Installing additional extensions

eb 3.9.4
Module: R-3.6.0-foss-2019a.eb

I have downloaded the following extensions to: .../path/R/extensions
poppr adegenet ape ggplot2 mmod treemap

trying to install them via:
$ eb R-3.6.0-foss-2019a.eb --skip --rebuild

'no differences found' (between backup and original files)

What am I doing wrong/missing?

[boegel]

@rg-roth If you want to install additional extensions, you'll need to (copy and) modify the R-3.6.0-foss-2019a.eb easyconfig file to list the additional extensions + accompanying version.

If done correctly, the necessary source tarballs for those extensions will be downloaded automatically, you don't need to do that yourself.

@boegel thanks for the prompt reply...

it seems a bit tricky (at least for me, a noob).

E.g.: poppr_2.8.3.tar.gz how would I know whether it is 'base', 'datasets ', 'graphics', etc (order of packages is important as stated in the R-3.6.0-foss-2019a.eb file).

Would you be able to put me in the right direction??

[boegel]

@rg-roth Just add additional extensions to the end of the list in exts_list.

exts_list = [
   ...
   ('poppr', '2.8.3'),
]

The first couple of entries are special (they're built-in packages which are just checked, not actually installed).

@boegel In fact the acutal module the users needs the extensions installed is: R-bundle-Bioconductor/3.9-foss-2019a-R-3.6.0

I added only poppr 2.8.3 to file: R-bundle-Bioconductor-3.9-foss-2019a-R-3.6.0.eb

('poppr', '2.8.3', { 'checksums': ['3f6c1badfed4655fea303e375ff1aa4386bd2f41ef6d170651d3563c76591a95'], }),
run
$ eb R-bundle-Bioconductor-3.9-foss-2019a-R-3.6.0.eb --skip --rebuild

run.py:219 INFO running cmd: R CMD INSTALL .../eb/sources/r/R-bundle-Bioconductor/extensions/poppr_2.8.3.tar.gz --library=.../eb/software/R-bundle-Bioconductor/3.9-foss-2019a-R-3.6.0/ --no-clean-on-error == 2019-11-12 13:09:49,301 build_log.py:164 ERROR EasyBuild crashed with an error (at easybuild/base/exceptions.py:124 in __init__): cmd " R CMD INSTALL .../eb/sources/r/R-bundle-Bioconductor/extensions/poppr_2.8.3.tar.gz --library=.../eb/software/R-bundle-Bioconductor/3.9-foss-2019a-R-3.6.0/ --no-clean-on-error " exited with exit code 1 and output: **ERROR: dependencies adegenet, pegas, polysat are not available for package poppr** == 2019-11-12 13:09:49,302 easyblock.py:3082 WARNING build failed (first 300 chars): cmd " R CMD INSTALL .../eb/sources/r/R-bundle-Bioconductor/extensions/poppr_2.8.3.tar.gz --library=.../eb/software/R-bundle-Bioconductor/3.9-foss-2019a-R-3.6.0/ --no-clean-on-error " exited with exit code 1 and output: == 2019-11-12 13:09:49,303 build_log.py:260 INFO FAILED: Installation ended unsuccessfully (build directory: .../eb/build/RbundleBioconductor/3.9/foss-2019a-R-3.6.0): build failed (first 300 chars): cmd " R CMD INSTALL .../eb/sources/r/R-bundle-Bioconductor/extensions/poppr_2.8.3.tar.gz --library=.../eb/software/R-bundle-Bioconductor/3.9-foss-2019a-R-3.6.0/ --no-clean-on-error " exited with exit code 1 and output: == 2019-11-12 13:09:49,306 build_log.py:164 ERROR EasyBuild crashed with an error (at easybuild/base/exceptions.py:124 in __init__): build failed (first 300 chars): cmd " R CMD INSTALL .../eb/sources/r/R-bundle-Bioconductor/extensions/poppr_2.8.3.tar.gz --library=.../eb/software/R-bundle-Bioconductor/3.9-foss-2019a-R-3.6.0/ --no-clean-on-error " exited with exit code 1 and output: == 2019-11-12 13:09:49,308 build_log.py:164 ERROR EasyBuild crashed with an error (at easybuild/base/exceptions.py:124 in __init__): Build of .../eb/ebfiles_repo/R-bundle-Bioconductor/R-bundle-Bioconductor-3.9-foss-2019a-R-3.6.0.eb failed (err: 'build failed (first 300 chars): cmd " R CMD INSTALL .../eb/sources/r/R-bundle-Bioconductor/extensions/poppr_2.8.3.tar.gz --library=.../eb/software/R-bundle-Bioconductor/3.9-foss-2019a-R-3.6.0/ --no-clean-on-error " exited with exit code 1 and output:\nERROR: dependencies adegenet, pegas, polysat are not available fo') (at easybuild/main.py:147 in build_and_install_software)

I then amended file: R-bundle-Bioconductor-3.9-foss-2019a-R-3.6.0.eb, inserting
('polysat', '1.7.4', {
'checksums': ['b721a790d3a079989c4e99e33e62035a4cf0c00691f071ed0f27084d669c5522'],
}),
('adegenet', '2.1.1', {
'checksums': ['3043fe5d731a38ff0e266f090dcda448640c3d0fd61934c76da32d082e5dce7a'],
}),`

then it complains that adegenet needs spdep 1.1-3; then amend again and it complains about sf 0.8-0

Does it mean that installing extensions is a trial and error exercise, with several iterations until you find all dependencies? (mind you https://cran.r-project.org/web/packages does not seem to list all dependencies).

Wondering if you/someone could assist?

[boegel]

@rg-roth Yes, it's a bit of a painful exercises indeed.

EasyBuild deliberately disables auto-installing the dependencies of R packages, and thus forces you to list all dependencies, and in the right order.
This is done to ensure reproducibility of installations.

Doing this manually through trial-and-error is annoying and time-consuming, but there is a better way: see the easy_update tool provided by @fizwit at https://github.com/fizwit/easy_update.

If I remember correctly it supports adding an additional extension to an existing easyconfig file + all required missing dependency packages with a single command.