[Debian-med-packaging] Bug#897716: canu: ftbfs with GCC-8

Fri May 4 13:20:59 BST 2018

Package: src:canu
Version: 1.7+dfsg-1
Severity: normal
Tags: sid buster
User: debian-gcc at lists.debian.org
Usertags: ftbfs-gcc-8

Please keep this issue open in the bug tracker for the package it
was filed for.  If a fix in another package is required, please
file a bug for the other package (or clone), and add a block in this
package. Please keep the issue open until the package can be built in
a follow-up test rebuild.

The package fails to build in a test rebuild on at least amd64 with
gcc-8/g++-8, but succeeds to build with gcc-7/g++-7. The
severity of this report will be raised before the buster release.

The full build log can be found at:
http://aws-logs.debian.net/2018/05/01/gcc8/canu_1.7+dfsg-1_unstable_gcc8.log.gz
The last lines of the build log are at the end of this report.

To build with GCC 8, either set CC=gcc-8 CXX=g++-8 explicitly,
or install the gcc, g++, gfortran, ... packages from experimental.

  apt-get -t=experimental install g++ 

Common build failures are new warnings resulting in build failures with
-Werror turned on, or new/dropped symbols in Debian symbols files.
For other C/C++ related build failures see the porting guide at
http://gcc.gnu.org/gcc-8/porting_to.html

