Re: Bug#956324: Clustalo bus error on mipsel (Was: Bug#956324: python-biopython: FTBFS on mipsel)
Hi Matthew,
thanks a lot for your detailed investigation.
On Fri, Apr 17, 2020 at 04:28:23PM -0700, Matthew Fernandez wrote:
> > Program received signal SIGBUS, Bus error.
> > 0x5556a1b8 in PairDistances (distmat=0x7fff278c, mseq=0x55692a30,
> > pairdist_type=, bPercID=, istart=0, iend=3,
> > jstart=0, jend=3, fdist_in=0x0,
> >fdist_out=0x0) at pair_dist.c:346
> > 346 NewProgress(&prProgress, LogGetFP(&rLog, LOG_INFO),
>
> OK, let me try a little harder :)
>
> $ # enable debugging symbols and Address Sanitizer
> $ CFLAGS="-g -fsanitize=address" CXXFLAGS="-g -fsanitize=address"
> ./configure
> …
> $ make clean && make
> …
> $ ./src/clustalo -i debian/tests/biopython_testdata/f002 --guidetree-out
> temp_test.dnd -o temp_test.aln --outfmt clustal --force
> =
> ==30264==ERROR: AddressSanitizer: dynamic-stack-buffer-overflow on
> address 0x7ffcfcbf5784 at pc 0x5620f0aa478c bp 0x7ffcfcbf56c0 sp
> 0x7ffcfcbf56b8
> WRITE of size 4 at 0x7ffcfcbf5784 thread T0
> #0 0x5620f0aa478b in PairDistances
> /home/matthew/clustal-omega-1.2.4/src/clustal/pair_dist.c:336
> #1 0x5620f0a91d9f in AlignmentOrder
> /home/matthew/clustal-omega-1.2.4/src/clustal-omega.c:835
> #2 0x5620f0a95c04 in Align
> /home/matthew/clustal-omega-1.2.4/src/clustal-omega.c:1221
> #3 0x5620f0a90d76 in MyMain
> /home/matthew/clustal-omega-1.2.4/src/mymain.c:1192
> #4 0x5620f0a88ca2 in main
> /home/matthew/clustal-omega-1.2.4/src/main.cpp:469
> #5 0x7f3773d9009a in __libc_start_main ../csu/libc-start.c:308
> #6 0x5620f0a89ad9 in _start
> (/home/matthew/clustal-omega-1.2.4/src/clustalo+0x2dad9)
>
> Address 0x7ffcfcbf5784 is located in stack of thread T0
> SUMMARY: AddressSanitizer: dynamic-stack-buffer-overflow
> /home/matthew/clustal-omega-1.2.4/src/clustal/pair_dist.c:336 in PairDistances
> Shadow bytes around the buggy address:
> 0x10001f976aa0: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00
> 0x10001f976ab0: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00
> 0x10001f976ac0: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00
> 0x10001f976ad0: 00 00 00 00 00 00 00 00 00 00 00 00 ca ca ca ca
> 0x10001f976ae0: 04 cb cb cb cb cb cb cb 00 00 00 00 ca ca ca ca
> =>0x10001f976af0:[04]cb cb cb cb cb cb cb 00 00 00 00 00 00 00 00
> 0x10001f976b00: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00
> 0x10001f976b10: f1 f1 f1 f1 00 f2 f2 f2 f2 f2 f2 f2 00 f2 f2 f2
> 0x10001f976b20: f2 f2 f2 f2 00 00 00 00 00 00 00 00 00 f2 f2 f2
> 0x10001f976b30: f3 f3 f3 f3 00 00 00 00 00 00 00 00 00 00 00 00
> 0x10001f976b40: 00 00 00 00 00 00 f1 f1 f1 f1 00 f2 f2 f2 f2 f2
> Shadow byte legend (one shadow byte represents 8 application bytes):
> Addressable: 00
> Partially addressable: 01 02 03 04 05 06 07
> Heap left redzone: fa
> Freed heap region: fd
> Stack left redzone: f1
> Stack mid redzone: f2
> Stack right redzone: f3
> Stack after return: f5
> Stack use after scope: f8
> Global redzone: f9
> Global init order: f6
> Poisoned by user:f7
> Container overflow: fc
> Array cookie:ac
> Intra object redzone:bb
> ASan internal: fe
> Left alloca redzone: ca
> Right alloca redzone:cb
> ==30264==ABORTING
>
> Looking at line 336 of pair_dist.c, it looks like the bound on the containing
> loop is wrong. So let’s try adjusting that:
>
> $ vim src/clustal/pair_dist.c
> $ git diff src/clustal/pair_dist.c
> diff --git a/src/clustal/pair_dist.c b/src/clustal/pair_dist.c
> index e6dbdc3..bb79e61 100644
> --- a/src/clustal/pair_dist.c
> +++ b/src/clustal/pair_dist.c
> @@ -321,7 +321,7 @@ PairDistances(symmatrix_t **distmat, mseq_t *mseq,
> int pairdist_type, bool bPerc
>
> /* FIXME: can get rid of iChunkStart, iChunkEnd now that we're
> using the arrays */
> iChunkStart = iend;
