Unable to install any packages in R/RStudio (on opensuse 42.2 with everything "up to date")

Dominga · October 8, 2019, 7:39pm

Hi!
I installed R and RStudio only a few days ago and yesterday I tried for the first time to install packages. I didn't work and I haven't been able to find out why.

The package install error message is the "non-zero status", for the package and all its dependencies.

My OS is OpenSuse LEAP 42.2, can't change that, it's a job issue.
Did an update of all repos and got this message:

Retrieving repository 'CRAN' metadata ...........................................................................................................................[error]
Repository 'CRAN' is invalid.
[CRAN|http://cran.r-project.org/] Valid metadata not found at specified URL
Please check if the URIs defined for this repository are pointing to a valid repository.
Skipping repository 'CRAN' because of the above error.
Retrieving repository 'R-base' metadata .........................................................................................................................[error]
Repository 'R-base' is invalid.
[R-base|http://download.opensuse.org/repositories/devel:/languages:/R:/patched//] Valid metadata not found at specified URL
Please check if the URIs defined for this repository are pointing to a valid repository.
Skipping repository 'R-base' because of the above error.
Repository 'Main Repository (NON-OSS)' is up to date.                                                                                                                   
Repository 'Update Repository (Non-Oss)' is up to date.                                                                                                                 
Repository 'Main Repository (DEBUG)' is up to date.                                                                                                                     
Repository 'Update Repository (DEBUG)' is up to date.                                                                                                                   
Repository 'Main Repository (OSS)' is up to date.                                                                                                                       
Repository 'Main Update Repository' is up to date.                                                                                                                      
Repository 'openSUSE:Leap:42.2' is up to date.                                                                                                                          
Repository 'Education' is up to date.                                                                                                                                   
Repository 'home:bgta:desktop' is up to date.                                                                                                                           
Repository 'server:php:extensions' is up to date.                                                                                                                       
Repository 'Packman Repository' is up to date.                                                                                                                          
Repository 'libdvdcss repository' is up to date.                                                                                                                        
Repository 'openSUSE-Leap-42.1-Update' is up to date.                                                                                                                   
Repository 'slack' is up to date.                                                                                                                                       
Some of the repositories have not been refreshed because of an error.

Any idea?
I'm desperate

Thanks

andresrcs · October 8, 2019, 7:59pm

Could you tell us how are you trying to install packages and the whole y error message you are getting? So far you are not giving us enough information to help you.

Dominga · October 8, 2019, 8:08pm

I try to install via RStudio -> "Install packages" by selecting the specific package from the list.

The "Install from" selection list contains only "Repository (CRAN)"
"Install to Library" is set to "‘/home/alligator/R/x86_64-suse-linux-gnu-library/3.6/Default’"

I could now paste the whole log, but it's far too long and repetitive for each dependency package, but it ends in this (which is what comes if I try to install without the dependencies):

Warning in install.packages :
  installation of package ‘rio’ had non-zero exit status
ERROR: dependencies ‘pbkrtest’, ‘quantreg’, ‘maptools’, ‘rio’, ‘lme4’ are not available for package ‘car’
* removing ‘/home/alligator/R/x86_64-suse-linux-gnu-library/3.6/car’
Warning in install.packages :
  installation of package ‘car’ had non-zero exit status.

andresrcs · October 8, 2019, 8:24pm

You are omitting the important parts, please post the whole error message

Dominga · October 8, 2019, 8:39pm

Sorry, I'm no pro in this

> install.packages("car", dependencies = FALSE)
Installing package into ‘/home/alligator/R/x86_64-suse-linux-gnu-library/3.6’
(as ‘lib’ is unspecified)
trying URL 'https://cran.rstudio.com/src/contrib/car_3.0-3.tar.gz'
Content type 'application/x-gzip' length 539020 bytes (526 KB)
==================================================
downloaded 526 KB

ERROR: dependencies ‘pbkrtest’, ‘quantreg’, ‘maptools’, ‘rio’, ‘lme4’ are not available for package ‘car’
* removing ‘/home/alligator/R/x86_64-suse-linux-gnu-library/3.6/car’
Warning in install.packages :
  installation of package ‘car’ had non-zero exit status

The downloaded source packages are in
	‘/tmp/Rtmph3XfSp/downloaded_packages’e

It doesn't help to try to install the named dependencies, as this resulkts in a similar error.

