[R-pkg-team] Bug#1097762: r-bioc-cner: ftbfs with GCC-15

Mon Feb 17 17:49:36 GMT 2025

Package: src:r-bioc-cner
Version: 1.42.0+dfsg-2
Severity: important
Tags: sid forky
User: debian-gcc at lists.debian.org
Usertags: ftbfs-gcc-15

[This bug is NOT targeted to the upcoming trixie release]

Please keep this issue open in the bug tracker for the package it
was filed for.  If a fix in another package is required, please
file a bug for the other package (or clone), and add a block in this
package. Please keep the issue open until the package can be built in
a follow-up test rebuild.

The package fails to build in a test rebuild on at least amd64 with
gcc-15/g++-15, but succeeds to build with gcc-14/g++-14. The
severity of this report will be raised before the forky release.

The full build log can be found at:
http://qa-logs.debian.net/2025/02/16/amd64exp/r-bioc-cner_1.42.0+dfsg-2_unstable_gccexp.log.gz
The last lines of the build log are at the end of this report.

To build with GCC 15, either set CC=gcc-15 CXX=g++-15 explicitly,
or install the gcc, g++, gfortran, ... packages from experimental.

  apt-get -t=experimental install g++ 

GCC 15 now defaults to the C23/C++23 standards, exposing many FTBFS.
Other Common build failures are new warnings resulting in build failures
with -Werror turned on, or new/dropped symbols in Debian symbols files.
For other C/C++ related build failures see the porting guide at
http://gcc.gnu.org/gcc-15/porting_to.html