> -for(iChunk = 0; iChunk <= iNumberOfThreads; iChunk++)
> +for(iChunk = 0; iChunk < iNumberOfThreads; iChunk++)
> {
> iChunkEnd = iChunkStart;
> if (iChunk == iNumberOfThreads - 1){
> $ make
> …
> $ ./src/clustalo -i debian/tests/biopython_testdata/f002 --guidetree-out
> temp_test.dnd -o temp_test.aln --outfmt clustal --force
> =
> ==30601==ERROR: AddressSanitizer: global-buffer-overflow on address
> 0x561188847864 at pc 0x5611886da6e7 bp 0x7fffe6d77ef0 sp 0x7fffe6d77ee8
> READ of size 4 at 0x561188847864 thread T0
> #0 0x5611886da6e6 in FullAlignment::Build(HMM&, Hit&, char*)
> /home/matthew/clustal-omega-1.2.
Bug#955323: RFS: atomic-chrome-el/2.0.0-1 [ITP] -- edit a web-browser text entry area with Emacs
Hello Nicholas! A few problems... these commands: git clone g...@salsa.debian.org:emacsen-team/atomic-chrome-el.git cd atomic-chrome-el uscan --download-current-version git bp give me this error: anarcat@angela:atomic-chrome-el(master)$ git bp dh clean --with elpa dh_clean gbp:info: Creating atomic-chrome_2.0.0.orig.tar.xz from 'v2.0.0' gbp:info: Exporting 'HEAD' to '/home/anarcat/src/build-area/atomic-chrome-tmp' gbp:info: Moving '/home/anarcat/src/build-area/atomic-chrome-tmp' to '/home/anarcat/src/build-area/atomic-chrome-2.0.0' gbp:info: Performing the build dpkg-source: error: source package has two conflicting values - atomic-chrome-el and atomic-chrome E: Failed to run dpkg-source --before-build /home/anarcat/src/build-area/atomic-chrome-2.0.0 i am not sure, but i suspect it is a mismatch between the debian/changelog and debian/control package names. indeed, with the following patch: From 419b3c708fbc41e727fc2dd880b7d90da8ada692 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Antoine=20Beaupr=C3=A9?= Date: Fri, 17 Apr 2020 20:52:07 -0400 Subject: [PATCH] fix package name to match debian/control --- debian/changelog | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/debian/changelog b/debian/changelog index d11e6c7..98e3daa 100644 --- a/debian/changelog +++ b/debian/changelog @@ -1,4 +1,4 @@ -atomic-chrome (2.0.0-1) unstable; urgency=medium +atomic-chrome-el (2.0.0-1) unstable; urgency=medium * Initial release. (Closes: #909336) -- 2.20.1 ... the package compiles. The other issue I found is what now seems to be a recurring disagreement between us. :) This is the tarball that `uscan` gives me when I run the above command: anarcat@angela:src(master)$ sha256sum atomic-chrome-2.0.0.tar.gz f239fabd2438df8d947b333453534e6ab76f946c8879df2e3f1151baf76dac97 atomic-chrome-2.0.0.tar.gz anarcat@angela:src(master)$ file atomic-chrome-2.0.0.tar.gz atomic-chrome-2.0.0.tar.gz: gzip compressed data, from Unix, original size 296960 Yet, git-buildpackage will not use that tarball. Because it has the following configuration: compression = xz compression-level = 9 It generates the following, different tarball: anarcat@angela:atomic-chrome-el(master)$ sha256sum ../build-area/atomic-chrome-el_2.0.0.orig.tar.xz 2d55a3646307be8c4b1703e3f353a358987592d6523a8de0ffb7be1292e678ab ../build-area/atomic-chrome-el_2.0.0.orig.tar.xz anarcat@angela:atomic-chrome-el(master)$ file ../build-area/atomic-chrome-el_2.0.0.orig.tar.xz ../build-area/atomic-chrome-el_2.0.0.orig.tar.xz: XZ compressed data There are a few things wrong here: 1. we should not needlessly differ from the upstream tarball 2. if we really have to, `uscan` should allow us to reconstruct our tarball reproducibly, or at least `README.source` should explain how. at minimum, `README.source` should explain *why* we differ 3. even if we insist on using `xz` (and I don't see why we do in this case), we don't need the maximum compression level. this is a small package and there's not reason to "crank it up to 11", so to speak :) The following patch should fix the problem: From a9dc9a10a4c1ea9024a70335232dd837d36738d1 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Antoine=20Beaupr=C3=A9?