[Bioc-devel] 49 software packages either have no vignettes or their vignettes are not built by R CMD build!

Karim Mezhoud kmezhoud at gmail.com
Fri Apr 1 02:09:37 CEST 2016 

Hi,
I repeated several times the clone ....And I success for one time the
commit but with mistakes. I can't repeat the steps again.

git merge master --log

And I had a conflict between versions. I omit conflicts and I

git svn dcommit --add-author-from

##############################
A....
A.....
A.....
All files are added


ERROR from SVN:
A repository hook failed: Commit blocked by pre-commit hook (exit code 1)
with output:
Traceback (most recent call last):
  File
"/extra/svndata/gentleman/svnroot/bioconductor/hooks/DESCRIPTION_hook/check_for_bad_version.py",
line 277, in <module>
    process_diff(diff)
  File
"/extra/svndata/gentleman/svnroot/bioconductor/hooks/DESCRIPTION_hook/check_for_bad_version.py",
line 112, in process_diff
    filename = segs0[1]
IndexError: list index out of range

W: bc9bed01f7b03d6da5b345d2699822d197b202b4 and refs/remotes/git-svn-devel
differ, using rebase:
:100644 100644 d4a2ec80b4623bc866606de39e06ff33e60056a8
cea7fa70e88adf9033fce5d7a846944c3431ee85 M    .gitignore
:100755 100755 6b7df529709f10184b376d69d5ea9f3ae9e1d3fe
15ac213b3484b967cceabc0c0e22bda2d654b27a M    DESCRIPTION
:040000 040000 e2c182ee6256b99e4c83e2dac8e7576fedeef302
7865b7a8f6a9e5e3b0bba7605de8f9e3abfb070a M    vignettes

It seems that there is already a rebase-apply directory, and
I wonder if you are in the middle of another rebase.  If that is the
case, please try
    git rebase (--continue | --abort | --skip)
If that is not the case, please
    rm -fr "/Volumes/DATA/canceRwrksp3/canceR/.git/rebase-apply"
and run me again.  I am stopping in case you still have something
valuable there.
rebase refs/remotes/git-svn-devel: command returned error: 1
@#####################################




I removed


rm -fr /Volumes/DATA/canceRwrksp3/canceR/.git/rebase-apply

and

git svn rebase

###########################
First, rewinding head to replay your work on top of it...
Applying: canceR0.99.1
Using index info to reconstruct a base tree...
.git/rebase-apply/patch:102: trailing whitespace.

.git/rebase-apply/patch:103: trailing whitespace.

.git/rebase-apply/patch:106: trailing whitespace.

.git/rebase-apply/patch:113: trailing whitespace.

.git/rebase-apply/patch:120: trailing whitespace.

warning: squelched 7388 whitespace errors
warning: 7393 lines add whitespace errors.
Falling back to patching base and 3-way merge...
error: The following untracked working tree files would be overwritten by
merge:
    vignettes/._canceR.pdf
Please move or remove them before you can merge.
Aborting
error: Failed to merge in the changes.
Patch failed at 0001 canceR0.99.1
The copy of the patch that failed is found in: .git/rebase-apply/patch

When you have resolved this problem, run "git rebase --continue".
If you prefer to skip this patch, run "git rebase --skip" instead.
To check out the original branch and stop rebasing, run "git rebase
--abort".

rebase refs/remotes/git-svn-devel: command returned error: 128
###############################

I did not found any whitespace in path file line: 102, 103, 106, 113, 120

patch file from 112 to 120:

*@@ -0,0 +1,73 @@*

*+Match_GeneList_MSigDB <- function(){*

*+    *

*+    *

*+    ttdialogMSigDB<-tktoplevel()*

*+    tktitle(ttdialogMSigDB) <- "Setting MSigDB Directory"*

*+    *

*+    fromDir <- function(){*

*+        ##Select directory which has MSigDB*

*+        myGlobalEnv$dirMSigDBPath <- tk_choose.dir()*

*+        tkdestroy(ttdialogMSigDB)*

*+        #return(dirMSigDBPath)*

*+    }*

*+    *

*+    fromExample <- function(){*

*+        ##Or select MSigDB from package*

*+        myGlobalEnv$dirMSigDBPath <-
paste(path.package("canceR"),"/extdata/MSigDB/",sep="")*

