Hi,
I used to work with rstan on rstudio and everything was working fine. However I was trying to install some basics R package and also some Stan related packages but I did not succeed.
So I tried to remove all Stan related packages, to install my classical R packages, but I still have the words “StanHeaders” or “rstan” in my error message even if I removed those packages.
Can you help me understand the error message I’m getting and how I can fix it? (see the error message below)
Thank you in advance,
Installing package into ‘/home/merlauda/R/x86_64-pc-linux-gnu-library/4.0.5-foss’
(as ‘lib’ is unspecified)
trying URL ‘https://cloud.r-project.org/src/contrib/rlang_1.1.1.tar.gz’
Content type ‘application/x-gzip’ length 762533 bytes (744 KB)
downloaded 744 KB
- installing source package ‘rlang’ …
** package ‘rlang’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
gcc -I"/apps/rocs/2020.08/cascadelake/software/R/4.0.5-foss-2020a/lib64/R/include" -DNDEBUG -I./rlang/ -I/apps/rocs/2020.08/cascadelake/software/nodejs/13.12.0-GCCcore-9.3.0/include -I/apps/rocs/2020.08/cascadelake/software/HDF5/1.10.6-gompi-2020a/include -I/apps/rocs/2020.08/cascadelake/software/PCRE2/10.34-GCCcore-9.3.0/include -I/apps/rocs/2020.08/cascadelake/software/XZ/5.2.5-GCCcore-9.3.0/include -I/apps/rocs/2020.08/cascadelake/software/NLopt/2.6.1-GCCcore-9.3.0/include -I/apps/rocs/2020.08/cascadelake/software/X11/20200222-GCCcore-9.3.0/include -I/apps/rocs/2020.08/cascadelake/software/Java/13.0.2/include -I/apps/rocs/2020.08/cascadelake/software/unixODBC/2.3.7-GCCcore-9.3.0/include -I/apps/rocs/2020.08/cascadelake/software/JAGS/4.3.0-foss-2020a/include -I/apps/rocs/2020.08/cascadelake/software/cairo/1.16.0-GCCcore-9.3.0/include -I/apps/rocs/2020.08/cascadelake/software/Pango/1.44.7-GCCcore-9.3.0/include -I/apps/rocs/2020.08/cascadelake/software/fontconfig/2.13.92-GCCcore-9.3.0/include -I/apps/rocs/2020.08/cascadelake/software/libxml2/2.9.10-GCCcore-9.3.0/include -I/apps/rocs/2020.08/cascadelake/software/cURL/7.69.1-GCCcore-9.3.0/include -I/apps/rocs/2020.08/cascadelake/software/Tk/8.6.10-GCCcore-9.3.0/include -I/apps/rocs/2020.08/cascadelake/software/Tcl/8.6.10-GCCcore-9.3.0/include -I/apps/rocs/2020.08/cascadelake/software/LibTIFF/4.1.0-GCCcore-9.3.0/include -I/apps/rocs/2020.08/cascadelake/software/libjpeg-turbo/2.0.4-GCCcore-9.3.0/include -I/apps/rocs/2020.08/cascadelake/software/libpng/1.6.37-GCCcore-9.3.0/include -I/apps/rocs/2020.08/cascadelake/software/zlib/1.2.11-GCCcore-9.3.0/include -I/apps/rocs/2020.08/cascadelake/software/libreadline/8.0-GCCcore-9.3.0/include -I/apps/rocs/2020.08/cascadelake/software/GSL/2.6-GCC-9.3.0/include -I/apps/rocs/2020.08/cascadelake/software/ICU/66.1-GCCcore-9.3.0/include -I/apps/rocs/2020.08/cascadelake/software/FFTW/3.3.8-gompi-2020a/include -I/apps/rocs/2020.08/cascadelake/software/ScaLAPACK/2.1.0-gompi-2020a/include -I/apps/rocs/2020.08/cascadelake/software/OpenBLAS/0.3.9-GCC-9.3.0/include -fvisibility=hidden -fpic -O2 -ftree-vectorize -march=cascadelake -fno-math-errno -c capture.c -o capture.o
