[Bioc-devel] mygene problems reported by the "Build/check report" for BioC 3.1

Mon Jul 6 23:56:24 CEST 2015

----- Original Message -----
> From: "Dan Tenenbaum" <dtenenba at fredhutch.org>
> To: "Adam Mark" <adam.maikai at gmail.com>
> Cc: "bioc-devel" <bioc-devel at 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.maikai at gmail.com>
> > To: "Dan Tenenbaum" <dtenenba at 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 <
> > dtenenba at 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.maikai at gmail.com >
> > > To: "Dan Tenenbaum" < dtenenba at 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 < cwu at 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.maikai at 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-noreply at bioconductor.org < BBS-noreply at bioconductor.org
> > > >
> > > To: Chunlei Wu < cwu at 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 at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>