*+        tkdestroy(ttdialogMSigDB)*

*+        #return(dirMSigDBPath)*



 after I    git svn rebase

It seems that there is already a rebase-apply directory, and
I wonder if you are in the middle of another rebase.  If that is the
case, please try
    git rebase (--continue | --abort | --skip)
If that is not the case, please
    rm -fr "/Volumes/DATA/canceRwrksp3/canceR/.git/rebase-apply"
and run me again.  I am stopping in case you still have something
valuable there.
rebase refs/remotes/git-svn-devel: command returned error: 1

On Tue, Mar 29, 2016 at 8:12 PM, Dan Tenenbaum <dtenenba at fredhutch.org>
wrote:

>
>
>
>
> ----- Original Message -----
> > From: "Karim Mezhoud" <kmezhoud at gmail.com>
> > To: "Dan Tenenbaum" <dtenenba at fredhutch.org>
> > Cc: "bioc-devel" <bioc-devel at r-project.org>
> > Sent: Tuesday, March 29, 2016 12:05:03 PM
> > Subject: Re: [Bioc-devel] 49 software packages either have no vignettes
> or their vignettes are not built by R CMD build!
>
> > Thank you,
> > I am in devel branch (git checkout devel) .
> >
> > when I "git svn rebase" I get all changed files with message: needs
> update.
>
> This doesn't happen with me:
>
> clone https://github.com/kmezhoud/canceR.git
> cd canceR/
> ../mirror/update_remotes.sh
> git checkout devel
> git svn rebase
>
>
> No error. You might try doing a fresh clone in another directory.
>
> Dan
>
>
>
> > How can I update.
> > km
> >
> >
> >
> >
> > On Tue, Mar 29, 2016 at 4:16 PM, Dan Tenenbaum <dtenenba at fredhutch.org>
> > wrote:
> >
> >>
> >>
> >> ----- Original Message -----
> >> > From: "Karim Mezhoud" <kmezhoud at gmail.com>
> >> > To: "bioc-devel" <bioc-devel at r-project.org>
> >> > Cc: "Dan Tenenbaum" <dtenenba at fredhutch.org>
> >> > Sent: Tuesday, March 29, 2016 6:11:15 AM
> >> > Subject: Re: [Bioc-devel] 49 software packages either have no
> vignettes
> >> or their vignettes are not built by R CMD build!
> >>
> >> > Dear Dr Dan,
> >> > Thank you for this note.
> >> > In my case (canceR), I am using sweave and having:
> >> >
> >> > checking PDF version of manual ... [8s/19s]   OK
> >> >
> >> > during R CMD Check.
> >> >
> >> > I need to sync devel version using git-mirrors (
> >> > https://www.bioconductor.org/developers/how-to/git-mirrors/).
> >> > I am following scenario 2.
> >> > When I fork bioc-mirror/canceR I get two repo with the same name in my
> >> > github.
> >> >
> >>
> >> It sounds like you already had a github repository before the fork. In
> >> this case, do not fork, just run the update_remotes.sh script.
> >> Dan
> >>
> >>
> >> > at step 4 of tutorial, I can not push some changes:
> >> >
> >> > error: unable to read askpass response from 'rpostback-askpass'
> >> > fatal: could not read Username for 'https://github.com': Device not
> >> > configured
> >> >
> >> > 1- How can I configure access to bioc-mirror/canceR.
> >> >
> >> > 2- What is the utility of the fork if we can commit directly to
> >> > bioc-mirror/canceR?
> >> >
> >> > Thank you
> >> > Karim
> >> >
> >> >
> >> > On Wed, Mar 23, 2016 at 10:44 PM, Dan Tenenbaum <
> dtenenba at fredhutch.org>
> >> > wrote:
> >> >
> >> >> Attention package maintainers,
> >> >>
> >> >> When building an R package, if R thinks there is a vignette, it will
> >> emit
> >> >> this line during R CMD build:
> >> >>
> >> >> * creating vignettes ... OK
> >> >>
> >> >> If there is either no vignette, or in the case of non-sweave
> vignettes,
> >> >> something is not set up correctly (there are many things that can go
> >> >> wrong), you won't see that line of output.
> >> >>
> >> >> This means your vignette will not be available on our web site, nor
> to
> >> end
> >> >> users who install your package.
> >> >>
