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igbucur / BFCS

Implementation of the approach described in "Large-Scale Local Causal Inference of Gene Regulatory Relationships" (https://doi.org/10.1016/j.ijar.2019.08.012)
GNU General Public License v3.0
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Compilation error on linux #1

Open jeales opened 4 years ago

jeales commented 4 years ago

Hello, I'm trying to test out BFCS on our HPC cluster. Currently I'm installing via devtools::install_github("https://github.com/igbucur/BFCS") Which generates the following error

* installing *source* package ‘bfcs’ ...
** using staged installation
** libs
/opt/gridware/depots/8e896c5a/el7/pkg/compilers/gcc/8.2.0/bin/g++ -std=gnu++11 -I"/opt/apps/apps/gcc/R/3.6.0/lib64/R/include" -DNDEBUG  -I"/opt/apps/apps/gcc/R/3.6.0/lib64/R/library/Rcpp/include" -I"/opt/apps/apps/gcc/R/3.6.0/lib64/R/library/RcppArmadillo/include" -I/opt/gridware/depots/8e896c5a/el7/pkg/compilers/gcc/8.2.0/include  -fpic  -g -O2  -c RcppExports.cpp -o RcppExports.o
/opt/gridware/depots/8e896c5a/el7/pkg/compilers/gcc/8.2.0/bin/g++ -std=gnu++11 -I"/opt/apps/apps/gcc/R/3.6.0/lib64/R/include" -DNDEBUG  -I"/opt/apps/apps/gcc/R/3.6.0/lib64/R/library/Rcpp/include" -I"/opt/apps/apps/gcc/R/3.6.0/lib64/R/library/RcppArmadillo/include" -I/opt/gridware/depots/8e896c5a/el7/pkg/compilers/gcc/8.2.0/include  -fpic  -g -O2  -c compute_BGe_score.cpp -o compute_BGe_score.o
/opt/gridware/depots/8e896c5a/el7/pkg/compilers/gcc/8.2.0/bin/g++ -std=gnu++11 -shared -L/opt/apps/apps/gcc/R/3.6.0/lib64/R/lib -L/opt/gridware/depots/8e896c5a/el7/pkg/compilers/gcc/8.2.0/lib -L/opt/gridware/depots/8e896c5a/el7/pkg/compilers/gcc/8.2.0/lib64 -o bfcs.so RcppExports.o compute_BGe_score.o -L/opt/apps/apps/gcc/R/3.6.0/lib64/R/lib -lR
/usr/bin/ld: skipping incompatible /opt/gridware/depots/8e896c5a/el7/pkg/compilers/gcc/8.2.0/lib/libstdc++.so when searching for -lstdc++
/usr/bin/ld: skipping incompatible /opt/gridware/depots/8e896c5a/el7/pkg/compilers/gcc/8.2.0/lib/libstdc++.a when searching for -lstdc++
/usr/bin/ld: skipping incompatible /opt/gridware/depots/8e896c5a/el7/pkg/compilers/gcc/8.2.0/lib/libgcc_s.so.1 when searching for libgcc_s.so.1
/usr/bin/ld: skipping incompatible /opt/gridware/depots/8e896c5a/el7/pkg/compilers/gcc/8.2.0/lib/libgcc_s.so.1 when searching for libgcc_s.so.1
installing to /mnt/iusers01/bk01-icvs/mobteje2/R/x86_64-pc-linux-gnu-library/3.6/00LOCK-bfcs/00new/bfcs/libs
** R
** exec
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
Error: package or namespace load failed for ‘bfcs’ in dyn.load(file, DLLpath = DLLpath, ...):
 unable to load shared object '/mnt/iusers01/bk01-icvs/mobteje2/R/x86_64-pc-linux-gnu-library/3.6/00LOCK-bfcs/00new/bfcs/libs/bfcs.so':
  /mnt/iusers01/bk01-icvs/mobteje2/R/x86_64-pc-linux-gnu-library/3.6/00LOCK-bfcs/00new/bfcs/libs/bfcs.so: undefined symbol: dgetrf_
Error: loading failed
Execution halted
ERROR: loading failed
* removing ‘/mnt/iusers01/bk01-icvs/mobteje2/R/x86_64-pc-linux-gnu-library/3.6/bfcs’
Error: Failed to install 'bfcs' from GitHub:
  (converted from warning) installation of package ‘/tmp/Rtmp9OZXTV/file3d73333529bd/bfcs_0.0.0.9000.tar.gz’ had non-zero exit status
igbucur commented 3 years ago

Hi jeales! Sorry it has taken me so long to answer your message, but I am not used to receiving issues on GitHub and I didn't really notice there was one until now. :)

Anyway, it looks like you are missing the LAPACK library on your system. Since March I have made significant changes to the package, so you might want to clone it again and have a look at the README for help.

Please let me know if you managed to fix the issue.