Unable to install arm and lme4 packages from OpenSUSE Leap 15.2

Question

I'm using OpenSUSE Leap 15.2 operating system together with pre-installed R v3.5.0. I did not have to install any package except rstudio.

Here are installation details:

> sessionInfo()

R version 3.5.0 (2018-04-23)
Platform: x86_64-suse-linux-gnu (64-bit)
Running under: openSUSE Leap 15.2

Matrix products: default
BLAS: /usr/lib64/R/lib/libRblas.so
LAPACK: /usr/lib64/R/lib/libRlapack.so

locale:
 [1] LC_CTYPE=fr_FR.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=fr_FR.UTF-8        LC_COLLATE=fr_FR.UTF-8    
 [5] LC_MONETARY=fr_FR.UTF-8    LC_MESSAGES=fr_FR.UTF-8   
 [7] LC_PAPER=fr_FR.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=fr_FR.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

loaded via a namespace (and not attached):
[1] compiler_3.5.0

I'm having difficulties installing two packages I need for my analysis: arm and lme4. I installed without any problem the ggplot2 package I also needed.

Either from the RStudio graphical interface or from R command line (within terminal), I get loads of errors I'm not able to interpret...

I have tried various repos in France, with the same issues. Note that the two packages installation is doing fine from a Windows 10 operating system.

The installation output end up with:

ERROR: compilation failed for package ‘RcppEigen’
* removing ‘/home/thomas/R/x86_64-suse-linux-gnu-library/3.5/RcppEigen’
Warning in install.packages :
  installation of package ‘RcppEigen’ had non-zero exit status
ERROR: dependency ‘latticeExtra’ is not available for package ‘Hmisc’
* removing ‘/home/thomas/R/x86_64-suse-linux-gnu-library/3.5/Hmisc’
Warning in install.packages :
  installation of package ‘Hmisc’ had non-zero exit status
ERROR: dependencies ‘minqa’, ‘nloptr’, ‘statmod’, ‘RcppEigen’ are not available for package ‘lme4’
* removing ‘/home/thomas/R/x86_64-suse-linux-gnu-library/3.5/lme4’
Warning in install.packages :
  installation of package ‘lme4’ had non-zero exit status
ERROR: dependencies ‘lme4’, ‘Hmisc’ are not available for package ‘arm’
* removing ‘/home/thomas/R/x86_64-suse-linux-gnu-library/3.5/arm’
Warning in install.packages :
  installation of package ‘arm’ had non-zero exit status

The downloaded source packages are in
    ‘/tmp/Rtmp5c12rX/downloaded_packages’

I do observe loads of error lines concerning Eigen stuff, like this:

../inst/include/Eigen/src/Core/CoreEvaluators.h:665:8:   required from ‘struct Eigen::internal::evaluator<Eigen::CwiseBinaryOp<Eigen::internal::scalar_product_op<double, double>, const Eigen::Transpose<const Eigen::Block<const Eigen::Matrix<double, -1, -1>, 1, -1, false> >, const Eigen::Block<const Eigen::Transpose<const Eigen::Matrix<double, -1, -1> >, -1, 1, false> > >’
../inst/include/Eigen/src/Core/Redux.h:349:39:   required from ‘class Eigen::internal::redux_evaluator<Eigen::CwiseBinaryOp<Eigen::internal::scalar_product_op<double, double>, const Eigen::Transpose<const Eigen::Block<const Eigen::Matrix<double, -1, -1>, 1, -1, false> >, const Eigen::Block<const Eigen::Transpose<const Eigen::Matrix<double, -1, -1> >, -1, 1, false> > >’
../inst/include/Eigen/src/Core/Redux.h:416:17:   required from ‘typename Eigen::internal::traits<T>::Scalar Eigen::DenseBase<Derived>::redux(const Func&) const [with BinaryOp = Eigen::internal::scalar_sum_op<double, double>; Derived = Eigen::CwiseBinaryOp<Eigen::internal::scalar_product_op<double, double>, const Eigen::Transpose<const Eigen::Block<const Eigen::Matrix<double, -1, -1>, 1, -1, false> >, const Eigen::Block<const Eigen::Transpose<const Eigen::Matrix<double, -1, -1> >, -1, 1, false> >; typename Eigen::internal::traits<T>::Scalar = double]’

I can't find how to export the full installation output in a file, so I can't give more details here...

Many thanks in advance for help and suggestions!

Thomas

-- EDIT --

To complete my issue:

1. I installed a Ubuntu Focal Fossa (21) on a Virtual Machine (via VirtualBox) and the package gets installed without any problems...

