----- Original Message ----- > From: "Dan Tenenbaum" <dtene...@fredhutch.org> > To: "Adam Mark" <adam.mai...@gmail.com> > Cc: "bioc-devel" <bioc-devel@r-project.org> > Sent: Monday, July 6, 2015 2:54:43 PM > Subject: Re: [Bioc-devel] mygene problems reported by the "Build/check > report" for BioC 3.1 > > > > ----- Original Message ----- > > From: "Adam Mark" <adam.mai...@gmail.com> > > To: "Dan Tenenbaum" <dtene...@fredhutch.org> > > Sent: Monday, July 6, 2015 2:43:51 PM > > Subject: Re: mygene problems reported by the "Build/check report" > > for BioC 3.1 > > > > > > Hi Dan, > > > > > > Thanks for your help. I was able to fix my issue. Also I am having > > trouble committing changes to my release branch. I usually get > > confused at this part. Here are the steps I take: > > > > > > cd devel > > svn update > > <make changes> > > svn commit -m "made some changes" > > cd ../release > > svn merge <last revision>:<latest revision> url of devel > > > > > > Be really careful when you do this. Whenever you make a change that > you want to propagate to our repositories (and to be available via > biocLite()) you need to increase its version number. You didn't > actually do that in devel (you want to change the value of the > Version field in DESCRIPTION to 1.4.1).
Oops, that should say 1.5.0, see below. Dan > > However, version numbers need to be different in release and devel, > see http://bioconductor.org/developers/how-to/version-numbering/ > > So, if you had bumped the version number in devel and then done svn > merge as above, and then committed, you would have copied the wrong > version number into release which would really mess things up. > Luckily you didn't do that. > > Since your change was relatively simple and just affected one file, I > would simply make the change manually in release. Or if that file > has no other differences between release and devel, just copy the > file (using cp) from devel/R to release/R. Then bump the version in > release (from 1.2.0 to 1.2.1). > > And don't forget to bump the version in devel as well. Note that > sometime in June you bumped the version from 1.3.0 to 1.4.0, which > you should not do. As mentioned at the link above, the y in the > x.y.z version number must always be even in release and odd in > devel. Also, version numbers can't go down, so you need to bump the > version in devel to 1.5.0. > > Dan > > > > > I have somehow completed this task and made it work but lately I am > > getting this: svn: E160005: Cannot replace a directory from within > > Thanks again for your advice. > > > > > > Adam > > > > > > > > > > On Mon, Jul 6, 2015 at 10:39 AM, Dan Tenenbaum < > > dtene...@fredhutch.org > wrote: > > > > > > [CC'ing bioc-devel because this kind of thing often happens and the > > info below is generally helpful in these cases.] > > > > ----- Original Message ----- > > > From: "Adam Mark" < adam.mai...@gmail.com > > > > To: "Dan Tenenbaum" < dtene...@fredhutch.org > > > > Sent: Monday, July 6, 2015 10:19:46 AM > > > Subject: Fwd: mygene problems reported by the "Build/check > > > report" > > > for BioC 3.1 > > > > > > > > > > > > Hello, > > > > > > > > > I received notification about this build error in the mygene > > > package. > > > Nothing has been changed recently so I am not sure why this error > > > is > > > occurring. Could it be due to an update from other packages? > > > > > > > Yes, it is very likely that a change in one of the packages you > > depend on has caused this. Or possibly the udpate to R-3.2.1. What > > you should try and do is see if you can reproduce the problem, by > > installing the same version of R used on the build system (in this > > case 3.2.1) and updating all packages to their latest version. You > > can see what version of packages are installed in the build system > > by going to (e.g.) > > http://bioconductor.org/checkResults/release/bioc-LATEST/zin2-R-instpkgs.html > > .. There is a link like this for each build machine. If you go to > > the main build report at > > http://bioconductor.org/checkResults/release/bioc-LATEST/ and then > > click on the number under "Installed pkgs" in the table at the top > > that describes each build machine you can get to the link that > > shows > > installed packages. Compare this to your sessionInfo(). > > > > You can now try and reproduce the problem. Install your package and > > stangle your vignette, then start R and source the resulting R > > file. > > > > Does it fail in chunk 4 like it does in the build report? If so, > > run > > traceback() and see where the error is. > > > > Since your package failed in release, and bioconductor packages > > typically don't change much in release, I would suspect a CRAN > > dependency. Looking at the CRAN dependencies that you have, it > > appears that httr had a major (from 0.6.1 to 1.0.0) update on June > > 25th. > > > > So the problem you are experiencing is either a bug in the new httr > > or some changed behavior that is perhaps documented in the httr > > NEWS > > file which is at https://github.com/hadley/httr/blob/master/NEWS.md > > . > > > > If it's a bug you can report it at > > https://github.com/hadley/httr/issues . > > > > Dan > > > > > > > > > > > > > > Adam Mark > > > > > > > > > > > > ---------- Forwarded message ---------- > > > From: Chunlei Wu < c...@scripps.edu > > > > Date: Wed, Jul 1, 2015 at 8:26 AM > > > Subject: Fwd: mygene problems reported by the "Build/check > > > report" > > > for BioC 3.1 > > > To: Adam Mark < adam.mai...@gmail.com > > > > > > > > > > > > > Hi, Adam, > > > > > > FYI. Any idea about this error? > > > > > > Chunlei > > > > > > > > > > > > -------- Forwarded Message -------- > > > Subject: mygene problems reported by the "Build/check report" for > > > BioC 3.1 > > > Date: Tue, 30 Jun 2015 11:13:17 -0700 > > > From: bbs-nore...@bioconductor.org < bbs-nore...@bioconductor.org > > > > > > > To: Chunlei Wu < c...@scripps.edu > > > > > > > [This is an automatically generated email. Please don't reply.] > > > > > > Hi mygene maintainer, > > > > > > According to the "Build/check report" for BioC 3.1, > > > the mygene package has the following problem(s): > > > > > > o ERROR for 'R CMD build' on zin2. See the details here: > > > http://bioconductor.org/checkResults/3.1/bioc-LATEST/mygene/zin2-buildsrc.html > > > Please take the time to address this then use your Subversion > > > account > > > when you are ready to commit a fix to your package. > > > > > > Notes: > > > > > > * This was the status of your package at the time this email was > > > sent to you. > > > Given that the online report is updated daily (in normal > > > conditions) you > > > could see something different when you visit the URL(s) above, > > > especially if > > > you do so several days after you received this email. > > > > > > * It is possible that the problems reported in this report are > > > false positives, > > > either because another package (from CRAN or Bioconductor) breaks > > > your > > > package (if yours depends on it) or because of a Build System > > > problem. > > > If this is the case, then you can ignore this email. > > > > > > * Please check the report again 24h after you've committed your > > > changes to the > > > package and make sure that all the problems have gone. > > > > > > * If you have questions about this report or need help with the > > > maintenance of your package, please use the Bioc-devel mailing > > > list: http://bioconductor.org/help/mailing-list/ (all package > > > maintainers are requested to subscribe to this list) > > > > > > For immediate notification of package build status, please > > > subscribe to your package's RSS feed. Information is at: > > > http://bioconductor.org/developers/rss-feeds/ Thanks for > > > contributing to the Bioconductor project! > > > > > > > > > > > > > > > _______________________________________________ > 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