Package: src:cufflinks Version: 2.2.1+dfsg.1-10 Severity: serious Tags: ftbfs forky sid
Dear maintainer: During a rebuild of all packages in unstable, your package failed to build. Below you will find how the build ends (probably the most relevant part, but not necessarily). If required, the full build log is available here: https://people.debian.org/~sanvila/build-logs/202509/ 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 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 add an affects on src:cufflinks, so that this is still visible in the BTS web page for this package. Thanks. -------------------------------------------------------------------------------- [...] debian/rules clean dh clean --with python3 debian/rules override_dh_auto_clean make[1]: Entering directory '/<<PKGBUILDDIR>>' dh_auto_clean rm -rf autom4te.cache make[1]: Leaving directory '/<<PKGBUILDDIR>>' dh_clean debian/rules binary dh binary --with python3 dh_update_autotools_config dh_autoreconf configure.ac:39: warning: AC_LANG_CONFTEST: no AC_LANG_SOURCE call detected in body ./lib/autoconf/lang.m4:199: AC_LANG_CONFTEST is expanded from... [... snipped ...] 812 | double tot_mass = accumulate( _rg_masses.begin(), _rg_masses.end(), 0.0 ); | ^~~~~~ In file included from GList.hh:8, from GFaSeqGet.h:3, from gff.h:10, from gtf_tracking.h:12, from bundles.h:22, from abundances.h:25, from biascorrection.cpp:12: GVec.hh: In instantiation of âvoid GVec<OBJ>::Grow(int, OBJ&) [with OBJ = GISeg]â: GVec.hh:422:9: required from âvoid GVec<OBJ>::Insert(int, OBJ*) [with OBJ = GISeg]â 422 | Grow(idx, *item); //expand and also copy/move data and insert the new item | ~~~~^~~~~~~~~~~~ GVec.hh:81:48: required from âvoid GVec<OBJ>::idxInsert(int, OBJ&) [with OBJ = GISeg]â 81 | void idxInsert(int idx, OBJ& item) { Insert(idx, &item); } | ~~~~~~^~~~~~~~~~~~ gtf_tracking.h:210:15: required from here 210 | idxInsert(result, *item); | ~~~~~~~~~^~~~~~~~~~~~~~~ GVec.hh:350:15: warning: âvoid* memset(void*, int, size_t)â clearing an object of non-trivial type âclass GISegâ; use assignment or value-initialization instead [-Wclass-memaccess] 350 | memset(&newList[fCount+1], 0, (NewCapacity-fCount-1)*sizeof(OBJ)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gtf_tracking.h:188:7: note: âclass GISegâ declared here 188 | class GISeg: public GSeg { | ^~~~~ GVec.hh: In instantiation of âvoid GVec<OBJ>::Grow(int, OBJ&) [with OBJ = GXSeg]â: GVec.hh:422:9: required from âvoid GVec<OBJ>::Insert(int, OBJ*) [with OBJ = GXSeg]â 422 | Grow(idx, *item); //expand and also copy/move data and insert the new item | ~~~~^~~~~~~~~~~~ GVec.hh:79:44: required from âvoid GVec<OBJ>::Insert(int, OBJ) [with OBJ = GXSeg]â 79 | void Insert(int idx, OBJ item) { Insert(idx, &item); } | ~~~~~~^~~~~~~~~~~~ GList.hh:230:21: required from âint GArray<OBJ>::Add(OBJ*) [with OBJ = GXSeg]â 230 | GVec<OBJ>::Insert(result, *item); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ GList.hh:51:36: required from âint GArray<OBJ>::Add(OBJ&) [with OBJ = GXSeg]â 51 | int Add(OBJ& item) { return Add(&item); } //both will CREATE a new OBJ and COPY to it | ~~~^~~~~~~ gtf_tracking.h:419:15: required from here 419 | uexons.Add(xseg); | ~~~~~~~~~~^~~~~~ GVec.hh:350:15: warning: âvoid* memset(void*, int, size_t)â clearing an object of non-trivial type âclass GXSegâ; use assignment or value-initialization instead [-Wclass-memaccess] 350 | memset(&newList[fCount+1], 0, (NewCapacity-fCount-1)*sizeof(OBJ)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ gtf_tracking.h:359:7: note: âclass GXSegâ declared here 359 | class GXSeg : public GSeg { | ^~~~~ GVec.hh: In instantiation of âvoid GVec<OBJ>::Grow(int, OBJ&) [with OBJ = GSeg]â: GVec.hh:422:9: required from âvoid GVec<OBJ>::Insert(int, OBJ*) [with OBJ = GSeg]â 422 | Grow(idx, *item); //expand and also copy/move data and insert the new item | ~~~~^~~~~~~~~~~~ GVec.hh:79:44: required from âvoid