r-lib/backports

backports installs on CentOS but cannot be loaded

Closed this issue · 2 comments

helske commented

I can install backports from CRAN without any problems (except Rd warning), but when I try to load it I get following:

install.packages("backports")
Installing package into ‘/usr/lib64/R/library’
(as ‘lib’ is unspecified)
Warning in install.packages("backports") :
  'lib = "/usr/lib64/R/library"' is not writable
Would you like to use a personal library instead? (yes/No/cancel) y
trying URL 'https://cloud.r-project.org/src/contrib/backports_1.1.5.tar.gz'
Content type 'application/x-gzip' length 14798 bytes (14 KB)
==================================================
downloaded 14 KB

* installing *source* package ‘backports’ ...
** package ‘backports’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG   -I/usr/local/include  -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 dotsElt.c -o dotsElt.o
gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG   -I/usr/local/include  -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 dotsLength.c -o dotsLength.o
gcc -m64 -std=gnu99 -I"/usr/include/R" -DNDEBUG   -I/usr/local/include  -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 init.c -o init.o
gcc -m64 -std=gnu99 -shared -L/usr/lib64/R/lib -Wl,-z,relro -o backports.so dotsElt.o dotsLength.o init.o -L/usr/lib64/R/lib -lR
installing to /home/jovetale/R/x86_64-redhat-linux-gnu-library/3.6/00LOCK-backports/00new/backports/libs
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package ‘backports’
    finding HTML links ... done
    URLencode                               html
    anyNA                                   html
    backports-package                       html
    capture.output                          html
    dir.exists                              html
    dotsElt                                 html
    dotsLength                              html
    endsWith                                html
    file.info                               html
    file.size                               html
    get0                                    html
    hasName                                 html
    import                                  html
Rd warning: /tmp/RtmplnHXa3/R.INSTALLf1a2542f7681/backports/man/import.Rd:47: file link ‘.onLoad’ in package ‘base’ does not exist and so has been treated as a topic
    isFALSE                                 html
    isTRUE                                  html
    lengths                                 html
    startsWith                              html
    strrep                                  html
    trimws                                  html
    valid.factor                            html
    warningCondition                        html
** building package indices
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (backports)

The downloaded source packages are in
        ‘/tmp/RtmpH7Ng8V/downloaded_packages’

library(backports)
Error in library(backports) : there is no package called ‘backports’

SessionInfo:

R version 3.6.0 (2019-04-26)
Platform: x86_64-redhat-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)

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

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.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_3.6.0 tools_3.6.0

Tried both with latest version in CRAN and one earlier version, both have the same issue. Any idea what is going on?

mllg commented 
Warning in install.packages("backports") :
  'lib = "/usr/lib64/R/library"' is not writable
Would you like to use a personal library instead? (yes/No/cancel) y

My best guess: this is a permission problem on the file system.

Can you verify that you have a personal library? Can you install other packages?

helske commented

Yeah that seemed to be (at least part of) the problem. Manual creation of personal library allowed me to install and load backports, but then when installing checkmate (in same session with same personal library) got

Error: package or namespace load failed for ‘checkmate’:
 .onLoad failed in loadNamespace() for 'checkmate', details:
  call: loadNamespace(name)
  error: there is no package called ‘backports’
Error: loading failed

But it looks like this isn't about backports but my fresh server configuration or something. Thanks.