Hello,
is Scientific linux or CentOS 7 supported for Bioconductor 3.8? When I run "BiocManager::install()
a lot of packages doesn't load with errors: "/lib64/libstdc++.so.6: version GLIBCXX_3.4.20 not found
or CXXABI_1.3.9 not found
. As I understand, there is no way to upgrade GLIBC in Centos.
Thanks
Best Regard
Michal
The problem is, that the latest GLIBC version that comes with Centos is GLIBCXX_3.4.19. It is not possible to install or upgrade GLIBC to newer version.
> BiocManager::install("EBImage")
Bioconductor version 3.7 (BiocManager 1.30.4), R 3.5.1 (2018-07-02)
Installing package(s) 'EBImage'
trying URL 'https://bioconductor.org/packages/3.7/bioc/src/contrib/EBImage_4.22.1.tar.gz'
Content type 'application/x-gzip' length 12560218 bytes (12.0 MB)
==================================================
downloaded 12.0 MB
* installing *source* package ‘EBImage’ ...
** libs
gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -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 EBImage.c -o EBImage.o
--- cut ---
** R
** inst
** byte-compile and prepare package for lazy loading
Creating a new generic function for ‘abind’ in package ‘EBImage’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Error: package or namespace load failed for ‘EBImage’ in dyn.load(file, DLLpath = DLLpath, ...):
unable to load shared object '/var/R/library/EBImage/libs/EBImage.so':
/lib64/libstdc++.so.6: version `CXXABI_1.3.8' not found (required by /var/R/library/EBImage/libs/EBImage.so)
Error: loading failed
Execution halted
ERROR: loading failed
* removing ‘/var/R/library/EBImage’
* restoring previous ‘/var/R/library/EBImage’
You cut out the most informative part of the installation (the c++ compilation step) but the problem is that your system (not R) has an incompatibility --- the libstdc++ library, installed on your system, cannot find the CXXABI version that your system advertised as available. Likely the solution is a variant of https://stackoverflow.com/a/20357035/547331 but maybe someone with direct centos experience will respond.
You were right ;-), there was another gcc installed in /usr/local/bin, which was causing the problems.
Thanks.
Best regrds