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 <[email protected]> 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)) ========================================
