Your message dated Wed, 23 Jan 2019 17:19:33 +0000
with message-id <[email protected]>
and subject line Bug#920240: fixed in abyss 2.1.5-4
has caused the Debian Bug report #920240,
regarding abyss fails to build on hurd due to missing header file
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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--
920240: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=920240
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Source: abyss
Version: 2.1.5-3
Severity: important
SUMMARY: abyss fails to build on hurd due to missing header file
DISCOVERY:
Build log of abyss-2.1.5-3 on mahler.debian.net (2019-01-09 22:47:19):
https://buildd.debian.org/status/fetch.php?pkg=abyss&arch=hurd-i386&ver=2.1.5-3&stamp=1547074039&raw=0
DESCRIPTION:
Abyss-2.1.5-3 gives the build error:
../Common/MemoryUtil.h:11:11: fatal error: mach/task.h: No such file or
directory
It seems that this is due to an out-of-date usage of mach include
files and possibly also linking with mach.
CONTEXT:
On the exodar GNU/hurd emulation:
$ uname -a
GNU exodar 0.9 GNU-Mach 1.8+git20181103-486-dbg/Hurd-0.9 i686-AT386 GNU
$ cat /proc/hostinfo
Basic info:
max_cpus = 1 /* max number of cpus possible */
avail_cpus = 1 /* number of cpus now available */
memory_size = 3221151744 /* size of memory in bytes */
cpu_type = 19 /* cpu type */
cpu_subtype = 1 /* cpu subtype */
Scheduling info:
min_timeout = 10 /* minimum timeout in milliseconds */
min_quantum = 100 /* minimum quantum in milliseconds */
Load info:
avenrun[3] = { 0.10, 0.28, 0.60 }
mach_factor[3] = { 0.89, 0.81, 0.64 }
$ dpkg -l |egrep "abyss|gcc|g\+\+"
ii g++ 4:8.2.0-2
hurd-i386 GNU C++ compiler
ii g++-8 8.2.0-14
hurd-i386 GNU C++ compiler
ii gcc 4:8.2.0-2
hurd-i386 GNU C compiler
ii gcc-8 8.2.0-14
hurd-i386 GNU C compiler
ii gcc-8-base:hurd-i386 8.2.0-14
hurd-i386 GCC, the GNU Compiler Collection (base package)
ii libgcc-8-dev:hurd-i386 8.2.0-14
hurd-i386 GCC support library (development files)
ii libgcc1:hurd-i386 1:8.2.0-14
hurd-i386 GCC support library
REPRODUCE:
On exodar:
$ apt-get source abyss
$ apt-get build-dep abyss
$ cd abyss-2.1.5
$ fakeroot debian/rules binary
...
g++ -Wall -Wextra -fopenmp -g -O2
-fdebug-prefix-map=/home/boud-guest/abyss-2.1.5=. -fstack-protector-strong
-Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -Wl,-z,relro
-Wl,-z,now -o abyss-align abyss_align-align.o ./libalign.a
../dialign/libdialign.a ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl
-lm
g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I../Common -I../DataLayer
-I/home/boud-guest/abyss-2.1.5 -Wdate-time -D_FORTIFY_SOURCE=2
-isystem/home/boud-guest/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -fopenmp -g -O2
-fdebug-prefix-map=/home/boud-guest/abyss-2.1.5=. -fstack-protector-strong
-Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o
abyss_mergepairs-mergepairs.o `test -f 'mergepairs.cc' || echo
'./'`mergepairs.cc
g++ -Wall -Wextra -fopenmp -g -O2
-fdebug-prefix-map=/home/boud-guest/abyss-2.1.5=. -fstack-protector-strong
-Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -Wl,-z,relro
-Wl,-z,now -o abyss-mergepairs abyss_mergepairs-mergepairs.o ./libalign.a
../dialign/libdialign.a ../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl
-lm
make[4]: Leaving directory '/home/boud-guest/abyss-2.1.5/Align'
Making all in ABYSS
make[4]: Entering directory '/home/boud-guest/abyss-2.1.5/ABYSS'
g++ -DHAVE_CONFIG_H -I. -I.. -I.. -I/home/boud-guest/abyss-2.1.5
-Wdate-time -D_FORTIFY_SOURCE=2
-isystem/home/boud-guest/abyss-2.1.5/boost_1_56_0 -Wall -Wextra -g -O2
-fdebug-prefix-map=/home/boud-guest/abyss-2.1.5=. -fstack-protector-strong
-Wformat -Werror=format-security -DGTEST_USE_OWN_TR1_TUPLE=0 -c -o
ABYSS-abyss.o `test -f 'abyss.cc' || echo './'`abyss.cc
In file included from ../Assembly/DBG.h:7,
from ../Assembly/SequenceCollection.h:22,
from abyss.cc:5:
../Common/MemoryUtil.h:11:11: fatal error: mach/task.h: No such file or
directory
# include <mach/task.h> // for task_info
^~~~~~~~~~~~~
compilation terminated.