GVec<OBJ>::Insert(int, OBJ) [with OBJ = GSeg]â 79 | void Insert(int idx, OBJ item) { Insert(idx, &item); } | ~~~~~~^~~~~~~~~~~~ GList.hh:230:21: required from âint GArray<OBJ>::Add(OBJ*) [with OBJ = GSeg]â 230 | GVec<OBJ>::Insert(result, *item); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ GList.hh:51:36: required from âint GArray<OBJ>::Add(OBJ&) [with OBJ = GSeg]â 51 | int Add(OBJ& item) { return Add(&item); } //both will CREATE a new OBJ and COPY to it | ~~~^~~~~~~ gtf_tracking.h:420:15: required from here 420 | mexons.Add(seg); | ~~~~~~~~~~^~~~~ GVec.hh:350:15: warning: âvoid* memset(void*, int, size_t)â clearing an object of non-trivial type âclass GSegâ; use assignment or value-initialization instead [-Wclass-memaccess] 350 | memset(&newList[fCount+1], 0, (NewCapacity-fCount-1)*sizeof(OBJ)); | ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from gff.h:7: GBase.h:279:7: note: âclass GSegâ declared here 279 | class GSeg { | ^~~~ In file included from bundles.h:23: progressbar.h: In function âvoid learn_bias(BundleFactory&, BiasLearner&, bool)â: progressbar.h:59:24: warning: âchar* __builtin_strncpy(char*, const char*, long unsigned int)â output may be truncated copying 27 bytes from a string of length 2047 [-Wstringop-truncation] 59 | strncpy(bundle_buf, bundle_label_buf, 27); | ^ progressbar.h:70:71: warning: â%3dâ directive output may be truncated writing between 3 and 11 bytes into a region of size between 6 and 33 [-Wformat-truncation=] 70 | snprintf(line_buf, 82, "\r> Processing Locus %-27s %s %3d%%", bundle_buf, _bar_buf, percent); | ^~~ In member function âvoid ProgressBar::update(const char*, double)â, inlined from âvoid learn_bias(BundleFactory&, BiasLearner&, bool)â at biascorrection.cpp:121:16: progressbar.h:70:40: note: directive argument in the range [-2147483648, 99] 70 | snprintf(line_buf, 82, "\r> Processing Locus %-27s %s %3d%%", bundle_buf, _bar_buf, percent); | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/stdio.h:970, from /usr/include/c++/15/cstdio:47, from /usr/include/c++/15/ext/string_conversions.h:47, from /usr/include/c++/15/bits/basic_string.h:4444, from /usr/include/c++/15/string:56, from /usr/include/c++/15/bits/locale_classes.h:42, from /usr/include/c++/15/bits/ios_base.h:43, from /usr/include/c++/15/streambuf:45, from /usr/include/c++/15/bits/streambuf_iterator.h:37, from /usr/include/c++/15/iterator:68, from /usr/include/boost/operators.hpp:98, from /usr/include/boost/serialization/strong_typedef.hpp:27, from /usr/include/boost/serialization/serialization.hpp:14, from /usr/include/boost/serialization/split_free.hpp:22, from /usr/include/boost/serialization/nvp.hpp:35, from /usr/include/boost/serialization/array_wrapper.hpp:17, from /usr/include/boost/serialization/array.hpp:26, from /usr/include/boost/numeric/ublas/storage.hpp:22: In function âint snprintf(char*, size_t, const char*, ...)â, inlined from âvoid ProgressBar::update(const char*, double)â at progressbar.h:70:11, inlined from âvoid learn_bias(BundleFactory&, BiasLearner&, bool)â at biascorrection.cpp:121:16: /usr/include/x86_64-linux-gnu/bits/stdio2.h:68:35: note: â__builtin___snprintf_chkâ output between 54 and 89 bytes into a destination of size 82 68 | return __builtin___snprintf_chk (__s, __n, __USE_FORTIFY_LEVEL - 1, | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 69 | __glibc_objsize (__s), __fmt, | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 70 | __va_arg_pack ()); | ~~~~~~~~~~~~~~~~~ g++ -DHAVE_CONFIG_H -I. -I.. -I../src -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++14 -DNDEBUG -pthread -I/usr/include -c -o sampling.o sampling.cpp cc1plus: warning: â-Werror=â argument â-Werror=implicit-function-declarationâ is not valid for C++ gcc -DHAVE_CONFIG_H -I. -I.. -I../src -Wdate-time -D_FORTIFY_SOURCE=2 -I/usr/include -Wall -Wno-strict-aliasing -g -gdwarf-2 -Wunused -Wuninitialized -ftemplate-depth-1024 -O3 -g -O2 -Werror=implicit-function-declaration -ffile-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -fstack-clash-protection -Wformat -Werror=format-security -fcf-protection -std=c++14 -DNDEBUG -c -o adap.o `test -f 'locfit/adap.c' || echo './'`locfit/adap.c cc1: warning: command-line option â-std=c++14â is valid for C++/ObjC++ but not for C cc1: warning: command-line option â-ftemplate-depth=1024â is valid for C++/ObjC++ but not for C locfit/adap.c: In function âacriâ: locfit/adap.c:17:8: warning: old-style function definition [-Wold-style-definition] 17 | double acri(lk,t0,t2,pen) | ^~~~ locfit/adap.c: In function âmmseâ: locfit/adap.c:26:8: warning: old-style function definition [-Wold-style-definition] 26 | double mmse(lf,des) | ^~~~ locfit/adap.c:32:3: error: too many arguments to function âwdiagâ; expected 0, have 6 32 | wdiag(lf,des,l,(INT)0,(INT)1,(INT)0); | ^~~~~ ~~ In file included from locfit/local.h:106, from locfit/adap.c:13: locfit/lffuns.h:151:12: note: declared here 151 | extern INT wdiag(), procvhatm(); | ^~~~~ locfit/adap.c:42:8: error: too many arguments to function âfactorialâ; expected 0, have 1 42 | p1 = factorial((int)lf->mi[MDEG]+1); | ^~~~~~~~~ ~~~~~~~~~~~~~~~~~~~ locfit/lffuns.h:108:12: note: declared here 108 | extern int factorial(); | ^~~~~~~~~ locfit/adap.c:29:17: warning: variable âpâ set but not used [-Wunused-but-set-variable] 29 | { int i, ii, j, p, p1; | ^ locfit/adap.c: In function âainitbandâ: locfit/adap.c:55:5: warning: old-style function definition [-Wold-style-definition] 55 | INT ainitband(des,lf) | ^~~~~~~~~ locfit/adap.c:58:1: error: number of arguments doesnât match prototype 58 | { INT lf_status = LF_OK, p, z, cri, noit, redo; | ^ locfit/lffuns.h:8:12: error: prototype declaration 8 | extern INT ainitband(); | ^~~~~~~~~ locfit/adap.c:67:9: error: too many arguments to function ânbhdâ; expected 0, have 5 67 | { h = nbhd(lf,des,z,lf->dp[DFXH],redo); | ^~~~ ~~ locfit/lffuns.h:114:27: note: declared here 114 | extern double kordstat(), nbhd(), rho(); | ^~~~ locfit/adap.c:69:27: error: too many arguments to function âlocfitâ; expected 0, have 4 69 | if (h>ho) lf_status = locfit(lf,des,h,noit); | ^~~~~~ ~~ locfit/lffuns.h:102:19: note: declared here 102 | extern int ident, locfit(), lf_iter(); | ^~~~~~ locfit/adap.c:78:7: error: too many arguments to function âlocal_dfâ; expected 0, have 3 78 | local_df(lf,des,t); | ^~~~~~~~ ~~ locfit/lffuns.h:89:26: note: declared here 89 | extern void comp_vari(), local_df(); | ^~~~~~~~ locfit/adap.c:82:7: error: too many arguments to function âlocal_dfâ; expected 0, have 3 82 | local_df(lf,des,t); | ^~~~~~~~ ~~ locfit/lffuns.h:89:26: note: declared here 89 | extern void comp_vari(), local_df(); | ^~~~~~~~ locfit/adap.c: In function âaband2â: locfit/adap.c:101:8: warning: old-style function definition [-Wold-style-definition] 101 | double aband2(des,lf,h0) | ^~~~~~ locfit/adap.c:105:1: error: number of arguments doesnât match prototype 105 | { double t[6], h, h1, nu1, cp, ncp, tlo, tup; | ^ locfit/lffuns.h:7:23: error: prototype declaration 7 | extern double afit(), aband2(), aband3(); | ^~~~~~ locfit/adap.c:112:9: error: too many arguments to function ânbhdâ; expected 0, have 5 112 | { h = nbhd(lf,des,0,(1+0.3/d)*h,1); | ^~~~ ~~ locfit/lffuns.h:114:27: note: declared here 114 | extern double kordstat(), nbhd(), rho(); | ^~~~ locfit/adap.c:113:9: error: too many arguments to function âlocfitâ; expected 0, have 4 113 | if (locfit(lf,des,h,1)>0) WARN(("aband2: failed fit")); | ^~~~~~ ~~ locfit/lffuns.h:102:19: note: declared here 102 | extern int ident, locfit(), lf_iter(); | ^~~~~~ locfit/adap.c:114:5: error: too many arguments to function âlocal_dfâ; expected 0, have 3 114 | local_df(lf,des,t); | ^~~~~~~~ ~~ locfit/lffuns.h:89:26: note: declared here 89 | extern void comp_vari(), local_df(); | ^~~~~~~~ locfit/adap.c: In function âaband3â: locfit/adap.c:152:8: warning: old-style function definition [-Wold-style-definition] 152 | double aband3(des,lf,h0) | ^~~~~~ locfit/adap.c:156:1: error: number of arguments doesnât match prototype 156 | { double t[6], h, h1, cp, tlo, tup; | ^ locfit/lffuns.h:7:33: error: prototype declaration 7 | extern double afit(), aband2(), aband3(); | ^~~~~~ locfit/adap.c:166:9: error: too many arguments to function ânbhdâ; expected 0, have 5 166 | h = nbhd(lf,des,0,h,1); | ^~~~ ~~ locfit/lffuns.h:114:27: note: declared here 114 | extern double kordstat(), nbhd(), rho(); | ^~~~ locfit/adap.c:167:9: error: too many arguments to function âlocfitâ; expected 0, have 4 167 | if (locfit(lf,des,h,1)>0) WARN(("aband3: failed fit")); | ^~~~~~ ~~ locfit/lffuns.h:102:19: note: declared here 102 | extern int ident, locfit(), lf_iter(); | ^~~~~~ locfit/adap.c:168:5: error: too many arguments to function âlocal_dfâ; expected 0, have 3 168 | local_df(lf,des,t); | ^~~~~~~~ ~~ locfit/lffuns.h:89:26: note: declared here 89 | extern void comp_vari(), local_df(); | ^~~~~~~~ locfit/adap.c:157:17: warning: variable ânâ set but not used [-Wunused-but-set-variable] 157 | INT i, i0, d, n; | ^ locfit/adap.c:157:14: warning: variable âdâ set but not used [-Wunused-but-set-variable] 157 | INT i, i0, d, n; | ^ make[3]: *** [Makefile:979: adap.o] Error 1 make[3]: *** Waiting for unfinished jobs.... In file included from sampling.cpp:9: sampling.h: In function âdouble boost::numeric::ublas::cholesky_factorize(M&)â: sampling.h:50:27: warning: typedef âmatrix_typeâ locally defined but not used [-Wunused-local-typedefs] 50 | typedef M matrix_type; | ^~~~~~~~~~~ sampling.h: In function âvoid boost::numeric::ublas::cholesky_substitute(const M&, vector_expression<E2>&)â: sampling.h:113:33: warning: typedef âconst_matrix_typeâ locally defined but not used [-Wunused-local-typedefs] 113 | typedef const M const_matrix_type; | ^~~~~~~~~~~~~~~~~ sampling.h:114:56: warning: typedef âvector_typeâ locally defined but not used [-Wunused-local-typedefs] 114 | typedef vector<typename E::value_type> vector_type; | ^~~~~~~~~~~ sampling.h: In function âvoid boost::numeric::ublas::cholesky_substitute(const M&, matrix_expression<E2>&)â: sampling.h:120:33: warning: typedef âconst_matrix_typeâ locally defined but not used [-Wunused-local-typedefs] 120 | typedef const M const_matrix_type; | ^~~~~~~~~~~~~~~~~ sampling.h:121:56: warning: typedef âmatrix_typeâ locally defined but not used [-Wunused-local-typedefs] 121 | typedef matrix<typename E::value_type> matrix_type; | ^~~~~~~~~~~ sampling.h: In function âvoid boost::numeric::ublas::cholesky_substitute_left(vector_expression<E>&, const M&)â: sampling.h:127:33: warning: typedef âconst_matrix_typeâ locally defined but not used [-Wunused-local-typedefs] 127 | typedef const M const_matrix_type; | ^~~~~~~~~~~~~~~~~ sampling.h:128:56: warning: typedef âvector_typeâ locally defined but not used [-Wunused-local-typedefs] 128 | typedef vector<typename E::value_type> vector_type; | ^~~~~~~~~~~ sampling.h: In function âvoid boost::numeric::ublas::cholesky_substitute_left(matrix_expression<E>&, const M&)â: sampling.h:134:33: warning: typedef âconst_matrix_typeâ locally defined but not used [-Wunused-local-typedefs] 134 | typedef const M const_matrix_type; | ^~~~~~~~~~~~~~~~~ sampling.h:135:56: warning: typedef âmatrix_typeâ locally defined but not used [-Wunused-local-typedefs] 135 | typedef matrix<typename E::value_type> matrix_type; | ^~~~~~~~~~~ make[3]: Leaving directory '/<<PKGBUILDDIR>>/src' make[2]: *** [Makefile:405: all-recursive] Error 1 make[2]: Leaving directory '/<<PKGBUILDDIR>>' make[1]: *** [Makefile:346: all] Error 2 make[1]: Leaving directory '/<<PKGBUILDDIR>>' dh_auto_build: error: make -j2 returned exit code 2 make: *** [debian/rules:12: binary] Error 25 dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2 --------------------------------------------------------------------------------
