[Bioc-devel] Git Problems and Dependence not available

[Yuan Tian]

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
repo on my personal Github and tried to push
<https://bioconductor.org/developers/how-to/git/push-to-github-bioc/> the
code. Finally I think I succeed, because my github repo
<https://github.com/JoshuaTian/ChAMP> shows version 2.9.10 now, and I also
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

	[[alternative HTML version deleted]]