD
These packages have more recent versions available.
It is recommended to update all of them.
Which would you like to update?

1: All                                             
2: CRAN packages only                              
3: None                                            
4: RcppArmad... (0.9.900.2.0 -> 0.9.900.3.0) [CRAN]

Enter one or more numbers, or an empty line to skip updates:3
✓  checking for file ‘/private/var/folders/0l/27166dcs57z48cjmt6y57r540000gp/T/RtmpmgcZaY/remotes14c7749f64993/RGLab-cytolib-94f2683/DESCRIPTION’ ...
─  preparing ‘cytolib’:
✓  checking DESCRIPTION meta-information ...
─  cleaning src
─  running ‘cleanup’
─  checking for LF line-endings in source and make files and shell scripts (455ms)
─  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/Cellar/gcc@8/8.4.0_1/lib/gcc/8 /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: 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: __ZN2H56H5FileC1ERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEjRKNS_17FileCreatPropListERKNS_15FileAccPropListE
  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//RtmpmgcZaY/file14c771b2afac7/cytolib_2.1.18.tar.gz’ had non-zero exit status

from cytolib.

mikejiang commented on July 25, 2024

Looks like the binary of your Rhdf5lib also mismatches on your system, try to recompile that as well

from cytolib.

mikejiang commented on July 25, 2024

Bioc devel should have the latest binaries of these packages. (the latest push was Sept 1st)

from cytolib.

masato-ogishi commented on July 25, 2024

Hmm... I installed the cytolib package from the bioc devel and it was installed without error. However, when I tried to install flowWorkspace (v.4.1.9) from bioc devel (this is my original purpose), it still caused a compilation error. So the problem is not likely due to the outdated version of cytolib.

from cytolib.

gfinak commented on July 25, 2024

For what it's worth, your error is here:
dlopen(/Library/Frameworks/R.framework/Versions/4.0/Resources/library/00LOCK-cytolib/00new/cytolib/libs/cytolib.so, 10): Symbol not found: __ZN2H56H5FileC1ERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEjRKNS_17FileCreatPropListERKNS_15FileAccPropListE
It's a dynamic linking error. Looks like it's related to Rhdf5lib. Please updated that package.
In general, you should pick: either the release branch of Bioc 3.11, or the devel branch of Bioc, or if you really know what you're doing, pull from our github sources.
But, don't mix and match packages from these sources.
The errors above indicate that the versions of different package dependencies are out of sync.
To deal with this, pick a source, download all flow packages and dependencies and install them. Either use binaries, or if you use the source, install with --preclean.

Finally one other point:
I noticed you're using R 4 on a mac with the gcc compiler installed via brew.
I don't know if you built R from source, but either way, starting with R 4, my understanding that on mac os the native tool chain (therefore clang) should be used (https://cran.r-project.org/bin/macosx/)

From that page:

Important: this release uses Xcode 10.1 and GNU Fortran 8.2. If you wish to compile R packages from sources, you will need to download and GNU Fortran 8.2 - see the tools directory.

Using mixed tool chains can lead to odd behavior and sometimes the types of errors you are seeing depending on what compiler was used to build the different libraries being linked.

If you're really unable to make headway,
my suggestion is: install R from the binaries and use the standard clang toolchain to build these packages on the Mac.

I'm afraid we won't be able to support your issue otherwise. We don't have the resources to debug non-standard toolchains.

from cytolib.

mikejiang commented on July 25, 2024

@gfinak is right. BioC binaries are built with clang++ -mmacosx-version-min=10.13 and yet you are using g++8, you should switch to the same compiler in order to keep the binaries ABI compatible. (if you do need to build the packages from source sometime)

from cytolib.

danxfreeman commented on July 25, 2024

I think I'm having the same issue installing flowCore onto an Amazon Linux 2 AMI for AWS Elastic Cloud (EC2). I've tried reinstalling Rhdf5lib and RProtoBufLib with remotes::install_github():

