[Debian-med-packaging] Bug#914814: spades: FTBFS with jemalloc/experimental

[Adam Borowski]

Source: spades
Version: 3.13.0+dfsg-1
Severity: normal
Tags: ftbfs

Hi!

I'm afraid that your package fails to build with jemalloc 5.1.0-1 (currently
in experimental).  Transitioning to jemalloc 5 is long overdue, and some
packages currently carry private copies of jemalloc which does not make the
security and release teams happy.  Your package is the only RB-Dep that
fails to build (not counting packages with long-standing unrelated bugs that
are not in testing).


cd /<<PKGBUILDDIR>>/build_spades/common/pipeline && /usr/bin/c++  -DJEMALLOC_NO_DEMANGLE -DUSE_GLIBCXX_PARALLEL=1 -I/<<PKGBUILDDIR>>/build_spades/common/pipeline -I/<<PKGBUILDDIR>>/src/common/pipeline -I/<<PKGBUILDDIR>>/src/include -I/<<PKGBUILDDIR>>/build_spades/include -I/<<PKGBUILDDIR>>/src -I/<<PKGBUILDDIR>>/src/common -isystem /<<PKGBUILDDIR>>/src/../ext/include  -g -O2 -fdebug-prefix-map=/<<PKGBUILDDIR>>=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fopenmp -std=c++14 -O2 -g -DNDEBUG   -UNDEBUG -Wno-deprecated -g3 -O2 -Wall -Wextra -Wconversion -Wno-sign-conversion -Wno-long-long -Wwrite-strings -o CMakeFiles/pipeline.dir/stage.cpp.o -c /<<PKGBUILDDIR>>/src/common/pipeline/stage.cpp
In file included from /<<PKGBUILDDIR>>/src/common/modules/alignment/kmer_mapper.hpp:11,
                 from /<<PKGBUILDDIR>>/src/common/modules/alignment/sequence_mapper.hpp:16,
                 from /<<PKGBUILDDIR>>/src/common/assembly_graph/graph_support/genomic_quality.hpp:12,
                 from /<<PKGBUILDDIR>>/src/common/pipeline/graph_pack.hpp:19,
                 from /<<PKGBUILDDIR>>/src/common/pipeline/stage.hpp:11,
                 from /<<PKGBUILDDIR>>/src/common/pipeline/stage.cpp:8:
/<<PKGBUILDDIR>>/src/common/adt/kmer_vector.hpp: In member function 'adt::KMerVector<Seq>::ElTy* adt::KMerVector<Seq>::realloc()':
/<<PKGBUILDDIR>>/src/common/adt/kmer_vector.hpp:31:89: error: 'ALLOCM_NO_MOVE' was not declared in this scope
             je_rallocm((void **) &storage_, NULL, sizeof(ElTy) * capacity_ * el_sz_, 0, ALLOCM_NO_MOVE) ==
                                                                                         ^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/common/adt/kmer_vector.hpp:31:89: note: suggested alternative: 'SPLICE_F_MOVE'
             je_rallocm((void **) &storage_, NULL, sizeof(ElTy) * capacity_ * el_sz_, 0, ALLOCM_NO_MOVE) ==
                                                                                         ^~~~~~~~~~~~~~
                                                                                         SPLICE_F_MOVE
/<<PKGBUILDDIR>>/src/common/adt/kmer_vector.hpp:31:13: error: there are no arguments to 'je_rallocm' that depend on a template parameter, so a declaration of 'je_rallocm' must be available [-fpermissive]
             je_rallocm((void **) &storage_, NULL, sizeof(ElTy) * capacity_ * el_sz_, 0, ALLOCM_NO_MOVE) ==
             ^~~~~~~~~~
/<<PKGBUILDDIR>>/src/common/adt/kmer_vector.hpp:31:13: note: (if you use '-fpermissive', G++ will accept your code, but allowing the use of an undeclared name is deprecated)
/<<PKGBUILDDIR>>/src/common/adt/kmer_vector.hpp:32:13: error: 'ALLOCM_SUCCESS' was not declared in this scope
             ALLOCM_SUCCESS)
             ^~~~~~~~~~~~~~
/<<PKGBUILDDIR>>/src/common/adt/kmer_vector.hpp:32:13: note: suggested alternative: 'EXIT_SUCCESS'
             ALLOCM_SUCCESS)
             ^~~~~~~~~~~~~~
             EXIT_SUCCESS



-- System Information:
Debian Release: buster/sid
  APT prefers unstable-debug
  APT policy: (500, 'unstable-debug'), (500, 'unstable'), (500, 'testing'), (150, 'experimental')
Architecture: amd64 (x86_64)
Foreign Architectures: i386

Kernel: Linux 4.20.0-rc2-debug-00035-g0f1e49a275c9 (SMP w/6 CPU cores)
Locale: LANG=C.UTF-8, LC_CTYPE=C.UTF-8 (charmap=UTF-8), LANGUAGE=C.UTF-8 (charmap=UTF-8)
Shell: /bin/sh linked to /bin/dash
Init: sysvinit (via /sbin/init)