Your message dated Sun, 14 Jul 2024 18:56:48 +0000
with message-id <[email protected]>
and subject line Bug#1071350: fixed in r-bioc-shortread 1.62.0-1~0exp
has caused the Debian Bug report #1071350,
regarding r-bioc-shortread: FTBFS: readBfaToc.cc:30:14: 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.)
--
1071350: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1071350
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Package: src:r-bioc-shortread
Version: 1.60.0-2
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
configure.ac:14: warning: The macro `AC_ERROR' is obsolete.
configure.ac:14: You should run autoupdate.
./lib/autoconf/oldnames.m4:34: AC_ERROR is expanded from...
configure.ac:14: the top level
configure.ac:17: warning: AC_OUTPUT should be used without arguments.
configure.ac:17: You should run autoupdate.
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-shortread/ -O--buildsystem=R
I: R Package: ShortRead Version: 1.60.0
I: Building using R version 4.4.0-2
I: R API version: r-api-4.0
I: Using built-time from d/changelog: Mon, 18 Dec 2023 07:49:58 +0100
mkdir -p /<<PKGBUILDDIR>>/debian/r-bioc-shortread/usr/lib/R/site-library
R CMD INSTALL -l /<<PKGBUILDDIR>>/debian/r-bioc-shortread/usr/lib/R/site-library
--clean . "--built-timestamp='Mon, 18 Dec 2023 07:49:58 +0100'"
* installing *source* package ‘ShortRead’ ...
** using staged installation
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether the compiler supports GNU C... yes
checking whether gcc accepts -g... yes
checking for gcc option to enable C11 features... none needed
checking for gzeof in -lz... yes
checking for stdio.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for strings.h... yes
checking for sys/stat.h... yes
checking for sys/types.h... yes
checking for unistd.h... yes
checking size of unsigned long... 8
configure: creating ./config.status
config.status: creating src/Makevars
** libs
using C compiler: ‘gcc (Debian 13.2.0-25) 13.2.0’
using C++ compiler: ‘g++ (Debian 13.2.0-25) 13.2.0’
make[1]: Entering directory '/<<PKGBUILDDIR>>/src'
gcc -I"/usr/share/R/include" -DNDEBUG
-I'/usr/lib/R/site-library/S4Vectors/include' -I'/usr/lib/R/site-library/IRanges/include'
-I'/usr/lib/R/site-library/XVector/include'
-I'/usr/lib/R/site-library/Biostrings/include'
-I'/usr/lib/R/site-library/Rhtslib/include' -I'/usr/lib/R/site-library/zlibbioc/include'
-fopenmp -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 Biostrings_stubs.c -o Biostrings_stubs.o
gcc -I"/usr/share/R/include" -DNDEBUG
-I'/usr/lib/R/site-library/S4Vectors/include' -I'/usr/lib/R/site-library/IRanges/include'
-I'/usr/lib/R/site-library/XVector/include'
-I'/usr/lib/R/site-library/Biostrings/include'
-I'/usr/lib/R/site-library/Rhtslib/include' -I'/usr/lib/R/site-library/zlibbioc/include'
-fopenmp -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 IRanges_stubs.c -o IRanges_stubs.o
gcc -I"/usr/share/R/include" -DNDEBUG
-I'/usr/lib/R/site-library/S4Vectors/include' -I'/usr/lib/R/site-library/IRanges/include'
-I'/usr/lib/R/site-library/XVector/include'
-I'/usr/lib/R/site-library/Biostrings/include'
-I'/usr/lib/R/site-library/Rhtslib/include' -I'/usr/lib/R/site-library/zlibbioc/include'
-fopenmp -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_ShortRead.c -o R_init_ShortRead.o
gcc -I"/usr/share/R/include" -DNDEBUG
-I'/usr/lib/R/site-library/S4Vectors/include' -I'/usr/lib/R/site-library/IRanges/include'
-I'/usr/lib/R/site-library/XVector/include'
-I'/usr/lib/R/site-library/Biostrings/include'
-I'/usr/lib/R/site-library/Rhtslib/include' -I'/usr/lib/R/site-library/zlibbioc/include'
-fopenmp -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 S4Vectors_stubs.c -o S4Vectors_stubs.o
gcc -I"/usr/share/R/include" -DNDEBUG
-I'/usr/lib/R/site-library/S4Vectors/include' -I'/usr/lib/R/site-library/IRanges/include'
-I'/usr/lib/R/site-library/XVector/include'
-I'/usr/lib/R/site-library/Biostrings/include'
-I'/usr/lib/R/site-library/Rhtslib/include' -I'/usr/lib/R/site-library/zlibbioc/include'
-fopenmp -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 XVector_stubs.c -o XVector_stubs.o
gcc -I"/usr/share/R/include" -DNDEBUG
-I'/usr/lib/R/site-library/S4Vectors/include' -I'/usr/lib/R/site-library/IRanges/include'
-I'/usr/lib/R/site-library/XVector/include'
-I'/usr/lib/R/site-library/Biostrings/include'
-I'/usr/lib/R/site-library/Rhtslib/include' -I'/usr/lib/R/site-library/zlibbioc/include'
-fopenmp -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 alphabet.c -o alphabet.o
gcc -I"/usr/share/R/include" -DNDEBUG
-I'/usr/lib/R/site-library/S4Vectors/include' -I'/usr/lib/R/site-library/IRanges/include'
-I'/usr/lib/R/site-library/XVector/include'
-I'/usr/lib/R/site-library/Biostrings/include'
-I'/usr/lib/R/site-library/Rhtslib/include' -I'/usr/lib/R/site-library/zlibbioc/include'
-fopenmp -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 count.c -o count.o
gcc -I"/usr/share/R/include" -DNDEBUG
