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 >> >>> >> >> _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