= Date: Fri, 17 Apr 2020 21:01:14 -0400 Subject: [PATCH] remove superfluous diff with upstream tarball --- debian/gbp.conf | 3 --- 1 file changed, 3 deletions(-) diff --git a/debian/gbp.conf b/debian/gbp.conf index 07b0329..839ffea 100644 --- a/debian/gbp.conf +++ b/debian/gbp.conf @@ -6,6 +6,3 @@ debian-tag = debian/%(version)s sign-tags = True pristine-tar = False pristine-tar-commit = False - -compression = xz -compression-level = 9 -- 2.20.1 I feel uncomfortable sponsoring a package if it doesn't use the upstream tarballs. I hope you'll understand. A. -- Nature hides her secret because of her essential loftiness, but not by means of ruse. - Albert Einstein signature.asc Description: PGP signature
Re: Bug#956324: Clustalo bus error on mipsel (Was: Bug#956324: python-biopython: FTBFS on mipsel)
> On Apr 17, 2020, at 13:18, Andreas Tille wrote: > > Hi Matthew, > > On Fri, Apr 17, 2020 at 08:18:29AM -0700, Matthew Fernandez wrote: >>> Thanks for the patch which I applied to packaging Git. I assume you >>> want to express that while these fixes are definitely good coding >>> practice the bus error problem is not fixed by it, right? >> >> Thanks, Andreas. It may fix the bus error, but I don’t have a MIPS machine >> to test on. Some of those logging calls had the potential to leave you with >> a misaligned stack pointer. IIUC unaligned loads on MIPS could cause such a >> bus error. > > I tried with hope ... but failed: > > (sid_mipsel-dchroot)tille@eller:~/clustalo$ gdb --args src/clustalo -i > debian/tests/biopython_testdata/f002 --guidetree-out temp_test.dnd -o > temp_test.aln --outfmt clustal --force > GNU gdb (Debian 9.1-3) 9.1 > ... > Reading symbols from src/clustalo... > (gdb) run > Starting program: /home/tille/clustalo/src/clustalo -i > debian/tests/biopython_testdata/f002 --guidetree-out temp_test.dnd -o > temp_test.aln --outfmt clustal --force > [Thread debugging using libthread_db enabled] > Using host libthread_db library "/lib/mipsel-linux-gnu/libthread_db.so.1". > > Program received signal SIGBUS, Bus error. > 0x5556a1b8 in PairDistances (distmat=0x7fff278c, mseq=0x55692a30, > pairdist_type=, bPercID=, istart=0, iend=3, > jstart=0, jend=3, fdist_in=0x0, >fdist_out=0x0) at pair_dist.c:346 > 346 NewProgress(&prProgress, LogGetFP(&rLog, LOG_INFO), OK, let me try a little harder :) $ # enable debugging symbols and Address Sanitizer $ CFLAGS="-g -fsanitize=address" CXXFLAGS="-g -fsanitize=address" ./configure … $ make clean && make … $ ./src/clustalo -i debian/tests/biopython_testdata/f002 --guidetree-out temp_test.dnd -o temp_test.aln --outfmt clustal --force = ==30264==ERROR: AddressSanitizer: dynamic-stack-buffer-overflow on address 0x7ffcfcbf5784 at pc 0x5620f0aa478c bp 0x7ffcfcbf56c0 sp 0x7ffcfcbf56b8 WRITE of size 4 at 0x7ffcfcbf5784 thread T0 #0 0x5620f0aa478b in PairDistances /home/matthew/clustal-omega-1.2.4/src/clustal/pair_dist.c:336 #1 0x5620f0a91d9f in AlignmentOrder /home/matthew/clustal-omega-1.2.4/src/clustal-omega.c:835 #2 0x5620f0a95c04 in Align /home/matthew/clustal-omega-1.2.4/src/clustal-omega.c:1221 #3 0x5620f0a90d76 in MyMain /home/matthew/clustal-omega-1.2.4/src/mymain.c:1192 #4 0x5620f0a88ca2 in main /home/matthew/clustal-omega-1.2.4/src/main.cpp:469 #5 0x7f3773d9009a in __libc_start_main ../csu/libc-start.c:308 #6 0x5620f0a89ad9 in _start (/home/matthew/clustal-omega-1.2.4/src/clustalo+0x2dad9) Address 0x7ffcfcbf5784 is located in stack of thread T0 SUMMARY: AddressSanitizer: dynamic-stack-buffer-overflow /home/matthew/clustal-omega-1.2.4/src/clustal/pair_dist.c:336 in PairDistances Shadow bytes around the buggy address: 0x10001f976aa0: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 0x10001f976ab0: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 