[root@ip-172-31-79-152 library]# R

R version 4.0.2 (2020-06-22) -- "Taking Off Again"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-koji-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

  Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> remotes::install_github("RGLab/cytolib", force = TRUE)
Downloading GitHub repo RGLab/cytolib@HEAD
   checking for file ‘/tmp/Rtmpzj3ruz/remotes49485fd3080c/RGLab-cytolib-b884a31/✔  checking for file ‘/tmp/Rtmpzj3ruz/remotes49485fd3080c/RGLab-cytolib-b884a31/DESCRIPTION’
─  preparing ‘cytolib’:
✔  checking DESCRIPTION meta-information ...
─  cleaning src
─  running ‘cleanup’
─  checking for LF line-endings in source and make files and shell scripts
─  checking for empty or unneeded directories
─  building ‘cytolib_2.3.2.tar.gz’
   
Installing package into ‘/usr/lib64/R/library’
(as ‘lib’ is unspecified)
* 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=2.3.2
configure: creating ./config.status
config.status: creating inst/include/cytolib/cytolibConfig.h
config.status: creating src/Makevars
** libs
g++ -m64 -std=gnu++11 -I"/usr/include/R" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/usr/lib64/R/library/Rcpp/include' -I'/usr/lib64/R/library/BH/include' -I'/usr/lib64/R/library/RProtoBufLib/include' -I'/usr/lib64/R/library/Rhdf5lib/include' -I'/usr/lib64/R/library/RcppArmadillo/include' -I'/usr/lib64/R/library/RcppParallel/include' -I/usr/local/include   -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches    -m64 -mtune=generic  -c CytoFrame.cpp -o CytoFrame.o
In file included from ../inst/include/cytolib/CytoFrame.hpp:16:0,
                 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 between signed and unsigned integer expressions [-Wsign-compare]
   if(valVec.size() != 1+n+n*n){
      ~~~~~~~~~~~~~~^~~~~~~~~~
../inst/include/cytolib/compensation.hpp:54:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    if(valVec.size() == 1+n+2*n*n){
       ~~~~~~~~~~~~~~^~~~~~~~~~~~
../inst/include/cytolib/compensation.hpp:60:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(int i = 1+n, j = 1+n; i < valVec_fixed.size(); i++, j+=2)
                               ~~^~~~~~~~~~~~~~~~~~~~~
g++ -m64 -std=gnu++11 -I"/usr/include/R" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/usr/lib64/R/library/Rcpp/include' -I'/usr/lib64/R/library/BH/include' -I'/usr/lib64/R/library/RProtoBufLib/include' -I'/usr/lib64/R/library/Rhdf5lib/include' -I'/usr/lib64/R/library/RcppArmadillo/include' -I'/usr/lib64/R/library/RcppParallel/include' -I/usr/local/include   -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches    -m64 -mtune=generic  -c CytoFrameView.cpp -o CytoFrameView.o
In file included from ../inst/include/cytolib/CytoFrame.hpp:16:0,
                 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 between signed and unsigned integer expressions [-Wsign-compare]
   if(valVec.size() != 1+n+n*n){
      ~~~~~~~~~~~~~~^~~~~~~~~~
../inst/include/cytolib/compensation.hpp:54:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    if(valVec.size() == 1+n+2*n*n){
       ~~~~~~~~~~~~~~^~~~~~~~~~~~
../inst/include/cytolib/compensation.hpp:60:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(int i = 1+n, j = 1+n; i < valVec_fixed.size(); i++, j+=2)
