fgeorgatos / easybuild.experimental

This repository is for easybuild open source contributions without restrictions - add your username under the /users directory

easybuild.experimental

This git repo is a playground area for easybuild developers, as long as we all talk "Open Source" with no redistribution limits.

Basic headlines:

• You can freely create a directory bearing your github name under ./users and work in it as you wish
• simply present yourself and ask to be added as a collaborator in this repo, via the "Issues" of github
• commit/push directly and avoid completely any pull/request cycles - we have no time for that here
• thousands of easyconfig files built in a bulk fashion may become available, for example see a2ps under [contrib/pkgsrc],
• If you cross the boundary of 100 buildable easyconfigs in some kind of provably intelligent way (Reverse Turing test, anyone?), the repo owner will owe you an EasyBuild towel, delivered on his birthday as per http://en.wikipedia.org/wiki/Towel_Day
• whatever you do, remember the words of this pal [http://www.ece.cmu.edu/~ganger/712.fall02/papers/p761-thompson.pdf]

Now, jump to the wiki for more details:

https://github.com/fgeorgatos/easybuild.experimental/wiki/

and/or:

easybuilders/easybuild-framework#222 # initial motivation for this repo is visible here

easybuild.experimental's Issues

Missing deps for R-3.3?

Saw the following when trying to build @pneerincx R-3.3 easyconfig:

 eb ./R-3.3.0-foss-2015b.eb -dr --robot=./
== temporary log file in case of crash /tmp/eb-_K8bn9/easybuild-Ssr_AP.log
== resolving dependencies ...
ERROR: Irresolvable dependencies encountered: XZ/5.2.2-foss-2015b, pixman/0.32.8-foss-2015b, fontconfig/2.11.94-foss-2015b

on a RHEL 6.2 (ahem) system.

Error relating to the logging package when trying to generate R easyconfigs?

I see the following error when trying to run the script to generate an updated easyconfig for R:

Error in as.environment(pos) : using 'as.environment(NULL)' is defunct
Calls: <Anonymous> -> assign
Execution halted

This is with the Fedora R RPM on a Fedora 23 system, with Bioconductor installed using BiocLite (to pick up the versions from the 3.2 release).

The R version is 3.2.2.

request to be added as a collaborator

Hi,

I am Dina Mahmoud From Cairo University, I would like to be added as a collaborator .

Gimme access!!!

Hello

World

small issue when generating an R easyconfig

@pneerincx thanks for the useful script to generate an easyconfig for R

The only small problem I found is that I had to comment out this line so it works for me:
https://github.com/fgeorgatos/easybuild.experimental/blob/master/users/pneerincx/generateEasyConfig.R#L104

Before commenting out that line it was crashing and printing the help. After commenting it I get the easyconfig and this output:

2015-10-30 17:34:56 INFO::Log level set to INFO.
2015-10-30 17:34:56 INFO::Will store EasyConfig in /import/bc2/home/schwede/escobar/generate-R-easyconfig/R-3.2.2-goolf-1.7.20.eb
Bioconductor version 3.2 (BiocInstaller 1.20.0), ?biocLite for help
2015-10-30 17:40:52 WARNING::Failed to determine repo origin for package NA .
2015-10-30 17:40:52 WARNING::Failed to determine repo origin for 1 package!
2015-10-30 17:40:52 INFO::==========================================================================
2015-10-30 17:40:52 INFO::: Total R packages processed:                                415
2015-10-30 17:40:52 INFO:::  * Resolved packages    (will be added to EasyConfig):     414  ( 99.76%)
2015-10-30 17:40:52 INFO:::  * Unavailable packages (missing from EasyConfig):           1  (  0.24%)
2015-10-30 17:40:52 INFO::==========================================================================
2015-10-30 17:40:52 INFO::Finished!

maybe the script is not parsing correctly the name of one of my libraries?

thanks again for this nice contribution

Hello

World

Add ak352 as a collaborator

Hi,

Please add me as a collaborator in this github repository.

My account details -

1. Username - ak352
2. SSH key
   ssh-rsa AAAAB3NzaC1yc2EAAAADAQABAAABAQDQAlzF//0bVTzOlklkjL7aTMNjRucWXM+XtSmiA+OHY8A7gOiXwrnl1BWj8iESIaMvd+5dKM09nNuhDWrHywYH2KNeKTqx+XLbp08Hy3Ltdjak80jknyXcWY8ngpTLSdv+4XgqeMO4kRvPfPNYDqWk+ipujuSVcyr5pWdP75DVNvy5favgnleOzqo20JOhd7Pfcm9kbr1EMAKKo1rRYif7eaOLtlTXLLKz4QlPYM7k6F3ixyKHW6gMwRh1YHx7T+fOZA9qGdvoQH6frPyze2KrF/rPTa1G2V4tedcbHZ8A5VNDs682KR7pPNyLg5jq5w7xcUBh+tZ6jxY5MoHqwVlp [email protected]

Abhimanyu Krishna

generateEasyConfig aborting

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.

New contributor

Hi EasyBuild experimentalists,

I'm working at the University Medical Center Groningen (UMCG) and would like to contribute to this repo; Can you please add https://github.com/pneerincx

Cheers,

Pi

Hello

World

hi this is xaver42

ssh-rsa AAAAB3NzaC1yc2EAAAADAQABAAABAQC+wo0PmGIaBjXw9jTS+XdbMlzK6+zpBuG+x0bQO5qz8ZJG7oHdAT96uX8rV5t99iJwBKWOouMHk/U5pUSlkHkWwu9DPNwQKNhqXn5sgTOAVRYGBG1E2q0b8Gj41ETe+x24UTYf2JPxZUvLgauYuggyqfdK4y7JfwsO8pFOuXPCzbspQWRlIaVaSEoavVc5ltYj4TBEqq6a1E47FC0QHSxEzuZvHT2zQuPIIcki1Io2VWqC8FJePBhoGO5KXkoy9isCrCE7dxY96uXLRqNPt5CkwbVsKCBZ2Ot2qarihZlG9C7nPmiO9akTIgu8YNjsVRDkRoDo5vtuOo8iYYtLLb nilsch@xaver

Add cedric as collaborator

Hi,

I have already prepared a couple dozens easyconfig files and easyblocks as we all know ;).
Please add me as a collaborator in this github repository.

My public ssh key is

ssh-dss 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 cedric.laczny@helloworld

Tia,

Cedric

New contributor request

Hello

Please add me as a contributor to this repo.

My GitHub account is at:

https://github.com/verdurin

Thanks,
Adam