generateEasyConfig aborting

[verdurin]

I've followed the procedure outlined by @pescobar in easybuilders/easybuild-easyconfigs#3079.

In my case, I want to install all the Bioconductor packages and generate an EasyConfig for that.

When I run the script, I see this error:

./generateEasyConfig.R --tc foss/2016b --od $TMPDIR -ll DEBUG
2016-07-19 14:13:30 INFO::Log level set to INFO.
2016-07-19 14:13:30 INFO::Will store EasyConfig in /home/camp/huffmaa/tmp/R-3.3.1-foss-2016b.eb
Bioconductor version 3.3 (BiocInstaller 1.22.3), ?biocLite for help
2016-07-19 14:25:22 CRITICAL::Package  is not installed. Aborting!

Description:
    Generates an EasyBuild EasyConfig file from an existing R environment.
    Optionally you can first load a specific version of R using module load before generating the *.eb EasyConfig

Example usage:
    module load EasyBuild
    module load R
    generateEasyConfig.R  --tc  goolf/1.7.20 \
                          --od  /path/to/my/EasyConfigs/r/R/ \
                          --ll  WARNING

Explanation of options:
    --tc toolchain/version  EasyBuild ToolChain (required).
                               To get a list of available toolchains (may or may not be already installed):
                                   module load EasyBuild
                                   eb --list-toolchains
                               To check if a toolchain is already installed and if yes which version is the default:
                                   module -r -t avail -d '^name_of_toolchain$'
    --od path               Output Directory where the generated *.eb EasyConfig file will be stored (optional).
                               Will default to the current working directory as determined with getwd().
                               Name of the output file follows strict rules
                               and is automatically generated based on R version and toolchain.
    --ll LEVEL              Log level (optional).
                               One of FINEST, FINER, FINE, DEBUG, INFO (default), WARNING, ERROR or CRITICAL.

Note that the request to see the logging level to DEBUG doesn't work either.

[pescobar]

I also had this issue I had to edit the generateEasyConfig.R to remove the if sentence were this warning is triggered. After this workaround I could generate the easyconfig and the script only complains about 1 missing library. I couldn't spend more time to look for the root cause of the issue.

[verdurin]

Thanks, @pescobar - commenting out that check worked for me:

2016-07-19 15:42:12 INFO::Log level set to INFO.
2016-07-19 15:42:12 INFO::Will store EasyConfig in /home/camp/huffmaa/tmp/R-3.3.1-foss-2016b.eb
Bioconductor version 3.3 (BiocInstaller 1.22.3), ?biocLite for help
2016-07-19 16:11:24 WARNING::Failed to determine repo origin for package NA .
2016-07-19 16:11:24 WARNING::Failed to determine repo origin for 1 package!
2016-07-19 16:11:24 INFO::===========================================================================
2016-07-19 16:11:24 INFO::: Total R packages processed:                                1938
2016-07-19 16:11:24 INFO:::  * Resolved packages    (will be added to EasyConfig):     1937  ( 99.95%)
2016-07-19 16:11:24 INFO:::  * Unavailable packages (missing from EasyConfig):            1  (  0.05%)
2016-07-19 16:11:24 INFO::===========================================================================
2016-07-19 16:11:24 INFO::Finished!

Would be nice to know which is the miscreant package...

[pescobar]

nice that it also worked for you. I get the same output and the generated easyconfig can be installed properly I didn't get any complain from my users. But I agree it would be nice to identify which package triggers the problem.