                               ~~^~~~~~~~~~~~~~~~~~~~~
g++ -m64 -std=gnu++11 -I"/usr/include/R" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/usr/lib64/R/library/Rcpp/include' -I'/usr/lib64/R/library/BH/include' -I'/usr/lib64/R/library/RProtoBufLib/include' -I'/usr/lib64/R/library/Rhdf5lib/include' -I'/usr/lib64/R/library/RcppArmadillo/include' -I'/usr/lib64/R/library/RcppParallel/include' -I/usr/local/include   -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches    -m64 -mtune=generic  -c CytoVFS.cpp -o CytoVFS.o
g++ -m64 -std=gnu++11 -I"/usr/include/R" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/usr/lib64/R/library/Rcpp/include' -I'/usr/lib64/R/library/BH/include' -I'/usr/lib64/R/library/RProtoBufLib/include' -I'/usr/lib64/R/library/Rhdf5lib/include' -I'/usr/lib64/R/library/RcppArmadillo/include' -I'/usr/lib64/R/library/RcppParallel/include' -I/usr/local/include   -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches    -m64 -mtune=generic  -c GatingHierarchy.cpp -o GatingHierarchy.o
In file included from ../inst/include/cytolib/CytoFrame.hpp:16:0,
                 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 between signed and unsigned integer expressions [-Wsign-compare]
   if(valVec.size() != 1+n+n*n){
      ~~~~~~~~~~~~~~^~~~~~~~~~
../inst/include/cytolib/compensation.hpp:54:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    if(valVec.size() == 1+n+2*n*n){
       ~~~~~~~~~~~~~~^~~~~~~~~~~~
../inst/include/cytolib/compensation.hpp:60:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(int i = 1+n, j = 1+n; i < valVec_fixed.size(); i++, j+=2)
                               ~~^~~~~~~~~~~~~~~~~~~~~
In file included from /usr/lib64/R/library/BH/include/boost/graph/adjacency_iterator.hpp:13:0,
                 from /usr/lib64/R/library/BH/include/boost/graph/detail/adjacency_list.hpp:37,
                 from /usr/lib64/R/library/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:
/usr/lib64/R/library/BH/include/boost/detail/iterator.hpp: At global scope:
/usr/lib64/R/library/BH/include/boost/detail/iterator.hpp:13:37: note: #pragma message: This header is deprecated. Use <iterator> instead.
 BOOST_HEADER_DEPRECATED("<iterator>")
                                     ^
g++ -m64 -std=gnu++11 -I"/usr/include/R" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/usr/lib64/R/library/Rcpp/include' -I'/usr/lib64/R/library/BH/include' -I'/usr/lib64/R/library/RProtoBufLib/include' -I'/usr/lib64/R/library/Rhdf5lib/include' -I'/usr/lib64/R/library/RcppArmadillo/include' -I'/usr/lib64/R/library/RcppParallel/include' -I/usr/local/include   -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches    -m64 -mtune=generic  -c GatingSet.cpp -o GatingSet.o
In file included from ../inst/include/cytolib/CytoFrame.hpp:16:0,
                 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 between signed and unsigned integer expressions [-Wsign-compare]
   if(valVec.size() != 1+n+n*n){
      ~~~~~~~~~~~~~~^~~~~~~~~~
../inst/include/cytolib/compensation.hpp:54:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    if(valVec.size() == 1+n+2*n*n){
       ~~~~~~~~~~~~~~^~~~~~~~~~~~
