Re: What happened to r-bioc-complexheatmap?
Well - eventually I understood that you did not mean the build tests. But
sh debian/tests/run-unit-test
also works:
...
> n = nrow(pos)
> pos[1:(n-1), 2] > pos[2:n, 1]
[1] TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE
>
>
> if(0) {
+ go_id = random_GO(500)
+ mat = GO_similarity(go_id)
+ invisible(simplify(mat, order_by_size = FALSE))
+ }
>
BEGIN TEST testthat-all.R
R version 4.0.2 (2020-06-22) -- "Taking Off Again"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
>
>
> suppressWarnings(suppressPackageStartupMessages(library(ComplexHeatmap)))
> library(testthat)
>
> test_check("ComplexHeatmap")
══ testthat results
═══════════════════════════════════════════════════════════
[ OK: 181 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
>
I suggest you just upload.
Steffen
On 11.07.20 15:02, Steffen Möller wrote:
> 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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