Your message dated Tue, 19 Aug 2014 13:35:44 +0000 with message-id <[email protected]> and subject line Bug#730722: fixed in t-coffee 11.00.8cbe486-1 has caused the Debian Bug report #730722, regarding t-coffee: please don't rely on legacy_blast's implementation language 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.) -- 730722: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=730722 Debian Bug Tracking System Contact [email protected] with problems
--- Begin Message ---Package: t-coffee Version: 10.00.r1613-1 Severity: wishlist Dear Maintainer, ncbi-blast+ package is installed and regarding t_coffee default output (see bellow), it doesn't seem to recognize it. I suspect the reason of this is that ncbi-blast+ provides /usr/bin/legacy_blast and not /usr/bin/legacy_blast.pl Is it possible to change this default in your package or is this a trouble with ncbi-blast+ package? (I remember discussion in Debian dev mailing list about having or not this kind of extension such as .pl in command name) And finally may be t_coffee is able to suggest it then? Regards, Patrice ****** Multiple Sequence Alignment Methods: -------------------------------------------- ktup_msa built_in [pg: t_coffee is Installed][built_in] blastp_msa ftp://ftp.ncbi.nih.gov/blast/executables/LATEST [pg: legacy_blast.pl is NOT Installed][] clustalo_msa http://www.clustal.org/omega/ [pg: clustalo is Installed][/usr/bin/clustalo] clustalw2_msa http://www.clustal.org [pg: clustalw2 is NOT Installed][] clustalw_msa http://www.clustal.org [pg: clustalw is Installed][/usr/bin/clustalw] mafftdef_msa http://align.bmr.kyushu-u.ac.jp/mafft/online/server/ [pg: mafft is Installed][/usr/bin/mafft] mafft_msa http://align.bmr.kyushu-u.ac.jp/mafft/online/server/ [pg: mafft is Installed][/usr/bin/mafft] mafftjtt_msa http://align.bmr.kyushu-u.ac.jp/mafft/online/server/ [pg: mafft is Installed][/usr/bin/mafft] mafftgins_msa http://align.bmr.kyushu-u.ac.jp/mafft/online/server/ [pg: mafft is Installed][/usr/bin/mafft] dialigntx_msa http://dialign-tx.gobics.de/ [pg: dialign-tx is Installed][/usr/bin/dialign-tx] dialignt_msa http://dialign-tx.gobics.de/ [pg: dialign-t is NOT Installed][] poa_msa http://www.bioinformatics.ucla.edu/poa/ [pg: poa is Installed][/usr/bin/poa] probcons_msa http://probcons.stanford.edu/ [pg: probcons is Installed][/usr/bin/probcons] probconsRNA_msa http://probcons.stanford.edu/ [pg: probcons-RNA is Installed][/usr/bin/probcons-RNA] muscle_msa http://www.drive5.com/muscle/ [pg: muscle is Installed][/usr/bin/muscle] mus4_msa http://www.drive5.com/muscle/ [pg: mus4 is NOT Installed][] t_coffee_msa http://www.tcoffee.org [pg: t_coffee is Installed][/usr/bin/t_coffee] pcma_msa ftp://iole.swmed.edu/pub/PCMA/ [pg: pcma is NOT Installed][] kalign_msa http://msa.cgb.ki.se [pg: kalign is Installed][/usr/bin/kalign] amap_msa http://bio.math.berkeley.edu/amap/ [pg: amap is Installed][/usr/bin/amap] proda_msa http://proda.stanford.edu [pg: proda is Installed][/usr/bin/proda] fsa_msa http://fsa.sourceforge.net/ [pg: fsa is NOT Installed][] tblastx_msa ftp://ftp.ncbi.nih.gov/blast/executables/LATEST [pg: