Your message dated Tue, 04 Sep 2018 13:21:35 +0000
with message-id <e1fxbgx-0003ek...@fasolo.debian.org>
and subject line Bug#907358: fixed in ncbi-vdb 2.9.2-1+dfsg-1
has caused the Debian Bug report #907358,
regarding ncbi-vdb: fix broken library on i386
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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--
907358: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=907358
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems
--- Begin Message ---
Package: ncbi-vdb
Version: 2.9.1-1+dfsg-1
Severity: grave
Tags: patch
User: ubuntu-de...@lists.ubuntu.com
Usertags: origin-ubuntu cosmic ubuntu-patch
Dear Andreas,
The libncbi-vdb2 library is broken on i386, because while it has managed to
build, it has unresolvable references:
$ ldd -d -r /usr/lib/i386-linux-gnu/libncbi-vdb.so.2
linux-gate.so.1 (0xf7f0d000)
libmbedx509.so.0 => /usr/lib/i386-linux-gnu/libmbedx509.so.0
(0xf7a33000)
libmbedtls.so.10 => /usr/lib/i386-linux-gnu/libmbedtls.so.10
(0xf7a03000)
libmbedcrypto.so.1 => /usr/lib/i386-linux-gnu/libmbedcrypto.so.1
(0xf7999000)
libz.so.1 => /lib/i386-linux-gnu/libz.so.1 (0xf797a000)
libbz2.so.1.0 => /lib/i386-linux-gnu/libbz2.so.1.0 (0xf7968000)
libdl.so.2 => /lib/i386-linux-gnu/libdl.so.2 (0xf7963000)
libpthread.so.0 => /lib/i386-linux-gnu/libpthread.so.0 (0xf7944000)
libxml2.so.2 => /usr/lib/i386-linux-gnu/libxml2.so.2 (0xf7757000)
libm.so.6 => /lib/i386-linux-gnu/libm.so.6 (0xf7655000)
libc.so.6 => /lib/i386-linux-gnu/libc.so.6 (0xf7479000)
/lib/ld-linux.so.2 (0xf7f0f000)
libicuuc.so.60 => /usr/lib/i386-linux-gnu/libicuuc.so.60 (0xf72b8000)
liblzma.so.5 => /lib/i386-linux-gnu/liblzma.so.5 (0xf728c000)
libicudata.so.60 => /usr/lib/i386-linux-gnu/libicudata.so.60
(0xf58e2000)
libstdc++.so.6 => /usr/lib/i386-linux-gnu/libstdc++.so.6 (0xf575b000)
libgcc_s.so.1 => /lib/i386-linux-gnu/libgcc_s.so.1 (0xf573d000)
undefined symbol: uint64_msbit (/usr/lib/i386-linux-gnu/libncbi-vdb.so.2)
$
This is because there is no implementation of uint64_msbit for the gcc/i386
target.
However, there doesn't appear to be anything about the gcc/x86_64
implementation which is 64-bit-specific, so attached is a patch that fixes
this bug by simply copying the x86_64 implementation to the i386 file.
This problem was discovered because it caused a build failure for sra-sdk on
i386 in Ubuntu when trying to link against the library at build time. The
same build failure appears to exist in Debian.
It would also be perfectly reasonable to drop i386 as a supported
architecture for ncbi-vdb if you prefer; but I suggest you then make sure to
actually do this, rather than shipping a broken library package on i386.
Also, this broken library package would have been detectable at build time
if you were building with -Wl,-z,defs in LDFLAGS, as that would have
prevented ever generating a shared library with missing symbols. That's a
good idea to do anyway, but in particular it would mean that if you didn't
want to support i386 anymore, you could just add this to build flags and not
have to worry about changing the architecture list explicitly.
Cheers,
--
Steve Langasek Give me a lever long enough and a Free OS
Debian Developer to set it on, and I can move the world.
Ubuntu Developer https://www.debian.org/
slanga...@ubuntu.com vor...@debian.org
diff -Nru ncbi-vdb-2.9.1-1+dfsg/debian/patches/i386-uint64_msbit.patch
ncbi-vdb-2.9.1-1+dfsg/debian/patches/i386-uint64_msbit.patch
--- ncbi-vdb-2.9.1-1+dfsg/debian/patches/i386-uint64_msbit.patch
1969-12-31 16:00:00.000000000 -0800
+++ ncbi-vdb-2.9.1-1+dfsg/debian/patches/i386-uint64_msbit.patch
2018-08-26 14:57:18.000000000 -0700
@@ -0,0 +1,25 @@
+Description: add missing implementation of uint64_msbit for i386
+ Without this definition, we get a "successful" library build with undefined
+ symbols on i386. We can use the same implementation of this function as on
+ x86_64.
