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: ucsc/common.c:360:9: error: too many arguments to
function 'free'
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: 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-cner/ -O--buildsystem=R
I: R Package: CNEr Version: 1.42.0
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 20:58:15 +0100
mkdir -p
/<<BUILDDIR>>/r-bioc-cner-1.42.0\+dfsg/debian/r-bioc-cner/usr/lib/R/site-library
R CMD INSTALL -l
/<<BUILDDIR>>/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 âCNErâ ...
** this is package âCNErâ version â1.42.0â
files âinst/doc/CNEr.htmlâ,
âinst/doc/PairwiseWholeGenomeAlignment.htmlâ are missing
files âtests/testthat/test_Axt.Râ, âtests/testthat/test_CNE.Râ,
âtests/testthat/test_GRangePairs.Râ, âtests/testthat/test_ceScan.Râ
have the wrong MD5 checksums
** using staged installation
** libs
using C compiler: âgcc (Debian 14.2.0-19) 14.2.0â
make[1]: Entering directory '/<<PKGBUILDDIR>>/src'
gcc -std=gnu23 -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=/<<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 S4Vectors_stubs.c -o S4Vectors_stubs.o
gcc -std=gnu23 -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=/<<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 IRanges_stubs.c -o IRanges_stubs.o
gcc -std=gnu23 -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=/<<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 XVector_stubs.c -o XVector_stubs.o
gcc -std=gnu23 -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=/<<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 R_init_CNEr.c -o R_init_CNEr.o
gcc -std=gnu23 -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=/<<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 utils.c -o utils.o
gcc -std=gnu23 -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=/<<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 io.c -o io.o
gcc -std=gnu23 -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=/<<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 ceScan.c -o ceScan.o
gcc -std=gnu23 -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=/<<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 ucsc/axt.c -o ucsc/axt.o
gcc -std=gnu23 -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=/<<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 ucsc/base64.c -o ucsc/base64.o
gcc -std=gnu23 -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=/<<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 ucsc/binRange.c -o ucsc/binRange.o
gcc -std=gnu23 -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=/<<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 ucsc/bits.c -o ucsc/bits.o
gcc -std=gnu23 -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=/<<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 ucsc/chain.c -o ucsc/chain.o
gcc -std=gnu23 -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=/<<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 ucsc/_cheapcgi.c -o ucsc/_cheapcgi.o
gcc -std=gnu23 -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=/<<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 ucsc/cirTree.c -o ucsc/cirTree.o
gcc -std=gnu23 -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=/<<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 ucsc/common.c -o ucsc/common.o
ucsc/common.c: In function âslUniqifyâ:
ucsc/common.c:360:9: error: too many arguments to function âfreeâ
360 | free(el);
| ^~~~
make[1]: *** [/usr/lib/R/etc/Makeconf:202: ucsc/common.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 âCNErâ
* removing â/<<PKGBUILDDIR>>/debian/r-bioc-cner/usr/lib/R/site-library/CNErâ
dh_auto_install: error: R CMD INSTALL -l
/<<BUILDDIR>>/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
--------------------------------------------------------------------------------
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-cner, so that this is still
visible in the BTS web page for this package.
Thanks.
--- 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
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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
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