Your message dated Thu, 14 Apr 2016 19:34:11 +0000
with message-id <[email protected]>
and subject line Bug#821015: fixed in harvest-tools 1.2-2
has caused the Debian Bug report #821015,
regarding harvest-tools: FTBFS with memcpy-related errors
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.
(NB: If you are a system administrator and have no idea what this
message is talking about, this may indicate a serious mail system
misconfiguration somewhere. Please contact [email protected]
immediately.)
--
821015: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=821015
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Source: harvest-tools
Version: 1.2-1
Severity: important
Justification: fails to build from source
Hi, Andreas.
Builds of harvest-tools fail on nearly all architectures with errors
related to memcpy. On most platforms, there are several errors of the
form
libharvest.a(AnnotationList.o): In function
`std::char_traits<char>::copy(char*, char const*, unsigned long)':
/usr/include/c++/5/bits/char_traits.h:290: undefined reference to
`memcpy@GLIBC_2.2.5'
On mips(el), the errors are instead
/usr/bin/ld: src/harvest/memcpyWrap.o: relocation R_MIPS_HI16 against
`__gnu_local_gp' can not be used when making a shared object; recompile with
-fPIC
src/harvest/memcpyWrap.o: error adding symbols: Bad value
These all look like fallout from attempting to deploy a memcpy
wrapper, which moreover appears to make no actual difference. I would
recommend the following build-system changes:
- Stop compiling with -include src/harvest/memcpyLink.h.
- Stop building memcpyWrap.c at all.
- Build harvesttools directly from the remaining object files,
as I see no need for an intermediate libharvest.a. (Alternatively,
pull harvest.cpp, which defines main, out of the library.)
- Stop linking with -Wl,--wrap=memcpy. While you're at it, please
also drop -static-libstdc++, which is inappropriate for Debian.
Could you please take a look?
Thanks!
--- End Message ---
--- Begin Message ---
Source: harvest-tools
Source-Version: 1.2-2
We believe that the bug you reported is fixed in the latest version of
harvest-tools, 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.
Gert Wollny <[email protected]> (supplier of updated harvest-tools 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: SHA512
Format: 1.8
Date: Thu, 14 Apr 2016 17:47:41 +0000
Source: harvest-tools
Binary: harvest-tools
Architecture: source amd64
Version: 1.2-2
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<[email protected]>
Changed-By: Gert Wollny <[email protected]>
Description:
harvest-tools - archiving and postprocessing for reference-compressed genomic
mul
Closes: 821015
Changes:
harvest-tools (1.2-2) unstable; urgency=medium
.
* team upload
* d/p/remove.. add patch to remove the memcpy wrapper and the intermediate
static library
Closes: #821015
Checksums-Sha1:
580148d374c51577ad645a28e674c315745c3f72 2103 harvest-tools_1.2-2.dsc
51c2b699ee0bc96a34a5c77e2ff151e1273eaac7 3749321 harvest-tools_1.2.orig.tar.gz
9319880ecc5f3d1d2e084a2be8a22ec572c7fc55 4568 harvest-tools_1.2-2.debian.tar.xz
9a8ca69b8c270f20bee2ed0854ef89ef6c729069 1403668
harvest-tools-dbgsym_1.2-2_amd64.deb
34e7244c1b6be817299e8792bd2a230f730c52df 112452 harvest-tools_1.2-2_amd64.deb
Checksums-Sha256:
6f128c0d6b49abc0c72ee59b1d5db5dd011679615456337abb156c2cc36b8581 2103
harvest-tools_1.2-2.dsc
6f9a7ab056d52fad78bdb7a93832ff8b509b77566c22481a2d81089736e10af4 3749321
harvest-tools_1.2.orig.tar.gz
d2f153da29e8365d6a01d046407a148cc545c63b69a66dcdd57ef0dae39de2a5 4568
harvest-tools_1.2-2.debian.tar.xz
b7498cc0b5bbdea50f44d5fa9894e45769a5c9da0248897b1f11c4251bb46306 1403668
harvest-tools-dbgsym_1.2-2_amd64.deb
731735845702d66b933a3773dff613a691d6b4416c8d18e55e7909f54f1801e8 112452
harvest-tools_1.2-2_amd64.deb
Files:
a164ed8fbca0dff06a9e3d7c11dd64ba 2103 science optional harvest-tools_1.2-2.dsc
4e27e06681dffae59fb64d613808d4bc 3749321 science optional
harvest-tools_1.2.orig.tar.gz
eaf81afb7338c4b92914bad5b8f42d07 4568 science optional
harvest-tools_1.2-2.debian.tar.xz
7b882dacd192a6968b20862101d2d6dc 1403668 debug extra
harvest-tools-dbgsym_1.2-2_amd64.deb
b6450e8c233377b74861658a11ce3cfb 112452 science optional
harvest-tools_1.2-2_amd64.deb
-----BEGIN PGP SIGNATURE-----
Version: GnuPG v1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=EXsc
-----END PGP SIGNATURE-----
--- End Message ---