andresrcs · October 8, 2019, 8:49pm

You have to try this with dependencies set to TRUE, and post the whole error message so we can identify which dependency is causing the issue

Dominga · October 8, 2019, 9:04pm

> install.packages("car")
Installing package into ‘/home/alligator/R/x86_64-suse-linux-gnu-library/3.6’
(as ‘lib’ is unspecified)
also installing the dependencies ‘backports’, ‘digest’, ‘glue’, ‘ellipsis’, ‘vctrs’, ‘utf8’, ‘forcats’, ‘hms’, ‘readr’, ‘cellranger’, ‘progress’, ‘zip’, ‘fansi’, ‘pillar’, ‘rlang’, ‘SparseM’, ‘sp’, ‘haven’, ‘curl’, ‘data.table’, ‘readxl’, ‘openxlsx’, ‘tibble’, ‘minqa’, ‘nloptr’, ‘Rcpp’, ‘RcppEigen’, ‘pbkrtest’, ‘quantreg’, ‘maptools’, ‘rio’, ‘lme4’

trying URL 'https://cran.rstudio.com/src/contrib/backports_1.1.5.tar.gz'
Content type 'application/x-gzip' length 14798 bytes (14 KB)
==================================================
downloaded 14 KB

trying URL 'https://cran.rstudio.com/src/contrib/digest_0.6.21.tar.gz'
Content type 'application/x-gzip' length 139987 bytes (136 KB)
==================================================
downloaded 136 KB

trying URL 'https://cran.rstudio.com/src/contrib/glue_1.3.1.tar.gz'
Content type 'application/x-gzip' length 122950 bytes (120 KB)
==================================================
downloaded 120 KB

trying URL 'https://cran.rstudio.com/src/contrib/ellipsis_0.3.0.tar.gz'
Content type 'application/x-gzip' length 7371 bytes
==================================================
downloaded 7371 bytes

trying URL 'https://cran.rstudio.com/src/contrib/vctrs_0.2.0.tar.gz'
Content type 'application/x-gzip' length 668258 bytes (652 KB)
==================================================
downloaded 652 KB

trying URL 'https://cran.rstudio.com/src/contrib/utf8_1.1.4.tar.gz'
Content type 'application/x-gzip' length 218882 bytes (213 KB)
==================================================
downloaded 213 KB

trying URL 'https://cran.rstudio.com/src/contrib/forcats_0.4.0.tar.gz'
Content type 'application/x-gzip' length 255097 bytes (249 KB)
==================================================
downloaded 249 KB

trying URL 'https://cran.rstudio.com/src/contrib/hms_0.5.1.tar.gz'
Content type 'application/x-gzip' length 136031 bytes (132 KB)
==================================================
downloaded 132 KB

trying URL 'https://cran.rstudio.com/src/contrib/readr_1.3.1.tar.gz'
Content type 'application/x-gzip' length 268853 bytes (262 KB)
==================================================
downloaded 262 KB

trying URL 'https://cran.rstudio.com/src/contrib/cellranger_1.1.0.tar.gz'
Content type 'application/x-gzip' length 63857 bytes (62 KB)
==================================================
downloaded 62 KB

trying URL 'https://cran.rstudio.com/src/contrib/progress_1.2.2.tar.gz'
Content type 'application/x-gzip' length 29506 bytes (28 KB)
==================================================
downloaded 28 KB

trying URL 'https://cran.rstudio.com/src/contrib/zip_2.0.4.tar.gz'
Content type 'application/x-gzip' length 97756 bytes (95 KB)
==================================================
downloaded 95 KB

trying URL 'https://cran.rstudio.com/src/contrib/fansi_0.4.0.tar.gz'
Content type 'application/x-gzip' length 266123 bytes (259 KB)
==================================================
downloaded 259 KB

trying URL 'https://cran.rstudio.com/src/contrib/pillar_1.4.2.tar.gz'
Content type 'application/x-gzip' length 228815 bytes (223 KB)
==================================================
downloaded 223 KB

trying URL 'https://cran.rstudio.com/src/contrib/rlang_0.4.0.tar.gz'
Content type 'application/x-gzip' length 859737 bytes (839 KB)
==================================================
downloaded 839 KB

trying URL 'https://cran.rstudio.com/src/contrib/SparseM_1.77.tar.gz'
Content type 'application/x-gzip' length 756317 bytes (738 KB)
==================================================
downloaded 738 KB