-I'/usr/lib/R/site-library/S4Vectors/include' -I'/usr/lib/R/site-library/IRanges/include'
-I'/usr/lib/R/site-library/XVector/include'
-I'/usr/lib/R/site-library/Biostrings/include'
-I'/usr/lib/R/site-library/Rhtslib/include' -I'/usr/lib/R/site-library/zlibbioc/include'
-fopenmp -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 io.c -o io.o
io.c: In function ‘read_prb_as_character’:
io.c:227:38: warning: format ‘%f’ expects argument of type ‘double’, but
argument 2 has type ‘const char *’ [-Wformat=]
227 | error("could not read file '%f'",
translateChar(STRING_ELT(fname, 0)));
| ~^
| |
| double
| %s
io.c: In function ‘_read_solexa_export_file’:
io.c:658:49: warning: format ‘%s’ expects argument of type ‘char *’, but
argument 2 has type ‘int’ [-Wformat=]
658 | error("invalid 'strand' field '%s', %s:%d",
| ~^
| |
| char *
| %d
659 | *elt[13], fname, lineno);
| ~~~~~~~~
| |
| int
io.c:676:48: warning: format ‘%s’ expects argument of type ‘char *’, but
argument 2 has type ‘int’ [-Wformat=]
676 | error("invalid 'filtering' field '%s', %s:%d",
| ~^
| |
| char *
| %d
677 | *elt[21], fname, lineno);
| ~~~~~~~~
| |
| int
gcc -I"/usr/share/R/include" -DNDEBUG
-I'/usr/lib/R/site-library/S4Vectors/include' -I'/usr/lib/R/site-library/IRanges/include'
-I'/usr/lib/R/site-library/XVector/include'
-I'/usr/lib/R/site-library/Biostrings/include'
-I'/usr/lib/R/site-library/Rhtslib/include' -I'/usr/lib/R/site-library/zlibbioc/include'
-fopenmp -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 io_bowtie.c -o io_bowtie.o
gcc -I"/usr/share/R/include" -DNDEBUG
-I'/usr/lib/R/site-library/S4Vectors/include' -I'/usr/lib/R/site-library/IRanges/include'
-I'/usr/lib/R/site-library/XVector/include'
-I'/usr/lib/R/site-library/Biostrings/include'
-I'/usr/lib/R/site-library/Rhtslib/include' -I'/usr/lib/R/site-library/zlibbioc/include'
-fopenmp -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 io_soap.c -o io_soap.o
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG -I'/usr/lib/R/site-library/S4Vectors/include'
-I'/usr/lib/R/site-library/IRanges/include' -I'/usr/lib/R/site-library/XVector/include' -I'/usr/lib/R/site-library/Biostrings/include'
-I'/usr/lib/R/site-library/Rhtslib/include' -I'/usr/lib/R/site-library/zlibbioc/include' -DPACKAGE_NAME=\"\"
-DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\"
-DPACKAGE_URL=\"\" -DHAVE_LIBZ=1 -DHAVE_STDIO_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1
-DHAVE_STRINGS_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_UNISTD_H=1 -DSTDC_HEADERS=1 -DSIZEOF_UNSIGNED_LONG=8 -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 readBfaToc.cc -o readBfaToc.o
cc1plus: warning: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’
is not valid for C++
readBfaToc.cc: In function ‘SEXPREC* readBfaToc(SEXP)’:
readBfaToc.cc:30:14: error: format not a string literal and no format arguments
[-Werror=format-security]
30 | error( buf );
| ^~~
readBfaToc.cc:35:19: warning: ignoring return value of ‘size_t fread(void*,
size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’
[-Wunused-result]
35 | (void) fread( seq_name, sizeof(char), name_len, fp );
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
readBfaToc.cc:36:19: warning: ignoring return value of ‘size_t fread(void*,
size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’
[-Wunused-result]
36 | (void) fread( &seq_ori_len, sizeof(int), 1, fp );
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
readBfaToc.cc:37:19: warning: ignoring return value of ‘size_t fread(void*,
size_t, size_t, FILE*)’ declared with attribute ‘warn_unused_result’
[-Wunused-result]
37 | (void) fread( &seq_len, sizeof(int), 1, fp );
| ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
cc1plus: some warnings being treated as errors
make[1]: *** [/usr/lib/R/etc/Makeconf:202: readBfaToc.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 ‘ShortRead’
* removing
‘/<<PKGBUILDDIR>>/debian/r-bioc-shortread/usr/lib/R/site-library/ShortRead’
dh_auto_install: error: R CMD INSTALL -l
/<<PKGBUILDDIR>>/debian/r-bioc-shortread/usr/lib/R/site-library --clean .
"--built-timestamp='Mon, 18 Dec 2023 07:49:58 +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/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-shortread
Source-Version: 1.62.0-1~0exp
Done: Michael R. Crusoe <[email protected]>
We believe that the bug you reported is fixed in the latest version of
r-bioc-shortread, 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-shortread
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 21:13:33 +0200
Source: r-bioc-shortread
Architecture: source
Version: 1.62.0-1~0exp
Distribution: experimental
Urgency: medium
Maintainer: Debian R Packages Maintainers <[email protected]>
Changed-By: Michael R. Crusoe <[email protected]>
Closes: 1071350
Changes:
r-bioc-shortread (1.62.0-1~0exp) experimental; urgency=medium
.
* Team upload
* New upstream version. Closes: #1071350
* d/control: Skip building on 32-bit systems.
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