[Debian-med-packaging] Bug#1129855: rsem: FTBFS with boost 1.90
Santiago Vila
sanvila at debian.org
Thu Mar 5 23:22:17 GMT 2026
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: ‘is_final’ has not been declared in ‘std’
206 | using std::is_final;
| ^~~~~~~~
/usr/include/boost/math/tools/type_traits.hpp:257:12: error: ‘remove_cv_t’ has not been declared in ‘std’
257 | using std::remove_cv_t;
| ^~~~~~~~~~~
/usr/include/boost/math/tools/type_traits.hpp:259:12: error: ‘remove_const_t’ has not been declared in ‘std’
259 | using std::remove_const_t;
| ^~~~~~~~~~~~~~
/usr/include/boost/math/tools/type_traits.hpp:261:12: error: ‘remove_volatile_t’ has not been declared in ‘std’
261 | using std::remove_volatile_t;
| ^~~~~~~~~~~~~~~~~
/usr/include/boost/math/tools/type_traits.hpp:263:12: error: ‘add_cv_t’ has not been declared in ‘std’
263 | using std::add_cv_t;
| ^~~~~~~~
/usr/include/boost/math/tools/type_traits.hpp:265:12: error: ‘add_const_t’ has not been declared in ‘std’
265 | using std::add_const_t;
| ^~~~~~~~~~~
/usr/include/boost/math/tools/type_traits.hpp:267:12: error: ‘add_volatile_t’ has not been declared in ‘std’
267 | using std::add_volatile_t;
| ^~~~~~~~~~~~~~
/usr/include/boost/math/tools/type_traits.hpp:271:12: error: ‘remove_reference_t’ has not been declared in ‘std’
271 | using std::remove_reference_t;
| ^~~~~~~~~~~~~~~~~~
/usr/include/boost/math/tools/type_traits.hpp:273:12: error: ‘add_lvalue_reference_t’ has not been declared in ‘std’
273 | using std::add_lvalue_reference_t;
| ^~~~~~~~~~~~~~~~~~~~~~
/usr/include/boost/math/tools/type_traits.hpp:275:12: error: ‘add_rvalue_reference_t’ has not been declared in ‘std’
275 | using std::add_rvalue_reference_t;
| ^~~~~~~~~~~~~~~~~~~~~~
/usr/include/boost/math/tools/type_traits.hpp:279:12: error: ‘remove_pointer_t’ has not been declared in ‘std’
279 | using std::remove_pointer_t;
| ^~~~~~~~~~~~~~~~
/usr/include/boost/math/tools/type_traits.hpp:281:12: error: ‘add_pointer_t’ has not been declared in ‘std’
281 | using std::add_pointer_t;
| ^~~~~~~~~~~~~
/usr/include/boost/math/tools/type_traits.hpp:285:12: error: ‘make_signed_t’ has not been declared in ‘std’
285 | using std::make_signed_t;
| ^~~~~~~~~~~~~
/usr/include/boost/math/tools/type_traits.hpp:287:12: error: ‘make_unsigned_t’ has not been declared in ‘std’
287 | using std::make_unsigned_t;
| ^~~~~~~~~~~~~~~
/usr/include/boost/math/tools/type_traits.hpp:291:12: error: ‘remove_extent_t’ has not been declared in ‘std’
291 | using std::remove_extent_t;
| ^~~~~~~~~~~~~~~
/usr/include/boost/math/tools/type_traits.hpp:293:12: error: ‘remove_all_extents_t’ has not been declared in ‘std’
293 | using std::remove_all_extents_t;
| ^~~~~~~~~~~~~~~~~~~~
/usr/include/boost/math/tools/type_traits.hpp:297:12: error: ‘decay_t’ has not been declared in ‘std’
297 | using std::decay_t;
| ^~~~~~~
/usr/include/boost/math/tools/type_traits.hpp:299:12: error: ‘enable_if_t’ has not been declared in ‘std’
299 | using std::enable_if_t;
| ^~~~~~~~~~~
/usr/include/boost/math/tools/type_traits.hpp:301:12: error: ‘conditional_t’ has not been declared in ‘std’
301 | using std::conditional_t;
| ^~~~~~~~~~~~~
/usr/include/boost/math/tools/type_traits.hpp:303:12: error: ‘common_type_t’ has not been declared in ‘std’
303 | using std::common_type_t;
| ^~~~~~~~~~~~~
/usr/include/boost/math/tools/type_traits.hpp:305:12: error: ‘underlying_type_t’ has not been declared in ‘std’
305 | using std::underlying_type_t;
| ^~~~~~~~~~~~~~~~~
/usr/include/boost/math/tools/type_traits.hpp:397:60: error: ‘is_final’ is not a member of ‘boost::math’; did you mean ‘is_final_v’?
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 ‘>’ 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: ‘::value’ 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: ‘common_type_t’ in namespace ‘boost::math’ does not name a template type; did you mean ‘common_type’? [-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: ‘remove_reference_t’ in namespace ‘boost::math’ does not name a template type; did you mean ‘remove_reference’? [-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 ‘>’ before ‘<’ 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: ‘boost::math::enable_if_t’ has not been declared; did you mean ‘boost::math::enable_if’?
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 ‘>’ before ‘<’ 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: ‘boost::math::enable_if_t’ has not been declared; did you mean ‘boost::math::enable_if’?
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 ‘>’ before ‘<’ 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: ‘enable_if_t’ in namespace ‘boost::math’ does not name a template type; did you mean ‘enable_if’?
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: ‘enable_if_t’ in namespace ‘boost::math’ does not name a template type; did you mean ‘enable_if’?
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: ‘enable_if_t’ in namespace ‘boost::math’ does not name a template type; did you mean ‘enable_if’?
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: ‘enable_if_t’ in namespace ‘boost::math’ does not name a template type; did you mean ‘enable_if’?
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: ‘enable_if_t’ in namespace ‘boost::math’ does not name a template type; did you mean ‘enable_if’?
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: ‘enable_if_t’ in namespace ‘boost::math’ does not name a template type; did you mean ‘enable_if’?
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 ‘<’ 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: ‘enable_if_t’ in namespace ‘boost::math’ does not name a template type; did you mean ‘enable_if’?
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: ‘enable_if_t’ in namespace ‘boost::math’ does not name a template type; did you mean ‘enable_if’?
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 ‘<’ 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 ‘constexpr typename boost::math::tools::promote_args<T2>::type boost::math::pow(T, const Policy&)’ differs in ‘constexpr’ 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 ‘boost::math::tools::promote_args_t<T> boost::math::pow(T, const Policy&)’
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 ‘constexpr typename boost::math::tools::promote_args<T2>::type boost::math::pow(T)’ differs in ‘constexpr’ 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 ‘boost::math::tools::promote_args_t<T> boost::math::pow(T)’
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 ‘void expand_data_size(bam1_t*)’:
sam_utils.h:34:17: warning: comparison of integer expressions of different signedness: ‘uint32_t’ {aka ‘unsigned int’} and ‘int’ [-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
--------------------------------------------------------------------------------
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