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!