trying URL 'https://cran.rstudio.com/src/contrib/sp_1.3-1.tar.gz'
Content type 'application/x-gzip' length 1133621 bytes (1.1 MB)
==================================================
downloaded 1.1 MB

trying URL 'https://cran.rstudio.com/src/contrib/haven_2.1.1.tar.gz'
Content type 'application/x-gzip' length 265123 bytes (258 KB)
==================================================
downloaded 258 KB

trying URL 'https://cran.rstudio.com/src/contrib/curl_4.2.tar.gz'
Content type 'application/x-gzip' length 667901 bytes (652 KB)
==================================================
downloaded 652 KB

trying URL 'https://cran.rstudio.com/src/contrib/data.table_1.12.4.tar.gz'
Content type 'application/x-gzip' length 5010321 bytes (4.8 MB)
==================================================
downloaded 4.8 MB

trying URL 'https://cran.rstudio.com/src/contrib/readxl_1.3.1.tar.gz'
Content type 'application/x-gzip' length 2056165 bytes (2.0 MB)
==================================================
downloaded 2.0 MB

trying URL 'https://cran.rstudio.com/src/contrib/openxlsx_4.1.0.1.tar.gz'
Content type 'application/x-gzip' length 1458738 bytes (1.4 MB)
==================================================
downloaded 1.4 MB

trying URL 'https://cran.rstudio.com/src/contrib/tibble_2.1.3.tar.gz'
Content type 'application/x-gzip' length 310774 bytes (303 KB)
==================================================
downloaded 303 KB

trying URL 'https://cran.rstudio.com/src/contrib/minqa_1.2.4.tar.gz'
Content type 'application/x-gzip' length 53548 bytes (52 KB)
==================================================
downloaded 52 KB

trying URL 'https://cran.rstudio.com/src/contrib/nloptr_1.2.1.tar.gz'
Content type 'application/x-gzip' length 2448313 bytes (2.3 MB)
==================================================
downloaded 2.3 MB

trying URL 'https://cran.rstudio.com/src/contrib/Rcpp_1.0.2.tar.gz'
Content type 'application/x-gzip' length 3699570 bytes (3.5 MB)
==================================================
downloaded 3.5 MB

trying URL 'https://cran.rstudio.com/src/contrib/RcppEigen_0.3.3.5.0.tar.gz'
Content type 'application/x-gzip' length 1633859 bytes (1.6 MB)
==================================================
downloaded 1.6 MB

trying URL 'https://cran.rstudio.com/src/contrib/pbkrtest_0.4-7.tar.gz'
Content type 'application/x-gzip' length 156406 bytes (152 KB)
==================================================
downloaded 152 KB

trying URL 'https://cran.rstudio.com/src/contrib/quantreg_5.51.tar.gz'
Content type 'application/x-gzip' length 995236 bytes (971 KB)
==================================================
downloaded 971 KB

trying URL 'https://cran.rstudio.com/src/contrib/maptools_0.9-8.tar.gz'
Content type 'application/x-gzip' length 1582038 bytes (1.5 MB)
==================================================
downloaded 1.5 MB

trying URL 'https://cran.rstudio.com/src/contrib/rio_0.5.16.tar.gz'
Content type 'application/x-gzip' length 420489 bytes (410 KB)
==================================================
downloaded 410 KB

trying URL 'https://cran.rstudio.com/src/contrib/lme4_1.1-21.tar.gz'
Content type 'application/x-gzip' length 4124154 bytes (3.9 MB)
==================================================
downloaded 3.9 MB

trying URL 'https://cran.rstudio.com/src/contrib/car_3.0-3.tar.gz'
Content type 'application/x-gzip' length 539020 bytes (526 KB)
==================================================
downloaded 526 KB

OK, here goes the full ERROR log:

