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 --------------------------------------------------------------------------------
