Your message dated Sun, 14 Jul 2024 18:33:40 +0000
with message-id <[email protected]>
and subject line Bug#1071344: fixed in r-bioc-oligo 1.68.2+ds-1~0exp
has caused the Debian Bug report #1071344,
regarding r-bioc-oligo: FTBFS: basecontent.c:54:15: 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.)
--
1071344: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1071344
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Package: src:r-bioc-oligo
Version: 1.66.0+ds-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
debian/rules override_dh_auto_install
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_auto_install
I: R Package: oligo Version: 1.66.0
I: Building using R version 4.4.0-2
I: R API version: r-api-4.0
I: Using built-time from d/changelog: Thu, 30 Nov 2023 17:58:01 +0100
mkdir -p
/<<BUILDDIR>>/r-bioc-oligo-1.66.0\+ds/debian/r-bioc-oligo/usr/lib/R/site-library
R CMD INSTALL -l
/<<BUILDDIR>>/r-bioc-oligo-1.66.0\+ds/debian/r-bioc-oligo/usr/lib/R/site-library --clean
. "--built-timestamp='Thu, 30 Nov 2023 17:58:01 +0100'"
* installing *source* package ‘oligo’ ...
** using staged installation
** libs
using C compiler: ‘gcc (Debian 13.2.0-25) 13.2.0’
make[2]: Entering directory '/<<PKGBUILDDIR>>/src'
gcc -I"/usr/share/R/include" -DNDEBUG
-I'/usr/lib/R/site-library/preprocessCore/include' -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 DABG.c -o DABG.o
gcc -I"/usr/share/R/include" -DNDEBUG
-I'/usr/lib/R/site-library/preprocessCore/include' -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 ParserGzXYS.c -o ParserGzXYS.o
ParserGzXYS.c: In function ‘gzcountLines’:
ParserGzXYS.c:18:17: warning: passing argument 1 of ‘gzeof’ from incompatible
pointer type [-Wincompatible-pointer-types]
18 | while (!gzeof(file)){
| ^~~~
| |
| struct gzFile_s **
In file included from ParserGzXYS.c:4:
/usr/include/zlib.h:1598:34: note: expected ‘gzFile’ {aka ‘struct gzFile_s *’}
but argument is of type ‘struct gzFile_s **’
1598 | ZEXTERN int ZEXPORT gzeof(gzFile file);
| ~~~~~~~^~~~
ParserGzXYS.c:19:12: warning: passing argument 1 of ‘gzgets’ from incompatible
pointer type [-Wincompatible-pointer-types]
19 | gzgets(file, buffer, 1000);
| ^~~~
| |
| struct gzFile_s **
/usr/include/zlib.h:1494:38: note: expected ‘gzFile’ {aka ‘struct gzFile_s *’}
but argument is of type ‘struct gzFile_s **’
1494 | ZEXTERN char * ZEXPORT gzgets(gzFile file, char *buf, int len);
| ~~~~~~~^~~~
ParserGzXYS.c: In function ‘gzxys_header_field’:
ParserGzXYS.c:46:6: warning: assignment to ‘struct gzFile_s **’ from
incompatible pointer type ‘gzFile’ {aka ‘struct gzFile_s *’}
[-Wincompatible-pointer-types]
46 | fp = gzopen(currentFile, "rb");
| ^
ParserGzXYS.c:50:10: warning: passing argument 1 of ‘gzgets’ from incompatible
pointer type [-Wincompatible-pointer-types]
50 | gzgets(fp, buffer, LINEMAX);
| ^~
| |
| struct gzFile_s **
/usr/include/zlib.h:1494:38: note: expected ‘gzFile’ {aka ‘struct gzFile_s *’}
but argument is of type ‘struct gzFile_s **’
1494 | ZEXTERN char * ZEXPORT gzgets(gzFile file, char *buf, int len);
| ~~~~~~~^~~~
ParserGzXYS.c:51:11: warning: passing argument 1 of ‘gzclose’ from incompatible
pointer type [-Wincompatible-pointer-types]
51 | gzclose(fp);
| ^~
| |
| struct gzFile_s **
/usr/include/zlib.h:1634:39: note: expected ‘gzFile’ {aka ‘struct gzFile_s *’}
but argument is of type ‘struct gzFile_s **’
1634 | ZEXTERN int ZEXPORT gzclose(gzFile file);
| ~~~~~~~^~~~
ParserGzXYS.c: In function ‘R_read_gzxys_files’:
ParserGzXYS.c:134:6: warning: assignment to ‘struct gzFile_s **’ from
incompatible pointer type ‘gzFile’ {aka ‘struct gzFile_s *’}
[-Wincompatible-pointer-types]
134 | fp = gzopen(CHAR(STRING_ELT(filenames, 0)), "rb");
| ^
ParserGzXYS.c:138:11: warning: passing argument 1 of ‘gzclose’ from
incompatible pointer type [-Wincompatible-pointer-types]
138 | gzclose(fp);
| ^~
| |
| struct gzFile_s **
/usr/include/zlib.h:1634:39: note: expected ‘gzFile’ {aka ‘struct gzFile_s *’}
but argument is of type ‘struct gzFile_s **’
1634 | ZEXTERN int ZEXPORT gzclose(gzFile file);
| ~~~~~~~^~~~
gcc -I"/usr/share/R/include" -DNDEBUG
-I'/usr/lib/R/site-library/preprocessCore/include' -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 ParserXYS.c -o ParserXYS.o
ParserXYS.c: In function ‘xys_header_field’:
ParserXYS.c:145:3: warning: ignoring return value of ‘fgets’ declared with
attribute ‘warn_unused_result’ [-Wunused-result]
145 | fgets(buffer, LINEMAX, fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
ParserXYS.c: In function ‘R_read_xys_header’:
ParserXYS.c:320:3: warning: ignoring return value of ‘fgets’ declared with
attribute ‘warn_unused_result’ [-Wunused-result]
320 | fgets(buffer, LINEMAX, fp);
| ^~~~~~~~~~~~~~~~~~~~~~~~~~
gcc -I"/usr/share/R/include" -DNDEBUG
-I'/usr/lib/R/site-library/preprocessCore/include' -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 baseProfile.c -o baseProfile.o
gcc -I"/usr/share/R/include" -DNDEBUG
-I'/usr/lib/R/site-library/preprocessCore/include' -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 basecontent.c -o basecontent.o
basecontent.c: In function ‘basecontent’:
basecontent.c:54:15: error: format not a string literal and no format arguments
[-Werror=format-security]
54 | error(errmess);
| ^~~~~~~
cc1: some warnings being treated as errors
make[2]: *** [/usr/lib/R/etc/Makeconf:195: basecontent.o] Error 1
make[2]: Leaving directory '/<<PKGBUILDDIR>>/src'
make[2]: Entering directory '/<<PKGBUILDDIR>>/src'
make[2]: Leaving directory '/<<PKGBUILDDIR>>/src'
ERROR: compilation failed for package ‘oligo’
* removing ‘/<<PKGBUILDDIR>>/debian/r-bioc-oligo/usr/lib/R/site-library/oligo’
dh_auto_install: error: R CMD INSTALL -l
/<<BUILDDIR>>/r-bioc-oligo-1.66.0\+ds/debian/r-bioc-oligo/usr/lib/R/site-library --clean
. "--built-timestamp='Thu, 30 Nov 2023 17:58:01 +0100'" returned exit code 1
make[1]: *** [debian/rules:7: override_dh_auto_install] Error 25
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
make: *** [debian/rules:4: binary] Error 2
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-oligo
Source-Version: 1.68.2+ds-1~0exp
Done: Michael R. Crusoe <[email protected]>
We believe that the bug you reported is fixed in the latest version of
r-bioc-oligo, 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-oligo 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: Fri, 12 Jul 2024 10:43:19 +0200
Source: r-bioc-oligo
Architecture: source
Version: 1.68.2+ds-1~0exp
Distribution: experimental
Urgency: low
Maintainer: Debian R Packages Maintainers <[email protected]>
Changed-By: Michael R. Crusoe <[email protected]>
Closes: 1071344
Changes:
r-bioc-oligo (1.68.2+ds-1~0exp) experimental; urgency=low
.
* Team upload.
* New upstream version. Closes: #1071344
* Set upstream metadata fields: Archive, Bug-Database, Bug-Submit,
Repository-Browse.
* d/control: Skip building on 32-bit systems.
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