0x10001f976ac0: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 0x10001f976ad0: 00 00 00 00 00 00 00 00 00 00 00 00 ca ca ca ca 0x10001f976ae0: 04 cb cb cb cb cb cb cb 00 00 00 00 ca ca ca ca =>0x10001f976af0:[04]cb cb cb cb cb cb cb 00 00 00 00 00 00 00 00 0x10001f976b00: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 0x10001f976b10: f1 f1 f1 f1 00 f2 f2 f2 f2 f2 f2 f2 00 f2 f2 f2 0x10001f976b20: f2 f2 f2 f2 00 00 00 00 00 00 00 00 00 f2 f2 f2 0x10001f976b30: f3 f3 f3 f3 00 00 00 00 00 00 00 00 00 00 00 00 0x10001f976b40: 00 00 00 00 00 00 f1 f1 f1 f1 00 f2 f2 f2 f2 f2 Shadow byte legend (one shadow byte represents 8 application bytes): Addressable: 00 Partially addressable: 01 02 03 04 05 06 07 Heap left redzone: fa Freed heap region: fd Stack left redzone: f1 Stack mid redzone: f2 Stack right redzone: f3 Stack after return: f5 Stack use after scope: f8 Global redzone: f9 Global init order: f6 Poisoned by user:f7 Container overflow: fc Array cookie:ac Intra object redzone:bb ASan internal: fe Left alloca redzone: ca Right alloca redzone:cb ==30264==ABORTING Looking at line 336 of pair_dist.c, it looks like the bound on the containing loop is wrong. So let’s try adjusting that: $ vim src/clustal/pair_dist.c $ git diff src/clustal/pair_dist.c diff --git a/src/clustal/pair_dist.c b/src/clustal/pair_dist.c index e6dbdc3..bb79e61 100644 --- a/src/clustal/pair_dist.c +++ b/src/clustal/pair_dist.c @@ -321,7 +321,7 @@ PairDistances(symmatrix_t **distmat, mseq_t *mseq, int pairdist_type, bool bPerc
Bug#958056: RFS: scanbd/1.5.1-6 [QA] -- Scanner button daemon
Package: sponsorship-requests Severity: normal Dear mentors, I am looking for a sponsor for my package "scanbd" * Package name: scanbd Version : 1.5.1-6 Upstream Author : Wilhelm Meier * URL : http://scanbd.sf.net/ * License : GPL-2+ * Vcs : https://salsa.debian.org/debian/scanbd Section : misc It builds those binary packages: scanbd - Scanner button daemon To access further information about this package, please visit the following URL: https://mentors.debian.net/package/scanbd Alternatively, one can download the package with dget using this command: dget -x https://mentors.debian.net/debian/pool/main/s/scanbd/scanbd_1.5.1-6.dsc Changes since the last upload: * QA upload. * Update Standards-Version to 4.5.0 * Fix ftbfs with GCC-10. (Closes: #957779) -- Regards Sudip
Re: Bug#956324: Clustalo bus error on mipsel (Was: Bug#956324: python-biopython: FTBFS on mipsel)
Hi Matthew, On Fri, Apr 17, 2020 at 08:18:29AM -0700, Matthew Fernandez wrote: > > Thanks for the patch which I applied to packaging Git. I assume you > > want to express that while these fixes are definitely good coding > > practice the bus error problem is not fixed by it, right? > > Thanks, Andreas. It may fix the bus error, but I don’t have a MIPS machine > to test on. Some of those logging calls had the potential to leave you with > a misaligned stack pointer. IIUC unaligned loads on MIPS could cause such a > bus error. I tried with hope ... but failed: (sid_mipsel-dchroot)tille@eller:~/clustalo$ gdb --args src/clustalo -i debian/tests/biopython_testdata/f002 --guidetree-out temp_test.dnd -o temp_test.aln --outfmt clustal --force GNU gdb (Debian 9.1-3) 9.1 ... Reading symbols from src/clustalo... (gdb) run Starting program: /home/tille/clustalo/src/clustalo -i debian/tests/biopython_testdata/f002 --guidetree-out temp_test.dnd -o temp_test.aln --outfmt clustal --force [Thread debugging using libthread_db enabled] Using host libthread_db library "/lib/mipsel-linux-gnu/libthread_db.so.1". Program received signal SIGBUS, Bus error. 0x5556a1b8 in PairDistances (distmat=0x7fff278c, mseq=0x55692a30, pairdist_type=, bPercID=, istart=0, iend=3, jstart=0, jend=3, fdist_in=0x0, fdist_out=0x0) at pair_dist.c:346 346 NewProgress(&prProgress, LogGetFP(&rLog, LOG_INFO), Thank you for the fixes anyway Andreas. -- http://fam-tille.de
