Closed HenrikBengtsson closed 2 years ago
Confirmed it fails also with R_LIBS_USER=~/tmp R
.
Works with R built with gcc 8.3.1;
[henrik@c4-dev3 ~]$ which R
/software/c4/cbi/software/R-4.1.0-gcc8/bin/R
[henrik@c4-dev3 ~]$ gcc --version
gcc (GCC) 8.3.1 20190311 (Red Hat 8.3.1-3)
Copyright (C) 2018 Free Software Foundation, Inc.
This is free software; see the source for copying conditions. There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
> install.packages("regsem", repos="https://cloud.r-project.org")
Installing package into ‘/c4/home/henrik/R/x86_64-pc-linux-gnu-library/4.1-CBI’
(as ‘lib’ is unspecified)
trying URL 'https://cloud.r-project.org/src/contrib/regsem_1.6.2.tar.gz'
Content type 'application/x-gzip' length 79501 bytes (77 KB)
==================================================
downloaded 77 KB
* installing *source* package ‘regsem’ ...
** package ‘regsem’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
g++ -std=gnu++14 -I"/software/c4/cbi/software/R-4.1.0-gcc8/lib64/R/include" -DNDEBUG -I'/c4/home/henrik/R/x86_64-pc-linux-gnu-library/4.1-CBI/Rcpp/include' -I'/c4/home/henrik/R/x86_64-pc-linux-gnu-library/4.1-CBI/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o
gcc -I"/software/c4/cbi/software/R-4.1.0-gcc8/lib64/R/include" -DNDEBUG -I'/c4/home/henrik/R/x86_64-pc-linux-gnu-library/4.1-CBI/Rcpp/include' -I'/c4/home/henrik/R/x86_64-pc-linux-gnu-library/4.1-CBI/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c regsem_init.c -o regsem_init.o
g++ -std=gnu++14 -I"/software/c4/cbi/software/R-4.1.0-gcc8/lib64/R/include" -DNDEBUG -I'/c4/home/henrik/R/x86_64-pc-linux-gnu-library/4.1-CBI/Rcpp/include' -I'/c4/home/henrik/R/x86_64-pc-linux-gnu-library/4.1-CBI/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c regsem_rcpp_RAMmult.cpp -o regsem_rcpp_RAMmult.o
g++ -std=gnu++14 -I"/software/c4/cbi/software/R-4.1.0-gcc8/lib64/R/include" -DNDEBUG -I'/c4/home/henrik/R/x86_64-pc-linux-gnu-library/4.1-CBI/Rcpp/include' -I'/c4/home/henrik/R/x86_64-pc-linux-gnu-library/4.1-CBI/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c regsem_rcpp_fit_fun.cpp -o regsem_rcpp_fit_fun.o
g++ -std=gnu++14 -I"/software/c4/cbi/software/R-4.1.0-gcc8/lib64/R/include" -DNDEBUG -I'/c4/home/henrik/R/x86_64-pc-linux-gnu-library/4.1-CBI/Rcpp/include' -I'/c4/home/henrik/R/x86_64-pc-linux-gnu-library/4.1-CBI/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c regsem_rcpp_grad_ram.cpp -o regsem_rcpp_grad_ram.o
g++ -std=gnu++14 -I"/software/c4/cbi/software/R-4.1.0-gcc8/lib64/R/include" -DNDEBUG -I'/c4/home/henrik/R/x86_64-pc-linux-gnu-library/4.1-CBI/Rcpp/include' -I'/c4/home/henrik/R/x86_64-pc-linux-gnu-library/4.1-CBI/RcppArmadillo/include' -I/usr/local/include -fpic -g -O2 -c regsem_rcpp_quasi_calc.cpp -o regsem_rcpp_quasi_calc.o
g++ -std=gnu++14 -shared -L/software/c4/cbi/software/R-4.1.0-gcc8/lib64/R/lib -L/usr/local/lib64 -o regsem.so RcppExports.o regsem_init.o regsem_rcpp_RAMmult.o regsem_rcpp_fit_fun.o regsem_rcpp_grad_ram.o regsem_rcpp_quasi_calc.o -L/software/c4/cbi/software/R-4.1.0-gcc8/lib64/R/lib -lRlapack -L/software/c4/cbi/software/R-4.1.0-gcc8/lib64/R/lib -lRblas -lgfortran -lm -lquadmath -L/software/c4/cbi/software/R-4.1.0-gcc8/lib64/R/lib -lR
installing to /c4/home/henrik/R/x86_64-pc-linux-gnu-library/4.1-CBI/00LOCK-regsem/00new/regsem/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
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (regsem)
The downloaded source packages are in
‘/scratch/henrik/RtmpTZ5snp/downloaded_packages’
>
Reported upstream to https://github.com/Rjacobucci/regsem/issues/15.
From this, it looks like it may be better if we use scl-devtoolset/8
for building/using R 4.1.0, cf. #16.
Possibly related to #16:
Action
R_LIBS_USER