[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 21:08:45 CEST 2016
NO thing in the file
On Fri, Apr 1, 2016 at 6:24 PM, Dan Tenenbaum <dtenenba at fredhutch.org>
wrote:
> 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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