I've been trying to install a R package, glmnet and having a installation issue. Here is an error output after I fired install.packages("glmnet") ;
/usr/bin/clang++ -std=gnu++14 -shared -L/usr/lib/R/lib -L/usr/lib/llvm-13/lib -Wl,-rpath,/usr/lib/llvm-13/lib -o glmnet.so RcppExports.o elnet_exp.o glmnet5dpclean.o glmnet_init.o pb.o pb_exp.o wls.o wls_exp.o -L/usr/lib/gcc/x86_64-linux-gnu/9 -lm -L/usr/lib/R/lib -lR
installing to /home/rstudio/R/x86_64-pc-linux-gnu-library/4.1/00LOCK-glmnet/00new/glmnet/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Error: package or namespace load failed for âglmnetâ in dyn.load(file, DLLpath = DLLpath, ...):
unable to load shared object '/home/rstudio/R/x86_64-pc-linux-gnu-library/4.1/00LOCK-glmnet/00new/glmnet/libs/glmnet.so':
/home/rstudio/R/x86_64-pc-linux-gnu-library/4.1/00LOCK-glmnet/00new/glmnet/libs/glmnet.so: undefined symbol: _gfortran_runtime_error_at
Error: loading failed
Execution halted
I noticed two things; undefined symbol: _gfortran_runtime_error_at, which indicates the complier can't find libgfortan and clang++. I thought glmnet specifically requests gfortran as a compiler but for some reasons, clang is kicked in.
I have a Makevars setup in my ~/.R as follows;
more .R/Makevars
C=/usr/bin/clang
#C89=/usr/bin/clang
#C99=/usr/bin/clang
CPP=/usr/bin/clang-cpp
CXX=/usr/bin/clang++
CXX11=/usr/bin/clang++
CXX14=/usr/bin/clang++
CXX17=/usr/bin/clang++
CXX1X=/usr/bin/clang++
SHLIB_OPENMP_CFLAGS = -fopenmp
CFLAGS=-g -O3 -Wall -pedantic -mtune=native -pipe
CXXFLAGS=-g -O3 -Wall -pedantic -mtune=native -pipe
LDFLAGS=-L"/usr/lib/llvm-13/lib/clang/13.0.1/lib/linux" -Wl,-rpath,/usr/lib/llvm-13/lib/clang/13.0.1/lib/linux
CPPFLAGS= -I"/usr/lib/llvm-13/lib/clang/13.0.1/include"
FC=/usr/bin/gfortran
F77=/usr/bin/gfortran
FLIBS=-L/usr/lib/gcc/x86_64-linux-gnu/9 -lm
MAKEFLAGS = -j12
Paths to gfortran and its libraries are defined, and gfortran and libgfrotran are installed;
gfortran --version
GNU Fortran (Ubuntu 9.3.0-17ubuntu1~20.04) 9.3.0
locate libgfortran
/usr/lib/gcc/x86_64-linux-gnu/9/libgfortran.a
/usr/lib/gcc/x86_64-linux-gnu/9/libgfortran.so
/usr/lib/gcc/x86_64-linux-gnu/9/libgfortran.spec
/usr/lib/x86_64-linux-gnu/libgfortran.so.5
/usr/lib/x86_64-linux-gnu/libgfortran.so.5.0.0
/usr/local/lib/python3.8/dist-packages/numpy.libs/libgfortran-2e0d59d6.so.5.0.0
/usr/local/lib/python3.8/dist-packages/scipy.libs/libgfortran-040039e1.so.5.0.0
/usr/local/lib/python3.9/dist-packages/numpy.libs/libgfortran-2e0d59d6.so.5.0.0
/usr/local/lib/python3.9/dist-packages/scipy.libs/libgfortran-040039e1.so.5.0.0
/usr/share/doc/libgfortran-9-dev
/usr/share/doc/libgfortran5
There is no alternative setup for gfortran;
sudo update-alternatives --config gfortran
update-alternatives: error: no alternatives for gfortran
I even added gfortran paths to a Makevars in the src directory of glmnet, and used R CMD INSTALL but got the same error.
I really appreciate any pointers to solve this issue.
sessionInfo()
R version 4.1.2 (2021-11-01)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.04.4 LTS
Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.9.0
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.9.0
locale:
[1] LC_CTYPE=C.UTF-8 LC_NUMERIC=C LC_TIME=C.UTF-8 LC_COLLATE=C.UTF-8
[5] LC_MONETARY=C.UTF-8 LC_MESSAGES=C.UTF-8 LC_PAPER=C.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=C.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] ggplot2_3.3.5 phyloseq_1.39.1
loaded via a namespace (and not attached):
[1] Rcpp_1.0.8 ape_5.6-2 lattice_0.20-45 prettyunits_1.1.1
[5] ps_1.6.0 Biostrings_2.62.0 rprojroot_2.0.2 assertthat_0.2.1
[9] foreach_1.5.2 utf8_1.2.2 R6_2.5.1 GenomeInfoDb_1.30.1
[13] plyr_1.8.6 stats4_4.1.2 pillar_1.7.0 zlibbioc_1.40.0
[17] rlang_1.0.1 curl_4.3.2 rstudioapi_0.13 data.table_1.14.3
[21] callr_3.7.0 vegan_2.5-7 S4Vectors_0.32.3 Matrix_1.4-0
[25] splines_4.1.2 stringr_1.4.0 igraph_1.2.11 RCurl_1.98-1.6
[29] munsell_0.5.0 compiler_4.1.2 pkgconfig_2.0.3 BiocGenerics_0.40.0
[33] pkgbuild_1.3.1 multtest_2.50.0 mgcv_1.8-39 biomformat_1.22.0
[37] tidyselect_1.1.2 tibble_3.1.6 GenomeInfoDbData_1.2.7 IRanges_2.28.0
[41] codetools_0.2-18 fansi_1.0.2 permute_0.9-7 crayon_1.5.0
[45] dplyr_1.0.8 withr_2.4.3 MASS_7.3-55 bitops_1.0-7
[49] rhdf5filters_1.6.0 grid_4.1.2 nlme_3.1-155 jsonlite_1.8.0
[53] gtable_0.3.0 lifecycle_1.0.1 DBI_1.1.2 magrittr_2.0.2
[57] scales_1.1.1 cli_3.2.0 stringi_1.7.6 XVector_0.34.0
[61] reshape2_1.4.4 remotes_2.4.2 ellipsis_0.3.2 generics_0.1.2
[65] vctrs_0.3.8 Rhdf5lib_1.16.0 iterators_1.0.14 tools_4.1.2
[69] ade4_1.7-18 Biobase_2.54.0 glue_1.6.2 purrr_0.3.4
[73] processx_3.5.2 parallel_4.1.2 survival_3.2-13 colorspace_2.0-3
[77] rhdf5_2.38.0 BiocManager_1.30.16 cluster_2.1.2
neofetch
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