Packages fail to install after migrating to Alma 9

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’

Thank you

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

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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’

trying URL 'https://positpkgmgrprd.strs.us/nystrs-cran/latest/src/contrib/Rcpp_1.0.12.tar.gz'
Content type 'application/x-gzip' length 3430499 bytes (3.3 MB)

downloaded 3.3 MB

trying URL 'https://positpkgmgrprd.strs.us/nystrs-cran/latest/src/contrib/digest_0.6.35.tar.gz'
Content type 'application/x-gzip' length 229176 bytes (223 KB)

downloaded 223 KB

trying URL 'https://positpkgmgrprd.strs.us/nystrs-cran/latest/src/contrib/ape_5.7-1.tar.gz'
Content type 'application/x-gzip' length 1583518 bytes (1.5 MB)

downloaded 1.5 MB

  • 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
  • installing source package ‘digest’ ...
    ** package ‘digest’ 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)’
    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. -I/usr/local/include -fpic -g -O2 -c SpookyV2.cpp -o SpookyV2.o
    gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I. -I/usr/local/include -fpic -g -O2 -c aes.c -o aes.o
    gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I. -I/usr/local/include -fpic -g -O2 -c blake3.c -o blake3.o
    gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I. -I/usr/local/include -fpic -g -O2 -c blake3_dispatch.c -o blake3_dispatch.o
    gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I. -I/usr/local/include -fpic -g -O2 -c blake3_portable.c -o blake3_portable.o
    gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I. -I/usr/local/include -fpic -g -O2 -c crc32.c -o crc32.o
    g++ -std=gnu++17 -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I. -I/usr/local/include -fpic -g -O2 -c crc32c.cpp -o crc32c.o
    g++ -std=gnu++17 -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I. -I/usr/local/include -fpic -g -O2 -c crc32c_portable.cpp -o crc32c_portable.o
    gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I. -I/usr/local/include -fpic -g -O2 -c digest.c -o digest.o
    gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I. -I/usr/local/include -fpic -g -O2 -c digest2int.c -o digest2int.o
    gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I. -I/usr/local/include -fpic -g -O2 -c init.c -o init.o
    gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I. -I/usr/local/include -fpic -g -O2 -c md5.c -o md5.o
    gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I. -I/usr/local/include -fpic -g -O2 -c pmurhash.c -o pmurhash.o
    gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I. -I/usr/local/include -fpic -g -O2 -c raes.c -o raes.o
    gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I. -I/usr/local/include -fpic -g -O2 -c sha1.c -o sha1.o
    gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I. -I/usr/local/include -fpic -g -O2 -c sha2.c -o sha2.o
    gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I. -I/usr/local/include -fpic -g -O2 -c sha256.c -o sha256.o
    g++ -std=gnu++17 -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I. -I/usr/local/include -fpic -g -O2 -c spooky_serialize.cpp -o spooky_serialize.o
    gcc -I"/opt/R/4.3.2/lib/R/include" -DNDEBUG -I. -I/usr/local/include -fpic -g -O2 -c xxhash.c -o xxhash.o
    g++ -std=gnu++17 -shared -L/opt/R/4.3.2/lib/R/lib -L/usr/local/lib -o digest.so SpookyV2.o aes.o blake3.o blake3_dispatch.o blake3_portable.o crc32.o crc32c.o crc32c_portable.o digest.o digest2int.o init.o md5.o pmurhash.o raes.o sha1.o sha2.o sha256.o spooky_serialize.o xxhash.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-digest/00new/digest/libs
    Warning in file.copy(files, dest, overwrite = TRUE) :
    problem copying ./digest.so to /home/echarbon/R/x86_64-pc-linux-gnu-library/4.3/00LOCK-digest/00new/digest/libs/digest.so: Operation not permitted
    ** R
    ** demo
    ** inst
    ** byte-compile and prepare package for lazy loading
    ** help
    *** installing help indices
    converting help for package ‘digest’
    finding HTML links ... done
    AES html
    digest html
    digest2int html
    hmac html
    makeRaw html
    sha1 html
    vdigest html
    ** building package indices
    ** installing vignettes
    ** testing if installed package can be loaded from temporary location
    Error: package or namespace load failed for ‘digest’ in library.dynam(lib, package, package.lib):
    shared object ‘digest.so’ not found
    Error: loading failed
    Execution halted
    ERROR: loading failed
  • 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"