Your message dated Thu, 26 Mar 2026 23:48:47 +0000
with message-id <[email protected]>
and subject line Bug#1129855: fixed in rsem 1.3.3+dfsg-4
has caused the Debian Bug report #1129855,
regarding rsem: FTBFS with boost 1.90
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.)
--
1129855: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1129855
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Package: src:rsem
Version: 1.3.3+dfsg-3
Severity: serious
Tags: ftbfs forky sid
Dear maintainer:
During a rebuild of all packages in unstable, this package failed to build.
Below you will find the last part of the build log (probably the most
relevant part, but not necessarily). If required, the full build log
is available here:
https://people.debian.org/~sanvila/build-logs/202603/
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 cannot 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:rsem, so that this is still
visible in the BTS web page for this package.
Thanks.
--------------------------------------------------------------------------------
[...]
debian/rules clean
dh clean
dh_auto_clean
make -j2 clean
make[1]: Entering directory '/<<PKGBUILDDIR>>'
rm -f *.o *~ rsem-extract-reference-transcripts
rsem-synthesis-reference-transcripts rsem-preref rsem-build-read-index
rsem-simulate-reads rsem-parse-alignments rsem-run-em rsem-tbam2gbam
rsem-bam2wig rsem-bam2readdepth rsem-get-unique rsem-sam-validator
rsem-scan-for-paired-end-reads rsem-run-gibbs
rsem-calculate-credibility-intervals
cd EBSeq && make clean
make[2]: Entering directory '/<<PKGBUILDDIR>>/EBSeq'
rm -rf EBSeq rsem-for-ebseq-calculate-clustering-info blockmodeling gplots
gtools gdata caTools bitops KernSmooth BiocInstaller *~
make[2]: Leaving directory '/<<PKGBUILDDIR>>/EBSeq'
cd pRSEM && make clean
make[2]: Entering directory '/<<PKGBUILDDIR>>/pRSEM'
rm -fr bigWigSummary RLib filterSam2Bed *.pyc
make[2]: Leaving directory '/<<PKGBUILDDIR>>/pRSEM'
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_clean
debian/rules binary
dh binary
dh_update_autotools_config
dh_autoreconf
dh_auto_configure
debian/rules override_dh_auto_build
make[1]: Entering directory '/<<PKGBUILDDIR>>'
dh_auto_build -- BOOST=/usr/include prefix=debian/tmp
make -j2 INSTALL="install --strip-program=true" BOOST=/usr/include
prefix=debian/tmp
make[2]: Entering directory '/<<PKGBUILDDIR>>'
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong
-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection
-std=gnu++11 -Wall -I. -I/usr/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -c -o
extractRef.o extractRef.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong
-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection
-std=gnu++11 -Wall -I. -I/usr/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -c -o
synthesisRef.o synthesisRef.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong
-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection
-std=gnu++11 -Wall -I. -I/usr/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -c -o
preRef.o preRef.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong
-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection
-std=gnu++11 -Wall -I. -I/usr/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3 -c -o
buildReadIndex.o buildReadIndex.cpp
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong
-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection
-std=gnu++11 -Wall -I. -I/usr/include -Wdate-time -D_FORTIFY_SOURCE=2 -O3
-ffast-math -c -o simulation.o simulation.cpp
In file included from /usr/include/boost/math/distributions/normal.hpp:18,
from LenDist.h:10,
from SingleModel.h:17,
from simulation.cpp:22:
/usr/include/boost/math/tools/config.hpp:28:6: warning: #warning "Boost.Math
