R: install R 4.2.3 with Bioconductor 3.16 [IN05922352]

[balston]

User cannot install Bioconductor package inferCNV in R 4.2.0 and neither can I. I've also tried it using the latest R 4.2.2 Myriad installation and it still doesn't work.

Doing this should I think resolve the problem. R 4.2.3 was released on 15th March.

Need this on Myriad first.

[balston]

This cannot really wait for the Spack R build process so firstly updating the base R plus recommended packages build script.

[balston]

Running from build_scripts:

module -f unload compilers mpi gcc-libs
./R-4.2.3_install 2>&1 | tee ~/Software/R/R-4.2.3_install.log-17042023

[balston]

Build finished without errors. It also runs checks and the R regression tests and they have worked without errors as well. Will update the R base module file and then get the additional packages build script updated.

[balston]

Running from build_scripts:

./R-4.2.3_packages_install 2>&1 | tee ~/Software/R/R-4.2.3_packages_install.log-17042023

[balston]

The additional packages build finished about 11pm last night. Today I will check the output for errors.

We add about 675 additional packages (including automatic dependencies) which is why it takes so long to run!

[balston]

There is at least one real error:

Package: rgl:

** R
** demo
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
sh: line 1: 208295 Segmentation fault      R_TESTS= '/shared/ucl/apps/R/R-4.2.3-OpenBLAS/lib64/R/bin/R' --no-save --no-restore --no-echo 2>&1 < '/tmp/RtmpVUcYfl/file2f3bb5766cdb8'
ERROR: loading failed
* removing �/lustre/shared/ucl/apps/R/R-4.2.3-OpenBLAS/lib64/R/library/rgl�

The downloaded source packages are in
	�/tmp/Rtmpgz3U7J/downloaded_packages�
Warning message:
In install.packages("rgl", lib = mainLib, repos = repros) :
  installation of package �rgl� had non-zero exit status

Not sure if this is a real error:

package RcppParallel:

** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
readelf: Error: /lustre/shared/ucl/apps/R/R-4.2.3-OpenBLAS/lib64/R/library/00LOCK-RcppParallel/00new/RcppParallel/lib/libtbb.so: Failed to read file header
readelf: Error: /lustre/shared/ucl/apps/R/R-4.2.3-OpenBLAS/lib64/R/library/00LOCK-RcppParallel/00new/RcppParallel/lib/libtbbmalloc.so: Failed to read file header
readelf: Error: /lustre/shared/ucl/apps/R/R-4.2.3-OpenBLAS/lib64/R/library/00LOCK-RcppParallel/00new/RcppParallel/lib/libtbbmalloc_proxy.so: Failed to read file header
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (RcppParallel)
*

[balston]

The error building the rgl packages was caused by the runtime test failing due to an issue with the XQuartz X server running on my MacBook - even running the glxgears example failed!

Solution - use a working X server supporting OpenGL - in my case a Linux VM. Now running:

./R-4.2.3_single_package_install rgl 2>&1 | tee ~/Software/R/R-4.2.3_rgl_install.log

from the VM works.

[balston]

The RcppParallel package appears to have been installed correctly.

[balston]

Added MPI support packages:

./R-4.2.3_MPI_install 2>&1 | tee ~/Software/R/R-4.2.3_MPI_install.log-18042023

without errors.

[balston]

Module bundle done and single Bioconductor package build script done. To use R 4.2.3 the following module command are needed:

module -f unload compilers mpi gcc-libs
module load beta-modules
module load r/r-4.2.3_bc-3.16

[balston]

OK I've now tried to install inferCNV with R 4.2.3 from my userid using:

module -f unload compilers mpi gcc-libs
module load beta-modules
module load r/r-4.2.3_bc-3.16
R

if (!requireNamespace ("BiocManager"))
    install.packages ("BiocManager")
BiocManager::install ()
BiocManager::install ("infercnv")

And it still fails but only with the following error (had several errors before):

ERROR: dependency �rjags� is not available for package �infercnv�
* removing �/lustre/home/ccaabaa/R/x86_64-pc-linux-gnu-library/4.2/infercnv�

This is because I don't have a version of jags that can be used with R 4.2.3.

Solution = build one!