[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 23:56:53 CEST 2016
Sorry, my bad! It really should be ok now. Thanks for your patience.
Dan
----- Original Message -----
> From: "Karim Mezhoud" <kmezhoud at gmail.com>
> To: "Dan Tenenbaum" <dtenenba at fredhutch.org>, "bioc-devel" <bioc-devel at 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 <dtenenba at fredhutch.org>
> wrote:
>
>> Sorry, about that, please try again.
>>
>> Dan
>>
>>
>> ----- Original Message -----
>> > From: "Karim Mezhoud" <kmezhoud at gmail.com>
>> > To: "Dan Tenenbaum" <dtenenba at 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 <dtenenba at 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" <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 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 <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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