2. I tried to install the small dependent package minqa and I get the following output:

I can see other error messages such as make: gfortran: command not found, which might be of any help....

-- EDIT --

I managed to export the output of arm package installation attempt. Note this is done from R version 4.1.0 I also installed on my OpenSUSE system (see comments):

thomas@localhost:~> sudo R

R version 4.1.0 (2021-05-18) -- "Camp Pontanezen"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-suse-linux-gnu (64-bit)

R est un logiciel libre livré sans AUCUNE GARANTIE.
Vous pouvez le redistribuer sous certaines conditions.
Tapez 'license()' ou 'licence()' pour plus de détails.

R est un projet collaboratif avec de nombreux contributeurs.
Tapez 'contributors()' pour plus d'information et
'citation()' pour la façon de le citer dans les publications.

Tapez 'demo()' pour des démonstrations, 'help()' pour l'aide
en ligne ou 'help.start()' pour obtenir l'aide au format HTML.
Tapez 'q()' pour quitter R.

> install.packages(pkgs="arm", repos="http://cran.univ-lyon1.fr/")

installation des dépendances ‘jpeg’, ‘latticeExtra’, ‘lme4’, ‘Hmisc’

essai de l'URL 'http://cran.univ-lyon1.fr/src/contrib/jpeg_0.1-8.1.tar.gz'
Content type 'application/x-gzip' length 18116 bytes (17 KB)
==================================================
downloaded 17 KB

essai de l'URL 'http://cran.univ-lyon1.fr/src/contrib/latticeExtra_0.6-29.tar.gz'
Content type 'application/x-gzip' length 1292315 bytes (1.2 MB)
==================================================
downloaded 1.2 MB

essai de l'URL 'http://cran.univ-lyon1.fr/src/contrib/lme4_1.1-27.tar.gz'
Content type 'application/x-gzip' length 3302287 bytes (3.1 MB)
==================================================
downloaded 3.1 MB

essai de l'URL 'http://cran.univ-lyon1.fr/src/contrib/Hmisc_4.5-0.tar.gz'
Content type 'application/x-gzip' length 775444 bytes (757 KB)
==================================================
downloaded 757 KB

essai de l'URL 'http://cran.univ-lyon1.fr/src/contrib/arm_1.11-2.tar.gz'
Content type 'application/x-gzip' length 79464 bytes (77 KB)
==================================================
downloaded 77 KB