../inst/include/cytolib/compensation.hpp:60:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(int i = 1+n, j = 1+n; i < valVec_fixed.size(); i++, j+=2)
                               ~~^~~~~~~~~~~~~~~~~~~~~
In file included from /usr/lib64/R/library/BH/include/boost/graph/adjacency_iterator.hpp:13:0,
                 from /usr/lib64/R/library/BH/include/boost/graph/detail/adjacency_list.hpp:37,
                 from /usr/lib64/R/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 GatingSet.cpp:3:
/usr/lib64/R/library/BH/include/boost/detail/iterator.hpp: At global scope:
/usr/lib64/R/library/BH/include/boost/detail/iterator.hpp:13:37: note: #pragma message: This header is deprecated. Use <iterator> instead.
 BOOST_HEADER_DEPRECATED("<iterator>")
                                     ^
In file included from ../inst/include/cytolib/compensation.hpp:19:0,
                 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>, std::allocator<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;
              ^~~
g++ -m64 -std=gnu++11 -I"/usr/include/R" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/usr/lib64/R/library/Rcpp/include' -I'/usr/lib64/R/library/BH/include' -I'/usr/lib64/R/library/RProtoBufLib/include' -I'/usr/lib64/R/library/Rhdf5lib/include' -I'/usr/lib64/R/library/RcppArmadillo/include' -I'/usr/lib64/R/library/RcppParallel/include' -I/usr/local/include   -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches    -m64 -mtune=generic  -c GatingSet.pb.cc -o GatingSet.pb.o
g++ -m64 -std=gnu++11 -I"/usr/include/R" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/usr/lib64/R/library/Rcpp/include' -I'/usr/lib64/R/library/BH/include' -I'/usr/lib64/R/library/RProtoBufLib/include' -I'/usr/lib64/R/library/Rhdf5lib/include' -I'/usr/lib64/R/library/RcppArmadillo/include' -I'/usr/lib64/R/library/RcppParallel/include' -I/usr/local/include   -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches    -m64 -mtune=generic  -c H5CytoFrame.cpp -o H5CytoFrame.o
In file included from ../inst/include/cytolib/CytoFrame.hpp:16:0,
                 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 between signed and unsigned integer expressions [-Wsign-compare]
   if(valVec.size() != 1+n+n*n){
      ~~~~~~~~~~~~~~^~~~~~~~~~
../inst/include/cytolib/compensation.hpp:54:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    if(valVec.size() == 1+n+2*n*n){
       ~~~~~~~~~~~~~~^~~~~~~~~~~~
../inst/include/cytolib/compensation.hpp:60:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(int i = 1+n, j = 1+n; i < valVec_fixed.size(); i++, j+=2)
                               ~~^~~~~~~~~~~~~~~~~~~~~
g++ -m64 -std=gnu++11 -I"/usr/include/R" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/usr/lib64/R/library/Rcpp/include' -I'/usr/lib64/R/library/BH/include' -I'/usr/lib64/R/library/RProtoBufLib/include' -I'/usr/lib64/R/library/Rhdf5lib/include' -I'/usr/lib64/R/library/RcppArmadillo/include' -I'/usr/lib64/R/library/RcppParallel/include' -I/usr/local/include   -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches    -m64 -mtune=generic  -c MemCytoFrame.cpp -o MemCytoFrame.o
MemCytoFrame.cpp:538:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
      #pragma omp parallel for
 