requires C++14" [-Wcpp]
28 | # warning "Boost.Math requires C++14"
| ^~~~~~~
In file included from /usr/include/boost/math/tools/promotion.hpp:28,
from /usr/include/boost/math/distributions/normal.hpp:21:
/usr/include/boost/math/tools/type_traits.hpp:206:12: error: âis_finalâ has
not been declared in âstdâ
206 | using std::is_final;
| ^~~~~~~~
/usr/include/boost/math/tools/type_traits.hpp:257:12: error: âremove_cv_tâ
has not been declared in âstdâ
257 | using std::remove_cv_t;
| ^~~~~~~~~~~
/usr/include/boost/math/tools/type_traits.hpp:259:12: error:
âremove_const_tâ has not been declared in âstdâ
259 | using std::remove_const_t;
| ^~~~~~~~~~~~~~
/usr/include/boost/math/tools/type_traits.hpp:261:12: error:
âremove_volatile_tâ has not been declared in âstdâ
261 | using std::remove_volatile_t;
| ^~~~~~~~~~~~~~~~~
/usr/include/boost/math/tools/type_traits.hpp:263:12: error: âadd_cv_tâ has
not been declared in âstdâ
263 | using std::add_cv_t;
| ^~~~~~~~
/usr/include/boost/math/tools/type_traits.hpp:265:12: error: âadd_const_tâ
has not been declared in âstdâ
265 | using std::add_const_t;
| ^~~~~~~~~~~
/usr/include/boost/math/tools/type_traits.hpp:267:12: error:
âadd_volatile_tâ has not been declared in âstdâ
267 | using std::add_volatile_t;
| ^~~~~~~~~~~~~~
/usr/include/boost/math/tools/type_traits.hpp:271:12: error:
âremove_reference_tâ has not been declared in âstdâ
271 | using std::remove_reference_t;
| ^~~~~~~~~~~~~~~~~~
/usr/include/boost/math/tools/type_traits.hpp:273:12: error:
âadd_lvalue_reference_tâ has not been declared in âstdâ
273 | using std::add_lvalue_reference_t;
| ^~~~~~~~~~~~~~~~~~~~~~
/usr/include/boost/math/tools/type_traits.hpp:275:12: error:
âadd_rvalue_reference_tâ has not been declared in âstdâ
275 | using std::add_rvalue_reference_t;
| ^~~~~~~~~~~~~~~~~~~~~~
/usr/include/boost/math/tools/type_traits.hpp:279:12: error:
âremove_pointer_tâ has not been declared in âstdâ
279 | using std::remove_pointer_t;
| ^~~~~~~~~~~~~~~~
/usr/include/boost/math/tools/type_traits.hpp:281:12: error:
âadd_pointer_tâ has not been declared in âstdâ
281 | using std::add_pointer_t;
| ^~~~~~~~~~~~~
/usr/include/boost/math/tools/type_traits.hpp:285:12: error:
âmake_signed_tâ has not been declared in âstdâ
285 | using std::make_signed_t;
| ^~~~~~~~~~~~~
/usr/include/boost/math/tools/type_traits.hpp:287:12: error:
âmake_unsigned_tâ has not been declared in âstdâ
287 | using std::make_unsigned_t;
| ^~~~~~~~~~~~~~~
/usr/include/boost/math/tools/type_traits.hpp:291:12: error:
âremove_extent_tâ has not been declared in âstdâ
291 | using std::remove_extent_t;
| ^~~~~~~~~~~~~~~
/usr/include/boost/math/tools/type_traits.hpp:293:12: error:
âremove_all_extents_tâ has not been declared in âstdâ
293 | using std::remove_all_extents_t;
| ^~~~~~~~~~~~~~~~~~~~
/usr/include/boost/math/tools/type_traits.hpp:297:12: error: âdecay_tâ has
not been declared in âstdâ
297 | using std::decay_t;
| ^~~~~~~
/usr/include/boost/math/tools/type_traits.hpp:299:12: error: âenable_if_tâ
has not been declared in âstdâ
299 | using std::enable_if_t;
| ^~~~~~~~~~~
/usr/include/boost/math/tools/type_traits.hpp:301:12: error:
âconditional_tâ has not been declared in âstdâ
301 | using std::conditional_t;
| ^~~~~~~~~~~~~
/usr/include/boost/math/tools/type_traits.hpp:303:12: error:
âcommon_type_tâ has not been declared in âstdâ
303 | using std::common_type_t;
| ^~~~~~~~~~~~~
/usr/include/boost/math/tools/type_traits.hpp:305:12: error:
âunderlying_type_tâ has not been declared in âstdâ
305 | using std::underlying_type_t;
| ^~~~~~~~~~~~~~~~~
/usr/include/boost/math/tools/type_traits.hpp:397:60: error: âis_finalâ is
not a member of âboost::mathâ; did you mean âis_final_vâ?
397 | BOOST_MATH_INLINE_CONSTEXPR bool is_final_v =
boost::math::is_final<T>::value;
| ^~~~~~~~
| is_final_v
/usr/include/boost/math/tools/type_traits.hpp:397:70: error: expected
primary-expression before â>â token
397 | BOOST_MATH_INLINE_CONSTEXPR bool is_final_v =
boost::math::is_final<T>::value;
| ^
/usr/include/boost/math/tools/type_traits.hpp:397:73: error: â::valueâ has
not been declared
397 | BOOST_MATH_INLINE_CONSTEXPR bool is_final_v =
boost::math::is_final<T>::value;
|
^~~~~
/usr/include/boost/math/tools/promotion.hpp:90:36: error: âcommon_type_tâ
in namespace âboost::mathâ does not name a template type; did you mean
âcommon_typeâ? [-Wtemplate-body]
90 | using type = boost::math::common_type_t<T1, T2, float>;
| ^~~~~~~~~~~~~
| common_type
In file included from /usr/include/boost/math/special_functions/math_fwd.hpp:31,
from /usr/include/boost/math/special_functions/erf.hpp:18,
from /usr/include/boost/math/distributions/normal.hpp:23:
/usr/include/boost/math/policies/policy.hpp:945:90: error:
âremove_reference_tâ in namespace âboost::mathâ does not name a
template type; did you mean âremove_referenceâ? [-Wtemplate-body]
945 | static constexpr bool value =
(sizeof(detail::test_is_policy(static_cast<boost::math::remove_reference_t<boost::math::remove_cv_t<P>>*>(nullptr)))
== sizeof(char));
|
^~~~~~~~~~~~~~~~~~
|
remove_reference
/usr/include/boost/math/policies/policy.hpp:945:108: error: expected â>â
before â<â token [-Wtemplate-body]
945 | static constexpr bool value =
(sizeof(detail::test_is_policy(static_cast<boost::math::remove_reference_t<boost::math::remove_cv_t<P>>*>(nullptr)))
== sizeof(char));
|
^
/usr/include/boost/math/special_functions/math_fwd.hpp:639:61: error:
âboost::math::enable_if_tâ has not been declared; did you mean
âboost::math::enable_ifâ?
639 | template <class T1, class T2, class Policy,
boost::math::enable_if_t<policies::is_policy_v<Policy>, bool> = true>
| ^~~~~~~~~~~
/usr/include/boost/math/special_functions/math_fwd.hpp:639:72: error: expected
â>â before â<â token
639 | template <class T1, class T2, class Policy,
boost::math::enable_if_t<policies::is_policy_v<Policy>, bool> = true>
| ^
/usr/include/boost/math/special_functions/math_fwd.hpp:643:57: error:
âboost::math::enable_if_tâ has not been declared; did you mean
âboost::math::enable_ifâ?
643 | template <class T1, class T2, class T3,
boost::math::enable_if_t<!policies::is_policy_v<T3>, bool> = true>
| ^~~~~~~~~~~
/usr/include/boost/math/special_functions/math_fwd.hpp:643:68: error: expected
â>â before â<â token
643 | template <class T1, class T2, class T3,
boost::math::enable_if_t<!policies::is_policy_v<T3>, bool> = true>
| ^
g++ -g -O2 -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong
-fstack-clash-protection -Wformat -Werror=format-security -fcf-protection
-std=gnu++11 -Wall -I. -I/usr/include -Wdate-time -D_FORTIFY_SOURCE=2 -O2 -c -o
parseIt.o parseIt.cpp
In file included from /usr/include/boost/math/special_functions/gamma.hpp:30,
from /usr/include/boost/math/special_functions/erf.hpp:19:
/usr/include/boost/math/special_functions/trunc.hpp:324:44: error:
âenable_if_tâ in namespace âboost::mathâ does not name a template type;
did you mean âenable_ifâ?
324 | BOOST_MATH_GPU_ENABLED inline
boost::math::enable_if_t<boost::math::is_constructible_v<int, T>, int>
| ^~~~~~~~~~~
| enable_if
/usr/include/boost/math/special_functions/trunc.hpp:331:44: error:
âenable_if_tâ in namespace âboost::mathâ does not name a template type;
did you mean âenable_ifâ?
331 | BOOST_MATH_GPU_ENABLED inline
boost::math::enable_if_t<!boost::math::is_constructible_v<int, T>, int>
| ^~~~~~~~~~~
| enable_if
/usr/include/boost/math/special_functions/trunc.hpp:339:44: error:
âenable_if_tâ in namespace âboost::mathâ does not name a template type;
did you mean âenable_ifâ?
339 | BOOST_MATH_GPU_ENABLED inline
boost::math::enable_if_t<boost::math::is_constructible_v<long, T>, long>
| ^~~~~~~~~~~
| enable_if
/usr/include/boost/math/special_functions/trunc.hpp:346:44: error:
âenable_if_tâ in namespace âboost::mathâ does not name a template type;
did you mean âenable_ifâ?