Bug#958047: RFS: mercantile/1.0-1 [ITP] -- python3-mercantile - Web mercator XYZ tile utilities
Hi Joachim, Your package seems to fit well inside Debian GIS Team [1]. You may contact the team regarding the sponsoring and team maintenance. [1] https://wiki.debian.org/Teams/DebianGis Best wishes, Andrius
Bug#958047: RFS: mercantile/1.0-1 [ITP] -- python3-mercantile - Web mercator XYZ tile utilities
Package: sponsorship-requests Severity: wishlist Dear mentors, I am looking for a sponsor for my package "mercantile" * Package name: mercantile Version : 1.1.3-1 Upstream Author : Sean Gillies * URL : https://github.com/mapbox/mercantile * License : BSD-3-clause * Vcs : None Section : utils It builds those binary packages: python3-mercantile - Web mercator XYZ tile utilities To access further information about this package, please visit the following URL: https://mentors.debian.net/package/mercantile Alternatively, one can download the package with dget using this command: dget -x https://mentors.debian.net/debian/pool/main/m/mercantile/ mercantile_1.1.3-1.dsc Changes since the last upload: * Initial release (Closes: #956911) Regards, Joachim
Bug#958046: RFS: connexion/1.0-1 [ITP] -- python3-connexion - API first applications with OpenAPI/Swagger and Flask
Package: sponsorship-requests Severity: wishlist Dear mentors, I am looking for a sponsor for my package "connexion" * Package name: connexion Version : 2.6.0-1 Upstream Author : Zalando SE * URL : https://github.com/zalando/connexion * License : Apache * Vcs : None Section : python It builds those binary packages: python3-connexion - API first applications with OpenAPI/Swagger and Flask To access further information about this package, please visit the following URL: https://mentors.debian.net/package/connexion Alternatively, one can download the package with dget using this command: dget -x https://mentors.debian.net/debian/pool/main/c/connexion/connexion_2.6.0-1.dsc Changes since the last upload: * Initial release (Closes: #958042) This package requires additional packages, which are not yet uploaded to debian. But I packaged those dependencies already and also uploaded them to mentors.debian.net: - https://mentors.debian.net/package/openapi-spec-validator[1] - https://mentors.debian.net/package/swagger-ui-bundle[2] - https://mentors.debian.net/package/clickclick[3] - https://mentors.debian.net/package/pytest-flake8[4] So I'm lokking for a sponsor for those packaging as well. If you like to sponsor them too, I wold be very glad. Otherwise I place an RFS for those packages to. Regards, Joachim [1] https://mentors.debian.net/package/openapi-spec-validator [2] https://mentors.debian.net/package/swagger-ui-bundle [3] https://mentors.debian.net/package/clickclick [4] https://mentors.debian.net/package/pytest-flake8
Bug#956965: RFS: sipxtapi/3.3.0~test18+dfsg.1-1.1 [NMU] -- SIP stack, RTP media framework and codecs
Thanks Tobi. On Fri, Apr 17, 2020 at 4:51 PM Tobias Frost wrote: > > Control: tags -1 moreinfo > > Hi Sudip, > > thanks for the updated package! > > Some remarks: > > The only thing that really needs fixing is that: > > - the version should be 3.3.0~test18+dfsg.1-0.1 (NMUing upstream versions > have > debian revision 0) sorry, missed this is in developers-reference. :( > I think all are done now. To access further information about this package, please visit the following URL: https://mentors.debian.net/package/sipxtapi Alternatively, one can download the package with dget using this command: dget -x https://mentors.debian.net/debian/pool/main/s/sipxtapi/sipxtapi_3.3.0~test18+dfsg.1-0.1.dsc Changes since the last upload: * Non-maintainer upload. * Update