gcc -I"/apps/rocs/2020.08/cascadelake/software/R/4.0.5-foss-2020a/lib64/R/include" -DNDEBUG -I./rlang/ -I/apps/rocs/2020.08/cascadelake/software/nodejs/13.12.0-GCCcore-9.3.0/include -I/apps/rocs/2020.08/cascadelake/software/HDF5/1.10.6-gompi-2020a/include -I/apps/rocs/2020.08/cascadelake/software/PCRE2/10.34-GCCcore-9.3.0/include -I/apps/rocs/2020.08/cascadelake/software/XZ/5.2.5-GCCcore-9.3.0/include -I/apps/rocs/2020.08/cascadelake/software/NLopt/2.6.1-GCCcore-9.3.0/include -I/apps/rocs/2020.08/cascadelake/software/X11/20200222-GCCcore-9.3.0/include -I/apps/rocs/2020.08/cascadelake/software/Java/13.0.2/include -I/apps/rocs/2020.08/cascadelake/software/unixODBC/2.3.7-GCCcore-9.3.0/include -I/apps/rocs/2020.08/cascadelake/software/JAGS/4.3.0-foss-2020a/include -I/apps/rocs/2020.08/cascadelake/software/cairo/1.16.0-GCCcore-9.3.0/include -I/apps/rocs/2020.08/cascadelake/software/Pango/1.44.7-GCCcore-9.3.0/include -I/apps/rocs/2020.08/cascadelake/software/fontconfig/2.13.92-GCCcore-9.3.0/include -I/apps/rocs/2020.08/cascadelake/software/libxml2/2.9.10-GCCcore-9.3.0/include -I/apps/rocs/2020.08/cascadelake/software/cURL/7.69.1-GCCcore-9.3.0/include -I/apps/rocs/2020.08/cascadelake/software/Tk/8.6.10-GCCcore-9.3.0/include -I/apps/rocs/2020.08/cascadelake/software/Tcl/8.6.10-GCCcore-9.3.0/include -I/apps/rocs/2020.08/cascadelake/software/LibTIFF/4.1.0-GCCcore-9.3.0/include -I/apps/rocs/2020.08/cascadelake/software/libjpeg-turbo/2.0.4-GCCcore-9.3.0/include -I/apps/rocs/2020.08/cascadelake/software/libpng/1.6.37-GCCcore-9.3.0/include -I/apps/rocs/2020.08/cascadelake/software/zlib/1.2.11-GCCcore-9.3.0/include -I/apps/rocs/2020.08/cascadelake/software/libreadline/8.0-GCCcore-9.3.0/include -I/apps/rocs/2020.08/cascadelake/software/GSL/2.6-GCC-9.3.0/include -I/apps/rocs/2020.08/cascadelake/software/ICU/66.1-GCCcore-9.3.0/include -I/apps/rocs/2020.08/cascadelake/software/FFTW/3.3.8-gompi-2020a/include -I/apps/rocs/2020.08/cascadelake/software/ScaLAPACK/2.1.0-gompi-2020a/include -I/apps/rocs/2020.08/cascadelake/software/OpenBLAS/0.3.9-GCC-9.3.0/include -fvisibility=hidden -fpic -O2 -ftree-vectorize -march=cascadelake -fno-math-errno -c internal.c -o internal.o
gcc -I"/apps/rocs/2020.08/cascadelake/software/R/4.0.5-foss-2020a/lib64/R/include" -DNDEBUG -I./rlang/ -I/apps/rocs/2020.08/cascadelake/software/nodejs/13.12.0-GCCcore-9.3.0/include -I/apps/rocs/2020.08/cascadelake/software/HDF5/1.10.6-gompi-2020a/include -I/apps/rocs/2020.08/cascadelake/software/PCRE2/10.34-GCCcore-9.3.0/include -I/apps/rocs/2020.08/cascadelake/software/XZ/5.2.5-GCCcore-9.3.0/include -I/apps/rocs/2020.08/cascadelake/software/NLopt/2.6.1-GCCcore-9.3.0/include -I/apps/rocs/2020.08/cascadelake/software/X11/20200222-GCCcore-9.3.0/include -I/apps/rocs/2020.08/cascadelake/software/Java/13.0.2/include -I/apps/rocs/2020.08/cascadelake/software/unixODBC/2.3.7-GCCcore-9.3.0/include -I/apps/rocs/2020.08/cascadelake/software/JAGS/4.3.0-foss-2020a/include -I/apps/rocs/2020.08/cascadelake/software/cairo/1.16.0-GCCcore-9.3.0/include -I/apps/rocs/2020.08/cascadelake/software/Pango/1.44.7-GCCcore-9.3.0/include -I/apps/rocs/2020.08/cascadelake/software/fontconfig/2.13.92-GCCcore-9.3.0/include -I/apps/rocs/2020.08/cascadelake/software/libxml2/2.9.10-GCCcore-9.3.0/include -I/apps/rocs/2020.08/cascadelake/software/cURL/7.69.1-GCCcore-9.3.0/include -I/apps/rocs/2020.08/cascadelake/software/Tk/8.6.10-GCCcore-9.3.0/include -I/apps/rocs/2020.08/cascadelake/software/Tcl/8.6.10-GCCcore-9.3.0/include -I/apps/rocs/2020.08/cascadelake/software/LibTIFF/4.1.0-GCCcore-9.3.0/include -I/apps/rocs/2020.08/cascadelake/software/libjpeg-turbo/2.0.4-GCCcore-9.3.0/include -I/apps/rocs/2020.08/cascadelake/software/libpng/1.6.37-GCCcore-9.3.0/include -I/apps/rocs/2020.08/cascadelake/software/zlib/1.2.11-GCCcore-9.3.0/include -I/apps/rocs/2020.08/cascadelake/software/libreadline/8.0-GCCcore-9.3.0/include -I/apps/rocs/2020.08/cascadelake/software/GSL/2.6-GCC-9.3.0/include -I/apps/rocs/2020.08/cascadelake/software/ICU/66.1-GCCcore-9.3.0/include -I/apps/rocs/2020.08/cascadelake/software/FFTW/3.3.8-gompi-2020a/include -I/apps/rocs/2020.08/cascadelake/software/ScaLAPACK/2.1.0-gompi-2020a/include -I/apps/rocs/2020.08/cascadelake/software/OpenBLAS/0.3.9-GCC-9.3.0/include -fvisibility=hidden -fpic -O2 -ftree-vectorize -march=cascadelake -fno-math-errno -c rlang.c -o rlang.o
gcc -I"/apps/rocs/2020.08/cascadelake/software/R/4.0.5-foss-2020a/lib64/R/include" -DNDEBUG -I./rlang/ -I/apps/rocs/2020.08/cascadelake/software/nodejs/13.12.0-GCCcore-9.3.0/include -I/apps/rocs/2020.08/cascadelake/software/HDF5/1.10.6-gompi-2020a/include -I/apps/rocs/2020.08/cascadelake/software/PCRE2/10.34-GCCcore-9.3.0/include -I/apps/rocs/2020.08/cascadelake/software/XZ/5.2.5-GCCcore-9.3.0/include -I/apps/rocs/2020.08/cascadelake/software/NLopt/2.6.1-GCCcore-9.3.0/include -I/apps/rocs/2020.08/cascadelake/software/X11/20200222-GCCcore-9.3.0/include -I/apps/rocs/2020.08/cascadelake/software/Java/13.0.2/include -I/apps/rocs/2020.08/cascadelake/software/unixODBC/2.3.7-GCCcore-9.3.0/include -I/apps/rocs/2020.08/cascadelake/software/JAGS/4.3.0-foss-2020a/include -I/apps/rocs/2020.08/cascadelake/software/cairo/1.16.0-GCCcore-9.3.0/include -I/apps/rocs/2020.08/cascadelake/software/Pango/1.44.7-GCCcore-9.3.0/include -I/apps/rocs/2020.08/cascadelake/software/fontconfig/2.13.92-GCCcore-9.3.0/include -I/apps/rocs/2020.08/cascadelake/software/libxml2/2.9.10-GCCcore-9.3.0/include -I/apps/rocs/2020.08/cascadelake/software/cURL/7.69.1-GCCcore-9.3.0/include -I/apps/rocs/2020.08/cascadelake/software/Tk/8.6.10-GCCcore-9.3.0/include -I/apps/rocs/2020.08/cascadelake/software/Tcl/8.6.10-GCCcore-9.3.0/include -I/apps/rocs/2020.08/cascadelake/software/LibTIFF/4.1.0-GCCcore-9.3.0/include -I/apps/rocs/2020.08/cascadelake/software/libjpeg-turbo/2.0.4-GCCcore-9.3.0/include -I/apps/rocs/2020.08/cascadelake/software/libpng/1.6.37-GCCcore-9.3.0/include -I/apps/rocs/2020.08/cascadelake/software/zlib/1.2.11-GCCcore-9.3.0/include -I/apps/rocs/2020.08/cascadelake/software/libreadline/8.0-GCCcore-9.3.0/include -I/apps/rocs/2020.08/cascadelake/software/GSL/2.6-GCC-9.3.0/include -I/apps/rocs/2020.08/cascadelake/software/ICU/66.1-GCCcore-9.3.0/include -I/apps/rocs/2020.08/cascadelake/software/FFTW/3.3.8-gompi-2020a/include -I/apps/rocs/2020.08/cascadelake/software/ScaLAPACK/2.1.0-gompi-2020a/include -I/apps/rocs/2020.08/cascadelake/software/OpenBLAS/0.3.9-GCC-9.3.0/include -fvisibility=hidden -fpic -O2 -ftree-vectorize -march=cascadelake -fno-math-errno -c version.c -o version.o