Makefile:410: recipe for target 'ABYSS-abyss.o' failed
make[4]: *** [ABYSS-abyss.o] Error 1
HYPOTHESES FOR FIXING:
Without knowing details of hurd/mach:
(1) My first guess was that <mach/task_info.h> should be included instead of
<mach/task.h>,
but some other updates look like they're needed too. Making this replacement
in Common/MemoryUtil.h and changing nothing else gives:
g++ -Wall -Wextra -g -O2 -fdebug-prefix-map=/home/boud-guest/abyss-2.1.5=.
-fstack-protector-strong -Wformat -Werror=format-security
-DGTEST_USE_OWN_TR1_TUPLE=0 -Wl,-z,relro -Wl,-z,now -o ABYSS ABYSS-abyss.o
../DataBase/libdb.a -lsqlite3 -ldl -lm ../Assembly/libassembly.a
../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm
/usr/bin/ld: ABYSS-abyss.o: in function `getMemoryUsage':
./ABYSS/../Common/MemoryUtil.h:22: undefined reference to `task_info(unsigned
long, int, int*, unsigned int*)'
collect2: error: ld returned 1 exit status
Makefile:372: recipe for target 'ABYSS' failed
make[4]: *** [ABYSS] Error 1
(2) Trying <mach.h> instead of both <mach/mach.h> and <mach/task.h>, and
putting '__task_info' instead of 'task_info', with both of these changes
in Common/MemoryUtil.h and modifying no other files, gives:
g++ -Wall -Wextra -g -O2 -fdebug-prefix-map=/home/boud-guest/abyss-2.1.5=.
-fstack-protector-strong -Wformat -Werror=format-security
-DGTEST_USE_OWN_TR1_TUPLE=0 -Wl,-z,relro -Wl,-z,now -o ABYSS ABYSS-abyss.o
../DataBase/libdb.a -lsqlite3 -ldl -lm ../Assembly/libassembly.a
../DataLayer/libdatalayer.a ../Common/libcommon.a -ldl -lm
/usr/bin/ld: ABYSS-abyss.o: in function `getMemoryUsage':
./ABYSS/../Common/MemoryUtil.h:22: undefined reference to `__task_info(unsigned
long, int, int*, unsigned int*)'
collect2: error: ld returned 1 exit status
Makefile:372: recipe for target 'ABYSS' failed
make[4]: *** [ABYSS] Error 1
(3) It looks like including only <mach.h> should automatically include
/usr/include/mach/mach_interface.h>, which includes a prototype
for
kern_return_t __task_info( ... )
but g++ doesn't find this when linking. Does g++ have something missing when
linking
to code created with mach-specific extensions?
COMMENT:
Since this software looks like it caters specifically to Mach, it would be a
pity
not to update this to the current recommended usage of Mach.
--- End Message ---
--- Begin Message ---
Source: abyss
Source-Version: 2.1.5-4
We believe that the bug you reported is fixed in the latest version of
abyss, which is due to be installed in the Debian FTP archive.
A summary of the changes between this version and the previous one is
attached.
Thank you for reporting the bug, which will now be closed. If you
have further comments please address them to [email protected],
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Andreas Tille <[email protected]> (supplier of updated abyss package)
(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing [email protected])
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA256
Format: 1.8
Date: Wed, 23 Jan 2019 15:49:21 +0100
Source: abyss
Binary: abyss
Architecture: source
Version: 2.1.5-4
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<[email protected]>
Changed-By: Andreas Tille <[email protected]>
Description:
abyss - de novo, parallel, sequence assembler for short reads
Closes: 920240
Changes:
abyss (2.1.5-4) unstable; urgency=medium
.
* Fix build on hurd due to missing header file (thanks for the patch
to Samuel Thibault <[email protected]>)
Closes: #920240
* debhelper 12
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Files:
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