NO thing in the file On Fri, Apr 1, 2016 at 6:24 PM, Dan Tenenbaum <dtene...@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" <kmezh...@gmail.com> > > To: "Dan Tenenbaum" <dtene...@fredhutch.org> > > Cc: "bioc-devel" <bioc-devel@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 <dtene...@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" <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 > >> >>> > >> >> > [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