* installing *source* package ‘backports’ ...
** package ‘backports’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
gcc -std=gnu99 -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 -funwind-tables -fasynchronous-unwind-tables -fstack-clash-protection -g  -c dotsElt.c -o dotsElt.o
gcc: error: unrecognized command line option ‘-fstack-clash-protection’
/usr/lib64/R/etc/Makeconf:167: recipe for target 'dotsElt.o' failed
make: *** [dotsElt.o] Error 1
ERROR: compilation failed for package ‘backports’
* removing ‘/home/alligator/R/x86_64-suse-linux-gnu-library/3.6/backports’
Warning in install.packages :
  installation of package ‘backports’ had non-zero exit status
* installing *source* package ‘digest’ ...
** package ‘digest’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
g++ -std=gnu++11 -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 -funwind-tables -fasynchronous-unwind-tables -fstack-clash-protection -g  -c SpookyV2.cpp -o SpookyV2.o
g++: error: unrecognized command line option ‘-fstack-clash-protection’
/usr/lib64/R/etc/Makeconf:176: recipe for target 'SpookyV2.o' failed
make: *** [SpookyV2.o] Error 1
ERROR: compilation failed for package ‘digest’
* removing ‘/home/alligator/R/x86_64-suse-linux-gnu-library/3.6/digest’
Warning in install.packages :
  installation of package ‘digest’ had non-zero exit status
* installing *source* package ‘glue’ ...
** package ‘glue’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
gcc -std=gnu99 -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 -funwind-tables -fasynchronous-unwind-tables -fstack-clash-protection -g  -c glue.c -o glue.o
gcc: error: unrecognized command line option ‘-fstack-clash-protection’
/usr/lib64/R/etc/Makeconf:167: recipe for target 'glue.o' failed
make: *** [glue.o] Error 1
ERROR: compilation failed for package ‘glue’
* removing ‘/home/alligator/R/x86_64-suse-linux-gnu-library/3.6/glue’
Warning in install.packages :
  installation of package ‘glue’ had non-zero exit status
* installing *source* package ‘utf8’ ...
** package ‘utf8’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
gcc -std=gnu99 -I"/usr/lib64/R/include" -DNDEBUG   -I/usr/local/include -Iutf8lite/src -fpic  -fmessage-length=0 -grecord-gcc-switches -O2 -Wall -D_FORTIFY_SOURCE=2 -fstack-protector -funwind-tables -fasynchronous-unwind-tables -fstack-clash-protection -g  -c as_utf8.c -o as_utf8.o
gcc: error: unrecognized command line option ‘-fstack-clash-protection’
/usr/lib64/R/etc/Makeconf:167: recipe for target 'as_utf8.o' failed
make: *** [as_utf8.o] Error 1
ERROR: compilation failed for package ‘utf8’
* removing ‘/home/alligator/R/x86_64-suse-linux-gnu-library/3.6/utf8’
Warning in install.packages :
  installation of package ‘utf8’ had non-zero exit status
* installing *source* package ‘zip’ ...
** package ‘zip’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
gcc -std=gnu99 -fmessage-length=0 -grecord-gcc-switches -O2 -Wall -D_FORTIFY_SOURCE=2 -fstack-protector -funwind-tables -fasynchronous-unwind-tables -fstack-clash-protection -g  miniz.c zip.c tools/cmdzip.c -o tools/cmdzip
gcc: error: unrecognized command line option ‘-fstack-clash-protection’
Makevars:9: recipe for target 'tools/cmdzip' failed
make: *** [tools/cmdzip] Error 1
ERROR: compilation failed for package ‘zip’
* removing ‘/home/alligator/R/x86_64-suse-linux-gnu-library/3.6/zip’
Warning in install.packages :
  installation of package ‘zip’ had non-zero exit status
* installing *source* package ‘fansi’ ...
** package ‘fansi’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
gcc -std=gnu99 -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 -funwind-tables -fasynchronous-unwind-tables -fstack-clash-protection -g  -c assumptions.c -o assumptions.o
gcc: error: unrecognized command line option ‘-fstack-clash-protection’
/usr/lib64/R/etc/Makeconf:167: recipe for target 'assumptions.o' failed
make: *** [assumptions.o] Error 1
ERROR: compilation failed for package ‘fansi’
