recountWorkflow

[lcolladotor]

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• Repository: https://github.com/LieberInstitute/recountWorkflow

Note that this package is a workflow and not a software package.

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[lcolladotor]

Hi,

I just pushed version 0.99.20 to https://github.com/LieberInstitute/recountWorkflow that includes the link to https://f1000research.com/articles/6-1558/v1 that was made public today.

Best, Leo

[vobencha]

Sorry this hasn't been added to the repo yet. I think I dropped the ball and forgot to ask @lshep to add this to the workflow repository.

Just fyi, the workflows will stay in svn for the time being. We'll migrate these to git after the dust from the software transition has settled.

[lshep]

Hi @lcolladotor I will look at adding recountWorkflow first thing tomorrow.

[lshep]

You should receive an additional email within the new few days with credentials for updating and maintaining. The recountWorkflow has been added and should appear shortly on the website. Cheers ~Lori

[vobencha]

Thanks Lori!

[lcolladotor]

Thanks Lori!

In the biocbuild emails I see errors like this:

* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
      -----------------------------------
* installing *source* package ‘recountWorkflow’ ...
** help
No man pages found in package  ‘recountWorkflow’
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Error: package or namespace load failed for ‘recountWorkflow’ in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]):
 namespace ‘recount’ 1.2.3 is being loaded, but >= 1.3.2 is required
Error: loading failed
Execution halted
ERROR: loading failed

I wrote the description file with Bioc-devel dependencies in mind since that's what was used by the SPB but I can switch it to Bioc-release if necessary.

Best, Leo

[lshep]

sorry about that. It is an issue we are trying to remedy as the workflow currently build on the release version of R. Can you please update to use the release?

[lshep]

Once Martin sends over credentials you will be able to make the changes on our system and it should kick off a new build automatically.

[lcolladotor]

Ok, will do! I'll wait for Martin to send over the credentials.

[mtmorgan]

The repos has been configured so that svn user l.collado-torres has access.

[lcolladotor]

Hi @lshep,

Most of the bioc-devel dependencies can be switched to bioc-release ones. The minor exceptions are:

• recount 1.3.3: same as 1.2.3 in release
• regionReport 1.11.2: same as 1.10.2 in release
• clusterProfiler 3.5.5: changing back to 3.4.4 requires changing the spelling of one argument. Easy.
• BiocStyle 2.5.19: requires changing the name of the HTML function used for the vignette. Easy.

However, there's a rather large change that I can't port back to bioc-release. That's the bumphunter 1.17.2 requirement. That's related to https://github.com/rafalab/bumphunter/issues/15 that hasn't been changed in the bioc-release branch. I had forgotten about it.

Since switching the workflow builder to bioc-devel is a work in progress, is there an option to add the workflow manually for now?

Otherwise I can ask bumphunter's maintainers to back-port 1.17.2 to the release branch.

A third option would be to stop evaluating the code chunks that depend on bumphunter and include the pre-made images (I use bumphunter's output to eventually make some images). But that doesn't sound right, since bioc-release users wouldn't be able to run the code (aka, there would be a mismatch between the session info and the output).

Best, Leo

[lshep]

@lcolladotor looking into this and will respond soon.

[mtmorgan]

The options are to make recountWorkflow work with current release dependencies, or to delay adding recountWorkflow until immediately after the next release (end of October?). In the 'short' term (several months) can't do anything other that that. What would you like to do?

[lcolladotor]

Hi,

I modified the workflow to work with bioc-release https://github.com/LieberInstitute/recountWorkflow/commit/7971b2c698197597707ce8cd7d0cc4cbc92a72e2 ** and hopefully bumphunter 1.17.2 will be merged to bioc-release (to say 1.16.1) following https://github.com/rafalab/bumphunter/issues/19. At that point or when Bioconductor 3.6 is released, I'll modify back the workflow.

Best, Leo

** And I pushed the changes using svn. I'm just keeping track of things with git separately.