Re: What happened to r-bioc-complexheatmap?
On 11.07.20 14:22, Andreas Tille wrote:
> On Wed, Jul 08, 2020 at 03:16:32PM +0200, Andreas Tille wrote:
>> Hi Steffen,
>>
>> On Wed, Jul 08, 2020 at 12:16:23PM +0200, Steffen Möller wrote:
>>> You seem to have addressed all its dependencies already (learned quite
>>> something about R while skimming through them) except for
>>> https://salsa.debian.org/r-pkg-team/r-bioc-complexheatmap which is on
>>> salsa but not in our distribution and not in the NEW queue. Is there by
>>> chance a rejection email somewhere buried in your inbox?
>> I admit I have no idea any more. No sign of this package in my in or
>> outbox. It needs r-cran-getoptlong which I'd upload immediately - but
> As I explained in debian-r list[1] there is an issue with the test
> suite. Please discuss the issue there.
Er - the default build does not have an issue for me. Added a bit to
d/u/metadata
and suggest you just upload. Are you building within cowbuilder? Maybe then
try in your regular environment where you have an X interface - just a
hunch.
Cheers,
Steffen
$ gbp buildpackage
gbp:info:Creating r-bioc-complexheatmap_2.4.2+dfsg.orig.tar.xz from
'upstream/2.4.2+dfsg'
gbp:info:Performing the build
dpkg-buildpackage -us -uc -ui -i -I
dpkg-buildpackage: info: source package r-bioc-complexheatmap
dpkg-buildpackage: info: source version 2.4.2+dfsg-1
dpkg-buildpackage: info: source distribution UNRELEASED
dpkg-buildpackage: info: source changed by Andreas Tille <tille@debian.org>
dpkg-source -i -I --before-build .
dpkg-buildpackage: info: host architecture amd64
debian/rules clean
dh clean --buildsystem R
dh_auto_clean -O--buildsystem=R
dh_autoreconf_clean -O--buildsystem=R
dh_clean -O--buildsystem=R
dpkg-source -i -I -b .
dpkg-source: info: using source format '3.0 (quilt)'
dpkg-source: info: building r-bioc-complexheatmap using existing
./r-bioc-complexheatmap_2.4.2+dfsg.orig.tar.xz
dpkg-source: info: building r-bioc-complexheatmap in
r-bioc-complexheatmap_2.4.2+dfsg-1.debian.tar.xz
dpkg-source: info: building r-bioc-complexheatmap in
r-bioc-complexheatmap_2.4.2+dfsg-1.dsc
debian/rules binary
dh binary --buildsystem R
dh_update_autotools_config -O--buildsystem=R
dh_autoreconf -O--buildsystem=R
dh_auto_configure -O--buildsystem=R
dh_auto_build -O--buildsystem=R
dh_auto_test -O--buildsystem=R
create-stamp debian/debhelper-build-stamp
dh_testroot -O--buildsystem=R
dh_prep -O--buildsystem=R
dh_auto_install -O--buildsystem=R
I: R packages needed for DEP8: testthat, dendextend
I: R Package: ComplexHeatmap Version: 2.4.2
I: Building using R version 4.0.2-1
I: R API version: r-api-4.0
I: Using built-time from d/changelog: Wed, 08 Jul 2020 15:09:30 +0200
mkdir -p
/home/moeller/builddir.r-bioc-complexheatmap.tREBOughn3/r-bioc-complexheatmap/debian/r-bioc-complexheatmap/usr/lib/R/site-library
R CMD INSTALL -l
/home/moeller/builddir.r-bioc-complexheatmap.tREBOughn3/r-bioc-complexheatmap/debian/r-bioc-complexheatmap/usr/lib/R/site-library
--clean . "--built-timestamp='Wed, 08 Jul 2020 15:09:30 +0200'"
* installing *source* package ‘ComplexHeatmap’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation
path
* DONE (ComplexHeatmap)
rm -f
