Just because git tells you to push, doesn't mean you should push! ;)
In the devel branch, the upstream repository is an svn repository, so instead
of pushing you want to do
git svn dcommit --add-author-from
I'll take a look at your earlier email later today.
Dan
----- Original Message -----
> From: "Karim Mezhoud" <kmezh...@gmail.com>
> To: "Dan Tenenbaum" <dtene...@fredhutch.org>
> Cc: "bioc-devel" <bioc-devel@r-project.org>
> Sent: Friday, April 1, 2016 5:17:32 AM
> Subject: Re: [Bioc-devel] 49 software packages either have no vignettes or
> their vignettes are not built by R CMD build!
> Hi,
> What is the meaning of this? Thanks
>
> git checkout devel
>
> Previous HEAD position was 1fe033d... add /image
> Switched to branch 'devel'
> Your branch is ahead of 'bioc/master' by 49 commits.
> (use "git push" to publish your local commits)
>
> git push
>
> fatal: The upstream branch of your current branch does not match
> the name of your current branch. To push to the upstream branch
> on the remote, use
>
> git push bioc HEAD:master
>
> To push to the branch of the same name on the remote, use
>
> git push HEAD:master
>
>
> ssh: Could not resolve hostname head: nodename nor servname provided, or
> not known
> fatal: Could not read from remote repository.
>
> Please make sure you have the correct access rights
>
>
>
> On Fri, Apr 1, 2016 at 1:09 AM, Karim Mezhoud <kmezh...@gmail.com> wrote:
>
>> 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 <dtene...@fredhutch.org>
>> wrote:
>>
>>>
>>>
>>>
>>>
>>> ----- Original Message -----
>>> > From: "Karim Mezhoud" <kmezh...@gmail.com>
>>> > To: "Dan Tenenbaum" <dtene...@fredhutch.org>
>>> > Cc: "bioc-devel" <bioc-devel@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 <dtene...@fredhutch.org>
>>> > wrote:
>>> >
>>> >>
>>> >>
>>> >> ----- Original Message -----
>>> >> > From: "Karim Mezhoud" <kmezh...@gmail.com>
>>> >> > To: "bioc-devel" <bioc-devel@r-project.org>
>>> >> > Cc: "Dan Tenenbaum" <dtene...@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 <
>>> dtene...@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@r-project.org mailing list
>>> >> >> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>>
>>
_______________________________________________
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
