[Bioc-devel] 49 software packages either have no vignettes or their vignettes are not built by R CMD build!
Karim Mezhoud
kmezhoud at gmail.com
Fri Apr 1 23:25:56 CEST 2016
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
> >> >> >> >>>
> >> >> >> >>
>
[[alternative HTML version deleted]]
More information about the Bioc-devel
mailing list