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

Dan Tenenbaum dtenenba at fredhutch.org
Tue Jul 21 20:44:17 CEST 2015

----- Original Message -----
> From: "Charles Determan" <cdetermanjr at gmail.com>
> To: bioc-devel at r-project.org
> Sent: Tuesday, July 21, 2015 11:23:00 AM
> Subject: [Bioc-devel] Fwd: OmicsMarkeR problems reported by the "Build/check report" for BioC 3.1
> I apologize if this is the incorrect place to post this but I need
> some
> assistance with the following build report.  I submitted my fix for
> this
> problem two days ago to my git repo which has the corresponding svn
> bridge.  Everything builds correctly on my system and Travis CI but
> doesn't
> appear to do so for bioconductor's servers.  I tried to access my svn
> to
> check if my updates were mirrored from my git repo at
> https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/OmicsMarkeR
> but
> after logging in all I get is an 'Internal Server Error'.

I can't reproduce this; if I paste that url into a web browser and log in either with my svn
username and password or readonly/readonly, I don't get an error.

> I want to address this problem but I don't know how to proceed at
> this
> point.

The error you were emailed about was in release. The problem here is that something in the CRAN package assertive has changed. It looks like you have not modified release at all.

The error in devel is different:


Not sure if this is related to the assertive package or if it's something introduced in your commit. As I recall, before this commit, both release and devel had the same error that we are now seeing in release.

FYI, to make changes to release, you need to check out



> Regards,
> Charles
> ---------- Forwarded message ----------
> From: <BBS-noreply at bioconductor.org>
> Date: Tue, Jul 21, 2015 at 1:12 PM
> Subject: OmicsMarkeR problems reported by the "Build/check report"
> for BioC
> 3.1
> To: cdetermanjr at gmail.com
> [This is an automatically generated email. Please don't reply.]
> Hi OmicsMarkeR maintainer,
> According to the "Build/check report" for BioC 3.1,
> the OmicsMarkeR 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/OmicsMarkeR/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
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