Hi I have a fresh Manjaro Linux KDE installation, with R 4.2.1 and RStudio 2022.02.3 Build 492 (AUR package: rstudio-desktop-bin).
I am trying to install packages but the installation fails (see below, that happens with any package).
I also have the following installed:
- clang 13.0.1
- gcc 12.1.0
- gcc-fortran 12.1.0
- gcc-libs 12.1.0
It feels like my system is missing a required package, or my library needs extra permissions or a symbolic link? Please let me know if you have any ideas
> install.packages("lmerTest", dependencies = TRUE)
Installing package into ‘/home/alpha/R/x86_64-pc-linux-gnu-library/4.2’
(as ‘lib’ is unspecified)
also installing the dependencies ‘diffobj’, ‘rematch2’, ‘brio’, ‘callr’, ‘cli’, ‘desc’, ‘pkgload’, ‘processx’, ‘ps’, ‘waldo’, ‘colorspace’, ‘utf8’, ‘testthat’, ‘farver’, ‘munsell’, ‘ellipsis’, ‘fansi’, ‘pillar’, ‘vctrs’, ‘backports’, ‘purrr’, ‘tidyr’, ‘tidyselect’, ‘minqa’, ‘nloptr’, ‘Rcpp’, ‘RcppEigen’, ‘isoband’, ‘scales’, ‘tibble’, ‘broom’, ‘dplyr’, ‘lme4’, ‘ggplot2’, ‘pbkrtest’
trying URL 'https://cran.curtin.edu.au/src/contrib/diffobj_0.3.5.tar.gz'
Content type 'application/x-gzip' length 479276 bytes (468 KB)
==================================================
downloaded 468 KB
trying URL 'https://cran.curtin.edu.au/src/contrib/rematch2_2.1.2.tar.gz'
Content type 'application/x-gzip' length 13366 bytes (13 KB)
==================================================
downloaded 13 KB
trying URL 'https://cran.curtin.edu.au/src/contrib/brio_1.1.3.tar.gz'
Content type 'application/x-gzip' length 12629 bytes (12 KB)
==================================================
downloaded 12 KB
trying URL 'https://cran.curtin.edu.au/src/contrib/callr_3.7.0.tar.gz'
Content type 'application/x-gzip' length 74518 bytes (72 KB)
==================================================
downloaded 72 KB
trying URL 'https://cran.curtin.edu.au/src/contrib/cli_3.3.0.tar.gz'
Content type 'application/x-gzip' length 495823 bytes (484 KB)
==================================================
downloaded 484 KB
trying URL 'https://cran.curtin.edu.au/src/contrib/desc_1.4.1.tar.gz'
Content type 'application/x-gzip' length 80670 bytes (78 KB)
==================================================
downloaded 78 KB
trying URL 'https://cran.curtin.edu.au/src/contrib/pkgload_1.3.0.tar.gz'
Content type 'application/x-gzip' length 76008 bytes (74 KB)
==================================================
downloaded 74 KB
trying URL 'https://cran.curtin.edu.au/src/contrib/processx_3.7.0.tar.gz'
Content type 'application/x-gzip' length 161751 bytes (157 KB)
==================================================
downloaded 157 KB
trying URL 'https://cran.curtin.edu.au/src/contrib/ps_1.7.1.tar.gz'
Content type 'application/x-gzip' length 128664 bytes (125 KB)
==================================================
downloaded 125 KB
trying URL 'https://cran.curtin.edu.au/src/contrib/waldo_0.4.0.tar.gz'
Content type 'application/x-gzip' length 37556 bytes (36 KB)
==================================================
downloaded 36 KB
trying URL 'https://cran.curtin.edu.au/src/contrib/colorspace_2.0-3.tar.gz'
Content type 'application/x-gzip' length 2199185 bytes (2.1 MB)
==================================================
downloaded 2.1 MB
trying URL 'https://cran.curtin.edu.au/src/contrib/utf8_1.2.2.tar.gz'
Content type 'application/x-gzip' length 240327 bytes (234 KB)
==================================================
downloaded 234 KB
trying URL 'https://cran.curtin.edu.au/src/contrib/testthat_3.1.4.tar.gz'
Content type 'application/x-gzip' length 700919 bytes (684 KB)
==================================================
downloaded 684 KB
trying URL 'https://cran.curtin.edu.au/src/contrib/farver_2.1.1.tar.gz'
Content type 'application/x-gzip' length 1274363 bytes (1.2 MB)
==================================================
downloaded 1.2 MB
trying URL 'https://cran.curtin.edu.au/src/contrib/munsell_0.5.0.tar.gz'
Content type 'application/x-gzip' length 182653 bytes (178 KB)
==================================================
downloaded 178 KB
trying URL 'https://cran.curtin.edu.au/src/contrib/ellipsis_0.3.2.tar.gz'