to new upstream 3.3.0_test18. (Closes: #956686) - Add Files-Excluded to repack source. - Add patch to skip building examples. - Remove patches applied upstream. - Remove lintian overrides not needed. - Update Standards-Version to 4.5.0 - Use debhelper-compat. - Update compat level to 12. - Update priority to optional. - Remove dependency on autotools-dev, dh-autoreconf. - Remove copyright information of file removed by update. - Fix copyright information for a header file. - Use secure copyright format uri. * Point Vcs to salsa. (Closes: #956685) * Add watch file. (Closes: #956687) -- Regards Sudip
Bug#956965: RFS: sipxtapi/3.3.0~test18+dfsg.1-1.1 [NMU] -- SIP stack, RTP media framework and codecs
Control: tags -1 moreinfo Hi Sudip, thanks for the updated package! Some remarks: The only thing that really needs fixing is that: - the version should be 3.3.0~test18+dfsg.1-0.1 (NMUing upstream versions have debian revision 0) The rest are minor things, but it would be nice if you could fix them as well: - There is prebuilt doxygen documentation in sipXcallLib/doc/sipXtapi/html/ As you anyway repacking, please remove them as well. - There are a lot of unwanted files un sipXcallLib/examples. Like pcre.a *.lib files or a ton of 3rd party library headers (wx, nss) As the examples are not installed anyway, I think it is ok just to strip them from the source and tweak the build system not looking for them. (I did a quick test by deleting the folder and tweaking configure.ac and sipXcallLib/Makefile.am and it builds at least. patch attached.) As a side benefit, this will also fix some linitan stuff ;-) - please add a "s" to fix: P: sipxtapi source: insecure-copyright-format-uri http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ Also easy to fix: I: sipxtapi source: unused-file-paragraph-in-dep5-copyright paragraph at line 37 I: sipxtapi source: unused-override license-problem-non-free-RFC sipXportLib/src/hmac-sha1/sha1.c I: sipxtapi source: unused-override license-problem-non-free-RFC sipXportLib/src/hmac-sha1/sha1.h I: sipxtapi source: wildcard-matches-nothing-in-dep5-copyright sipXtackLib/include/*.c (paragraph at line 37) -- Cheers, tobi --- sipxtapi-3.3.0~test18+dfsg.1/configure.ac 2020-04-17 17:39:04.724141006 +0200 +++ sipxtapi-3.3.0~test18+dfsg.1_/configure.ac 2020-04-17 17:38:18.183321746 +0200 @@ -189,8 +189,6 @@ bin/Makefile sipXcallLib/Makefile sipXcallLib/doc/Makefile - sipXcallLib/examples/Makefile - sipXcallLib/examples/sipXezPhone/Makefile sipXcallLib/include/Makefile sipXcallLib/src/Makefile sipXcallLib/src/test/Makefile --- sipxtapi-3.3.0~test18+dfsg.1/sipXcallLib/Makefile.am 2020-04-17 17:39:04.724141006 +0200 +++ sipxtapi-3.3.0~test18+dfsg.1_/sipXcallLib/Makefile.am 2020-04-17 17:38:18.187322097 +0200 @@ -9,7 +9,7 @@ config/sipXcommon.am.inc \ CONTRIBUTORS -unconditional_SUBDIRS = . src examples include +unconditional_SUBDIRS = . src include # bin is not really needed now that we have a top-level build system #unconditional_SUBDIRS += bin
Re: Bug#956324: Clustalo bus error on mipsel (Was: Bug#956324: python-biopython: FTBFS on mipsel)
On Fri, 17 Apr 2020 at 08:09, Andreas Tille wrote: > Hi Matthew, > > On Fri, Apr 17, 2020 at 07:40:54AM -0700, Matthew Fernandez wrote: > > > > As a jumping off point, the attached patch fixes some issues with > logging calls in the upstream 1.2.4 source release. > > Thanks for the patch which I applied to packaging Git. I assume you > want to express that while these fixes are definitely good coding > practice the bus error problem is not fixed by it, right? Thanks, Andreas. It may fix the bus error, but I don’t have a MIPS machine to test on. Some of those logging calls had the potential to leave you with a misaligned stack pointer. IIUC unaligned loads on MIPS could cause such a bus error.
