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Question

Can anyone tell me why I am having the following error when I am trying to install the mvtnorm package in R from my HPC terminal that is Linux (CentOS) based?

ERROR: compilation failed for package 'mvtnorm'
* removing '/mnt/beegfs/home/apiya2021/.conda/envs/test_env/lib/R/library/mvtnorm

I have pasted the full error below in case anyone wants to have a look.

> install.packages("mvtnorm")
trying URL 'https://mirrors.nics.utk.edu/cran/src/contrib/mvtnorm_1.2-4.tar.gz'
Content type 'application/x-gzip' length 663517 bytes (647 KB)
==================================================
downloaded 647 KB

* installing *source* package 'mvtnorm' ...
** package 'mvtnorm' successfully unpacked and MD5 sums checked
** using staged installation
** libs
x86_64-conda_cos6-linux-gnu-cc -I"/mnt/beegfs/home/apiya2021/.conda/envs/test_env/lib/R/include" -DNDEBUG   -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /mnt/beegfs/home/apiya2021/.conda/envs/test_env/include -I/mnt/beegfs/home/apiya2021/.conda/envs/test_env/include -Wl,-rpath-link,/mnt/beegfs/home/apiya2021/.conda/envs/test_env/lib -fvisibility=hidden -fpic  -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /mnt/beegfs/home/apiya2021/.conda/envs/test_env/include -fdebug-prefix-map=/tmp/build/80754af9/r-base_1589917437985/work=/usr/local/src/conda/r-base-3.6.1 -fdebug-prefix-map=/mnt/beegfs/home/apiya2021/.conda/envs/test_env=/usr/local/src/conda-prefix  -c C_FORTRAN_interface.c -o C_FORTRAN_interface.o
x86_64-conda_cos6-linux-gnu-cc -I"/mnt/beegfs/home/apiya2021/.conda/envs/test_env/lib/R/include" -DNDEBUG   -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /mnt/beegfs/home/apiya2021/.conda/envs/test_env/include -I/mnt/beegfs/home/apiya2021/.conda/envs/test_env/include -Wl,-rpath-link,/mnt/beegfs/home/apiya2021/.conda/envs/test_env/lib -fvisibility=hidden -fpic  -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /mnt/beegfs/home/apiya2021/.conda/envs/test_env/include -fdebug-prefix-map=/tmp/build/80754af9/r-base_1589917437985/work=/usr/local/src/conda/r-base-3.6.1 -fdebug-prefix-map=/mnt/beegfs/home/apiya2021/.conda/envs/test_env=/usr/local/src/conda-prefix  -c lpmvnorm.c -o lpmvnorm.o
x86_64-conda_cos6-linux-gnu-cc -I"/mnt/beegfs/home/apiya2021/.conda/envs/test_env/lib/R/include" -DNDEBUG   -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /mnt/beegfs/home/apiya2021/.conda/envs/test_env/include -I/mnt/beegfs/home/apiya2021/.conda/envs/test_env/include -Wl,-rpath-link,/mnt/beegfs/home/apiya2021/.conda/envs/test_env/lib -fvisibility=hidden -fpic  -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /mnt/beegfs/home/apiya2021/.conda/envs/test_env/include -fdebug-prefix-map=/tmp/build/80754af9/r-base_1589917437985/work=/usr/local/src/conda/r-base-3.6.1 -fdebug-prefix-map=/mnt/beegfs/home/apiya2021/.conda/envs/test_env=/usr/local/src/conda-prefix  -c ltMatrices.c -o ltMatrices.o
ltMatrices.c: In function 'R_ltMatrices_solve':
ltMatrices.c:139:57: error: expected ')' before 'FCONE'
             F77_CALL(dtptri)(&lo, &di, &iJ, dans, &info FCONE FCONE);
                                                         ^~~~~
ltMatrices.c:144:67: error: expected ')' before 'FCONE'
             F77_CALL(dtpsv)(&lo, &tr, &di, &iJ, dans, dansx, &ONE FCONE FCONE FCONE);
                                                                   ^~~~~
ltMatrices.c: In function 'R_syMatrices_chol':
ltMatrices.c:375:48: error: expected ')' before 'FCONE'
         F77_CALL(dpptrf)(&lo, &iJ, dans, &info FCONE);
                                                ^~~~~
ltMatrices.c: In function 'R_vectrick':
ltMatrices.c:464:35: error: expected ')' before 'FCONE'
                         dans, &iJ FCONE FCONE FCONE FCONE);
                                   ^~~~~
ltMatrices.c:475:35: error: expected ')' before 'FCONE'
                         dans, &iJ FCONE FCONE FCONE FCONE);
                                   ^~~~~
make: *** [/mnt/beegfs/home/apiya2021/.conda/envs/test_env/lib/R/etc/Makeconf:168: ltMatrices.o] Error 1
ERROR: compilation failed for package 'mvtnorm'
* removing '/mnt/beegfs/home/apiya2021/.conda/envs/test_env/lib/R/library/mvtnorm'

The downloaded source packages are in
    '/tmp/RtmpcxjtcG/downloaded_packages'
Updating HTML index of packages in '.Library'
Making 'packages.html' ... done
Warning message:
In install.packages("mvtnorm") :
  installation of package 'mvtnorm' had non-zero exit status

I am running the command in the R session in a miniconda environment on hpc cause I will need to run some python libraries as well later. Can anyone tell me how to solve this issue with mvtnorm here?

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Danh mục

Error in mvtnorm package installation in R on Linux (CentOS)