Content type 'application/x-gzip' length 8066 bytes
==================================================
downloaded 8066 bytes
trying URL 'https://cran.curtin.edu.au/src/contrib/fansi_1.0.3.tar.gz'
Content type 'application/x-gzip' length 481163 bytes (469 KB)
==================================================
downloaded 469 KB
trying URL 'https://cran.curtin.edu.au/src/contrib/pillar_1.7.0.tar.gz'
Content type 'application/x-gzip' length 529668 bytes (517 KB)
==================================================
downloaded 517 KB
trying URL 'https://cran.curtin.edu.au/src/contrib/vctrs_0.4.1.tar.gz'
Content type 'application/x-gzip' length 916782 bytes (895 KB)
==================================================
downloaded 895 KB
trying URL 'https://cran.curtin.edu.au/src/contrib/backports_1.4.1.tar.gz'
Content type 'application/x-gzip' length 26201 bytes (25 KB)
==================================================
downloaded 25 KB
trying URL 'https://cran.curtin.edu.au/src/contrib/purrr_0.3.4.tar.gz'
Content type 'application/x-gzip' length 375062 bytes (366 KB)
==================================================
downloaded 366 KB
trying URL 'https://cran.curtin.edu.au/src/contrib/tidyr_1.2.0.tar.gz'
Content type 'application/x-gzip' length 744570 bytes (727 KB)
==================================================
downloaded 727 KB
trying URL 'https://cran.curtin.edu.au/src/contrib/tidyselect_1.1.2.tar.gz'
Content type 'application/x-gzip' length 92085 bytes (89 KB)
==================================================
downloaded 89 KB
trying URL 'https://cran.curtin.edu.au/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.curtin.edu.au/src/contrib/nloptr_2.0.3.tar.gz'
Content type 'application/x-gzip' length 2219877 bytes (2.1 MB)
==================================================
downloaded 2.1 MB
trying URL 'https://cran.curtin.edu.au/src/contrib/Rcpp_1.0.8.3.tar.gz'
Content type 'application/x-gzip' length 3086192 bytes (2.9 MB)
==================================================
downloaded 2.9 MB
trying URL 'https://cran.curtin.edu.au/src/contrib/RcppEigen_0.3.3.9.2.tar.gz'
Content type 'application/x-gzip' length 1476004 bytes (1.4 MB)
==================================================
downloaded 1.4 MB
trying URL 'https://cran.curtin.edu.au/src/contrib/isoband_0.2.5.tar.gz'
Content type 'application/x-gzip' length 1671911 bytes (1.6 MB)
==================================================
downloaded 1.6 MB
trying URL 'https://cran.curtin.edu.au/src/contrib/scales_1.2.0.tar.gz'
Content type 'application/x-gzip' length 270188 bytes (263 KB)
==================================================
downloaded 263 KB
trying URL 'https://cran.curtin.edu.au/src/contrib/tibble_3.1.7.tar.gz'
Content type 'application/x-gzip' length 674873 bytes (659 KB)
==================================================
downloaded 659 KB
trying URL 'https://cran.curtin.edu.au/src/contrib/broom_1.0.0.tar.gz'
Content type 'application/x-gzip' length 641539 bytes (626 KB)
==================================================
downloaded 626 KB
trying URL 'https://cran.curtin.edu.au/src/contrib/dplyr_1.0.9.tar.gz'
Content type 'application/x-gzip' length 957637 bytes (935 KB)
==================================================
downloaded 935 KB
trying URL 'https://cran.curtin.edu.au/src/contrib/lme4_1.1-30.tar.gz'
Content type 'application/x-gzip' length 3307884 bytes (3.2 MB)
==================================================
downloaded 3.2 MB
trying URL 'https://cran.curtin.edu.au/src/contrib/ggplot2_3.3.6.tar.gz'
Content type 'application/x-gzip' length 3061989 bytes (2.9 MB)
==================================================
downloaded 2.9 MB
trying URL 'https://cran.curtin.edu.au/src/contrib/pbkrtest_0.5.1.tar.gz'
Content type 'application/x-gzip' length 246327 bytes (240 KB)
==================================================
downloaded 240 KB
trying URL 'https://cran.curtin.edu.au/src/contrib/lmerTest_3.1-3.tar.gz'
Content type 'application/x-gzip' length 195633 bytes (191 KB)
==================================================
downloaded 191 KB
* installing *source* package ‘diffobj’ ...
