[Bioc-devel] 49 software packages either have no vignettes or their vignettes are not built by R CMD build!
Dan Tenenbaum
dtenenba at fredhutch.org
Fri Apr 1 19:24:54 CEST 2016
Can you send me the output of
git diff?
So:
git diff > diff.txt
and send me diff.txt?
Dan
----- 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: Friday, April 1, 2016 9:27:52 AM
> Subject: Re: [Bioc-devel] 49 software packages either have no vignettes or their vignettes are not built by R CMD build!
> Hi,
> I tried the scenario 1:
> git clone https://github.com/Bioconductor-mirror/canceR
> cd canceR
>
> bash ../update_remotes.sh
> add files/dir in /vignette
> pump version in DESCRIPTION
>
> commit -m "fix vignette"
> git svn rebase
> git svn dcommit --add-author-from
>
>
> MBP-de-MacBook:canceR Mezhoud$ git svn dcommit --add-author-from
> Committing to
> https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/canceR ...
> A inst/doc/canceR.pdf
> A vignettes/canceR.Rnw
> A vignettes/canceR.latex
> A vignettes/image/BrstPrstGSEAlm.png
> A vignettes/image/BrstPrstGSEAlm1.jpeg
> A vignettes/image/BrstPrstGSEAlm2.jpeg
> A vignettes/image/BrstPrstGSEAlm3.jpeg
> A vignettes/image/BrstPrstGSEAlm4.jpeg
> A vignettes/image/Circos.png
> A vignettes/image/Coxph.png
> A vignettes/image/GSEA-R.png
> A vignettes/image/Mutation1.png
> A vignettes/image/clinicalDataDialog.png
> A vignettes/image/dialogCircos.png
> A vignettes/image/gct_cls.png
> ..............
> A vignettes/image/setWorkspace.jpeg
> A vignettes/image/stadGSEAlm4.jpeg
> A vignettes/image/stadGSEAlm5.jpeg
> A vignettes/image/stadGSEAlm6.jpeg
> A vignettes/image/stadGSEAlm7.jpeg
> A vignettes/image/stadGSEAlm8.jpeg
> A vignettes/image/stadGSEAlm9.jpeg
> A vignettes/image/stadGSEAlmCNA.png
> A vignettes/image/starting.png
> A vignettes/image/starting.svg
> A vignettes/image/startingWindow.jpeg
> A vignettes/image/whichMSigDB.png
> A vignettes/image/whichMSigDB1.jpeg
> A vignettes/image/whichMSigDB2.jpeg
> A vignettes/image/workspace.png
> M DESCRIPTION
>
> 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: e980c09a87a818a1736f38304e18325b7c0362f5 and refs/remotes/git-svn
> differ, using rebase:
> :100755 100755 d4a308bbf85b4f0ba06ee27af51f1e76804bad2a
> 6b7df529709f10184b376d69d5ea9f3ae9e1d3fe M DESCRIPTION
> :040000 040000 de5dbdd606d8758565afcadbaf04e5821e71b461
> 870588b10784e8f5169b2f7bf6377985edd3a735 M inst
> :040000 040000 056451883aa9ba2af9e19f8dd2a285d412b9ae60
> 7865b7a8f6a9e5e3b0bba7605de8f9e3abfb070a M vignettes
> Current branch master is up to date.
> ERROR: Not all changes have been committed into SVN, however the committed
> ones (if any) seem to be successfully integrated into the working tree.
> Please see the above messages for details.
>
>
> On Fri, Apr 1, 2016 at 4:27 PM, Dan Tenenbaum <dtenenba at fredhutch.org>
> wrote:
>
>> 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" <kmezhoud at gmail.com>
>> > To: "Dan Tenenbaum" <dtenenba at fredhutch.org>
>> > Cc: "bioc-devel" <bioc-devel at 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 <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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