Re: Bug#956324: Clustalo bus error on mipsel (Was: Bug#956324: python-biopython: FTBFS on mipsel)
Hi Matthew, On Fri, Apr 17, 2020 at 07:40:54AM -0700, Matthew Fernandez wrote: > > As a jumping off point, the attached patch fixes some issues with logging > calls in the upstream 1.2.4 source release. Thanks for the patch which I applied to packaging Git. I assume you want to express that while these fixes are definitely good coding practice the bus error problem is not fixed by it, right? Kind regards and thank a lot in any case Andreas. -- http://fam-tille.de
Re: Bug#956324: Clustalo bus error on mipsel (Was: Bug#956324: python-biopython: FTBFS on mipsel)
> On Apr 17, 2020, at 04:20, Andreas Tille wrote: > > Control: tags -1 help > > Hi, > > as it can be seen on the recent build log of clustalo on mips[1] the > build fails with > > > # Run additional test from python-biopython package to verify that > # this will work as well > src/clustalo -i debian/tests/biopython_testdata/f002 --guidetree-out > temp_test.dnd -o temp_test.aln --outfmt clustal --force > make[1]: *** [debian/rules:25: override_dh_auto_test-arch] Bus error > > > I injected that extra test since this very test failed inside the > python-biopython package. To track it down I logged in to > eller.debian.org tried to build the package and was able to reproduce > the error. Thus I fired up gdb in this session and got: > > > (sid_mipsel-dchroot)tille@eller:~/clustalo-1.2.4$ gdb --args src/clustalo -i > debian/tests/biopython_testdata/f002 --guidetree-out temp_test.dnd -o > temp_test.aln --outfmt clustal --force > GNU gdb (Debian 9.1-3) 9.1 > ... > Reading symbols from src/clustalo... > (gdb) run > Starting program: /home/tille/clustalo-1.2.4/src/clustalo -i > debian/tests/biopython_testdata/f002 --guidetree-out temp_test.dnd -o > temp_test.aln --outfmt clustal --force > [Thread debugging using libthread_db enabled] > Using host libthread_db library "/lib/mipsel-linux-gnu/libthread_db.so.1". > > Program received signal SIGBUS, Bus error. > 0x5556a188 in PairDistances (distmat=0x7fff278c, mseq=0x55692a38, > pairdist_type=, bPercID=, istart=0, iend=3, > jstart=0, jend=3, fdist_in=0x0, fdist_out=0x0) at pair_dist.c:346 > 346 NewProgress(&prProgress, LogGetFP(&rLog, LOG_INFO), > (gdb) > > > So it seems the bus error occures somehow here: > > > https://salsa.debian.org/med-team/clustalo/-/blob/master/src/clustal/pair_dist.c#L346 > > > I have no idea how to continue from here. I'm hoping that someone with > some more detailed knowledge might have a clue how to fix this issue on > mipsel. Otherwise I personally do not see any better solution than to > remove clustalo from mipsel architecture. As a jumping off point, the attached patch fixes some issues with logging calls in the upstream 1.2.4 source release. clustalo-log-format-calls.patch Description: Binary data
Bug#956907: RFS: ace/6.5.8+dfsg-1 [RC] -- makefile, project, and workspace creator
Thanks Tobi for pointing out the transition. I did not know that. :( On Thu, Apr 16, 2020 at 4:35 PM Tobias Frost wrote: > > Control: tags -1 moreinfo > > Hi Sudip, > > here's a review, no specific order: > > - it seems that there is an ABI bump in the libraries (as packages get > renamed and so on…). > Please target "experimental" for this upload, as this will trigger an > transistion [1] and also > needs to clear "NEW". done > > - d/copyright needs some years updated. Bonus points for converting it to > dep5 (its almost already dep5, so likely quickly converted) I only noticed one change of year, which has been updated now. And, I could not convert it to dep5 as I could not decide on the license of debian/* that the previous people wanted to use. I will ping Johny (upstream) about it and check if he knows something and then have it updated in the next release. > > [1] https://wiki.debian.org/Teams/ReleaseTeam/Transitions > > - you should probably close #878198; I see the change but it is not mentioned > in the changelog. done. > > - you should probably also close #954252 (at least the bts says it is fixed > by the new upstream version) closed separately as it was already fixed by #946853. > > Regarding the symbols: Be aware that symbols are tricky for C++ code, > especially for different architectures… Lets see and wait how it turns out, > but > do not hesitate to undo that if you feel it becomes a burden. upstream was also not too much enthusiastic about having symbols and was telling me about problems that it might cause. dropped for now. :) Changes since the last upload: * Team upload. * Update to upstream v6.5.8 - Remove old patches applied upstream. - Use debian/* from upstream. * Update Standards-Version to 4.5.0 * Use debhelper-compat. - Update compat level to 12. * Update debian/rules. - Remove --list-missing. - Add -g for debug symbols. - Stop modifying flags directly. - Install shared library in multiarch location. - Remove LD_LIBRARY_PATH. * Update doc-base location. * Remove lintian overrides. - for symbols. - for debhelper. * Update maintainer to valid team email. (Closes: #899440) * Update Vcs link to salsa. * Update copyright year. * Drop transitional package gperf-ace. (Closes: #878198) -- Regards Sudip