* installing *source* package ‘jpeg’ ...
** package ‘jpeg’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
gcc -I"/usr/lib64/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -fmessage-length=0 -grecord-gcc-switches -O2 -Wall -D_FORTIFY_SOURCE=2 -fstack-protector-strong -funwind-tables -fasynchronous-unwind-tables -fstack-clash-protection  -c read.c -o read.o
In file included from read.c:1:0:
rjcommon.h:11:10: fatal error: jpeglib.h: Aucun fichier ou dossier de ce type
 #include <jpeglib.h>
          ^~~~~~~~~~~
compilation terminated.
make: *** [/usr/lib64/R/etc/Makeconf:168: read.o] Error 1
ERROR: compilation failed for package ‘jpeg’
* removing ‘/usr/lib64/R/library/jpeg’
* installing *source* package ‘lme4’ ...
** package ‘lme4’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
g++ -std=gnu++14 -I"/usr/lib64/R/include" -DNDEBUG  -I'/usr/lib64/R/library/Rcpp/include' -I'/usr/lib64/R/library/RcppEigen/include' -I/usr/local/include  -DNDEBUG -DEIGEN_DONT_VECTORIZE -fpic  -fmessage-length=0 -grecord-gcc-switches -O2 -Wall -D_FORTIFY_SOURCE=2 -fstack-protector-strong -funwind-tables -fasynchronous-unwind-tables -fstack-clash-protection  -c external.cpp -o external.o
g++ -std=gnu++14 -I"/usr/lib64/R/include" -DNDEBUG  -I'/usr/lib64/R/library/Rcpp/include' -I'/usr/lib64/R/library/RcppEigen/include' -I/usr/local/include  -DNDEBUG -DEIGEN_DONT_VECTORIZE -fpic  -fmessage-length=0 -grecord-gcc-switches -O2 -Wall -D_FORTIFY_SOURCE=2 -fstack-protector-strong -funwind-tables -fasynchronous-unwind-tables -fstack-clash-protection  -c glmFamily.cpp -o glmFamily.o
g++ -std=gnu++14 -I"/usr/lib64/R/include" -DNDEBUG  -I'/usr/lib64/R/library/Rcpp/include' -I'/usr/lib64/R/library/RcppEigen/include' -I/usr/local/include  -DNDEBUG -DEIGEN_DONT_VECTORIZE -fpic  -fmessage-length=0 -grecord-gcc-switches -O2 -Wall -D_FORTIFY_SOURCE=2 -fstack-protector-strong -funwind-tables -fasynchronous-unwind-tables -fstack-clash-protection  -c optimizer.cpp -o optimizer.o
g++ -std=gnu++14 -I"/usr/lib64/R/include" -DNDEBUG  -I'/usr/lib64/R/library/Rcpp/include' -I'/usr/lib64/R/library/RcppEigen/include' -I/usr/local/include  -DNDEBUG -DEIGEN_DONT_VECTORIZE -fpic  -fmessage-length=0 -grecord-gcc-switches -O2 -Wall -D_FORTIFY_SOURCE=2 -fstack-protector-strong -funwind-tables -fasynchronous-unwind-tables -fstack-clash-protection  -c predModule.cpp -o predModule.o
g++ -std=gnu++14 -I"/usr/lib64/R/include" -DNDEBUG  -I'/usr/lib64/R/library/Rcpp/include' -I'/usr/lib64/R/library/RcppEigen/include' -I/usr/local/include  -DNDEBUG -DEIGEN_DONT_VECTORIZE -fpic  -fmessage-length=0 -grecord-gcc-switches -O2 -Wall -D_FORTIFY_SOURCE=2 -fstack-protector-strong -funwind-tables -fasynchronous-unwind-tables -fstack-clash-protection  -c respModule.cpp -o respModule.o
Erreur : le package ‘Rcpp’ a été installé avant R 4.0.0 : veuillez le réinstaller, s'il-vous-plait
Exécution arrêtée
g++ -std=gnu++14 -shared -L/usr/lib64/R/lib -L/usr/local/lib64 -o lme4.so external.o glmFamily.o optimizer.o predModule.o respModule.o -L/usr/lib64/R/lib -lR
Erreur : le package ‘Rcpp’ a été installé avant R 4.0.0 : veuillez le réinstaller, s'il-vous-plait
Exécution arrêtée
installing to /usr/lib64/R/library/00LOCK-lme4/00new/lme4/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
Error: le chargement du package ou de l'espace de noms a échoué pour ‘Matrix’ :
le package ‘Matrix’ a été installé avant R 4.0.0 : veuillez le réinstaller, s'il-vous-plait
Erreur : le package ‘Matrix’ ne peut être chargé
Exécution arrêtée
ERROR: lazy loading failed for package ‘lme4’
* removing ‘/usr/lib64/R/library/lme4’
ERROR: dependency ‘jpeg’ is not available for package ‘latticeExtra’
* removing ‘/usr/lib64/R/library/latticeExtra’
ERROR: dependency ‘latticeExtra’ is not available for package ‘Hmisc’
* removing ‘/usr/lib64/R/library/Hmisc’
ERROR: dependencies ‘lme4’, ‘Hmisc’ are not available for package ‘arm’
* removing ‘/usr/lib64/R/library/arm’

The downloaded source packages are in
    ‘/tmp/Rtmpz1IryW/downloaded_packages’
Updating HTML index of packages in '.Library'
Making 'packages.html' ... done
Messages d'avis :
1: Dans install.packages(pkgs = "arm", repos = "http://cran.univ-lyon1.fr/") :
  installation of package ‘jpeg’ had non-zero exit status
2: Dans install.packages(pkgs = "arm", repos = "http://cran.univ-lyon1.fr/") :
  installation of package ‘lme4’ had non-zero exit status
3: Dans install.packages(pkgs = "arm", repos = "http://cran.univ-lyon1.fr/") :
  installation of package ‘latticeExtra’ had non-zero exit status
4: Dans install.packages(pkgs = "arm", repos = "http://cran.univ-lyon1.fr/") :
  installation of package ‘Hmisc’ had non-zero exit status
5: Dans install.packages(pkgs = "arm", repos = "http://cran.univ-lyon1.fr/") :
  installation of package ‘arm’ had non-zero exit status

Answer 1

In my experience, these errors on Unix often stem from missing external libraries. For example, installing the R xml2 package requires libxml2-dev to be installed via the system package manager (i.e. outside R) otherwise installation will fail.

I can't read French, but it looks to me as though the dependency jpeg failed, due to a missing external jpeg library, and then everything cascaded from there. You could try installing some version of the libjpeg library. I know it comes pre-installed in Ubuntu which may be why that worked for you. I'm a little surprised it doesn't come installed already in OpenSUSE, but I have no experience with OpenSUSE.