We have an R environemnt running the latest versions of
Posit Workbench
Posit Connect
Posit Package Manger
each running on its own server. The servers are Alma Linux 9
When we try to install packages from our internal package manager, we get permissions errors on the Workbench server. It seems like its a global permission issue for all packages and users. Can someone please offer some assistance with this?
Blockquote
with_handlers html
wref_key html
zap html
zap_srcref html
*** copying figures
** building package indices
** testing if installed package can be loaded from temporary location
Error: package or namespace load failed for ‘rlang’ in library.dynam(lib, package, package.lib):
shared object ‘rlang.so’ not found
Error: loading failed
Execution halted
ERROR: loading failed
removing ‘/home/echarbon/R/x86_64-pc-linux-gnu-library/4.3/rlang’
Warning in install.packages :
installation of package ‘rlang’ had non-zero exit status
installing source package ‘yaml’ ...
** package ‘yaml’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘gcc (GCC) 11.4.1 20230605 (Red Hat 11.4.1-2)’
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I. -DNDEBUG -I/usr/local/include -fpic -g -O2 -c api.c -o api.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I. -DNDEBUG -I/usr/local/include -fpic -g -O2 -c dumper.c -o dumper.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I. -DNDEBUG -I/usr/local/include -fpic -g -O2 -c emitter.c -o emitter.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I. -DNDEBUG -I/usr/local/include -fpic -g -O2 -c implicit.c -o implicit.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I. -DNDEBUG -I/usr/local/include -fpic -g -O2 -c loader.c -o loader.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I. -DNDEBUG -I/usr/local/include -fpic -g -O2 -c parser.c -o parser.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I. -DNDEBUG -I/usr/local/include -fpic -g -O2 -c r_emit.c -o r_emit.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I. -DNDEBUG -I/usr/local/include -fpic -g -O2 -c r_ext.c -o r_ext.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I. -DNDEBUG -I/usr/local/include -fpic -g -O2 -c r_parse.c -o r_parse.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I. -DNDEBUG -I/usr/local/include -fpic -g -O2 -c reader.c -o reader.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I. -DNDEBUG -I/usr/local/include -fpic -g -O2 -c scanner.c -o scanner.o
gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I. -DNDEBUG -I/usr/local/include -fpic -g -O2 -c writer.c -o writer.o
gcc -shared -L/opt/R/4.3.2/lib/R/lib -L/usr/local/lib -o yaml.so api.o dumper.o emitter.o implicit.o loader.o parser.o r_emit.o r_ext.o r_parse.o reader.o scanner.o writer.o -L/opt/R/4.3.2/lib/R/lib -lR
installing to /home/echarbon/R/x86_64-pc-linux-gnu-library/4.3/00LOCK-yaml/00new/yaml/libs
Warning in file.copy(files, dest, overwrite = TRUE) :
problem copying ./yaml.so to /home/echarbon/R/x86_64-pc-linux-gnu-library/4.3/00LOCK-yaml/00new/yaml/libs/yaml.so: Operation not permitted
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package ‘yaml’
finding HTML links ... done
as.yaml html
read_yaml html
verbatim_logical html
write_yaml html
yaml.load html
** building package indices
** testing if installed package can be loaded from temporary location
Error: package or namespace load failed for ‘yaml’ in library.dynam(lib, package, package.lib):
shared object ‘yaml.so’ not found
Error: loading failed
Execution halted
ERROR: loading failed
removing ‘/home/echarbon/R/x86_64-pc-linux-gnu-library/4.3/yaml’
Warning in install.packages :
installation of package ‘yaml’ had non-zero exit status
ERROR: dependency ‘sys’ is not available for package ‘askpass’
removing ‘/home/echarbon/R/x86_64-pc-linux-gnu-library/4.3/askpass’
Warning in install.packages :
installation of package ‘askpass’ had non-zero exit status
ERROR: dependency ‘askpass’ is not available for package ‘openssl’
removing ‘/home/echarbon/R/x86_64-pc-linux-gnu-library/4.3/openssl’
Warning in install.packages :
installation of package ‘openssl’ had non-zero exit status
ERROR: dependencies ‘cli’, ‘curl’, ‘digest’, ‘jsonlite’, ‘openssl’, ‘rlang’, ‘yaml’ are not available for package ‘rsconnect’
removing ‘/home/echarbon/R/x86_64-pc-linux-gnu-library/4.3/rsconnect’
Warning in install.packages :
installation of package ‘rsconnect’ had non-zero exit status
The downloaded source packages are in
‘/tmp/RtmpdHkaZ3/downloaded_packages’
R version 4.3.2 (2023-10-31) -- "Eye Holes"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
Natural language support but running in an English locale
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
install.packages("abind")
Installing package into ‘/home/echarbon/R/x86_64-pc-linux-gnu-library/4.3’
(as ‘lib’ is unspecified)
trying URL 'https://positpkgmgrprd.strs.us/nystrs-cran/latest/src/contrib/abind_1.4-5.tar.gz'
Content type 'application/x-gzip' length 21877 bytes (21 KB)
==================================================
downloaded 21 KB
installing source package ‘abind’ ...
