Sorry, my bad! It really should be ok now. Thanks for your patience. Dan
----- Original Message ----- > From: "Karim Mezhoud" <kmezh...@gmail.com> > To: "Dan Tenenbaum" <dtene...@fredhutch.org>, "bioc-devel" > <bioc-devel@r-project.org> > Sent: Friday, April 1, 2016 2:25:56 PM > Subject: Re: [Bioc-devel] 49 software packages either have no vignettes or > their vignettes are not built by R CMD build! > git clone https://github.com/Bioconductor-mirror/canceR > cd canceR/ > bash ../update_remotes.sh > Already on 'master' > Your branch is up-to-date with 'origin/master'. > Rebuilding > .git/svn/refs/remotes/git-svn/.rev_map.bc3139a8-67e5-0310-9ffc-ced21a209358 > ... > r100351 = 942469704de53586b277926f1b3d358ffd808152 > r100809 = 0aa2b86471d49cace7d4baa504684c2e86f47830 > r100810 = 3940d764844e9051172fd1d05fe606ee56764e67 > r100984 = 55fba8349ef754fc51a78367c19a8bc8f29b881e > r100985 = b313b60029281d2c8486d0dc9e6a34c2f68fd9be > r100987 = a8cd3e44badee5b04548fff7a9faeca2f8448489 > r101023 = f625ce6a1d225016103768be2e051593ba785832 > r102448 = a2c8236451c5e04cc1e43f4568472de8ea8361ba > r102571 = f6fc58dd50aa611f3b1930fd850df9c5471c7f94 > r102584 = fdd1ce259835d1325645a17e80affa4f0656fc41 > r102591 = 2e2874d3ad1d00f3599dcdc6ef7347199dc8b651 > r102594 = 363ea15b52e2c00cc063c1bffeb167c70390769c > r102693 = 535c658791a5218ad341b329c2e049c4b04c9584 > r102694 = 26c26df43c2ddf12008543e4f647f135bde63cf7 > r102695 = af7cd2771d0695bb92c4d6a433b545cf63940463 > r102854 = 954b8510e0fe68211fc315787a1c866ad237e8a5 > r103140 = f042db172a7f04f00c04ca9e233df54bbc1746a1 > r103142 = efb740a41e489809c91cd6f3a42516adddb6b050 > r103607 = 1b9435efea2dd8d14593ad500f59623bcecbe155 > r106326 = c9a8e4f83e33c277e26b58b03848c8bb304b9571 > r106461 = 9726cf88862426c96fbbd238321599e99444fd12 > r109589 = 88ef0e88bb6ab106d53100787d698672d6f44bac > r109592 = a8299618231a8ce2891e20310f4cbf2fddc24526 > r115378 = 1da8432c11ae9cbc38950c22e16093fc4c97853f > r115379 = 2592b6a5ac7c41003611ce44b93ff9b6ac8c5a54 > r115385 = 7fbc307287b25ff7efe7235001921791f2668898 > r115387 = 1fe033d9fdd765f6c7e6a2a884053721bbd5691a > r115608 = 025a596f5f717b527b9a5c92612d48a09e93f0a8 > Done rebuilding > .git/svn/refs/remotes/git-svn/.rev_map.bc3139a8-67e5-0310-9ffc-ced21a209358 > Current branch master is up to date. > Commit to git as normal, when you want to push your commits to svn > 1. `git svn rebase` to get the latest SVN changes. > 2. `git svn dcommit --add-author-from` to commit your changes to SVN. > > > add files/forder to /vignette > pump version DESCRIPTION > > git commit -m "fix vignette" > git svn rebase > Current branch master is up to date. > > git svn dcommit --add-author-from > Committing to > https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/canceR ... > A vignettes/canceR.Rnw > A vignettes/canceR.latex > A vignettes/image/BrstPrstGSEAlm.png > A vignettes/image/whichMSigDB2.jpeg > A vignettes/image/workspace.png > M vignettes/.gitignore > > 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 283, in <module> > myexit(0) > TypeError: myexit() takes exactly 2 arguments (1 given) > > W: 35d29461f59277e54461a31161c6522053c666ad and refs/remotes/git-svn > differ, using rebase: > :040000 040000 e29c612e777ebd221293caaccbfb810b293addd0 > 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. > > git diff > > > No thing > > > > On Fri, Apr 1, 2016 at 9:48 PM, Dan Tenenbaum <dtene...@fredhutch.org> > wrote: > >> Sorry, about that, please try again. >> >> Dan >> >> >> ----- Original Message ----- >> > From: "Karim Mezhoud" <kmezh...@gmail.com> >> > To: "Dan Tenenbaum" <dtene...@fredhutch.org> >> > Sent: Friday, April 1, 2016 1:36:30 PM >> > Subject: Re: [Bioc-devel] 49 software packages either have no vignettes >> or their vignettes are not built by R CMD build! >> >> > git reset --hard HEAD~ >> > bash ../update_remotes.sh >> > >> > add files/folder to / vignette >> > pump version in DESCRIPTION >> > check all change >> > git commit -m "fix vignette" >> > git svn rebase >> > git svn dcommit --add-author-from >> > Committing to >> > https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/canceR ... >> > 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/stadGSEAlm2.jpeg >> > A vignettes/image/stadGSEAlm3.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 283, in <module> >> > process_diff(diff) >> > File >> > >> "/extra/svndata/gentleman/svnroot/bioconductor/hooks/DESCRIPTION_hook/check_for_bad_version.py", >> > line 118, in process_diff >> > filename = segs0[1] >> > IndexError: list index out of range >> > >> > W: 989187ef342a32768b73a4a852bf20aaee9f2dec and refs/remotes/git-svn >> > differ, using rebase: >> > :100755 100755 47dcc306473ddd67eb11ec42423b30991b72099c >> > 6b7df529709f10184b376d69d5ea9f3ae9e1d3fe M DESCRIPTION >> > :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. >> > >> > MBP-de-MacBook:canceR Mezhoud$ git diff >> > MBP-de-MacBook:canceR Mezhoud$ >> > >> > NO THING IN DIFF >> > >> > >> > On Fri, Apr 1, 2016 at 8:13 PM, Dan Tenenbaum <dtene...@fredhutch.org> >> > wrote: >> > >> >> [removing bioc-devel from the thread] >> >> >> >> Please try the git svn dcommit again, I have modified the post commit >> hook. >> >> >> >> 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 12:08:45 PM >> >> > Subject: Re: [Bioc-devel] 49 software packages either have no >> vignettes >> >> or their vignettes are not built by R CMD build! >> >> >> >> > 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 >> >> >> >> >>> >> >> >> >> >> _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel