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configure.ac:14: warning: The macro `AC_ERROR' is obsolete.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.
