[R-pkg-team] Bug#1144179: r-bioc-genomicalignments: FTBFS: dh_auto_install: error: R CMD INSTALL -l /<<PKGBUILDDIR>>/debian/r-bioc-genomicalignments/usr/lib/R/site-library --clean . --built-timestamp="'Tue, 04 Aug 2026 16:12:48 +0200'" returned exit code 1

[Santiago Vila]

Package: src:r-bioc-genomicalignments
Version: 1.48.0-1
Severity: serious
Tags: ftbfs forky sid

Dear maintainer:

During a rebuild of all packages in unstable, this package failed to build.

Below you will find the last part of the build log (probably the most
relevant part, but not necessarily). If required, the full build log
is available here:

https://people.debian.org/~sanvila/build-logs/202608/

About the archive rebuild: The build was made on virtual machines from AWS,
using sbuild and a reduced chroot with only build-essential packages.

If you cannot reproduce the bug please contact me privately, as I
am willing to provide ssh access to a virtual machine where the bug is
fully reproducible.

If this is really a bug in one of the build-depends, please use
reassign and add an affects on src:r-bioc-genomicalignments, so that this is still
visible in the BTS web page for this package.

Thanks.

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[...]
 debian/rules clean
dh clean --buildsystem R
dh: warning: Implicitly activating single-binary dh addon for backwards compatibility.  In compat 14+,
dh: warning: this fallback will *not* happen automatically via dh_auto_install will instead use a
dh: warning: different default for --destdir unless the single-binary add-on is active,
dh: warning: which can cause the source to produce an empty binary package
dh: warning: 
dh: warning: To keep the existing behaviour (compat 13), please activate the single-binary addon explicitly.
dh: warning: This can be done by adding "dh-sequence-single-binary" to Build-Depends or passing
dh: warning: --with=single-binary to dh.
dh: warning: 
dh: warning: If you have solved this issue differently (e.g., by passing --destdir explicitly to
dh: warning: dh_auto_install or not using dh_auto_install at all) and want to silence this warning
dh: warning: without activating the addon, you can do that by passing --without=single-binary to dh
dh: warning: to explicitly acknowledge the change.
dh: warning: 
dh: warning: Please see the description of the "single-binary" in "man dh" for more details of what
dh: warning: it does and why this is changing from implicit behaviour to explicitly opt-in.
   dh_auto_clean -O--buildsystem=R
   dh_autoreconf_clean -O--buildsystem=R
   dh_clean -O--buildsystem=R
 debian/rules binary
dh binary --buildsystem R
dh: warning: Implicitly activating single-binary dh addon for backwards compatibility.  In compat 14+,
dh: warning: this fallback will *not* happen automatically via dh_auto_install will instead use a
dh: warning: different default for --destdir unless the single-binary add-on is active,
dh: warning: which can cause the source to produce an empty binary package
dh: warning: 
dh: warning: To keep the existing behaviour (compat 13), please activate the single-binary addon explicitly.
dh: warning: This can be done by adding "dh-sequence-single-binary" to Build-Depends or passing
dh: warning: --with=single-binary to dh.
dh: warning: 
dh: warning: If you have solved this issue differently (e.g., by passing --destdir explicitly to
dh: warning: dh_auto_install or not using dh_auto_install at all) and want to silence this warning
dh: warning: without activating the addon, you can do that by passing --without=single-binary to dh
dh: warning: to explicitly acknowledge the change.
dh: warning: 
dh: warning: Please see the description of the "single-binary" in "man dh" for more details of what
dh: warning: it does and why this is changing from implicit behaviour to explicitly opt-in.
   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 --destdir=debian/r-bioc-genomicalignments/ -O--buildsystem=R
I: R Package: GenomicAlignments Version: 1.48.0
I: Building using R version 4.6.1-4
I: R API version: r-api-4.0
I: Using built-time from d/changelog: Tue, 04 Aug 2026 16:12:48 +0200
	mkdir -p /<<PKGBUILDDIR>>/debian/r-bioc-genomicalignments/usr/lib/R/site-library
	R CMD INSTALL -l /<<PKGBUILDDIR>>/debian/r-bioc-genomicalignments/usr/lib/R/site-library --clean . --built-timestamp="'Tue, 04 Aug 2026 16:12:48 +0200'"
ERROR: dependency ‘cigarillo’ is not available for package ‘GenomicAlignments’
Perhaps try a variation of:
install.packages('cigarillo')
* removing ‘/<<PKGBUILDDIR>>/debian/r-bioc-genomicalignments/usr/lib/R/site-library/GenomicAlignments’
dh_auto_install: error: R CMD INSTALL -l /<<PKGBUILDDIR>>/debian/r-bioc-genomicalignments/usr/lib/R/site-library --clean . --built-timestamp="'Tue, 04 Aug 2026 16:12:48 +0200'" returned exit code 1
make: *** [debian/rules:4: binary] Error 25
dpkg-buildpackage: error: debian/rules binary subprocess failed with exit status 2
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