** package ‘diffobj’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
sh: line 1: make: command not found
Warning in system(cmd) : error in running command
ERROR: compilation failed for package ‘diffobj’
* removing ‘/home/alpha/R/x86_64-pc-linux-gnu-library/4.2/diffobj’
Warning in install.packages :
installation of package ‘diffobj’ had non-zero exit status
* installing *source* package ‘brio’ ...
** package ‘brio’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
sh: line 1: make: command not found
Warning in system(cmd) : error in running command
ERROR: compilation failed for package ‘brio’
* removing ‘/home/alpha/R/x86_64-pc-linux-gnu-library/4.2/brio’
Warning in install.packages :
installation of package ‘brio’ had non-zero exit status
* installing *source* package ‘cli’ ...
** package ‘cli’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
sh: line 1: make: command not found
Warning in system(cmd) : error in running command
ERROR: compilation failed for package ‘cli’
* removing ‘/home/alpha/R/x86_64-pc-linux-gnu-library/4.2/cli’
Warning in install.packages :
installation of package ‘cli’ had non-zero exit status
* installing *source* package ‘ps’ ...
** package ‘ps’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
sh: line 1: make: command not found
Warning in system(cmd) : error in running command
ERROR: compilation failed for package ‘ps’
* removing ‘/home/alpha/R/x86_64-pc-linux-gnu-library/4.2/ps’
Warning in install.packages :
installation of package ‘ps’ had non-zero exit status
* installing *source* package ‘colorspace’ ...
** package ‘colorspace’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
sh: line 1: make: command not found
Warning in system(cmd) : error in running command
ERROR: compilation failed for package ‘colorspace’
* removing ‘/home/alpha/R/x86_64-pc-linux-gnu-library/4.2/colorspace’
Warning in install.packages :
installation of package ‘colorspace’ had non-zero exit status
* installing *source* package ‘utf8’ ...
** package ‘utf8’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
sh: line 1: make: command not found
Warning in system(cmd) : error in running command
ERROR: compilation failed for package ‘utf8’
* removing ‘/home/alpha/R/x86_64-pc-linux-gnu-library/4.2/utf8’
Warning in install.packages :
installation of package ‘utf8’ had non-zero exit status
* installing *source* package ‘farver’ ...
** package ‘farver’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
sh: line 1: make: command not found
Warning in system(cmd) : error in running command
ERROR: compilation failed for package ‘farver’
* removing ‘/home/alpha/R/x86_64-pc-linux-gnu-library/4.2/farver’
Warning in install.packages :
installation of package ‘farver’ had non-zero exit status
* installing *source* package ‘ellipsis’ ...
** package ‘ellipsis’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
sh: line 1: make: command not found
Warning in system(cmd) : error in running command
ERROR: compilation failed for package ‘ellipsis’
* removing ‘/home/alpha/R/x86_64-pc-linux-gnu-library/4.2/ellipsis’
Warning in install.packages :
installation of package ‘ellipsis’ had non-zero exit status
* installing *source* package ‘fansi’ ...
** package ‘fansi’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
sh: line 1: make: command not found
Warning in system(cmd) : error in running command
ERROR: compilation failed for package ‘fansi’
* removing ‘/home/alpha/R/x86_64-pc-linux-gnu-library/4.2/fansi’
Warning in install.packages :
installation of package ‘fansi’ had non-zero exit status
* installing *source* package ‘backports’ ...
** package ‘backports’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
sh: line 1: make: command not found
Warning in system(cmd) : error in running command
ERROR: compilation failed for package ‘backports’
* removing ‘/home/alpha/R/x86_64-pc-linux-gnu-library/4.2/backports’
Warning in install.packages :
installation of package ‘backports’ had non-zero exit status
* installing *source* package ‘purrr’ ...
