[Debian-med-packaging] Bug#837235: r-bioc-deseq2: FTBFS: build-dependency not installable: r-cran-knitr

[Andreas Tille]

Hi Lucas,

before you keep on filing bug reports against lots of R packages are you sure
that your build environment is correct.  r-cran-knitr is available as far as
I can see.

Kind regards

    Andreas.

On Sat, Sep 10, 2016 at 09:37:31AM +0200, Lucas Nussbaum wrote:
> Source: r-bioc-deseq2
> Version: 1.12.3-2
> Severity: serious
> Tags: stretch sid
> User: debian-qa at lists.debian.org
> Usertags: qa-ftbfs-20160910 qa-ftbfs
> Justification: FTBFS on amd64
> 
> Hi,
> 
> During a rebuild of all packages in sid, your package failed to build on
> amd64.
> 
> Relevant part (hopefully):
> > +------------------------------------------------------------------------------+
> > | Install package build dependencies                                           |
> > +------------------------------------------------------------------------------+
> > 
> > 
> > Setup apt archive
> > -----------------
> > 
> > Merged Build-Depends: debhelper (>= 9), cdbs, r-base-dev, r-bioc-genefilter, r-cran-ggplot2, r-cran-hmisc, r-cran-rcpparmadillo, r-cran-foreign, r-cran-nnet, r-bioc-genomicranges, r-bioc-summarizedexperiment, r-bioc-biocparallel, r-bioc-geneplotter, r-cran-knitr
> > Filtered Build-Depends: debhelper (>= 9), cdbs, r-base-dev, r-bioc-genefilter, r-cran-ggplot2, r-cran-hmisc, r-cran-rcpparmadillo, r-cran-foreign, r-cran-nnet, r-bioc-genomicranges, r-bioc-summarizedexperiment, r-bioc-biocparallel, r-bioc-geneplotter, r-cran-knitr
> > dpkg-deb: building package 'sbuild-build-depends-r-bioc-deseq2-dummy' in '/<<BUILDDIR>>/resolver-V1enNf/apt_archive/sbuild-build-depends-r-bioc-deseq2-dummy.deb'.
> > dpkg-scanpackages: warning: Packages in archive but missing from override file:
> > dpkg-scanpackages: warning:   sbuild-build-depends-r-bioc-deseq2-dummy
> > dpkg-scanpackages: info: Wrote 1 entries to output Packages file.
> > Ign:1 copy:/<<BUILDDIR>>/resolver-V1enNf/apt_archive ./ InRelease
> > Get:2 copy:/<<BUILDDIR>>/resolver-V1enNf/apt_archive ./ Release [957 B]
> > Ign:3 copy:/<<BUILDDIR>>/resolver-V1enNf/apt_archive ./ Release.gpg
> > Get:4 copy:/<<BUILDDIR>>/resolver-V1enNf/apt_archive ./ Sources [448 B]
> > Get:5 copy:/<<BUILDDIR>>/resolver-V1enNf/apt_archive ./ Packages [536 B]
> > Fetched 1941 B in 0s (0 B/s)
> > Reading package lists...
> > W: No sandbox user '_apt' on the system, can not drop privileges
> > Reading package lists...
> > 
> > Install r-bioc-deseq2 build dependencies (apt-based resolver)
> > -------------------------------------------------------------
> > 
> > Installing build dependencies
> > Reading package lists...
> > Building dependency tree...
> > Reading state information...
> > Some packages could not be installed. This may mean that you have
> > requested an impossible situation or if you are using the unstable
> > distribution that some required packages have not yet been created
> > or been moved out of Incoming.
> > The following information may help to resolve the situation:
> > 
> > The following packages have unmet dependencies:
> >  sbuild-build-depends-r-bioc-deseq2-dummy : Depends: r-cran-knitr but it is not going to be installed
> > E: Unable to correct problems, you have held broken packages.
> > apt-get failed.
> 
> The full build log is available from:
>    http://aws-logs.debian.net/2016/09/10/r-bioc-deseq2_1.12.3-2_unstable.log
> (That DNS record was just updated. Use
> http://ec2-52-58-237-241.eu-central-1.compute.amazonaws.com if it
> doesn't work)
> 
> A list of current common problems and possible solutions is available at
> http://wiki.debian.org/qa.debian.org/FTBFS . You're welcome to contribute!
> 
> About the archive rebuild: The rebuild was done on EC2 VM instances from
> Amazon Web Services, using a clean, minimal and up-to-date chroot. Every
> failed build was retried once to eliminate random failures.
> 
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> 

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