[Debian-med-packaging] Bug#978928: zalign: ftbfs with autoconf 2.70
Matthias Klose
doko at debian.org
Thu Dec 31 14:29:29 GMT 2020
Package: src:zalign
Version: 0.9.1-4
Severity: normal
Tags: sid bookworm
User: doko at debian.org
Usertags: ftbfs-ac270
[This bug report is not targeted to the upcoming bullseye release]
The package fails to build in a test rebuild on at least amd64 with
autoconf 2.70, but succeeds to build with autoconf 2.69. The
severity of this report will be raised before the bookworm release,
so nothing has to be done for the bullseye release.
The full build log can be found at:
http://qa-logs.debian.net/2020/09/26.ac270/zalign_0.9.1-4_unstable_ac270.log
The last lines of the build log are at the end of this report.
To build with autoconf 2.70, please install the autoconf package from
experimental: apt-get -t=experimental install autoconf
[...]
../include/linearfickettaligner.h: In member function ‘void LinearFickettAligner::LinearFickettTable<T>::allocateCache(count_t)’:
../include/linearfickettaligner.h:174:32: error: there are no arguments to ‘malloc’ that depend on a template parameter, so a declaration of ‘malloc’ must be available [-fpermissive]
174 | mCache[segment] = (T *)malloc(size);
| ^~~~~~
mpialign.cpp: In function ‘void gatherBestScores()’:
mpialign.cpp:146:34: error: ‘malloc’ was not declared in this scope
146 | root_CountArray = (count_t *)malloc(comm_size * sizeof(count_t));
| ^~~~~~
mpialign.cpp:41:1: note: ‘malloc’ is defined in header ‘<cstdlib>’; did you forget to ‘#include <cstdlib>’?
40 | #include "score.h"
+++ |+#include <cstdlib>
41 |
mpialign.cpp:198:33: error: ‘malloc’ was not declared in this scope
198 | local_BoundsArray = (char*) malloc (local_BufferSize);
| ^~~~~~
mpialign.cpp:198:33: note: ‘malloc’ is defined in header ‘<cstdlib>’; did you forget to ‘#include <cstdlib>’?
mpialign.cpp:212:32: error: ‘malloc’ was not declared in this scope
212 | root_BoundsArray = (char *)malloc(root_BufferSize);
| ^~~~~~
mpialign.cpp:212:32: note: ‘malloc’ is defined in header ‘<cstdlib>’; did you forget to ‘#include <cstdlib>’?
mpialign.cpp:248:33: warning: format ‘%d’ expects argument of type ‘int’, but argument 2 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=]
248 | printf ("Alignments found: %d\n", root_BufferCount);
| ~^ ~~~~~~~~~~~~~~~~
| | |
| int size_t {aka long unsigned int}
| %ld
mpialign.cpp: In function ‘void mpialign_stage1()’:
mpialign.cpp:361:32: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 2 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=]
361 | printf (" S sequence: %u characters\n", strlen(s));
| ~^ ~~~~~~~~~
| | |
| unsigned int size_t {aka long unsigned int}
| %lu
mpialign.cpp:363:32: warning: format ‘%u’ expects argument of type ‘unsigned int’, but argument 2 has type ‘size_t’ {aka ‘long unsigned int’} [-Wformat=]
363 | printf (" T sequence: %u characters\n", strlen(t));
| ~^ ~~~~~~~~~
| | |
| unsigned int size_t {aka long unsigned int}
| %lu
make[3]: *** [Makefile:497: mpialign.o] Error 1
make[3]: *** Waiting for unfinished jobs....
In file included from /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx/mpicxx.h:277,
from /usr/lib/x86_64-linux-gnu/openmpi/include/mpi.h:2887,
from ../include/alignbounds.h:23,
from mpialignslave.cpp:23:
/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx/op_inln.h: In member function ‘virtual void MPI::Op::Init(void (*)(const void*, void*, int, const MPI::Datatype&), bool)’:
/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx/op_inln.h:121:25: warning: cast between incompatible function types from ‘void (*)(void*, void*, int*, ompi_datatype_t**, void (*)(void*, void*, int*, ompi_datatype_t**))’ to ‘void (*)(void*, void*, int*, ompi_datatype_t**)’ [-Wcast-function-type]
121 | (void)MPI_Op_create((MPI_User_function*) ompi_mpi_cxx_op_intercept,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx/op_inln.h:123:38: warning: cast between incompatible function types from ‘void (*)(const void*, void*, int, const MPI::Datatype&)’ to ‘void (*)(void*, void*, int*, ompi_datatype_t**)’ [-Wcast-function-type]
123 | ompi_op_set_cxx_callback(mpi_op, (MPI_User_function*) func);
| ^~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx/mpicxx.h:277,
from /usr/lib/x86_64-linux-gnu/openmpi/include/mpi.h:2887,
from mpialignmaster.cpp:22:
/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx/op_inln.h: In member function ‘virtual void MPI::Op::Init(void (*)(const void*, void*, int, const MPI::Datatype&), bool)’:
/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx/op_inln.h:121:25: warning: cast between incompatible function types from ‘void (*)(void*, void*, int*, ompi_datatype_t**, void (*)(void*, void*, int*, ompi_datatype_t**))’ to ‘void (*)(void*, void*, int*, ompi_datatype_t**)’ [-Wcast-function-type]
121 | (void)MPI_Op_create((MPI_User_function*) ompi_mpi_cxx_op_intercept,
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/ompi/mpi/cxx/op_inln.h:123:38: warning: cast between incompatible function types from ‘void (*)(const void*, void*, int, const MPI::Datatype&)’ to ‘void (*)(void*, void*, int*, ompi_datatype_t**)’ [-Wcast-function-type]
123 | ompi_op_set_cxx_callback(mpi_op, (MPI_User_function*) func);
| ^~~~~~~~~~~~~~~~~~~~~~~~~
make[3]: Leaving directory '/<<PKGBUILDDIR>>/src'
make[2]: *** [Makefile:408: all-recursive] Error 1
make[2]: Leaving directory '/<<PKGBUILDDIR>>'
make[1]: *** [Makefile:340: all] Error 2
make[1]: Leaving directory '/<<PKGBUILDDIR>>'
dh_auto_build: error: make -j4 returned exit code 2
make: *** [debian/rules:12: build] Error 25
dpkg-buildpackage: error: debian/rules build subprocess returned exit status 2
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