In file included from ../inst/include/cytolib/CytoFrame.hpp:16:0,
                 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 between signed and unsigned integer expressions [-Wsign-compare]
   if(valVec.size() != 1+n+n*n){
      ~~~~~~~~~~~~~~^~~~~~~~~~
../inst/include/cytolib/compensation.hpp:54:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    if(valVec.size() == 1+n+2*n*n){
       ~~~~~~~~~~~~~~^~~~~~~~~~~~
../inst/include/cytolib/compensation.hpp:60:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(int i = 1+n, j = 1+n; i < valVec_fixed.size(); i++, j+=2)
                               ~~^~~~~~~~~~~~~~~~~~~~~
g++ -m64 -std=gnu++11 -I"/usr/include/R" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/usr/lib64/R/library/Rcpp/include' -I'/usr/lib64/R/library/BH/include' -I'/usr/lib64/R/library/RProtoBufLib/include' -I'/usr/lib64/R/library/Rhdf5lib/include' -I'/usr/lib64/R/library/RcppArmadillo/include' -I'/usr/lib64/R/library/RcppParallel/include' -I/usr/local/include   -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches    -m64 -mtune=generic  -c POPINDICES.cpp -o POPINDICES.o
In file included from ../inst/include/cytolib/CytoFrame.hpp:16:0,
                 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 between signed and unsigned integer expressions [-Wsign-compare]
   if(valVec.size() != 1+n+n*n){
      ~~~~~~~~~~~~~~^~~~~~~~~~
../inst/include/cytolib/compensation.hpp:54:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    if(valVec.size() == 1+n+2*n*n){
       ~~~~~~~~~~~~~~^~~~~~~~~~~~
../inst/include/cytolib/compensation.hpp:60:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(int i = 1+n, j = 1+n; i < valVec_fixed.size(); i++, j+=2)
                               ~~^~~~~~~~~~~~~~~~~~~~~
g++ -m64 -std=gnu++11 -I"/usr/include/R" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/usr/lib64/R/library/Rcpp/include' -I'/usr/lib64/R/library/BH/include' -I'/usr/lib64/R/library/RProtoBufLib/include' -I'/usr/lib64/R/library/Rhdf5lib/include' -I'/usr/lib64/R/library/RcppArmadillo/include' -I'/usr/lib64/R/library/RcppParallel/include' -I/usr/local/include   -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches    -m64 -mtune=generic  -c calibrationTable.cpp -o calibrationTable.o
g++ -m64 -std=gnu++11 -I"/usr/include/R" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/usr/lib64/R/library/Rcpp/include' -I'/usr/lib64/R/library/BH/include' -I'/usr/lib64/R/library/RProtoBufLib/include' -I'/usr/lib64/R/library/Rhdf5lib/include' -I'/usr/lib64/R/library/RcppArmadillo/include' -I'/usr/lib64/R/library/RcppParallel/include' -I/usr/local/include   -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches    -m64 -mtune=generic  -c compensation.cpp -o compensation.o
In file included from compensation.cpp:3:0:
../inst/include/cytolib/compensation.hpp: In constructor ‘cytolib::compensation::compensation(const string&)’:
../inst/include/cytolib/compensation.hpp:50:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   if(valVec.size() != 1+n+n*n){
      ~~~~~~~~~~~~~~^~~~~~~~~~
../inst/include/cytolib/compensation.hpp:54:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    if(valVec.size() == 1+n+2*n*n){
       ~~~~~~~~~~~~~~^~~~~~~~~~~~
../inst/include/cytolib/compensation.hpp:60:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(int i = 1+n, j = 1+n; i < valVec_fixed.size(); i++, j+=2)
                               ~~^~~~~~~~~~~~~~~~~~~~~
g++ -m64 -std=gnu++11 -I"/usr/include/R" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/usr/lib64/R/library/Rcpp/include' -I'/usr/lib64/R/library/BH/include' -I'/usr/lib64/R/library/RProtoBufLib/include' -I'/usr/lib64/R/library/Rhdf5lib/include' -I'/usr/lib64/R/library/RcppArmadillo/include' -I'/usr/lib64/R/library/RcppParallel/include' -I/usr/local/include   -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches    -m64 -mtune=generic  -c dummy.cpp -o dummy.o