gcc -shared -L/apps/rocs/2020.08/cascadelake/software/R/4.0.5-foss-2020a/lib64/R/lib -L/apps/rocs/2020.08/cascadelake/software/nodejs/13.12.0-GCCcore-9.3.0/lib64 -L/apps/rocs/2020.08/cascadelake/software/nodejs/13.12.0-GCCcore-9.3.0/lib -L/apps/rocs/2020.08/cascadelake/software/HDF5/1.10.6-gompi-2020a/lib64 -L/apps/rocs/2020.08/cascadelake/software/HDF5/1.10.6-gompi-2020a/lib -L/apps/rocs/2020.08/cascadelake/software/Oracle_InstantClient/19.6.0.0.0/lib64 -L/apps/rocs/2020.08/cascadelake/software/Oracle_InstantClient/19.6.0.0.0/lib -L/apps/rocs/2020.08/cascadelake/software/PCRE2/10.34-GCCcore-9.3.0/lib64 -L/apps/rocs/2020.08/cascadelake/software/PCRE2/10.34-GCCcore-9.3.0/lib -L/apps/rocs/2020.08/cascadelake/software/XZ/5.2.5-GCCcore-9.3.0/lib64 -L/apps/rocs/2020.08/cascadelake/software/XZ/5.2.5-GCCcore-9.3.0/lib -L/apps/rocs/2020.08/cascadelake/software/NLopt/2.6.1-GCCcore-9.3.0/lib64 -L/apps/rocs/2020.08/cascadelake/software/NLopt/2.6.1-GCCcore-9.3.0/lib -L/apps/rocs/2020.08/cascadelake/software/X11/20200222-GCCcore-9.3.0/lib64 -L/apps/rocs/2020.08/cascadelake/software/X11/20200222-GCCcore-9.3.0/lib -L/apps/rocs/2020.08/cascadelake/software/Java/13.0.2/lib64 -L/apps/rocs/2020.08/cascadelake/software/Java/13.0.2/lib -L/apps/rocs/2020.08/cascadelake/software/texinfo/6.7-GCCcore-9.3.0/lib64 -L/apps/rocs/2020.08/cascadelake/software/texinfo/6.7-GCCcore-9.3.0/lib -L/apps/rocs/2020.08/cascadelake/software/unixODBC/2.3.7-GCCcore-9.3.0/lib64 -L/apps/rocs/2020.08/cascadelake/software/unixODBC/2.3.7-GCCcore-9.3.0/lib -L/apps/rocs/2020.08/cascadelake/software/JAGS/4.3.0-foss-2020a/lib64 -L/apps/rocs/2020.08/cascadelake/software/JAGS/4.3.0-foss-2020a/lib -L/apps/rocs/2020.08/cascadelake/software/cairo/1.16.0-GCCcore-9.3.0/lib64 -L/apps/rocs/2020.08/cascadelake/software/cairo/1.16.0-GCCcore-9.3.0/lib -L/apps/rocs/2020.08/cascadelake/software/Pango/1.44.7-GCCcore-9.3.0/lib64 -L/apps/rocs/2020.08/cascadelake/software/Pango/1.44.7-GCCcore-9.3.0/lib -L/apps/rocs/2020.08/cascadelake/software/fontconfig/2.13.92-GCCcore-9.3.0/lib64 -L/apps/rocs/2020.08/cascadelake/software/fontconfig/2.13.92-GCCcore-9.3.0/lib -L/apps/rocs/2020.08/cascadelake/software/libxml2/2.9.10-GCCcore-9.3.0/lib64 -L/apps/rocs/2020.08/cascadelake/software/libxml2/2.9.10-GCCcore-9.3.0/lib -L/apps/rocs/2020.08/cascadelake/software/cURL/7.69.1-GCCcore-9.3.0/lib64 -L/apps/rocs/2020.08/cascadelake/software/cURL/7.69.1-GCCcore-9.3.0/lib -L/apps/rocs/2020.08/cascadelake/software/Tk/8.6.10-GCCcore-9.3.0/lib64 -L/apps/rocs/2020.08/cascadelake/software/Tk/8.6.10-GCCcore-9.3.0/lib -L/apps/rocs/2020.08/cascadelake/software/Tcl/8.6.10-GCCcore-9.3.0/lib64 -L/apps/rocs/2020.08/cascadelake/software/Tcl/8.6.10-GCCcore-9.3.0/lib -L/apps/rocs/2020.08/cascadelake/software/LibTIFF/4.1.0-GCCcore-9.3.0/lib64 -L/apps/rocs/2020.08/cascadelake/software/LibTIFF/4.1.0-GCCcore-9.3.0/lib -L/apps/rocs/2020.08/cascadelake/software/libjpeg-turbo/2.0.4-GCCcore-9.3.0/lib64 -L/apps/rocs/2020.08/cascadelake/software/libpng/1.6.37-GCCcore-9.3.0/lib64 -L/apps/rocs/2020.08/cascadelake/software/libpng/1.6.37-GCCcore-9.3.0/lib -L/apps/rocs/2020.08/cascadelake/software/zlib/1.2.11-GCCcore-9.3.0/lib64 -L/apps/rocs/2020.08/cascadelake/software/zlib/1.2.11-GCCcore-9.3.0/lib -L/apps/rocs/2020.08/cascadelake/software/libreadline/8.0-GCCcore-9.3.0/lib64 -L/apps/rocs/2020.08/cascadelake/software/libreadline/8.0-GCCcore-9.3.0/lib -L/apps/rocs/2020.08/cascadelake/software/GSL/2.6-GCC-9.3.0/lib64 -L/apps/rocs/2020.08/cascadelake/software/GSL/2.6-GCC-9.3.0/lib -L/apps/rocs/2020.08/cascadelake/software/ICU/66.1-GCCcore-9.3.0/lib64 -L/apps/rocs/2020.08/cascadelake/software/ICU/66.1-GCCcore-9.3.0/lib -L/apps/rocs/2020.08/cascadelake/software/FFTW/3.3.8-gompi-2020a/lib64 -L/apps/rocs/2020.08/cascadelake/software/FFTW/3.3.8-gompi-2020a/lib -L/apps/rocs/2020.08/cascadelake/software/ScaLAPACK/2.1.0-gompi-2020a/lib64 -L/apps/rocs/2020.08/cascadelake/software/ScaLAPACK/2.1.0-gompi-2020a/lib -L/apps/rocs/2020.08/cascadelake/software/OpenBLAS/0.3.9-GCC-9.3.0/lib64 -L/apps/rocs/2020.08/cascadelake/software/OpenBLAS/0.3.9-GCC-9.3.0/lib -L/apps/rocs/2020.08/cascadelake/software/GCCcore/9.3.0/lib64 -L/apps/rocs/2020.08/cascadelake/software/GCCcore/9.3.0/lib -o rlang.so capture.o internal.o rlang.o version.o /home/merlauda/R/x86_64-pc-linux-gnu-library/4.0.5-foss/rstan/lib//libStanServices.a -L/home/merlauda/R/x86_64-pc-linux-gnu-library/4.0.5-foss/StanHeaders/lib/ -lStanHeaders -L/apps/rocs/2020.08/cascadelake/software/R/4.0.5-foss-2020a/lib64/R/library/RcppParallel/lib/ -ltbb -L/apps/rocs/2020.08/cascadelake/software/R/4.0.5-foss-2020a/lib64/R/lib -lR
gcc: error: /home/merlauda/R/x86_64-pc-linux-gnu-library/4.0.5-foss/rstan/lib//libStanServices.a: No such file or directory
make: *** [/apps/rocs/2020.08/cascadelake/software/R/4.0.5-foss-2020a/lib64/R/share/make/shlib.mk:10: rlang.so] Error 1
ERROR: compilation failed for package ‘rlang’ - removing ‘/home/merlauda/R/x86_64-pc-linux-gnu-library/4.0.5-foss/rlang’
Warning in install.packages :
installation of package ‘rlang’ had non-zero exit status
The downloaded source packages are in
‘/tmp/RtmpKKIkK4/downloaded_packages’
sessionInfo()
R version 4.0.5 (2021-03-31)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Red Hat Enterprise Linux 8.6 (Ootpa)
Matrix products: default
BLAS/LAPACK: /apps/rocs/2020.08/cascadelake/software/OpenBLAS/0.3.9-GCC-9.3.0/lib/libopenblas_skylakexp-r0.3.9.so
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] loo_2.6.0 outbreaks_1.9.0
loaded via a namespace (and not attached):
[1] compiler_4.0.5 backports_1.2.1 cli_3.6.1 parallel_4.0.5
[5] tools_4.0.5 grid_4.0.5 checkmate_2.0.0 matrixStats_0.58.0