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error when install flowCore through Rstudio on MAC #248

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klutzzzOOyyyq opened this issue Mar 2, 2023 · 0 comments
Open

error when install flowCore through Rstudio on MAC #248

klutzzzOOyyyq opened this issue Mar 2, 2023 · 0 comments

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@klutzzzOOyyyq
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sorry, when I run"devtools::install_github("RGLab/cytolib")",there is still an error:

devtools::install_github("RGLab/cytolib")
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: Rhdf5lib (1.18.2 -> 1.20.0 ) [CRAN]
5: BH (1.78.0-0 -> 1.81.0-1) [CRAN]

Enter one or more numbers, or an empty line to skip updates: 3
✔ checking for file ‘/private/var/folders/st/7qpxbzfj6gl6tpcp2739bwnr0000gn/T/RtmpFXGz0O/remotes7a4760258550/RGLab-cytolib-24e6c07/DESCRIPTION’ ...
─ preparing ‘cytolib’:
✔ checking DESCRIPTION meta-information
─ cleaning src
─ running ‘cleanup’
─ checking for LF line-endings in source and make files and shell scripts (1.5s)
─ checking for empty or unneeded directories
─ building ‘cytolib_2.11.1.tar.gz’

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=2.11.1
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 -DBOOST_FILESYSTEM_NO_CXX20_ATOMIC_REF -DBOOST_FILESYSTEM_SINGLE_THREADED -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RProtoBufLib/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhdf5lib/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 -DBOOST_FILESYSTEM_NO_CXX20_ATOMIC_REF -DBOOST_FILESYSTEM_SINGLE_THREADED -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RProtoBufLib/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhdf5lib/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 -DBOOST_FILESYSTEM_NO_CXX20_ATOMIC_REF -DBOOST_FILESYSTEM_SINGLE_THREADED -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/BH/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/RProtoBufLib/include' -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rhdf5lib/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
boost/libs/filesystem/src/codecvt_error_category.cpp:18:10: fatal error: 'boost/filesystem/detail/path_traits.hpp' file not found
#include <boost/filesystem/detail/path_traits.hpp>
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1 error generated.
make: *** [boost/libs/filesystem/src/codecvt_error_category.o] Error 1
ERROR: compilation failed for package ‘cytolib’
removing ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library/cytolib’
restoring previous ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library/cytolib’
Warning message:
In i.p(...) :
‘/var/folders/st/7qpxbzfj6gl6tpcp2739bwnr0000gn/T//RtmpFXGz0O/file7a473f537880/cytolib_2.11.1.tar.gz’ had non-zero exit status

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