** package ‘abind’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package ‘abind’
finding HTML links ... done
abind html
acorn html
adrop html
afill html
asub html
** building package indices
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
DONE (abind)
The downloaded source packages are in
‘/opt/RPackages.tmp/Rtmp411zJf/downloaded_packages’
detach("package:base", unload = TRUE)
Error in detach("package:base", unload = TRUE) :
detaching "package:base" is not allowed
install.packages("ape")
Installing package into ‘/home/echarbon/R/x86_64-pc-linux-gnu-library/4.3’
(as ‘lib’ is unspecified)
also installing the dependencies ‘Rcpp’, ‘digest’
installing source package ‘Rcpp’ ...
** package ‘Rcpp’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘g++ (GCC) 11.4.1 20230605 (Red Hat 11.4.1-2)’
g++ -std=gnu++17 -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I../inst/include/ -I/usr/local/include -fpic -g -O2 -c api.cpp -o api.o
g++ -std=gnu++17 -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I../inst/include/ -I/usr/local/include -fpic -g -O2 -c attributes.cpp -o attributes.o
g++ -std=gnu++17 -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I../inst/include/ -I/usr/local/include -fpic -g -O2 -c barrier.cpp -o barrier.o
g++ -std=gnu++17 -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I../inst/include/ -I/usr/local/include -fpic -g -O2 -c date.cpp -o date.o
g++ -std=gnu++17 -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I../inst/include/ -I/usr/local/include -fpic -g -O2 -c module.cpp -o module.o
g++ -std=gnu++17 -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I../inst/include/ -I/usr/local/include -fpic -g -O2 -c rcpp_init.cpp -o rcpp_init.o
g++ -std=gnu++17 -shared -L/opt/R/4.3.2/lib/R/lib -L/usr/local/lib -o Rcpp.so api.o attributes.o barrier.o date.o module.o rcpp_init.o -L/opt/R/4.3.2/lib/R/lib -lR
installing to /home/echarbon/R/x86_64-pc-linux-gnu-library/4.3/00LOCK-Rcpp/00new/Rcpp/libs
Warning in file.copy(files, dest, overwrite = TRUE) :
problem copying ./Rcpp.so to /home/echarbon/R/x86_64-pc-linux-gnu-library/4.3/00LOCK-Rcpp/00new/Rcpp/libs/Rcpp.so: Operation not permitted
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package ‘Rcpp’
finding HTML links ... done
CppClass-class html
CppConstructor-class html
CppField-class html
CppFunction-class html
CppObject-class html
CppOverloadedMethods-class html
DollarNames-methods html
Module-class html
Module html
Rcpp-deprecated html
Rcpp-internal html
Rcpp-package html
Rcpp.package.skeleton html
Rcpp.plugin.maker html
RcppLdFlags html
RcppUnitTests html
compileAttributes html
compilerCheck html
cppFunction html
demangle html
dependsAttribute html
evalCpp html
exportAttribute html
exposeClass html
formals html
getRcppVersion html
interfacesAttribute html
loadModule html
loadRcppModules-deprecated html
pluginsAttribute html
populate html
registerPlugin html
setRcppClass html
sourceCpp html
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Error: package or namespace load failed for ‘Rcpp’ in library.dynam(lib, package, package.lib):
shared object ‘Rcpp.so’ not found
Error: loading failed
Execution halted
ERROR: loading failed
removing ‘/home/echarbon/R/x86_64-pc-linux-gnu-library/4.3/Rcpp’
Warning in install.packages :
installation of package ‘Rcpp’ had non-zero exit status
removing ‘/home/echarbon/R/x86_64-pc-linux-gnu-library/4.3/digest’
Warning in install.packages :
installation of package ‘digest’ had non-zero exit status
ERROR: dependencies ‘Rcpp’, ‘digest’ are not available for package ‘ape’
removing ‘/home/echarbon/R/x86_64-pc-linux-gnu-library/4.3/ape’
Warning in install.packages :
installation of package ‘ape’ had non-zero exit status
The downloaded source packages are in
‘/opt/RPackages.tmp/Rtmp411zJf/downloaded_packages’
.libpaths()
Error in .libpaths() : could not find function ".libpaths"