* removing ‘/home/alligator/R/x86_64-suse-linux-gnu-library/3.6/fansi’
Warning in install.packages :
  installation of package ‘fansi’ had non-zero exit status
* installing *source* package ‘rlang’ ...
** package ‘rlang’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
gcc -std=gnu99 -I"/usr/lib64/R/include" -DNDEBUG -I./lib/  -I/usr/local/include  -fpic  -fmessage-length=0 -grecord-gcc-switches -O2 -Wall -D_FORTIFY_SOURCE=2 -fstack-protector -funwind-tables -fasynchronous-unwind-tables -fstack-clash-protection -g  -c capture.c -o capture.o
gcc: error: unrecognized command line option ‘-fstack-clash-protection’
/usr/lib64/R/etc/Makeconf:167: recipe for target 'capture.o' failed
make: *** [capture.o] Error 1
ERROR: compilation failed for package ‘rlang’
* removing ‘/home/alligator/R/x86_64-suse-linux-gnu-library/3.6/rlang’
Warning in install.packages :
  installation of package ‘rlang’ had non-zero exit status
* installing *source* package ‘SparseM’ ...
** package ‘SparseM’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
gfortran  -fpic  -fmessage-length=0 -grecord-gcc-switches -O2 -Wall -D_FORTIFY_SOURCE=2 -fstack-protector -funwind-tables -fasynchronous-unwind-tables -fstack-clash-protection -g  -c bckslv.f -o bckslv.o
make: gfortran: Command not found
/usr/lib64/R/etc/Makeconf:190: recipe for target 'bckslv.o' failed
make: *** [bckslv.o] Error 127
ERROR: compilation failed for package ‘SparseM’
* removing ‘/home/alligator/R/x86_64-suse-linux-gnu-library/3.6/SparseM’
Warning in install.packages :
  installation of package ‘SparseM’ had non-zero exit status
* installing *source* package ‘sp’ ...
** package ‘sp’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
gcc -std=gnu99 -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 -funwind-tables -fasynchronous-unwind-tables -fstack-clash-protection -g  -c Rcentroid.c -o Rcentroid.o
gcc: error: unrecognized command line option ‘-fstack-clash-protection’
/usr/lib64/R/etc/Makeconf:167: recipe for target 'Rcentroid.o' failed
make: *** [Rcentroid.o] Error 1
ERROR: compilation failed for package ‘sp’
* removing ‘/home/alligator/R/x86_64-suse-linux-gnu-library/3.6/sp’
Warning in install.packages :
  installation of package ‘sp’ had non-zero exit status
* installing *source* package ‘curl’ ...
** package ‘curl’ successfully unpacked and MD5 sums checked
** using staged installation
Package libcurl was not found in the pkg-config search path.
Perhaps you should add the directory containing `libcurl.pc'
to the PKG_CONFIG_PATH environment variable
No package 'libcurl' found
Package libcurl was not found in the pkg-config search path.
Perhaps you should add the directory containing `libcurl.pc'
to the PKG_CONFIG_PATH environment variable
No package 'libcurl' found
Using PKG_CFLAGS=
Using PKG_LIBS=-lcurl
------------------------- ANTICONF ERROR ---------------------------
Configuration failed because libcurl was not found. Try installing:
 * deb: libcurl4-openssl-dev (Debian, Ubuntu, etc)
 * rpm: libcurl-devel (Fedora, CentOS, RHEL)
 * csw: libcurl_dev (Solaris)
If libcurl is already installed, check that 'pkg-config' is in your
PATH and PKG_CONFIG_PATH contains a libcurl.pc file. If pkg-config
is unavailable you can set INCLUDE_DIR and LIB_DIR manually via:
R CMD INSTALL --configure-vars='INCLUDE_DIR=... LIB_DIR=...'
--------------------------------------------------------------------
ERROR: configuration failed for package ‘curl’
* removing ‘/home/alligator/R/x86_64-suse-linux-gnu-library/3.6/curl’
Warning in install.packages :
  installation of package ‘curl’ had non-zero exit status
* installing *source* package ‘data.table’ ...
** package ‘data.table’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
gcc -std=gnu99 -I"/usr/lib64/R/include" -DNDEBUG   -I/usr/local/include -fopenmp -fpic  -fmessage-length=0 -grecord-gcc-switches -O2 -Wall -D_FORTIFY_SOURCE=2 -fstack-protector -funwind-tables -fasynchronous-unwind-tables -fstack-clash-protection -g  -c assign.c -o assign.o