> >> >> So going to the build system and looking through all R CMD build
> output
> >> to
> >> >> see which output files do NOT have that line, returns 49 matches:
> >> >>
> >> >> $ grep -L "creating vignettes ..." *.buildsrc-out.txt
> >> >> a4Base.buildsrc-out.txt
> >> >> a4Classif.buildsrc-out.txt
> >> >> a4Core.buildsrc-out.txt
> >> >> a4Preproc.buildsrc-out.txt
> >> >> a4Reporting.buildsrc-out.txt
> >> >> affxparser.buildsrc-out.txt
> >> >> affyio.buildsrc-out.txt
> >> >> AffyTiling.buildsrc-out.txt
> >> >> aroma.light.buildsrc-out.txt
> >> >> arrayQuality.buildsrc-out.txt
> >> >> bigmemoryExtras.buildsrc-out.txt
> >> >> BiocCaseStudies.buildsrc-out.txt
> >> >> BiocGenerics.buildsrc-out.txt
> >> >> BiocInstaller.buildsrc-out.txt
> >> >> BufferedMatrixMethods.buildsrc-out.txt
> >> >> canceR.buildsrc-out.txt
> >> >> CGHbase.buildsrc-out.txt
> >> >> CoCiteStats.buildsrc-out.txt
> >> >> daMA.buildsrc-out.txt
> >> >> dcGSA.buildsrc-out.txt
> >> >> DynDoc.buildsrc-out.txt
> >> >> ExperimentHub.buildsrc-out.txt
> >> >> flipflop.buildsrc-out.txt
> >> >> GraphAT.buildsrc-out.txt
> >> >> HDF5Array.buildsrc-out.txt
> >> >> hypergraph.buildsrc-out.txt
> >> >> Icens.buildsrc-out.txt
> >> >> impute.buildsrc-out.txt
> >> >> mcaGUI.buildsrc-out.txt
> >> >> microRNA.buildsrc-out.txt
> >> >> minet.buildsrc-out.txt
> >> >> MSstats.buildsrc-out.txt
> >> >> multtest.buildsrc-out.txt
> >> >> netresponse.buildsrc-out.txt
> >> >> nondetects.buildsrc-out.txt
> >> >> normalize450K.buildsrc-out.txt
> >> >> oligoClasses.buildsrc-out.txt
> >> >> parglms.buildsrc-out.txt
> >> >> plier.buildsrc-out.txt
> >> >> preprocessCore.buildsrc-out.txt
> >> >> ProtGenerics.buildsrc-out.txt
> >> >> QUALIFIER.buildsrc-out.txt
> >> >> RPA.buildsrc-out.txt
> >> >> scde.buildsrc-out.txt
> >> >> seqplots.buildsrc-out.txt
> >> >> SJava.buildsrc-out.txt
> >> >> spotSegmentation.buildsrc-out.txt
> >> >> stepNorm.buildsrc-out.txt
> >> >> XVector.buildsrc-out.txt
> >> >>
> >> >> Some of these (a4Base, a4Classif and many more) just have no
> vignettes/
> >> >> directory so no vignettes at all.
> >> >>
> >> >>
> >> >> Others (ExperimentHub for example) have an empty vignettes directory.
> >> >>
> >> >> But others (QUALIFIER for example) have a vignettes directory with
> >> >> vignette files.
> >> >>
> >> >> If any packages you maintain do not have a vignette, please add one.
> >> >>
> >> >> If your package has a vignette in the vignettes/ directory but is in
> the
> >> >> above list, then you need to fix it.
> >> >>
> >> >> This page is a good place to start tracking down the problem:
> >> >>
> >> >> http://yihui.name/knitr/demo/vignette/
> >> >>
> >> >> For non-sweave (usually knitr) vignettes, the important things to
> check
> >> >> are:
> >> >>
> >> >> - knitr should be in the Suggests field in DESCRIPTION
> >> >>   (if using BiocStyle with rmarkdown, be sure BiocStyle and rmarkdown
> >> are
> >> >>   also in Suggests).
> >> >> - VignetteBuilder: knitr should be in DESCRIPTION
> >> >> - The actual vignette file should have a %\VignetteEngine line; see
> link
> >> >> above
> >> >>   for more information.
> >> >>
> >> >> How can you tell if you've fixed the problem?
> >> >> run R CMD build on your package and look for the line
> >> >>
> >> >> * creating vignettes ... OK
> >> >>
> >> >> In the output. If you don't see that line, your vignette has not been
> >> >> built.
> >> >>
> >> >> If you've tried all these things and are still running into problems,
> >> >> contact bioc-devel.
> >> >>
> >> >> Dan
> >> >>
> >> >> _______________________________________________
> >> >> Bioc-devel at r-project.org mailing list
> >> >> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>

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