[Bioc-devel] Git Problems and Dependence not available

Thu Nov 2 13:55:16 CET 2017

Hi Yuan,

To address your concerns:

1) The version bumps occur when we do a release.  You can see a similar thread here:

https://stat.ethz.ch/pipermail/bioc-devel/2017-November/012268.html

with main answers describing the version bumps that happen during a Bioconductor release

https://stat.ethz.ch/pipermail/bioc-devel/2017-November/012269.html

and

https://stat.ethz.ch/pipermail/bioc-devel/2017-November/012270.html

The version in release should increment from 2.10.0 if you would like the changes reflected on our build machine. So the next version bump in RELEASE_3_6 should be 2.10.1

The version in devel should increment from 2.11.0 to be consistent with the release branch.  Please correct the versioning to be higher than 2.11.0 (i.e 2.11.1) .  You seemed to have reverted back to 2.9.10.

To get the version bumps locally, and any changes that may have occurred from our end,

You should always start with a pull or fetch/merge from the upstream as documented here:

http://bioconductor.org/developers/how-to/git/pull-upstream-changes/

Before modifying local repositories, this will also help avoid git merge conflicts.

2) There is code for how to modify in both release and devel not having to change every file twice is documented here:

http://bioconductor.org/developers/how-to/git/bug-fix-in-release-and-devel/

The release is RELEASE_3_6  for every place that has RELEASE_X_Y

alternatively, you could change to the release branch and manually change all the files by

git fetch --all

git checkout RELEASE_3_6

<doing whatever changes necessary>

git commit

git push upstream <RELEASE_X_Y>
git push origin <RELEASE_X_Y>

3) Besides checkout out the upstream repository in a new location to verify the changes there is not a web version to look at like svn.  The build report should reflect the updated version numbers (provided they are higher than the previous version number) within 24 hours of pushing changes.

4) For now this is expected. There was a mailing list post sent out https://stat.ethz.ch/pipermail/bioc-devel/2017-November/012265.html

If the other two platforms build cleanly than you don't have to worry about windows at this time.

Lori Shepherd

Bioconductor Core Team

Roswell Park Cancer Institute

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263

________________________________
From: Bioc-devel <bioc-devel-bounces at r-project.org> on behalf of Yuan Tian <tianyuan1991hit at gmail.com>
Sent: Wednesday, November 1, 2017 11:58 PM
To: bioc-devel at r-project.org
Subject: [Bioc-devel] Git Problems and Dependence not available

Hello Dear Bioconductor Team and developers:

Sorry to interrupt all of you here. It's my first time to ask question via
bioc-devel email.

I am confused by current git-control version system. I am the author of ChAMP
package <https://bioconductor.org/packages/release/bioc/html/ChAMP.html> .
Previous I used an online CSS file in vignette from google. Now it seems
that css link is failed because Bioconductor check
<http://www.bioconductor.org/checkResults/3.6/bioc-LATEST/ChAMP/malbec1-buildsrc.html>
always
fail on that point.  It's easy to fix but now I don't know how to sent
fixed file to your system. I only used SVN before, never use git to
maintain Bioconductor package.

(1): In package link
<https://bioconductor.org/packages/release/bioc/html/ChAMP.html>, it shows
the ChAMP version is 2.9.9. However, in the Bioconducter check page
<http://www.bioconductor.org/checkResults/3.6/bioc-LATEST/ChAMP/malbec1-buildsrc.html>,
the version showing is 2.10.0? So where does this 2.10.0 version come from?

(2): I followed guild
<https://bioconductor.org/developers/how-to/git/maintain-bioc-only/> created
Bioconductor - Bioconductor -only repository<https://bioconductor.org/developers/how-to/git/maintain-bioc-only/>
bioconductor.org
Maintain a Bioconductor-only repository for an existing package. Goal: Developer wishes to maintain their Bioconductor repository without using GitHub.

repo on my personal Github and tried to push
<https://bioconductor.org/developers/how-to/git/push-to-github-bioc/> the
Push to GitHub and Bioconductor repositories<https://bioconductor.org/developers/how-to/git/push-to-github-bioc/>
bioconductor.org
Push to GitHub and Bioconductor repositories. Goal: During everyday development, you commit changes to your local repository master branch, and wish to push these ...

code. Finally I think I succeed, because my github repo
<https://github.com/JoshuaTian/ChAMP> shows version 2.9.10 now, and I also
[https://avatars1.githubusercontent.com/u/2176883?s=400&v=4]<https://github.com/JoshuaTian/ChAMP>

JoshuaTian/ChAMP<https://github.com/JoshuaTian/ChAMP>
github.com
Contribute to ChAMP development by creating an account on GitHub.

pushed upstream to Bioconductor, also seems succeed.  Now I can see
Bioconductor version 3.7 has been modified, and new package
<https://www.bioconductor.org/packages/3.7/bioc/html/ChAMP.html> and
vignette
<https://www.bioconductor.org/packages/3.7/bioc/vignettes/ChAMP/inst/doc/ChAMP.html>
is online. *But how to fix bug in Bioconductor version 3.6?* Previously,
when I use SVN system, I always modify both release version and development
version at the same time.

(3): Previously when I used SVN, after committing, I can always refresh the
SVN webpage to confirm changes, but now seems I can only see github change
on my github account, but not sure if Bioconductor have changed correctly?
Is there anyway I can see that? like old svn one
<https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/ChAMP/>
?

(4): Currently for Bioconductor version 3.7, ChAMP successfully compiled on
two system, but failed on windows, the error shows:

BioC 3.7: BUILD report for ChAMP on tokay2

##############################################################################
##############################################################################
###
### Running command:
###
###   chmod a+r ChAMP -R &&
C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD build
--keep-empty-dirs --no-resave-data ChAMP
###
##############################################################################
##############################################################################

* checking for file 'ChAMP/DESCRIPTION' ... OK
* preparing 'ChAMP':
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
      -----------------------------------
ERROR: dependencies 'minfi', 'ChAMPdata', 'FEM', 'DMRcate',
'IlluminaHumanMethylationEPICmanifest', 'sva',
'IlluminaHumanMethylation450kmanifest',
'IlluminaHumanMethylationEPICanno.ilm10b2.hg19', 'wateRmelon',
'goseq', 'missMethyl', 'GenomicRanges', 'bumphunter' are not available
for package 'ChAMP'
* removing 'C:/Users/biocbuild/bbs-3.7-bioc/tmpdir/RtmpiMSE8e/Rinst2efc5e455811/ChAMP'
In R CMD INSTALL
      -----------------------------------
ERROR: package installation failed

Why these dependencies are not available only on windows system? Is that
because I missed something? But seems Mac and Linux are both succeed.

Thanks for your helping. ^_^

Best
Yuan Tian

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