Your message dated Sun, 14 Jul 2024 18:55:30 +0000
with message-id <[email protected]>
and subject line Bug#1071349: fixed in r-bioc-s4vectors 0.42.1+dfsg-1~0exp
has caused the Debian Bug report #1071349,
regarding r-bioc-s4vectors: FTBFS: Rle_class.c:1136:17: error: format not a
string literal and no format arguments
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 [email protected]
immediately.)
--
1071349: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1071349
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Package: src:r-bioc-s4vectors
Version: 0.40.2+dfsg-1
Severity: serious
Tags: ftbfs
Dear maintainer:
During a rebuild of all packages in unstable, your package failed to build:
--------------------------------------------------------------------------------
[...]
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-s4vectors/ -O--buildsystem=R
I: R Package: S4Vectors Version: 0.40.2
I: Building using R version 4.4.0-2
I: R API version: r-api-4.0
I: Using built-time from d/changelog: Wed, 29 Nov 2023 17:40:04 +0100
mkdir -p
/<<BUILDDIR>>/r-bioc-s4vectors-0.40.2\+dfsg/debian/r-bioc-s4vectors/usr/lib/R/site-library
R CMD INSTALL -l
/<<BUILDDIR>>/r-bioc-s4vectors-0.40.2\+dfsg/debian/r-bioc-s4vectors/usr/lib/R/site-library
--clean . "--built-timestamp='Wed, 29 Nov 2023 17:40:04 +0100'"
* installing *source* package ‘S4Vectors’ ...
** using staged installation
** libs
using C compiler: ‘gcc (Debian 13.2.0-25) 13.2.0’
make[1]: Entering directory '/<<PKGBUILDDIR>>/src'
gcc -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2
-Werror=implicit-function-declaration
-ffile-prefix-map=/build/reproducible-path/r-base-4.4.0=. -fstack-protector-strong
-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time
-D_FORTIFY_SOURCE=2 -c AEbufs.c -o AEbufs.o
gcc -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2
-Werror=implicit-function-declaration
-ffile-prefix-map=/build/reproducible-path/r-base-4.4.0=. -fstack-protector-strong
-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time
-D_FORTIFY_SOURCE=2 -c DataFrame_class.c -o DataFrame_class.o
gcc -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2
-Werror=implicit-function-declaration
-ffile-prefix-map=/build/reproducible-path/r-base-4.4.0=. -fstack-protector-strong
-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time
-D_FORTIFY_SOURCE=2 -c Hits_class.c -o Hits_class.o
gcc -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2
-Werror=implicit-function-declaration
-ffile-prefix-map=/build/reproducible-path/r-base-4.4.0=. -fstack-protector-strong
-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time
-D_FORTIFY_SOURCE=2 -c LLint_class.c -o LLint_class.o
gcc -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2
-Werror=implicit-function-declaration
-ffile-prefix-map=/build/reproducible-path/r-base-4.4.0=. -fstack-protector-strong
-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time
-D_FORTIFY_SOURCE=2 -c List_class.c -o List_class.o
gcc -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2
-Werror=implicit-function-declaration
-ffile-prefix-map=/build/reproducible-path/r-base-4.4.0=. -fstack-protector-strong
-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time
-D_FORTIFY_SOURCE=2 -c R_init_S4Vectors.c -o R_init_S4Vectors.o
gcc -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2
-Werror=implicit-function-declaration
-ffile-prefix-map=/build/reproducible-path/r-base-4.4.0=. -fstack-protector-strong
-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -Wdate-time
-D_FORTIFY_SOURCE=2 -c Rle_class.c -o Rle_class.o
Rle_class.c: In function ‘_subset_Rle_by_ranges’:
Rle_class.c:1136:17: error: format not a string literal and no format arguments
[-Werror=format-security]
1136 | error(errmsg);
| ^~~~~
Rle_class.c: In function ‘_subset_Rle_by_positions’:
Rle_class.c:1161:17: error: format not a string literal and no format arguments
[-Werror=format-security]
1161 | error(errmsg);
| ^~~~~
Rle_class.c: In function ‘Rle_extract_range’:
Rle_class.c:1190:17: error: format not a string literal and no format arguments
[-Werror=format-security]
1190 | error(errmsg);
| ^~~~~
cc1: some warnings being treated as errors
make[1]: *** [/usr/lib/R/etc/Makeconf:195: Rle_class.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 ‘S4Vectors’
* removing
‘/<<PKGBUILDDIR>>/debian/r-bioc-s4vectors/usr/lib/R/site-library/S4Vectors’
dh_auto_install: error: R CMD INSTALL -l
/<<BUILDDIR>>/r-bioc-s4vectors-0.40.2\+dfsg/debian/r-bioc-s4vectors/usr/lib/R/site-library
--clean . "--built-timestamp='Wed, 29 Nov 2023 17:40:04 +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/202405/
About the archive rebuild: The build was made on virtual machines
of type m6a.large and r6a.large 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 affects, so that this is still visible in the BTS web
page for this package.