/home/moeller/builddir.r-bioc-complexheatmap.tREBOughn3/r-bioc-complexheatmap/debian/r-bioc-complexheatmap/usr/lib/R/site-library/ComplexHeatmap/LICENSE
W: Ignoring specified R dependency: R (>= 3.1.2)
I: Using r-cran-testthat for Recommends:testthat (>= 1.0.0)
I: Using r-cran-dendextend for Recommends:dendextend (>= 1.0.1)
I: Using r-cran-knitr for Suggests:knitr
I: Using r-cran-markdown for Suggests:markdown
W: Cannot find a debian package for Suggests:dendsort
I: Using r-cran-cairo for Suggests:Cairo
I: Using r-cran-jpeg for Suggests:jpeg
I: Using r-cran-tiff for Suggests:tiff
I: Using r-cran-fastcluster for Suggests:fastcluster
W: Cannot find a debian package for Suggests:grImport
I: Using r-cran-grimport2 for Suggests:grImport2
I: Using r-cran-glue for Suggests:glue
I: Using r-bioc-genomicranges for Suggests:GenomicRanges
I: Using r-cran-gridtext for Suggests:gridtext
I: Using r-cran-circlize for Imports:circlize (>= 0.4.5)
I: Using r-cran-getoptlong for Imports:GetoptLong
I: Using r-cran-colorspace for Imports:colorspace
I: Using r-cran-clue for Imports:clue
I: Using r-cran-rcolorbrewer for Imports:RColorBrewer
I: Using r-cran-globaloptions for Imports:GlobalOptions (>= 0.1.0)
I: Using r-cran-png for Imports:png
I: BioConductor API version: r-api-bioc-3.11
I: Use r-bioc-complexheatmap as Debian binary package for variables
substitution
dh_installdocs -O--buildsystem=R
dh_installchangelogs -O--buildsystem=R
dh_installsystemduser -O--buildsystem=R
dh_perl -O--buildsystem=R
dh_link -O--buildsystem=R
dh_strip_nondeterminism -O--buildsystem=R
dh_compress -O--buildsystem=R
debian/rules override_dh_fixperms
make[1]: Entering directory
'/home/moeller/builddir.r-bioc-complexheatmap.tREBOughn3/r-bioc-complexheatmap'
dh_fixperms
find debian \( -name "*.rds" -o -name "*.txt" \) -exec chmod -x \{\} \;
make[1]: Leaving directory
'/home/moeller/builddir.r-bioc-complexheatmap.tREBOughn3/r-bioc-complexheatmap'
dh_missing -O--buildsystem=R
dh_installdeb -O--buildsystem=R
dh_gencontrol -O--buildsystem=R
dh_md5sums -O--buildsystem=R
dh_builddeb -O--buildsystem=R
dpkg-deb: building package 'r-bioc-complexheatmap' in
'../r-bioc-complexheatmap_2.4.2+dfsg-1_all.deb'.
dpkg-genbuildinfo
dpkg-genchanges >../r-bioc-complexheatmap_2.4.2+dfsg-1_amd64.changes
dpkg-genchanges: info: including full source code in upload
dpkg-source -i -I --after-build .
dpkg-buildpackage: info: full upload (original source is included)
Now running lintian r-bioc-complexheatmap_2.4.2+dfsg-1_amd64.changes ...
E: r-bioc-complexheatmap: requires-r-api
Finished running lintian.
... [Starting R]...
> library(ComplexHeatmap)
Loading required package: grid
========================================
ComplexHeatmap version 2.4.2
Bioconductor page: http://bioconductor.org/packages/ComplexHeatmap/
Github page: https://github.com/jokergoo/ComplexHeatmap
Documentation: http://jokergoo.github.io/ComplexHeatmap-reference
If you use it in published research, please cite:
Gu, Z. Complex heatmaps reveal patterns and correlations in
multidimensional
genomic data. Bioinformatics 2016.
This message can be suppressed by:
suppressPackageStartupMessages(library(ComplexHeatmap))
========================================
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