Package: src:r-bioc-grohmm
Version: 1.40.3-2
Severity: serious
Tags: ftbfs trixie sid

Dear maintainer:

During a rebuild of all packages in unstable, your package failed to build:

--------------------------------------------------------------------------------
[...]
debian/rules clean
dh clean --buildsystem R
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_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-grohmm/ -O--buildsystem=R
I: R Package: groHMM Version: 1.40.3
I: Building using R version 4.5.0-1
I: R API version: r-api-4.0
I: Using built-time from d/changelog: Mon, 13 Jan 2025 21:17:46 +0100
mkdir -p /<<PKGBUILDDIR>>/debian/r-bioc-grohmm/usr/lib/R/site-library
R CMD INSTALL -l /<<PKGBUILDDIR>>/debian/r-bioc-grohmm/usr/lib/R/site-library --clean . "--built-timestamp='Mon, 13 Jan 2025 21:17:46 +0100'"
* installing *source* package ‘groHMM’ ...
** this is package ‘groHMM’ version ‘1.40.3’
** package ‘groHMM’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘gcc (Debian 14.2.0-19) 14.2.0’
make[1]: Entering directory '/<<PKGBUILDDIR>>/src'
gcc -std=gnu23 -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/r-base-4.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -c
AnnotateProbes.c -o AnnotateProbes.o
gcc -std=gnu23 -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -ffile-prefix-map=/<<BUILDDIR>>/r-base-4.5.0=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2 -c
DecayAlgorithm.c -o DecayAlgorithm.o
DecayAlgorithm.c: In function ‘getTranscriptPositions’: DecayAlgorithm.c:94:15: error: expected identifier or ‘(’ before ‘false’
94 | const int false= 0;
| ^~~~~
make[1]: *** [/usr/lib/R/etc/Makeconf:202: DecayAlgorithm.o] Error 1
make[1]: Leaving directory '/<<PKGBUILDDIR>>/src'
make[1]: Entering directory '/<<PKGBUILDDIR>>/src'
make[1]: Leaving directory '/<<PKGBUILDDIR>>/src'
ERROR: compilation failed for package ‘groHMM’
* removing ‘/<<PKGBUILDDIR>>/debian/r-bioc-grohmm/usr/lib/R/site-library/groHMM’
dh_auto_install: error: R CMD INSTALL -l /<<PKGBUILDDIR>>/debian/r-bioc-grohmm/usr/lib/R/site-library --clean . "--built-timestamp='Mon, 13 Jan 2025 21:17:46 +0100'" returned exit code 1
make: *** [debian/rules:4: binary] Error 25
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2 --------------------------------------------------------------------------------

The above is just how the build ends and not necessarily the most relevant part.
If required, the full build log is available here:

https://people.debian.org/~sanvila/build-logs/202504/

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 could not 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-grohmm, so that this is still
visible in the BTS web page for this package.

Thanks.

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This is a multi-part message in MIME format.
Package: src:r-bioc-grohmm
Version: 1.40.3-2
Severity: serious
Tags: ftbfs trixie sid

Dear maintainer:

I founded a commit on the upstream for fixing this problem:

Bioconductor Code: groHMM <https://code.bioconductor.org/browse/groHMM/commit/261791bdd2802badced2ba6dc1f0bdddd07a85df>

Or you might prefer to upgrade the major version to their lastest release 1.42.0.

Bioconductor Code: groHMM <https://code.bioconductor.org/browse/groHMM/RELEASE_3_21/>

Best Regards,

liwenjun

<!DOCTYPE html>
<html>
<head>

<meta http-equiv="content-type" content="text/html; charset=UTF-8">
</head>
<body>
<pre class="message"
style="font-family: monospace; padding-top: 8px; margin-top: 0px; border-top: 0px; white-space: pre-wrap; color: rgb(0, 0, 0); font-style: normal; font-variant-ligatures: normal; font-variant-caps: normal; font-weight: 400; letter-spacing: normal;
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grohmm
Version: 1.40.3-2
Severity: serious
Tags: ftbfs trixie sid

Dear maintainer:

I founded a commit on the upstream for fixing this problem:

<a href="https://code.bioconductor.org/browse/groHMM/commit/261791bdd2802badced2ba6dc1f0bdddd07a85df">Bioconductor Code: groHMM</a>

Or you might prefer to upgrade the major version to their lastest release 1.42.0.

<a href="https://code.bioconductor.org/browse/groHMM/RELEASE_3_21/">Bioconductor Code: groHMM</a>

Best Regards,

liwenjun</pre>
</body>
</html>

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