g++ -m64 -std=gnu++11 -I"/usr/include/R" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/usr/lib64/R/library/Rcpp/include' -I'/usr/lib64/R/library/BH/include' -I'/usr/lib64/R/library/RProtoBufLib/include' -I'/usr/lib64/R/library/Rhdf5lib/include' -I'/usr/lib64/R/library/RcppArmadillo/include' -I'/usr/lib64/R/library/RcppParallel/include' -I/usr/local/include   -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches    -m64 -mtune=generic  -c ellipse2points.cpp -o ellipse2points.o
g++ -m64 -std=gnu++11 -I"/usr/include/R" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/usr/lib64/R/library/Rcpp/include' -I'/usr/lib64/R/library/BH/include' -I'/usr/lib64/R/library/RProtoBufLib/include' -I'/usr/lib64/R/library/Rhdf5lib/include' -I'/usr/lib64/R/library/RcppArmadillo/include' -I'/usr/lib64/R/library/RcppParallel/include' -I/usr/local/include   -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches    -m64 -mtune=generic  -c gate.cpp -o gate.o
In file included from ../inst/include/cytolib/CytoFrame.hpp:16:0,
                 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 between signed and unsigned integer expressions [-Wsign-compare]
   if(valVec.size() != 1+n+n*n){
      ~~~~~~~~~~~~~~^~~~~~~~~~
../inst/include/cytolib/compensation.hpp:54:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    if(valVec.size() == 1+n+2*n*n){
       ~~~~~~~~~~~~~~^~~~~~~~~~~~
../inst/include/cytolib/compensation.hpp:60:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(int i = 1+n, j = 1+n; i < valVec_fixed.size(); i++, j+=2)
                               ~~^~~~~~~~~~~~~~~~~~~~~
g++ -m64 -std=gnu++11 -I"/usr/include/R" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/usr/lib64/R/library/Rcpp/include' -I'/usr/lib64/R/library/BH/include' -I'/usr/lib64/R/library/RProtoBufLib/include' -I'/usr/lib64/R/library/Rhdf5lib/include' -I'/usr/lib64/R/library/RcppArmadillo/include' -I'/usr/lib64/R/library/RcppParallel/include' -I/usr/local/include   -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches    -m64 -mtune=generic  -c global.cpp -o global.o
global.cpp: In function ‘std::__cxx11::string cytolib::s3_to_http(std::__cxx11::string)’:
global.cpp:46:20: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for(int i = 1; i < tokens.size(); i++)
                  ~~^~~~~~~~~~~~~~~
g++ -m64 -std=gnu++11 -I"/usr/include/R" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/usr/lib64/R/library/Rcpp/include' -I'/usr/lib64/R/library/BH/include' -I'/usr/lib64/R/library/RProtoBufLib/include' -I'/usr/lib64/R/library/Rhdf5lib/include' -I'/usr/lib64/R/library/RcppArmadillo/include' -I'/usr/lib64/R/library/RcppParallel/include' -I/usr/local/include   -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches    -m64 -mtune=generic  -c in_polygon.cpp -o in_polygon.o
g++ -m64 -std=gnu++11 -I"/usr/include/R" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/usr/lib64/R/library/Rcpp/include' -I'/usr/lib64/R/library/BH/include' -I'/usr/lib64/R/library/RProtoBufLib/include' -I'/usr/lib64/R/library/Rhdf5lib/include' -I'/usr/lib64/R/library/RcppArmadillo/include' -I'/usr/lib64/R/library/RcppParallel/include' -I/usr/local/include   -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches    -m64 -mtune=generic  -c nodeProperties.cpp -o nodeProperties.o
In file included from ../inst/include/cytolib/CytoFrame.hpp:16:0,
                 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 between signed and unsigned integer expressions [-Wsign-compare]
   if(valVec.size() != 1+n+n*n){
      ~~~~~~~~~~~~~~^~~~~~~~~~
../inst/include/cytolib/compensation.hpp:54:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    if(valVec.size() == 1+n+2*n*n){
       ~~~~~~~~~~~~~~^~~~~~~~~~~~
../inst/include/cytolib/compensation.hpp:60:33: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(int i = 1+n, j = 1+n; i < valVec_fixed.size(); i++, j+=2)
                               ~~^~~~~~~~~~~~~~~~~~~~~