[...]
make[2]: Leaving directory '/<<BUILDDIR>>/canu-1.7+dfsg/src'
make[2]: Entering directory '/<<BUILDDIR>>/canu-1.7+dfsg/src'
g++ -o /<<BUILDDIR>>/canu-1.7+dfsg/Linux-amd64/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-1.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/<<BUILDDIR>>/canu-1.7+dfsg/src -IAS_UTL -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -Imeryl/libleaff -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap -Ifalcon_sense/libfalcon utgcns/libNDalign/NDalgorithm.C
make[2]: Leaving directory '/<<BUILDDIR>>/canu-1.7+dfsg/src'
make[2]: Entering directory '/<<BUILDDIR>>/canu-1.7+dfsg/src'
g++ -o /<<BUILDDIR>>/canu-1.7+dfsg/Linux-amd64/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm-allocateMoreSpace.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-1.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/<<BUILDDIR>>/canu-1.7+dfsg/src -IAS_UTL -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -Imeryl/libleaff -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap -Ifalcon_sense/libfalcon utgcns/libNDalign/NDalgorithm-allocateMoreSpace.C
make[2]: Leaving directory '/<<BUILDDIR>>/canu-1.7+dfsg/src'
make[2]: Entering directory '/<<BUILDDIR>>/canu-1.7+dfsg/src'
g++ -o /<<BUILDDIR>>/canu-1.7+dfsg/Linux-amd64/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm-extend.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-1.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/<<BUILDDIR>>/canu-1.7+dfsg/src -IAS_UTL -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -Imeryl/libleaff -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap -Ifalcon_sense/libfalcon utgcns/libNDalign/NDalgorithm-extend.C
make[2]: Leaving directory '/<<BUILDDIR>>/canu-1.7+dfsg/src'
make[2]: Entering directory '/<<BUILDDIR>>/canu-1.7+dfsg/src'
g++ -o /<<BUILDDIR>>/canu-1.7+dfsg/Linux-amd64/obj/lib/libcanu.a/utgcns/libNDalign/NDalign.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-1.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/<<BUILDDIR>>/canu-1.7+dfsg/src -IAS_UTL -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -Imeryl/libleaff -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap -Ifalcon_sense/libfalcon utgcns/libNDalign/NDalign.C
In file included from utgcns/libNDalign/NDalign.C:39:
AS_UTL/stddev.H: In member function 'std::vector<long unsigned int>& genericStatistics<TT>::histogram()':
AS_UTL/stddev.H:341:12: error: invalid initialization of non-const reference of type 'std::vector<long unsigned int>&' from an rvalue of type 'std::vector<long unsigned int>*'
     return(&_histogram);
           ~^~~~~~~~~~~~
AS_UTL/stddev.H: In member function 'std::vector<long unsigned int>& genericStatistics<TT>::Nstatistics()':
AS_UTL/stddev.H:346:12: error: invalid initialization of non-const reference of type 'std::vector<long unsigned int>&' from an rvalue of type 'std::vector<long unsigned int>*'
     return(&_Nstatistics);
           ~^~~~~~~~~~~~~~
make[2]: *** [Makefile:658: /<<BUILDDIR>>/canu-1.7+dfsg/Linux-amd64/obj/lib/libcanu.a/utgcns/libNDalign/NDalign.o] Error 1
make[2]: Leaving directory '/<<BUILDDIR>>/canu-1.7+dfsg/src'
make[2]: *** Waiting for unfinished jobs....
make[2]: Entering directory '/<<BUILDDIR>>/canu-1.7+dfsg/src'
g++ -o /<<BUILDDIR>>/canu-1.7+dfsg/Linux-amd64/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm-reverse.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-1.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/<<BUILDDIR>>/canu-1.7+dfsg/src -IAS_UTL -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -Imeryl/libleaff -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap -Ifalcon_sense/libfalcon utgcns/libNDalign/NDalgorithm-reverse.C
make[2]: Leaving directory '/<<BUILDDIR>>/canu-1.7+dfsg/src'
make[2]: Entering directory '/<<BUILDDIR>>/canu-1.7+dfsg/src'
g++ -o /<<BUILDDIR>>/canu-1.7+dfsg/Linux-amd64/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm-forward.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-1.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/<<BUILDDIR>>/canu-1.7+dfsg/src -IAS_UTL -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -Imeryl/libleaff -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap -Ifalcon_sense/libfalcon utgcns/libNDalign/NDalgorithm-forward.C
make[2]: Leaving directory '/<<BUILDDIR>>/canu-1.7+dfsg/src'
make[2]: Entering directory '/<<BUILDDIR>>/canu-1.7+dfsg/src'
g++ -o /<<BUILDDIR>>/canu-1.7+dfsg/Linux-amd64/obj/lib/libcanu.a/utgcns/libcns/abAbacus-appendBases.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-1.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/<<BUILDDIR>>/canu-1.7+dfsg/src -IAS_UTL -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -Imeryl/libleaff -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap -Ifalcon_sense/libfalcon utgcns/libcns/abAbacus-appendBases.C
make[2]: Leaving directory '/<<BUILDDIR>>/canu-1.7+dfsg/src'
make[2]: Entering directory '/<<BUILDDIR>>/canu-1.7+dfsg/src'
g++ -o /<<BUILDDIR>>/canu-1.7+dfsg/Linux-amd64/obj/lib/libcanu.a/utgcns/libcns/abAbacus-addRead.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-1.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/<<BUILDDIR>>/canu-1.7+dfsg/src -IAS_UTL -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -Imeryl/libleaff -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap -Ifalcon_sense/libfalcon utgcns/libcns/abAbacus-addRead.C
make[2]: Leaving directory '/<<BUILDDIR>>/canu-1.7+dfsg/src'
make[2]: Entering directory '/<<BUILDDIR>>/canu-1.7+dfsg/src'
g++ -o /<<BUILDDIR>>/canu-1.7+dfsg/Linux-amd64/obj/lib/libcanu.a/overlapInCore/libedlib/edlib.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-1.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/<<BUILDDIR>>/canu-1.7+dfsg/src -IAS_UTL -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -Imeryl/libleaff -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap -Ifalcon_sense/libfalcon overlapInCore/libedlib/edlib.C
make[2]: Leaving directory '/<<BUILDDIR>>/canu-1.7+dfsg/src'
make[2]: Entering directory '/<<BUILDDIR>>/canu-1.7+dfsg/src'
g++ -o /<<BUILDDIR>>/canu-1.7+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/tgTigSizeAnalysis.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-1.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/<<BUILDDIR>>/canu-1.7+dfsg/src -IAS_UTL -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -Imeryl/libleaff -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap -Ifalcon_sense/libfalcon stores/tgTigSizeAnalysis.C
make[2]: Leaving directory '/<<BUILDDIR>>/canu-1.7+dfsg/src'
make[2]: Entering directory '/<<BUILDDIR>>/canu-1.7+dfsg/src'
g++ -o /<<BUILDDIR>>/canu-1.7+dfsg/Linux-amd64/obj/lib/libcanu.a/stores/tgTigMultiAlignDisplay.o -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fdebug-prefix-map=/<<BUILDDIR>>/canu-1.7+dfsg=. -fstack-protector-strong -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations -finline-functions -fomit-frame-pointer -DNOBACKTRACE -I/<<BUILDDIR>>/canu-1.7+dfsg/src -IAS_UTL -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -Imeryl/libleaff -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap -Ifalcon_sense/libfalcon stores/tgTigMultiAlignDisplay.C
make[2]: Leaving directory '/<<BUILDDIR>>/canu-1.7+dfsg/src'
dh_auto_build: cd src && make -j8 -Oline returned exit code 2
make[1]: *** [debian/rules:16: override_dh_auto_build] Error 25
make[1]: Leaving directory '/<<BUILDDIR>>/canu-1.7+dfsg'
make: *** [debian/rules:13: build-arch] Error 2
dpkg-buildpackage: error: debian/rules build-arch subprocess returned exit status 2