Install Request: Upgrade R to 4.2.0 and Bioconductor to 3.15 [IN05264358]

[balston]

The latest R version currently on the clusters (R 4.1.1) cannot install the nlmixr package (Nonlinear Mixed Effects Models in Population PK/PD) as it depends on at least one other package (symengine) that requires at least R 4.2. This type of problem will become an increasing problem with older R versions.

• R 4.2.0 was released on 22nd April 2022 - https://cran.r-project.org/
• Bioconductor 3.15 was released on 27th April 2022 - http://bioconductor.org/

Note: This is the R version we should have as the default on RStudio from September 2022.

[balston]

Linked to Jira issue:

https://ucldata.atlassian.net/browse/RCE-877

[balston]

Building base R on Myriad first.

[balston]

Build script updated and uploaded to Myriad.

Building base R and recommended packages using:

cd /shared/ucl/apps/build_scripts
module unload -f compilers mpi gcc-libs
module load beta-modules
module load gcc-libs/10.2.0
module load compilers/gnu/10.2.0
module load openblas/0.3.13-serial/gnu-10.2.0
module load java/1.8.0_92
module load fftw/3.3.9/gnu-10.2.0
module load ghostscript/9.19/gnu-4.9.2
module load texinfo/6.6/gnu-4.9.2
module load texlive/2019
module load gsl/2.7/gnu-10.2.0
module load hdf/5-1.10.6/gnu-10.2.0
module load udunits/2.2.28/gnu-10.2.0
module load netcdf/4.8.1/gnu-10.2.0
module load pcre2/10.37/gnu-10.2.0
./R-4.2.0_install 2>&1 | tee ~/Software/R/R-4.2.0_install.log-25052022

[balston]

Build has completed. Looks OK so will make a module ready for the next stage of the build.

[balston]

Building additional packages using:

./R-4.2.0_packages_install 2>&1 | tee ~/Software//R//R-4.2.0_packages_install.log-25052022

Note: this will probably need running more than once.

[balston]

Myriad is now running the extra R packages build after a couple of minor issues - I had forgotten that Myriad needs extra modules for OpenMPI 4.0.5 and I had to remove the old adapt package as it fails to compile now (it is no longer on CRAN anyway).

[balston]

It has failed at attempting to build another old package not on CRAN (Design). Will remove and rerun tomorrow.

[balston]

Additional R and Bioconductor packages build completed. Now checking the log for problems.

[balston]

Possible problems:

readelf: Error: /lustre/shared/ucl/apps/R/R-4.2.0-OpenBLAS/lib64/R/library/00LOCK-RcppParallel/00new/RcppParallel/lib/libtbb.so: Failed to read file header
readelf: Error: /lustre/shared/ucl/apps/R/R-4.2.0-OpenBLAS/lib64/R/library/00LOCK-RcppParallel/00new/RcppParallel/lib/libtbbmalloc.so: Failed to read file header
readelf: Error: /lustre/shared/ucl/apps/R/R-4.2.0-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)

Install RcppParallel again to check.

* installing *source* package �protolite� ...
** package �protolite� successfully unpacked and MD5 sums checked
** using staged installation
Package protobuf was not found in the pkg-config search path.
Perhaps you should add the directory containing `protobuf.pc'
to the PKG_CONFIG_PATH environment variable
No package 'protobuf' found
Using PKG_CFLAGS=
Using PKG_LIBS=-lprotobuf
<stdin>:1:10: fatal error: google/protobuf/message.h: No such file or directory
compilation terminated.
------------------------- ANTICONF ERROR ---------------------------
Configuration failed because protobuf was not found. Try installing:
 * deb: libprotobuf-dev (Debian, Ubuntu, etc)
 * rpm: protobuf-devel (Fedora, EPEL)
 * csw: protobuf_dev (Solaris)
 * brew: protobuf (OSX)
If protobuf is already installed, check that 'pkg-config' is in your
PATH and PKG_CONFIG_PATH contains a protobuf.pc file. If pkg-config
is unavailable you can set INCLUDE_DIR and LIB_DIR manually via:
R CMD INSTALL --configure-vars='INCLUDE_DIR=... LIB_DIR=...'
--------------------------------------------------------------------
ERROR: configuration failed for package �protolite�

This one needs fixing because:

ERROR: dependency �protolite� is not available for package �geojson�
* removing �/lustre/shared/ucl/apps/R/R-4.2.0-OpenBLAS/lib64/R/library/geojson�

[balston]

I've reinstalled RcppParallel using:

./R-4.2.0_single_package_install RcppParallel

and it has installed correctly as far as I can tell.

[balston]

Protobuf protobuf/3.17.3/gnu-10.2.0 wasn't installed on Myriad. Installing with:

module -f unload compilers mpi gcc-libs
module load beta-modules
module load gcc-libs/10.2.0
module load compilers/gnu/10.2.0
module load python3/3.9-gnu-10.2.0
./protobuf-3.17.3_install

[balston]

Redone geojsonio using:

./R-4.2.0_single_package_install geojsonio