346 | BOOST_MATH_GPU_ENABLED inline
boost::math::enable_if_t<!boost::math::is_constructible_v<long, T>, long>
| ^~~~~~~~~~~
| enable_if
/usr/include/boost/math/special_functions/trunc.hpp:354:44: error:
âenable_if_tâ in namespace âboost::mathâ does not name a template type;
did you mean âenable_ifâ?
354 | BOOST_MATH_GPU_ENABLED inline
boost::math::enable_if_t<boost::math::is_constructible_v<long long, T>, long
long>
| ^~~~~~~~~~~
| enable_if
/usr/include/boost/math/special_functions/trunc.hpp:361:53: error:
âenable_if_tâ in namespace âboost::mathâ does not name a template type;
did you mean âenable_ifâ?
361 | BOOST_MATH_GPU_ENABLED inline typename
boost::math::enable_if_t<!boost::math::is_constructible_v<long long, T>, long
long>
| ^~~~~~~~~~~
| enable_if
/usr/include/boost/math/special_functions/trunc.hpp:361:64: error: expected
unqualified-id before â<â token
361 | BOOST_MATH_GPU_ENABLED inline typename
boost::math::enable_if_t<!boost::math::is_constructible_v<long long, T>, long
long>
| ^
/usr/include/boost/math/special_functions/trunc.hpp:369:76: error:
âenable_if_tâ in namespace âboost::mathâ does not name a template type;
did you mean âenable_ifâ?
369 | BOOST_MATH_GPU_ENABLED [[deprecated("Use llconvert")]] inline
boost::math::enable_if_t<boost::math::is_constructible_v<long long, T>, long
long>
|
^~~~~~~~~~~
|
enable_if
/usr/include/boost/math/special_functions/trunc.hpp:376:85: error:
âenable_if_tâ in namespace âboost::mathâ does not name a template type;
did you mean âenable_ifâ?
376 | BOOST_MATH_GPU_ENABLED [[deprecated("Use llconvert")]] inline typename
boost::math::enable_if_t<!boost::math::is_constructible_v<long long, T>, long
long>
|
^~~~~~~~~~~
|
enable_if
/usr/include/boost/math/special_functions/trunc.hpp:376:96: error: expected
unqualified-id before â<â token
376 | BOOST_MATH_GPU_ENABLED [[deprecated("Use llconvert")]] inline typename
boost::math::enable_if_t<!boost::math::is_constructible_v<long long, T>, long
long>
|
^
In file included from
/usr/include/boost/math/special_functions/detail/polygamma.hpp:24,
from
/usr/include/boost/math/special_functions/polygamma.hpp:15,
from /usr/include/boost/math/special_functions/gamma.hpp:42:
/usr/include/boost/math/special_functions/pow.hpp:126:79: error: redeclaration
âconstexpr typename boost::math::tools::promote_args<T2>::type
boost::math::pow(T, const Policy&)â differs in âconstexprâ from previous
declaration
126 | BOOST_MATH_GPU_ENABLED constexpr inline typename
tools::promote_args<T>::type pow(T base, const Policy& policy)
|
^~~
/usr/include/boost/math/special_functions/math_fwd.hpp:1181:79: note: previous
declaration âboost::math::tools::promote_args_t<T> boost::math::pow(T, const
Policy&)â
1181 | BOOST_MATH_GPU_ENABLED BOOST_MATH_CXX14_CONSTEXPR
tools::promote_args_t<T> pow(T base, const Policy& policy);
|
^~~
/usr/include/boost/math/special_functions/pow.hpp:133:79: error: redeclaration
âconstexpr typename boost::math::tools::promote_args<T2>::type
boost::math::pow(T)â differs in âconstexprâ from previous declaration
133 | BOOST_MATH_GPU_ENABLED constexpr inline typename
tools::promote_args<T>::type pow(T base)
|
^~~
/usr/include/boost/math/special_functions/math_fwd.hpp:1184:79: note: previous
declaration âboost::math::tools::promote_args_t<T> boost::math::pow(T)â
1184 | BOOST_MATH_GPU_ENABLED BOOST_MATH_CXX14_CONSTEXPR
tools::promote_args_t<T> pow(T base);
|
^~~
In file included from SamParser.h:13,
from parseIt.cpp:27:
sam_utils.h: In function âvoid expand_data_size(bam1_t*)â:
sam_utils.h:34:17: warning: comparison of integer expressions of different
signedness: âuint32_tâ {aka âunsigned intâ} and âintâ
[-Wsign-compare]
34 | if (b->m_data < b->l_data) {
| ~~~~~~~~~~^~~~~~~~~~~
make[2]: *** [Makefile:73: simulation.o] Error 1
make[2]: *** Waiting for unfinished jobs....