Thanks.
--- End Message ---
--- Begin Message ---
Source: r-bioc-s4vectors
Source-Version: 0.42.1+dfsg-1~0exp
Done: Michael R. Crusoe <[email protected]>
We believe that the bug you reported is fixed in the latest version of
r-bioc-s4vectors, 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 [email protected],
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Michael R. Crusoe <[email protected]> (supplier of updated r-bioc-s4vectors
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 [email protected])
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Format: 1.8
Date: Tue, 09 Jul 2024 17:21:49 +0200
Source: r-bioc-s4vectors
Architecture: source
Version: 0.42.1+dfsg-1~0exp
Distribution: experimental
Urgency: medium
Maintainer: Debian R Packages Maintainers <[email protected]>
Changed-By: Michael R. Crusoe <[email protected]>
Closes: 1070843 1071349
Changes:
r-bioc-s4vectors (0.42.1+dfsg-1~0exp) experimental; urgency=medium
.
* Team upload
* New upstream version. Closes: #1070843, #1071349
* d/copyright: Exclude inst/doc/S4VectorsOverview.html
Checksums-Sha1:
3e7c300f676cb928a6f4849c20f7fa5cbc486113 2186
r-bioc-s4vectors_0.42.1+dfsg-1~0exp.dsc
3e04d7bfc8798a9667414e571acaa85f719cd16c 353260
r-bioc-s4vectors_0.42.1+dfsg.orig.tar.xz
9f901b3b36f399461643f5781c16cecf2dee0f87 22860
r-bioc-s4vectors_0.42.1+dfsg-1~0exp.debian.tar.xz
5f21ee9e4b295e5ced29f2d6eb1884a05af96e84 11588
r-bioc-s4vectors_0.42.1+dfsg-1~0exp_source.buildinfo
Checksums-Sha256:
92f38bff8eae44f01ecb0d51ae2abe226216a3394be7726d05c6c5648cbc23ad 2186
r-bioc-s4vectors_0.42.1+dfsg-1~0exp.dsc
44f52c38c4fedc71f8228905d8e4472a08180f1660ad99cd8d2090ff70cec736 353260
r-bioc-s4vectors_0.42.1+dfsg.orig.tar.xz
0f8629db550b1f2d43ecc1da2fc76ab1accef31d1f2cb6a1ea3388a185186828 22860
r-bioc-s4vectors_0.42.1+dfsg-1~0exp.debian.tar.xz
5a9c473fb17ce610de6295751bc6dd84663b44cc1e25e1f07517e5ad7e53a1d5 11588
r-bioc-s4vectors_0.42.1+dfsg-1~0exp_source.buildinfo
Files:
89ce6ca6472be4d09d4e26ad267e7062 2186 gnu-r optional
r-bioc-s4vectors_0.42.1+dfsg-1~0exp.dsc
7052b99d4b00b39432c7095b38d87f42 353260 gnu-r optional
r-bioc-s4vectors_0.42.1+dfsg.orig.tar.xz
fd7d89883b30f1eaf881315b76b2e31d 22860 gnu-r optional
r-bioc-s4vectors_0.42.1+dfsg-1~0exp.debian.tar.xz
3c62736016f3c14e5acd9d42b863755d 11588 gnu-r optional
r-bioc-s4vectors_0.42.1+dfsg-1~0exp_source.buildinfo
-----BEGIN PGP SIGNATURE-----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=xGxo
-----END PGP SIGNATURE-----
pgpmeB7aJO2_A.pgp
Description: PGP signature
--- End Message ---
