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.