Your message dated Thu, 24 Apr 2025 12:37:29 +0000
with message-id <e1u7vpz-00hxuh...@fasolo.debian.org>
and subject line Bug#1103198: fixed in r-bioc-cner 1.42.0+dfsg-3
has caused the Debian Bug report #1103198,
regarding r-bioc-cner: ftbfs with GCC-15
to be marked as done.
This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.
(NB: If you are a system administrator and have no idea what this
message is talking about, this may indicate a serious mail system
misconfiguration somewhere. Please contact ow...@bugs.debian.org
immediately.)
--
1103198: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1103198
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems
--- Begin Message ---
Package: src:r-bioc-cner
Version: 1.42.0+dfsg-2
Severity: important
Tags: sid forky
User: debian-...@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 <cru...@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
--- End Message ---
--- Begin Message ---
Source: r-bioc-cner
Source-Version: 1.42.0+dfsg-3
Done: Rebecca N. Palmer <rebecca_pal...@zoho.com>
We believe that the bug you reported is fixed in the latest version of
r-bioc-cner, which is due to be installed in the Debian FTP archive.
A summary of the changes between this version and the previous one is
attached.
Thank you for reporting the bug, which will now be closed. If you
have further comments please address them to 1103...@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Rebecca N. Palmer <rebecca_pal...@zoho.com> (supplier of updated r-bioc-cner
package)
(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing ftpmas...@ftp-master.debian.org)
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Format: 1.8
Date: Wed, 23 Apr 2025 19:15:22 +0100
Source: r-bioc-cner
Architecture: source
Version: 1.42.0+dfsg-3
Distribution: unstable
Urgency: medium
Maintainer: Debian R Packages Maintainers <r-pkg-t...@alioth-lists.debian.net>
Changed-By: Rebecca N. Palmer <rebecca_pal...@zoho.com>
Closes: 1103198
Changes:
r-bioc-cner (1.42.0+dfsg-3) unstable; urgency=medium
.
* Team upload.
* Avoid pointer type mismatch FTBFS. (Closes: #1103198)
Checksums-Sha1:
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r-bioc-cner_1.42.0+dfsg-3.debian.tar.xz
ad93186cbe4cd523a343ea6313b4571fe0e61096 15149
r-bioc-cner_1.42.0+dfsg-3_amd64.buildinfo
Checksums-Sha256:
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r-bioc-cner_1.42.0+dfsg-3.dsc
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r-bioc-cner_1.42.0+dfsg-3.debian.tar.xz
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r-bioc-cner_1.42.0+dfsg-3_amd64.buildinfo
Files:
b8534abea09c8b337a08a0c181140936 2437 gnu-r optional
r-bioc-cner_1.42.0+dfsg-3.dsc
3efc4af1ac1b1e8da139d5401ee798eb 6076 gnu-r optional
r-bioc-cner_1.42.0+dfsg-3.debian.tar.xz
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r-bioc-cner_1.42.0+dfsg-3_amd64.buildinfo
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