RStudio libraries msm and mvtnorm are not installing on Linux RH RStudio Server 2023.06.0 Build 4.2.1

mo_marikar · June 13, 2023, 8:06pm

Error Information:

installing source package ‘mvtnorm’ ...
** package ‘mvtnorm’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c C_FORTRAN_interface.c -o C_FORTRAN_interface.o
gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c lpmvnorm.c -o lpmvnorm.o
gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -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: *** [ltMatrices.o] Error 1
ERROR: compilation failed for package ‘mvtnorm’
removing ‘/home/mmarikar/R/x86_64-redhat-linux-gnu-library/3.6/mvtnorm’
Warning in install.packages :
installation of package ‘mvtnorm’ had non-zero exit status
ERROR: dependency ‘mvtnorm’ is not available for package ‘msm’
removing ‘/home/mmarikar/R/x86_64-redhat-linux-gnu-library/3.6/msm’
Warning in install.packages :
installation of package ‘msm’ had non-zero exit status

The downloaded source packages are in
‘/tmp/Rtmpr9qQp0/downloaded_packages’

install.packages("mvtnorm")
Installing package into ‘/home/mmarikar/R/x86_64-redhat-linux-gnu-library/3.6’
(as ‘lib’ is unspecified)
trying URL 'https://cran.rstudio.com/src/contrib/mvtnorm_1.2-2.tar.gz'
Content type 'application/x-gzip' length 662749 bytes (647 KB)
==================================================
downloaded 647 KB

installing source package ‘mvtnorm’ ...
** package ‘mvtnorm’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c C_FORTRAN_interface.c -o C_FORTRAN_interface.o
gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c lpmvnorm.c -o lpmvnorm.o
gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -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: *** [ltMatrices.o] Error 1
ERROR: compilation failed for package ‘mvtnorm’
removing ‘/home/mmarikar/R/x86_64-redhat-linux-gnu-library/3.6/mvtnorm’
Warning in install.packages :
installation of package ‘mvtnorm’ had non-zero exit status

Description of issue -

Steps taken so far -

System Information:

RStudio Edition: (Desktop or Server)
RStudio Version:
OS Version:
R Version:

Also:

RStudio diagnostics report:
Your sessionInfo():
RStudio crash report:
RStudio application log files:

From Troubleshooting Guide: Using RStudio

technocrat · June 13, 2023, 8:42pm

Precompiled binaries might be available as described here.

mo_marikar · June 13, 2023, 9:59pm

Precompiled version of mvtnorm mvtnorm_1.2-2.tar.gzfrom CRAN produced similar error messages.

install.packages("~/R/httk_caco2_June13_2023/mvtnorm_1.2-2.tar.gz", repos = NULL, type = "source")
Installing package into ‘/home/mmarikar/R/x86_64-redhat-linux-gnu-library/3.6’
(as ‘lib’ is unspecified)

installing source package ‘mvtnorm’ ...
** package ‘mvtnorm’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c C_FORTRAN_interface.c -o C_FORTRAN_interface.o
gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c lpmvnorm.c -o lpmvnorm.o
gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG -I/usr/local/include -fvisibility=hidden -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -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: *** [ltMatrices.o] Error 1
ERROR: compilation failed for package ‘mvtnorm’
removing ‘/home/mmarikar/R/x86_64-redhat-linux-gnu-library/3.6/mvtnorm’

technocrat · June 13, 2023, 11:14pm

Those were not binaries. Fedora Packages of R Software see the ref to cran2copr. It might be that by using the EPEL rpm repo access there will be source code versions tweaked for the Fedora platforms.

Gabor · June 14, 2023, 6:48am

I would be surprised if you could "just" use Fedora binaries on RedHat Linux, especially for R 3.6. (But maybe you can, I don't know anything about cran2copr.)

FWIW, Posit Package Manager supports R 3.6.x and also RedHat Linux, so if you can install R as documented at GitHub - rstudio/r-builds: an opinionated environment for compiling R and then set up RStudio PPM, then you would get binary R packages for most CRAN and Bioconductor packages.

Nevertheless, even if you don't use the RStudio R builds, that README has some tips to enable the EPEL and the CRB repos to get a newer C compiler, that will be able to compile mvtnorm.

system · July 5, 2023, 6:49am

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