** package ‘purrr’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
sh: line 1: make: command not found
Warning in system(cmd) : error in running command
ERROR: compilation failed for package ‘purrr’
* removing ‘/home/alpha/R/x86_64-pc-linux-gnu-library/4.2/purrr’
Warning in install.packages :
installation of package ‘purrr’ had non-zero exit status
* installing *source* package ‘Rcpp’ ...
** package ‘Rcpp’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
sh: line 1: make: command not found
Warning in system(cmd) : error in running command
ERROR: compilation failed for package ‘Rcpp’
* removing ‘/home/alpha/R/x86_64-pc-linux-gnu-library/4.2/Rcpp’
Warning in install.packages :
installation of package ‘Rcpp’ had non-zero exit status
* installing *source* package ‘isoband’ ...
** package ‘isoband’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
sh: line 1: make: command not found
Warning in system(cmd) : error in running command
ERROR: compilation failed for package ‘isoband’
* removing ‘/home/alpha/R/x86_64-pc-linux-gnu-library/4.2/isoband’
Warning in install.packages :
installation of package ‘isoband’ had non-zero exit status
ERROR: dependency ‘cli’ is not available for package ‘desc’
* removing ‘/home/alpha/R/x86_64-pc-linux-gnu-library/4.2/desc’
Warning in install.packages :
installation of package ‘desc’ had non-zero exit status
ERROR: dependency ‘ps’ is not available for package ‘processx’
* removing ‘/home/alpha/R/x86_64-pc-linux-gnu-library/4.2/processx’
Warning in install.packages :
installation of package ‘processx’ had non-zero exit status
ERROR: dependency ‘colorspace’ is not available for package ‘munsell’
* removing ‘/home/alpha/R/x86_64-pc-linux-gnu-library/4.2/munsell’
Warning in install.packages :
installation of package ‘munsell’ had non-zero exit status
ERROR: dependency ‘cli’ is not available for package ‘vctrs’
* removing ‘/home/alpha/R/x86_64-pc-linux-gnu-library/4.2/vctrs’
Warning in install.packages :
installation of package ‘vctrs’ had non-zero exit status
ERROR: dependency ‘Rcpp’ is not available for package ‘minqa’
* removing ‘/home/alpha/R/x86_64-pc-linux-gnu-library/4.2/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/alpha/R/x86_64-pc-linux-gnu-library/4.2/RcppEigen’
Warning in install.packages :
installation of package ‘RcppEigen’ had non-zero exit status
ERROR: dependency ‘processx’ is not available for package ‘callr’
* removing ‘/home/alpha/R/x86_64-pc-linux-gnu-library/4.2/callr’
Warning in install.packages :
installation of package ‘callr’ had non-zero exit status
ERROR: dependencies ‘cli’, ‘desc’ are not available for package ‘pkgload’
* removing ‘/home/alpha/R/x86_64-pc-linux-gnu-library/4.2/pkgload’
Warning in install.packages :
installation of package ‘pkgload’ had non-zero exit status
ERROR: dependencies ‘cli’, ‘ellipsis’, ‘fansi’, ‘utf8’, ‘vctrs’ are not available for package ‘pillar’
* removing ‘/home/alpha/R/x86_64-pc-linux-gnu-library/4.2/pillar’
Warning in install.packages :
installation of package ‘pillar’ had non-zero exit status
ERROR: dependencies ‘ellipsis’, ‘purrr’, ‘vctrs’ are not available for package ‘tidyselect’
* removing ‘/home/alpha/R/x86_64-pc-linux-gnu-library/4.2/tidyselect’
Warning in install.packages :
installation of package ‘tidyselect’ had non-zero exit status
ERROR: dependencies ‘farver’, ‘munsell’ are not available for package ‘scales’
* removing ‘/home/alpha/R/x86_64-pc-linux-gnu-library/4.2/scales’
Warning in install.packages :
installation of package ‘scales’ had non-zero exit status
ERROR: dependencies ‘ellipsis’, ‘fansi’, ‘pillar’, ‘vctrs’ are not available for package ‘tibble’