g++ -m64 -std=gnu++11 -I"/usr/include/R" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/usr/lib64/R/library/Rcpp/include' -I'/usr/lib64/R/library/BH/include' -I'/usr/lib64/R/library/RProtoBufLib/include' -I'/usr/lib64/R/library/Rhdf5lib/include' -I'/usr/lib64/R/library/RcppArmadillo/include' -I'/usr/lib64/R/library/RcppParallel/include' -I/usr/local/include   -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches    -m64 -mtune=generic  -c spline.cpp -o spline.o
g++ -m64 -std=gnu++11 -I"/usr/include/R" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/usr/lib64/R/library/Rcpp/include' -I'/usr/lib64/R/library/BH/include' -I'/usr/lib64/R/library/RProtoBufLib/include' -I'/usr/lib64/R/library/Rhdf5lib/include' -I'/usr/lib64/R/library/RcppArmadillo/include' -I'/usr/lib64/R/library/RcppParallel/include' -I/usr/local/include   -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches    -m64 -mtune=generic  -c trans_group.cpp -o trans_group.o
g++ -m64 -std=gnu++11 -I"/usr/include/R" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/usr/lib64/R/library/Rcpp/include' -I'/usr/lib64/R/library/BH/include' -I'/usr/lib64/R/library/RProtoBufLib/include' -I'/usr/lib64/R/library/Rhdf5lib/include' -I'/usr/lib64/R/library/RcppArmadillo/include' -I'/usr/lib64/R/library/RcppParallel/include' -I/usr/local/include   -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches    -m64 -mtune=generic  -c transformation.cpp -o transformation.o
g++ -m64 -std=gnu++11 -I"/usr/include/R" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/usr/lib64/R/library/Rcpp/include' -I'/usr/lib64/R/library/BH/include' -I'/usr/lib64/R/library/RProtoBufLib/include' -I'/usr/lib64/R/library/Rhdf5lib/include' -I'/usr/lib64/R/library/RcppArmadillo/include' -I'/usr/lib64/R/library/RcppParallel/include' -I/usr/local/include   -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches    -m64 -mtune=generic  -c boost/libs/system/src/error_code.cpp -o boost/libs/system/src/error_code.o
g++ -m64 -std=gnu++11 -I"/usr/include/R" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/usr/lib64/R/library/Rcpp/include' -I'/usr/lib64/R/library/BH/include' -I'/usr/lib64/R/library/RProtoBufLib/include' -I'/usr/lib64/R/library/Rhdf5lib/include' -I'/usr/lib64/R/library/RcppArmadillo/include' -I'/usr/lib64/R/library/RcppParallel/include' -I/usr/local/include   -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches    -m64 -mtune=generic  -c boost/libs/filesystem/src/path_traits.cpp -o boost/libs/filesystem/src/path_traits.o
g++ -m64 -std=gnu++11 -I"/usr/include/R" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/usr/lib64/R/library/Rcpp/include' -I'/usr/lib64/R/library/BH/include' -I'/usr/lib64/R/library/RProtoBufLib/include' -I'/usr/lib64/R/library/Rhdf5lib/include' -I'/usr/lib64/R/library/RcppArmadillo/include' -I'/usr/lib64/R/library/RcppParallel/include' -I/usr/local/include   -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches    -m64 -mtune=generic  -c boost/libs/filesystem/src/codecvt_error_category.cpp -o boost/libs/filesystem/src/codecvt_error_category.o
g++ -m64 -std=gnu++11 -I"/usr/include/R" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/usr/lib64/R/library/Rcpp/include' -I'/usr/lib64/R/library/BH/include' -I'/usr/lib64/R/library/RProtoBufLib/include' -I'/usr/lib64/R/library/Rhdf5lib/include' -I'/usr/lib64/R/library/RcppArmadillo/include' -I'/usr/lib64/R/library/RcppParallel/include' -I/usr/local/include   -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches    -m64 -mtune=generic  -c boost/libs/filesystem/src/utf8_codecvt_facet.cpp -o boost/libs/filesystem/src/utf8_codecvt_facet.o
g++ -m64 -std=gnu++11 -I"/usr/include/R" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/usr/lib64/R/library/Rcpp/include' -I'/usr/lib64/R/library/BH/include' -I'/usr/lib64/R/library/RProtoBufLib/include' -I'/usr/lib64/R/library/Rhdf5lib/include' -I'/usr/lib64/R/library/RcppArmadillo/include' -I'/usr/lib64/R/library/RcppParallel/include' -I/usr/local/include   -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches    -m64 -mtune=generic  -c boost/libs/filesystem/src/windows_file_codecvt.cpp -o boost/libs/filesystem/src/windows_file_codecvt.o