gcc: error: unrecognized command line option ‘-fstack-clash-protection’
/usr/lib64/R/etc/Makeconf:167: recipe for target 'assign.o' failed
make: *** [assign.o] Error 1
ERROR: compilation failed for package ‘data.table’
* removing ‘/home/alligator/R/x86_64-suse-linux-gnu-library/3.6/data.table’
Warning in install.packages :
  installation of package ‘data.table’ had non-zero exit status
* installing *source* package ‘nloptr’ ...
** package ‘nloptr’ successfully unpacked and MD5 sums checked
** using staged installation
configure: loading site script /usr/share/site/x86_64-unknown-linux-gnu
checking whether the C++ compiler works... no
configure: error: in `/tmp/RtmpFRJgIv/R.INSTALL560c73cd89d2/nloptr':
configure: error: C++ compiler cannot create executables
See `config.log' for more details
ERROR: configuration failed for package ‘nloptr’
* removing ‘/home/alligator/R/x86_64-suse-linux-gnu-library/3.6/nloptr’
Warning in install.packages :
  installation of package ‘nloptr’ had non-zero exit status
* installing *source* package ‘Rcpp’ ...
** package ‘Rcpp’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
g++ -std=gnu++11 -I"/usr/lib64/R/include" -DNDEBUG -I../inst/include/  -I/usr/local/include  -fpic  -fmessage-length=0 -grecord-gcc-switches -O2 -Wall -D_FORTIFY_SOURCE=2 -fstack-protector -funwind-tables -fasynchronous-unwind-tables -fstack-clash-protection -g  -c api.cpp -o api.o
g++: error: unrecognized command line option ‘-fstack-clash-protection’
/usr/lib64/R/etc/Makeconf:176: recipe for target 'api.o' failed
make: *** [api.o] Error 1
ERROR: compilation failed for package ‘Rcpp’
* removing ‘/home/alligator/R/x86_64-suse-linux-gnu-library/3.6/Rcpp’
Warning in install.packages :
  installation of package ‘Rcpp’ had non-zero exit status
ERROR: dependency ‘rlang’ is not available for package ‘ellipsis’
* removing ‘/home/alligator/R/x86_64-suse-linux-gnu-library/3.6/ellipsis’
Warning in install.packages :
  installation of package ‘ellipsis’ had non-zero exit status
ERROR: dependencies ‘Rcpp’, ‘zip’ are not available for package ‘openxlsx’
* removing ‘/home/alligator/R/x86_64-suse-linux-gnu-library/3.6/openxlsx’
Warning in install.packages :
  installation of package ‘openxlsx’ had non-zero exit status
ERROR: dependency ‘Rcpp’ is not available for package ‘minqa’
* removing ‘/home/alligator/R/x86_64-suse-linux-gnu-library/3.6/minqa’
Warning in install.packages :
  installation of package ‘minqa’ had non-zero exit status
ERROR: dependency ‘Rcpp’ is not available for package ‘RcppEigen’
* removing ‘/home/alligator/R/x86_64-suse-linux-gnu-library/3.6/RcppEigen’
Warning in install.packages :
  installation of package ‘RcppEigen’ had non-zero exit status
ERROR: dependency ‘SparseM’ is not available for package ‘quantreg’
* removing ‘/home/alligator/R/x86_64-suse-linux-gnu-library/3.6/quantreg’
Warning in install.packages :
  installation of package ‘quantreg’ had non-zero exit status
ERROR: dependency ‘sp’ is not available for package ‘maptools’
* removing ‘/home/alligator/R/x86_64-suse-linux-gnu-library/3.6/maptools’
Warning in install.packages :
  installation of package ‘maptools’ had non-zero exit status
ERROR: dependencies ‘backports’, ‘ellipsis’, ‘digest’, ‘glue’, ‘rlang’ are not available for package ‘vctrs’
* removing ‘/home/alligator/R/x86_64-suse-linux-gnu-library/3.6/vctrs’
Warning in install.packages :
  installation of package ‘vctrs’ had non-zero exit status
ERROR: dependencies ‘minqa’, ‘nloptr’, ‘Rcpp’, ‘RcppEigen’ are not available for package ‘lme4’
* removing ‘/home/alligator/R/x86_64-suse-linux-gnu-library/3.6/lme4’
Warning in install.packages :
  installation of package ‘lme4’ had non-zero exit status
ERROR: dependencies ‘rlang’, ‘vctrs’ are not available for package ‘hms’
* removing ‘/home/alligator/R/x86_64-suse-linux-gnu-library/3.6/hms’
Warning in install.packages :
  installation of package ‘hms’ had non-zero exit status
ERROR: dependencies ‘fansi’, ‘rlang’, ‘utf8’, ‘vctrs’ are not available for package ‘pillar’