Re: Bug#956324: Clustalo bus error on mipsel (Was: Bug#956324: python-biopython: FTBFS on mipsel)
Control: tags -1 help Hi, as it can be seen on the recent build log of clustalo on mips[1] the build fails with # Run additional test from python-biopython package to verify that # this will work as well src/clustalo -i debian/tests/biopython_testdata/f002 --guidetree-out temp_test.dnd -o temp_test.aln --outfmt clustal --force make[1]: *** [debian/rules:25: override_dh_auto_test-arch] Bus error I injected that extra test since this very test failed inside the python-biopython package. To track it down I logged in to eller.debian.org tried to build the package and was able to reproduce the error. Thus I fired up gdb in this session and got: (sid_mipsel-dchroot)tille@eller:~/clustalo-1.2.4$ gdb --args src/clustalo -i debian/tests/biopython_testdata/f002 --guidetree-out temp_test.dnd -o temp_test.aln --outfmt clustal --force GNU gdb (Debian 9.1-3) 9.1 ... Reading symbols from src/clustalo... (gdb) run Starting program: /home/tille/clustalo-1.2.4/src/clustalo -i debian/tests/biopython_testdata/f002 --guidetree-out temp_test.dnd -o temp_test.aln --outfmt clustal --force [Thread debugging using libthread_db enabled] Using host libthread_db library "/lib/mipsel-linux-gnu/libthread_db.so.1". Program received signal SIGBUS, Bus error. 0x5556a188 in PairDistances (distmat=0x7fff278c, mseq=0x55692a38, pairdist_type=, bPercID=, istart=0, iend=3, jstart=0, jend=3, fdist_in=0x0, fdist_out=0x0) at pair_dist.c:346 346 NewProgress(&prProgress, LogGetFP(&rLog, LOG_INFO), (gdb) So it seems the bus error occures somehow here: https://salsa.debian.org/med-team/clustalo/-/blob/master/src/clustal/pair_dist.c#L346 I have no idea how to continue from here. I'm hoping that someone with some more detailed knowledge might have a clue how to fix this issue on mipsel. Otherwise I personally do not see any better solution than to remove clustalo from mipsel architecture. Kind regards Andreas. [1] https://buildd.debian.org/status/fetch.php?pkg=clustalo&arch=mipsel&ver=1.2.4-5&stamp=1586883766&raw=0 -- http://fam-tille.de
Bug#956965: RFS: sipxtapi/3.3.0~test18+dfsg.1-1.1 [NMU] -- SIP stack, RTP media framework and codecs
Package: sponsorship-requests Severity: normal X-Debbugs-CC: t...@debian.org Dear mentors, I am looking for a sponsor for my package "sipxtapi" * Package name: sipxtapi Version : 3.3.0~test18+dfsg.1-1.1 Upstream Author : sipXtapi community * URL : http://www.sipxtapi.org * License : LGPL-2.1 * Vcs : https://salsa.debian.org/pkg-voip-team/sipxtapi Section : libs It builds those binary packages: libsipxtapi - SIP stack, RTP media framework and codecs libsipxtapi-dev - SIP stack, RTP media framework and codecs (headers) libsipxtapi-doc - SIP stack, RTP media framework and codecs (API documentation) To access further information about this package, please visit the following URL: https://mentors.debian.net/package/sipxtapi Alternatively, one can download the package with dget using this command: dget -x https://mentors.debian.net/debian/pool/main/s/sipxtapi/sipxtapi_3.3.0~test18+dfsg.1-1.1.dsc Changes since the last upload: * Non-maintainer upload. * Update to new upstream 3.3.0_test18. (Closes: #956686) - Add Files-Excluded to repack source. - Remove patches applied upstream. - Remove lintian override for removed patch. - Update Standards-Version to 4.5.0 - Use debhelper-compat. - Update compat level to 12. - Update priority to optional. - Remove dependency on autotools-dev, dh-autoreconf. - Remove copyright information of file removed by update. * Point Vcs to salsa. (Closes: #956685) * Add watch file. (Closes: #956687) -- Regards Sudip
Bug#956935: RFS: grok-jpeg2000/5.1.0-0 -- development files for Grok, a JPEG 2000 image library
Hi Aaron, On 4/17/20 12:28 AM, Aaron Boxer wrote: > I am looking for a sponsor for my package "grok-jpeg2000" [...] > To access further information about this package, please visit the > following URL: > > https://mentors.debian.net/package/grok-jpeg2000 Please fix all tags reported by lintian on your package before seeking a sponsor. Debian expects high-quality, well maintained packages. -- Baptiste BEAUPLAT - lyknode signature.asc Description: OpenPGP digital signature