+Author: Steve Langasek <steve.langa...@ubuntu.com>
+Last-Modified: 2018-08-26
+
+Index: ncbi-vdb-2.9.1-1+dfsg/interfaces/cc/gcc/i386/arch-impl.h
+===================================================================
+--- ncbi-vdb-2.9.1-1+dfsg.orig/interfaces/cc/gcc/i386/arch-impl.h
++++ ncbi-vdb-2.9.1-1+dfsg/interfaces/cc/gcc/i386/arch-impl.h
+@@ -127,6 +127,13 @@ int32_t uint32_msbit ( uint32_t self )
+ return rtn;
+ }
+
++static __inline__
++int32_t uint64_msbit ( uint64_t self )
++{
++ if (self==0) return -1;
++ return 63 - __builtin_clzll ( self );
++}
++
+ typedef struct int128_t int128_t;
+ struct int128_t
+ {
diff -Nru ncbi-vdb-2.9.1-1+dfsg/debian/patches/series
ncbi-vdb-2.9.1-1+dfsg/debian/patches/series
--- ncbi-vdb-2.9.1-1+dfsg/debian/patches/series 2018-06-27 20:41:16.000000000
-0700
+++ ncbi-vdb-2.9.1-1+dfsg/debian/patches/series 2018-08-26 14:58:11.000000000
-0700
@@ -9,3 +9,4 @@
add_-msse2.patch
use_debian_packaged_libmbedx.patch
mbedtls_ssl_init.patch
+i386-uint64_msbit.patch
--- End Message ---
--- Begin Message ---
Source: ncbi-vdb
Source-Version: 2.9.2-1+dfsg-1
We believe that the bug you reported is fixed in the latest version of
ncbi-vdb, 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 907...@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Andreas Tille <ti...@debian.org> (supplier of updated ncbi-vdb 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 ftpmas...@ftp-master.debian.org)
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA256
Format: 1.8
Date: Tue, 04 Sep 2018 14:14:44 +0200
Source: ncbi-vdb
Binary: libncbi-vdb2 libncbi-vdb-dev libkdf5-2 libkdf5-dev libncbi-wvdb2
libncbi-wvdb-dev libvdb-sqlite2 libvdb-sqlite-dev
Architecture: source
Version: 2.9.2-1+dfsg-1
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<debian-med-packag...@lists.alioth.debian.org>
Changed-By: Andreas Tille <ti...@debian.org>
Description:
libkdf5-2 - hdf5 access to data in the INSDC Sequence Read Archives
libkdf5-dev - hdf5 access to data in the INSDC Sequence Read Archives (devel)
libncbi-vdb-dev - libraries for using data in the INSDC Sequence Read Archives
(dev
libncbi-vdb2 - libraries for using data in the INSDC Sequence Read Archives
libncbi-wvdb-dev - virtual layer update modul of ncbi-vdb library (devel)
libncbi-wvdb2 - virtual layer update modul of ncbi-vdb library
libvdb-sqlite-dev - sqlite modul of ncbi-vdb library (devel)
libvdb-sqlite2 - sqlite modul of ncbi-vdb library
Closes: 907358
Changes:
ncbi-vdb (2.9.2-1+dfsg-1) unstable; urgency=medium
.
* New upstream version
.
[ Steve Langasek ]
* add missing implementation of uint64_msbit for i386
Closes: #907358
.
[ Andreas Tille ]
* d/rules:
- DEB_LDFLAGS_MAINT_APPEND := -Wl,--as-needed
- Considered using
DEB_LDFLAGS_MAINT_APPEND := -Wl,-z,defs
which should prevent successful build of a broken library (thanks
for the hint to Steve Langasek) Unfortunately this uncovers several
other build failures - volunteers to provide the correct linker
flags are welcome
- dh_auto_build --no-parallel
* Standards-Version: 4.2.1
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ncbi-vdb_2.9.2-1+dfsg-1.debian.tar.xz
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