[...]
SHELL=/bin/sh
USER=user42

dpkg-buildpackage
-----------------

Command: dpkg-buildpackage --sanitize-env -us -uc -b
dpkg-buildpackage: info: source package r-bioc-cner
dpkg-buildpackage: info: source version 1.42.0+dfsg-2
dpkg-buildpackage: info: source distribution unstable
dpkg-buildpackage: info: source changed by Michael R. Crusoe <crusoe at debian.org>
 dpkg-source --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
 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-cner/ -O--buildsystem=R
I: R Package: CNEr Version: 1.42.0
I: Building using R version 4.4.2-1
I: R API version: r-api-4.0
I: Using built-time from d/changelog: Mon, 13 Jan 2025 20:58:15 +0100
	mkdir -p /build/reproducible-path/r-bioc-cner-1.42.0\+dfsg/debian/r-bioc-cner/usr/lib/R/site-library
	R CMD INSTALL -l /build/reproducible-path/r-bioc-cner-1.42.0\+dfsg/debian/r-bioc-cner/usr/lib/R/site-library --clean . "--built-timestamp='Mon, 13 Jan 2025 20:58:15 +0100'"
* installing *source* package ‘CNEr’ ...
files ‘inst/doc/CNEr.html’, ‘inst/doc/PairwiseWholeGenomeAlignment.html’ are missing
files ‘tests/testthat/test_Axt.R’, ‘tests/testthat/test_CNE.R’, ‘tests/testthat/test_GRangePairs.R’, ‘tests/testthat/test_ceScan.R’ have the wrong MD5 checksums
** using staged installation
** libs
using C compiler: ‘gcc (Debian 15-20250213-1) 15.0.1 20250213 (experimental) [master r15-7502-g26baa2c09b3]’
make[1]: Entering directory '/build/reproducible-path/r-bioc-cner-1.42.0+dfsg/src'
gcc -I"/usr/share/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib/R/site-library/S4Vectors/include' -I'/usr/lib/R/site-library/IRanges/include' -I'/usr/lib/R/site-library/XVector/include'    -g -fpic  -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.4.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2  -c S4Vectors_stubs.c -o S4Vectors_stubs.o
gcc -I"/usr/share/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib/R/site-library/S4Vectors/include' -I'/usr/lib/R/site-library/IRanges/include' -I'/usr/lib/R/site-library/XVector/include'    -g -fpic  -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.4.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2  -c IRanges_stubs.c -o IRanges_stubs.o
gcc -I"/usr/share/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib/R/site-library/S4Vectors/include' -I'/usr/lib/R/site-library/IRanges/include' -I'/usr/lib/R/site-library/XVector/include'    -g -fpic  -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.4.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2  -c XVector_stubs.c -o XVector_stubs.o
gcc -I"/usr/share/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib/R/site-library/S4Vectors/include' -I'/usr/lib/R/site-library/IRanges/include' -I'/usr/lib/R/site-library/XVector/include'    -g -fpic  -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.4.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2  -c R_init_CNEr.c -o R_init_CNEr.o
gcc -I"/usr/share/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib/R/site-library/S4Vectors/include' -I'/usr/lib/R/site-library/IRanges/include' -I'/usr/lib/R/site-library/XVector/include'    -g -fpic  -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.4.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2  -c utils.c -o utils.o
gcc -I"/usr/share/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib/R/site-library/S4Vectors/include' -I'/usr/lib/R/site-library/IRanges/include' -I'/usr/lib/R/site-library/XVector/include'    -g -fpic  -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.4.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2  -c io.c -o io.o
gcc -I"/usr/share/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib/R/site-library/S4Vectors/include' -I'/usr/lib/R/site-library/IRanges/include' -I'/usr/lib/R/site-library/XVector/include'    -g -fpic  -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.4.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2  -c ceScan.c -o ceScan.o
gcc -I"/usr/share/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib/R/site-library/S4Vectors/include' -I'/usr/lib/R/site-library/IRanges/include' -I'/usr/lib/R/site-library/XVector/include'    -g -fpic  -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.4.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2  -c ucsc/axt.c -o ucsc/axt.o
gcc -I"/usr/share/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib/R/site-library/S4Vectors/include' -I'/usr/lib/R/site-library/IRanges/include' -I'/usr/lib/R/site-library/XVector/include'    -g -fpic  -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.4.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2  -c ucsc/base64.c -o ucsc/base64.o
gcc -I"/usr/share/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib/R/site-library/S4Vectors/include' -I'/usr/lib/R/site-library/IRanges/include' -I'/usr/lib/R/site-library/XVector/include'    -g -fpic  -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.4.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2  -c ucsc/binRange.c -o ucsc/binRange.o
gcc -I"/usr/share/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib/R/site-library/S4Vectors/include' -I'/usr/lib/R/site-library/IRanges/include' -I'/usr/lib/R/site-library/XVector/include'    -g -fpic  -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.4.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2  -c ucsc/bits.c -o ucsc/bits.o
gcc -I"/usr/share/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib/R/site-library/S4Vectors/include' -I'/usr/lib/R/site-library/IRanges/include' -I'/usr/lib/R/site-library/XVector/include'    -g -fpic  -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.4.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2  -c ucsc/chain.c -o ucsc/chain.o
gcc -I"/usr/share/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib/R/site-library/S4Vectors/include' -I'/usr/lib/R/site-library/IRanges/include' -I'/usr/lib/R/site-library/XVector/include'    -g -fpic  -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.4.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2  -c ucsc/_cheapcgi.c -o ucsc/_cheapcgi.o
gcc -I"/usr/share/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib/R/site-library/S4Vectors/include' -I'/usr/lib/R/site-library/IRanges/include' -I'/usr/lib/R/site-library/XVector/include'    -g -fpic  -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.4.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2  -c ucsc/cirTree.c -o ucsc/cirTree.o
gcc -I"/usr/share/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'/usr/lib/R/site-library/S4Vectors/include' -I'/usr/lib/R/site-library/IRanges/include' -I'/usr/lib/R/site-library/XVector/include'    -g -fpic  -g -O2 -ffile-prefix-map=/build/reproducible-path/r-base-4.4.2=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time -D_FORTIFY_SOURCE=2  -c ucsc/common.c -o ucsc/common.o
ucsc/common.c: In function ‘slUniqify’:
ucsc/common.c:360:9: error: too many arguments to function ‘free’; expected 0, have 1
  360 |         free(el);
      |         ^~~~ ~~
make[1]: *** [/usr/lib/R/etc/Makeconf:195: ucsc/common.o] Error 1
make[1]: Leaving directory '/build/reproducible-path/r-bioc-cner-1.42.0+dfsg/src'
make[1]: Entering directory '/build/reproducible-path/r-bioc-cner-1.42.0+dfsg/src'
make[1]: Leaving directory '/build/reproducible-path/r-bioc-cner-1.42.0+dfsg/src'
ERROR: compilation failed for package ‘CNEr’
* removing ‘/build/reproducible-path/r-bioc-cner-1.42.0+dfsg/debian/r-bioc-cner/usr/lib/R/site-library/CNEr’
dh_auto_install: error: R CMD INSTALL -l /build/reproducible-path/r-bioc-cner-1.42.0\+dfsg/debian/r-bioc-cner/usr/lib/R/site-library --clean . "--built-timestamp='Mon, 13 Jan 2025 20:58:15 +0100'" returned exit code 1
make: *** [debian/rules:6: binary] Error 25
dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2