Your message dated Fri, 18 Jan 2019 11:16:29 +0200
with message-id
<CAD=WrcKj9KYvq5tsc2Ma=shvUsi-SS=je0pddytrlku2s42...@mail.gmail.com>
and subject line Re: Bug#914814: spades: FTBFS with jemalloc/experimental
has caused the Debian Bug report #914814,
regarding spades: FTBFS with jemalloc 5
to be marked as done.
This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.
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--
914814: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=914814
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems
--- Begin Message ---
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)
--- End Message ---
--- Begin Message ---
On Fri, 11 Jan 2019 11:35:31 +0200 Michael Crusoe <michael.cru...@gmail.com>
wrote:
> On Sat, 5 Jan 2019 11:05:38 +0200 Faidon Liambotis <parav...@debian.org>
> wrote:
> > Therefore attached is a patch that addresses this using the je_rallocx
> > API. It also deals with the deprecation of the stats.cactive statistic
> > (as of jemalloc 4.0), using the stats.active instead.
> >
> > The patch should be 3.6.0-compatible as well and can go in anytime and
> > ahead of a potential jemalloc transition. It is lightly tested (i.e.
> > builds and runs the test suite).
>
> Dear Faidon,
>
> Thank you for your patch. I was unable to get the tests to complete
> locally. Via an upload to experimental I confirmed that they do hang on
the
> build machines as well:
>
https://buildd.debian.org/status/fetch.php?pkg=spades&arch=amd64&ver=3.13.0%2Bdfsg-2%7E0jemalloc5&stamp=1547148149&raw=0
>
> I see a couple paths forward:
>
> 1. The patch is evolved so that the tests pass
> 2. jemalloc is rolled back from 5 to 3 as it breaks an established package
> and the archive is starting to freeze for Buster
> 3. Same as 2, but a jemalloc5 package is introduced for packages that are
> compatible.
For now I've taken path 4, which is to re-include upstream's patched (and
older) copy of jemalloc. Patches that restore compatibility with the Debian
package for jemalloc are still welcome, as long as the tests still pass.
--- End Message ---
