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 ‘void GVec<OBJ>::Grow(int, OBJ&) [with OBJ = GISeg]’:
GVec.hh:422:9: required from ‘void GVec<OBJ>::Insert(int, OBJ*) [with OBJ = GISeg]’
422 | Grow(idx, *item); //expand and also copy/move data and insert the new item
| ~~~~^~~~~~~~~~~~
GVec.hh:81:48: required from ‘void GVec<OBJ>::idxInsert(int, OBJ&) [with OBJ = GISeg]’
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: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘class GISeg’; 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: ‘class GISeg’ declared here
188 | class GISeg: public GSeg {
| ^~~~~
GVec.hh: In instantiation of ‘void GVec<OBJ>::Grow(int, OBJ&) [with OBJ = GXSeg]’:
GVec.hh:422:9: required from ‘void GVec<OBJ>::Insert(int, OBJ*) [with OBJ = GXSeg]’
422 | Grow(idx, *item); //expand and also copy/move data and insert the new item
| ~~~~^~~~~~~~~~~~
GVec.hh:79:44: required from ‘void GVec<OBJ>::Insert(int, OBJ) [with OBJ = GXSeg]’
79 | void Insert(int idx, OBJ item) { Insert(idx, &item); }
| ~~~~~~^~~~~~~~~~~~
GList.hh:230:21: required from ‘int GArray<OBJ>::Add(OBJ*) [with OBJ = GXSeg]’
230 | GVec<OBJ>::Insert(result, *item);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~
GList.hh:51:36: required from ‘int GArray<OBJ>::Add(OBJ&) [with OBJ = GXSeg]’
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: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘class GXSeg’; 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: ‘class GXSeg’ declared here
359 | class GXSeg : public GSeg {
| ^~~~~
GVec.hh: In instantiation of ‘void GVec<OBJ>::Grow(int, OBJ&) [with OBJ = GSeg]’:
GVec.hh:422:9: required from ‘void GVec<OBJ>::Insert(int, OBJ*) [with OBJ = GSeg]’
422 | Grow(idx, *item); //expand and also copy/move data and insert the new item
| ~~~~^~~~~~~~~~~~
GVec.hh:79:44: required from ‘void GVec<OBJ>::Insert(int, OBJ) [with OBJ = GSeg]’
79 | void Insert(int idx, OBJ item) { Insert(idx, &item); }
| ~~~~~~^~~~~~~~~~~~
GList.hh:230:21: required from ‘int GArray<OBJ>::Add(OBJ*) [with OBJ = GSeg]’
230 | GVec<OBJ>::Insert(result, *item);
| ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~
GList.hh:51:36: required from ‘int GArray<OBJ>::Add(OBJ&) [with OBJ = GSeg]’
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: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘class GSeg’; 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: ‘class GSeg’ declared here
279 | class GSeg {
| ^~~~
In file included from bundles.h:23:
progressbar.h: In function ‘void learn_bias(BundleFactory&, BiasLearner&, bool)’:
progressbar.h:59:24: warning: ‘char* __builtin_strncpy(char*, const char*, long unsigned int)’ 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: ‘%3d’ 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 ‘void ProgressBar::update(const char*, double)’,
inlined from ‘void learn_bias(BundleFactory&, BiasLearner&, bool)’ 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 ‘int snprintf(char*, size_t, const char*, ...)’,
inlined from ‘void ProgressBar::update(const char*, double)’ at progressbar.h:70:11,
inlined from ‘void learn_bias(BundleFactory&, BiasLearner&, bool)’ at biascorrection.cpp:121:16:
/usr/include/x86_64-linux-gnu/bits/stdio2.h:68:35: note: ‘__builtin___snprintf_chk’ 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: ‘-Werror=’ argument ‘-Werror=implicit-function-declaration’ 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 ‘-std=c++14’ is valid for C++/ObjC++ but not for C
cc1: warning: command-line option ‘-ftemplate-depth=1024’ is valid for C++/ObjC++ but not for C
locfit/adap.c: In function ‘acri’:
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 ‘mmse’:
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 ‘wdiag’; 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 ‘factorial’; 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 ‘p’ set but not used [-Wunused-but-set-variable]
29 | { int i, ii, j, p, p1;
| ^
locfit/adap.c: In function ‘ainitband’:
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 doesn’t 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 ‘nbhd’; 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 ‘locfit’; 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 ‘local_df’; 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 ‘local_df’; 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 ‘aband2’:
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 doesn’t 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 ‘nbhd’; 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 ‘locfit’; 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 ‘local_df’; 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 ‘aband3’:
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 doesn’t 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 ‘nbhd’; 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 ‘locfit’; 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 ‘local_df’; 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 ‘n’ set but not used [-Wunused-but-set-variable]
157 | INT i, i0, d, n;
| ^
locfit/adap.c:157:14: warning: variable ‘d’ 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 ‘double boost::numeric::ublas::cholesky_factorize(M&)’:
sampling.h:50:27: warning: typedef ‘matrix_type’ locally defined but not used [-Wunused-local-typedefs]
50 | typedef M matrix_type;
| ^~~~~~~~~~~
sampling.h: In function ‘void boost::numeric::ublas::cholesky_substitute(const M&, vector_expression<E2>&)’:
sampling.h:113:33: warning: typedef ‘const_matrix_type’ locally defined but not used [-Wunused-local-typedefs]
113 | typedef const M const_matrix_type;
| ^~~~~~~~~~~~~~~~~
sampling.h:114:56: warning: typedef ‘vector_type’ locally defined but not used [-Wunused-local-typedefs]
114 | typedef vector<typename E::value_type> vector_type;
| ^~~~~~~~~~~
sampling.h: In function ‘void boost::numeric::ublas::cholesky_substitute(const M&, matrix_expression<E2>&)’:
sampling.h:120:33: warning: typedef ‘const_matrix_type’ locally defined but not used [-Wunused-local-typedefs]
120 | typedef const M const_matrix_type;
| ^~~~~~~~~~~~~~~~~
sampling.h:121:56: warning: typedef ‘matrix_type’ locally defined but not used [-Wunused-local-typedefs]
121 | typedef matrix<typename E::value_type> matrix_type;
| ^~~~~~~~~~~
sampling.h: In function ‘void boost::numeric::ublas::cholesky_substitute_left(vector_expression<E>&, const M&)’:
sampling.h:127:33: warning: typedef ‘const_matrix_type’ locally defined but not used [-Wunused-local-typedefs]
127 | typedef const M const_matrix_type;
| ^~~~~~~~~~~~~~~~~
sampling.h:128:56: warning: typedef ‘vector_type’ locally defined but not used [-Wunused-local-typedefs]
128 | typedef vector<typename E::value_type> vector_type;
| ^~~~~~~~~~~
sampling.h: In function ‘void boost::numeric::ublas::cholesky_substitute_left(matrix_expression<E>&, const M&)’:
sampling.h:134:33: warning: typedef ‘const_matrix_type’ locally defined but not used [-Wunused-local-typedefs]
134 | typedef const M const_matrix_type;
| ^~~~~~~~~~~~~~~~~
sampling.h:135:56: warning: typedef ‘matrix_type’ 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
--------------------------------------------------------------------------------