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

[Dan Tenenbaum]

----- 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).

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
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> > 
> > 
> > 
> 
>