* removing ‘/home/alpha/R/x86_64-pc-linux-gnu-library/4.2/tibble’
Warning in install.packages :
installation of package ‘tibble’ had non-zero exit status
ERROR: dependency ‘tibble’ is not available for package ‘rematch2’
* removing ‘/home/alpha/R/x86_64-pc-linux-gnu-library/4.2/rematch2’
Warning in install.packages :
installation of package ‘rematch2’ had non-zero exit status
ERROR: dependencies ‘tibble’, ‘tidyselect’, ‘vctrs’, ‘pillar’ are not available for package ‘dplyr’
* removing ‘/home/alpha/R/x86_64-pc-linux-gnu-library/4.2/dplyr’
Warning in install.packages :
installation of package ‘dplyr’ had non-zero exit status
ERROR: dependencies ‘isoband’, ‘scales’, ‘tibble’ are not available for package ‘ggplot2’
* removing ‘/home/alpha/R/x86_64-pc-linux-gnu-library/4.2/ggplot2’
Warning in install.packages :
installation of package ‘ggplot2’ had non-zero exit status
ERROR: dependencies ‘cli’, ‘diffobj’, ‘fansi’, ‘rematch2’, ‘tibble’ are not available for package ‘waldo’
* removing ‘/home/alpha/R/x86_64-pc-linux-gnu-library/4.2/waldo’
Warning in install.packages :
installation of package ‘waldo’ had non-zero exit status
ERROR: dependencies ‘dplyr’, ‘ellipsis’, ‘purrr’, ‘tibble’, ‘tidyselect’, ‘vctrs’ are not available for package ‘tidyr’
* removing ‘/home/alpha/R/x86_64-pc-linux-gnu-library/4.2/tidyr’
Warning in install.packages :
installation of package ‘tidyr’ had non-zero exit status
ERROR: dependencies ‘brio’, ‘callr’, ‘cli’, ‘desc’, ‘ellipsis’, ‘pkgload’, ‘processx’, ‘ps’, ‘waldo’ are not available for package ‘testthat’
* removing ‘/home/alpha/R/x86_64-pc-linux-gnu-library/4.2/testthat’
Warning in install.packages :
installation of package ‘testthat’ had non-zero exit status
ERROR: dependencies ‘backports’, ‘dplyr’, ‘ellipsis’, ‘purrr’, ‘tibble’, ‘tidyr’, ‘ggplot2’ are not available for package ‘broom’
* removing ‘/home/alpha/R/x86_64-pc-linux-gnu-library/4.2/broom’
Warning in install.packages :
installation of package ‘broom’ had non-zero exit status
ERROR: dependency ‘testthat’ is not available for package ‘nloptr’
* removing ‘/home/alpha/R/x86_64-pc-linux-gnu-library/4.2/nloptr’
Warning in install.packages :
installation of package ‘nloptr’ had non-zero exit status
ERROR: dependencies ‘minqa’, ‘nloptr’, ‘Rcpp’, ‘RcppEigen’ are not available for package ‘lme4’
* removing ‘/home/alpha/R/x86_64-pc-linux-gnu-library/4.2/lme4’
Warning in install.packages :
installation of package ‘lme4’ had non-zero exit status
ERROR: dependencies ‘lme4’, ‘broom’, ‘dplyr’ are not available for package ‘pbkrtest’
* removing ‘/home/alpha/R/x86_64-pc-linux-gnu-library/4.2/pbkrtest’
Warning in install.packages :
installation of package ‘pbkrtest’ had non-zero exit status
ERROR: dependencies ‘lme4’, ‘ggplot2’ are not available for package ‘lmerTest’
* removing ‘/home/alpha/R/x86_64-pc-linux-gnu-library/4.2/lmerTest’
Warning in install.packages :
installation of package ‘lmerTest’ had non-zero exit status
The downloaded source packages are in
‘/tmp/Rtmpu9oIUf/downloaded_packages’
Also if it helps
sessionInfo()
R version 4.2.1 (2022-06-23)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Manjaro Linux
Matrix products: default
BLAS: /usr/lib/libblas.so.3.10.1
LAPACK: /usr/lib/liblapack.so.3.10.1
locale:
[1] LC_CTYPE=en_AU.UTF-8 LC_NUMERIC=C LC_TIME=en_AU.UTF-8 LC_COLLATE=en_AU.UTF-8
[5] LC_MONETARY=en_AU.UTF-8 LC_MESSAGES=en_AU.UTF-8 LC_PAPER=en_AU.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=en_AU.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_4.2.1 fastmap_1.1.0 magrittr_2.0.3 htmltools_0.5.2 tools_4.2.1 yaml_2.3.5 rmarkdown_2.14
[8] stringi_1.7.6 knitr_1.39 digest_0.6.29 stringr_1.4.0 xfun_0.31 rlang_1.0.3 evaluate_0.15