g++ -m64 -std=gnu++11 -I"/usr/include/R" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/usr/lib64/R/library/Rcpp/include' -I'/usr/lib64/R/library/BH/include' -I'/usr/lib64/R/library/RProtoBufLib/include' -I'/usr/lib64/R/library/Rhdf5lib/include' -I'/usr/lib64/R/library/RcppArmadillo/include' -I'/usr/lib64/R/library/RcppParallel/include' -I/usr/local/include   -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches    -m64 -mtune=generic  -c boost/libs/filesystem/src/exception.cpp -o boost/libs/filesystem/src/exception.o
g++ -m64 -std=gnu++11 -I"/usr/include/R" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/usr/lib64/R/library/Rcpp/include' -I'/usr/lib64/R/library/BH/include' -I'/usr/lib64/R/library/RProtoBufLib/include' -I'/usr/lib64/R/library/Rhdf5lib/include' -I'/usr/lib64/R/library/RcppArmadillo/include' -I'/usr/lib64/R/library/RcppParallel/include' -I/usr/local/include   -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches    -m64 -mtune=generic  -c boost/libs/filesystem/src/directory.cpp -o boost/libs/filesystem/src/directory.o
g++ -m64 -std=gnu++11 -I"/usr/include/R" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/usr/lib64/R/library/Rcpp/include' -I'/usr/lib64/R/library/BH/include' -I'/usr/lib64/R/library/RProtoBufLib/include' -I'/usr/lib64/R/library/Rhdf5lib/include' -I'/usr/lib64/R/library/RcppArmadillo/include' -I'/usr/lib64/R/library/RcppParallel/include' -I/usr/local/include   -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches    -m64 -mtune=generic  -c boost/libs/filesystem/src/path.cpp -o boost/libs/filesystem/src/path.o
g++ -m64 -std=gnu++11 -I"/usr/include/R" -DNDEBUG -DROUT -I../inst/include -DBOOST_NO_AUTO_PTR -I'/usr/lib64/R/library/Rcpp/include' -I'/usr/lib64/R/library/BH/include' -I'/usr/lib64/R/library/RProtoBufLib/include' -I'/usr/lib64/R/library/Rhdf5lib/include' -I'/usr/lib64/R/library/RcppArmadillo/include' -I'/usr/lib64/R/library/RcppParallel/include' -I/usr/local/include   -fpic  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches    -m64 -mtune=generic  -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:
/usr/lib64/R/library/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:
/usr/lib64/R/library/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);
      ^~~~~~~~
/usr/lib64/R/library/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:842:41: 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:
/usr/lib64/R/library/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);
      ^~~~~~~~~~~~~~~~
/usr/lib64/R/library/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*’
/usr/lib64/R/library/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
      ^~~~~~~~~~~~~~~~
/usr/lib64/R/library/BH/include/boost/filesystem/operations.hpp:388:6: note:   candidate expects 3 arguments, 2 provided
/usr/lib64/R/library/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)
      ^~~~~~~~~~~~~~~~
/usr/lib64/R/library/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&’
/usr/lib64/R/library/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
      ^~~~~~~~~~~~~~~~
/usr/lib64/R/library/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&’
/usr/lib64/R/library/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);}
      ^~~~~~~~~~~~~~~~
/usr/lib64/R/library/BH/include/boost/filesystem/operations.hpp:379:6: note:   candidate expects 1 argument, 2 provided
boost/libs/filesystem/src/operations.cpp: At global scope:
boost/libs/filesystem/src/operations.cpp:381:1: warning: ‘bool boost::filesystem::detail::{anonymous}::copy_file_api(const string&, const string&, bool)’ defined but not used [-Wunused-function]
 copy_file_api(const std::string& from_p,
 ^~~~~~~~~~~~~
make: *** [boost/libs/filesystem/src/operations.o] Error 1
ERROR: compilation failed for package ‘cytolib’
* removing ‘/usr/lib64/R/library/cytolib’
Error: Failed to install 'cytolib' from GitHub:
  (converted from warning) installation of package ‘/tmp/Rtmpzj3ruz/file4948561f90b7/cytolib_2.3.2.tar.gz’ had non-zero exit status

from cytolib.

Installation error in macOS about cytolib HOT 16 CLOSED

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