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
dh_auto_build: error: make -j2 INSTALL="install --strip-program=true"
BOOST=/usr/include prefix=debian/tmp returned exit code 2
make[1]: *** [debian/rules:13: override_dh_auto_build] Error 25
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
make: *** [debian/rules:10: binary] Error 2
dpkg-buildpackage: error: debian/rules binary subprocess failed with exit
status 2
--------------------------------------------------------------------------------
--- End Message ---
--- Begin Message ---
Source: rsem
Source-Version: 1.3.3+dfsg-4
Done: Santiago Vila <[email protected]>
We believe that the bug you reported is fixed in the latest version of
rsem, 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.
Santiago Vila <[email protected]> (supplier of updated rsem 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: Thu, 26 Mar 2026 23:50:00 +0100
Source: rsem
Architecture: source
Version: 1.3.3+dfsg-4
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<[email protected]>
Changed-By: Santiago Vila <[email protected]>
Closes: 1129855
Changes:
rsem (1.3.3+dfsg-4) unstable; urgency=medium
.
* Team upload.
.
[ Adrian Bunk ]
* Fix FTBFS with Boost 1.90. Closes: #1129855.
.
[ Santiago Vila ]
* Drop "Rules-Requires-Root: no" (default).
* Drop "Priority: optional" (default).
* Update standards-version.
* Disable redundant/duplicate jobs in salsa-ci.yml.
Checksums-Sha1:
9d8accbec65330a686bdf907c1e72d18c04c8322 1760 rsem_1.3.3+dfsg-4.dsc
58ffaeac24185972b2e90830a6f29a2720ed27cb 35661072
rsem_1.3.3+dfsg-4.debian.tar.xz
37b31fc9b0263385afabc88e1b1c7f2f55bf5465 4939
rsem_1.3.3+dfsg-4_source.buildinfo
Checksums-Sha256:
e73111f6080318d53119027a903b46d887e5293ecb988afa6c22ec50f0df7cc8 1760
rsem_1.3.3+dfsg-4.dsc
b665d5d10223825ae1e421e8d27eaeb6231a5ca2d24d8547287721ed1dc67420 35661072
rsem_1.3.3+dfsg-4.debian.tar.xz
33f545738a6c169516aae1e737a78894732ac1e87d5abf2ae9f5d8029313ae6b 4939
rsem_1.3.3+dfsg-4_source.buildinfo
Files:
aaa0dd54da3378499069123744cd6880 1760 science optional rsem_1.3.3+dfsg-4.dsc
d082549f96dd7714d8aad81c203fb05f 35661072 science optional
rsem_1.3.3+dfsg-4.debian.tar.xz
709f6e3985a55a1a8e798c8c72372172 4939 science optional
rsem_1.3.3+dfsg-4_source.buildinfo
-----BEGIN PGP SIGNATURE-----
iQEzBAEBCgAdFiEE1Uw7+v+wQt44LaXXQc5/C58bizIFAmnFwIwACgkQQc5/C58b
izITNwf+K3v+r9XkvPKC7jqjisKxNehYzT7Zf9Vx9nWSHxDxY7WDLDjj8/RxAppX
RZ4AIE7H/TIKIhu5FZwzSGJKsU+HFHLk4XR9P0QTghWAITGSmLNrSUVwdgKwF2JP
AVqethLbyj6R75BxSt6jTjYLk116keQ6vclGVUAiXgZ/pvAKowUcmmi9eKhUPsux
rUySCciZU8UyxtYbQKjQe4iAfmZZcEm3RpXFbBFJYLnWyNqJqRXBVM2CtdF1NnWG
J5LvcNrjudYG/pmV1jByK1gxVF/sJ8WJrWASqu2mSjYWy+JI6klmXkd+eCBL3pCI
wuRbvg350haDJdDApHVMVLFqXZLK9A==
=J0kU
-----END PGP SIGNATURE-----
pgpRMxJZwi8Yq.pgp
Description: PGP signature
--- End Message ---
