[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 14:17:32 CEST 2016
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 <kmezhoud at 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 <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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