* removing ‘/home/alligator/R/x86_64-suse-linux-gnu-library/3.6/pillar’
Warning in install.packages :
  installation of package ‘pillar’ had non-zero exit status
ERROR: dependency ‘lme4’ is not available for package ‘pbkrtest’
* removing ‘/home/alligator/R/x86_64-suse-linux-gnu-library/3.6/pbkrtest’
Warning in install.packages :
  installation of package ‘pbkrtest’ had non-zero exit status
ERROR: dependency ‘hms’ is not available for package ‘progress’
* removing ‘/home/alligator/R/x86_64-suse-linux-gnu-library/3.6/progress’
Warning in install.packages :
  installation of package ‘progress’ had non-zero exit status
ERROR: dependencies ‘fansi’, ‘pillar’, ‘rlang’ are not available for package ‘tibble’
* removing ‘/home/alligator/R/x86_64-suse-linux-gnu-library/3.6/tibble’
Warning in install.packages :
  installation of package ‘tibble’ had non-zero exit status
ERROR: dependencies ‘ellipsis’, ‘rlang’, ‘tibble’ are not available for package ‘forcats’
* removing ‘/home/alligator/R/x86_64-suse-linux-gnu-library/3.6/forcats’
Warning in install.packages :
  installation of package ‘forcats’ had non-zero exit status
ERROR: dependencies ‘Rcpp’, ‘tibble’, ‘hms’ are not available for package ‘readr’
* removing ‘/home/alligator/R/x86_64-suse-linux-gnu-library/3.6/readr’
Warning in install.packages :
  installation of package ‘readr’ had non-zero exit status
ERROR: dependency ‘tibble’ is not available for package ‘cellranger’
* removing ‘/home/alligator/R/x86_64-suse-linux-gnu-library/3.6/cellranger’
Warning in install.packages :
  installation of package ‘cellranger’ had non-zero exit status
ERROR: dependencies ‘forcats’, ‘hms’, ‘Rcpp’, ‘readr’, ‘tibble’ are not available for package ‘haven’
* removing ‘/home/alligator/R/x86_64-suse-linux-gnu-library/3.6/haven’
Warning in install.packages :
  installation of package ‘haven’ had non-zero exit status
ERROR: dependencies ‘cellranger’, ‘Rcpp’, ‘tibble’, ‘progress’ are not available for package ‘readxl’
* removing ‘/home/alligator/R/x86_64-suse-linux-gnu-library/3.6/readxl’
Warning in install.packages :
  installation of package ‘readxl’ had non-zero exit status
ERROR: dependencies ‘haven’, ‘curl’, ‘data.table’, ‘readxl’, ‘openxlsx’, ‘tibble’ are not available for package ‘rio’
* removing ‘/home/alligator/R/x86_64-suse-linux-gnu-library/3.6/rio’
Warning in install.packages :
  installation of package ‘rio’ had non-zero exit status
ERROR: dependencies ‘pbkrtest’, ‘quantreg’, ‘maptools’, ‘rio’, ‘lme4’ are not available for package ‘car’
* removing ‘/home/alligator/R/x86_64-suse-linux-gnu-library/3.6/car’
Warning in install.packages :
  installation of package ‘car’ had non-zero exit status

The downloaded source packages are in
	‘/tmp/Rtmph3XfSp/downloaded_packages’

andresrcs · October 8, 2019, 9:23pm

It seems like you have an incompatible or old version of gcc installed in your system, try updating or reinstalling gcc I can't give you any specific command since I don't have experience with opensuse

Dominga · October 9, 2019, 8:27pm

I did that and some research on what version of gcc is needed.Only found a reference that it must be > 4 and I have gcc version 4.8.x
I also checked the PATH variables, which seem to be ok

Now I have gcc 6.1.1 20160707 installed and set the pointer to it (so that's what appears if I check the version of gcc in the terminal.)

Still not able to install any packages in RStudio.
I'm desperate because I need this to work somehow. Is there a posiibility to use RsTudio online, on a server?

andresrcs · October 9, 2019, 8:46pm

Yes, you can use RStudio Cloud for free, but have in minde that it has a 1GB RAM memory limit so you can't do nothing memory intensive.

Dominga · October 9, 2019, 8:50pm

It's for Statistics 101, I don't think I will need that much memory at the beginning. Until I find a solution for the problem.

Thanks very much for your help!

system · October 30, 2019, 8:51pm

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