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

[Lucas Nussbaum]

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.