legacy_blast.pl is NOT Installed][] tblastpx_msa ftp://ftp.ncbi.nih.gov/blast/executables/LATEST [pg: legacy_blast.pl is NOT Installed][] plib_msa www.tcoffee.org [pg: t_coffee is Installed][/usr/bin/t_coffee] -- System Information: Debian Release: jessie/sid APT prefers unstable APT policy: (500, 'unstable') Architecture: amd64 (x86_64) Foreign Architectures: i386 Kernel: Linux 3.11-2-amd64 (SMP w/24 CPU cores) Locale: LANG=fr_FR.UTF-8, LC_CTYPE=fr_FR.UTF-8 (charmap=UTF-8) Shell: /bin/sh linked to /bin/dash Versions of packages t-coffee depends on: ii libc6 2.17-96 ii libgcc1 1:4.8.2-5 ii libstdc++6 4.8.2-5 Versions of packages t-coffee recommends: ii libsoap-lite-perl 0.716-1 ii libxml-simple-perl 2.20-1 ii tm-align 20130511+dfsg-1 Versions of packages t-coffee suggests: ii amap-align 2.2-4 ii boxshade 3.3.1-8 ii clustalw 2.1+lgpl-3 ii dialign-tx 1.0.2-3 ii kalign 1:2.03+20110620-2 ii mafft 7.123-1 ii muscle 1:3.8.31-1 ii poa 2.0+20060928-3 ii probcons 1.12-9 ii proda 1.0-8 pn seaview <none> pn t-coffee-examples <none> -- no debconf information
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--- Begin Message ---Source: t-coffee Source-Version: 11.00.8cbe486-1 We believe that the bug you reported is fixed in the latest version of t-coffee, 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 t-coffee 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: Sat, 16 Aug 2014 00:20:06 +0200 Source: t-coffee Binary: t-coffee t-coffee-examples Architecture: source amd64 all Version: 11.00.8cbe486-1 Distribution: unstable Urgency: low Maintainer: Debian Med Packaging Team <[email protected]> Changed-By: Andreas Tille <[email protected]> Description: t-coffee - Multiple Sequence Alignment t-coffee-examples - annotated examples for the use of T-Coffee Closes: 730722 Changes: t-coffee (11.00.8cbe486-1) unstable; urgency=low . [ Charles Plessy ] * Suggest ncbi-blast+. . [ Andreas Tille ] * New upstream version * debian/patches/ncbi-blast++_has_dropped_pl_extension.patch: since ncbi-blast++ has renamed some perl scripts according to Debian policy t-coffee needs to be adapted: s/legacy_blast\.pl/legacy_blast/ s/blastpgp\.pl/blastpgp/ Closes: #730722 * Move some suggested packages to Recommends since these are recommended when calling t_coffee --help * Suggests: fsa (will be packaged soon) Checksums-Sha1: 9a27445148f570ff3fa73251267d0d572e31053c 2155 t-coffee_11.00.8cbe486-1.dsc be0a430c4a4326982f8a0e1ab3e5c7a4c4a28a48 3526354 t-coffee_11.00.8cbe486.orig.tar.gz 330fb7e5f9a24cbce061a71bc377309189f7d439 10312 t-coffee_11.00.8cbe486-1.debian.tar.xz acd82a516a25986f20d3e6eebeabb84138e9fac8 921258 t-coffee_11.00.8cbe486-1_amd64.deb 7e19f173fc8edbe5d6b438b9bc7e123bbabbd08b 525856 t-coffee-examples_11.00.8cbe486-1_all.deb Checksums-Sha256: eed53c5097d50967a20b2c6e0e2e497a062b5de77711c578294352d9cd87f6a6 2155 t-coffee_11.00.8cbe486-1.dsc b8018433574ff7705c49cd974bebb06a48eb8bc5e38aaa9eb4f53f2e7778e72c 3526354 t-coffee_11.00.8cbe486.orig.tar.gz ed0dbf1591b7e0544b8341ea98ee552dd7e365eae21372dbd54f591b7cc7c5d8 10312 t-coffee_11.00.8cbe486-1.debian.tar.xz 9d2663a8eb3f48410cc507bab4b3d10aabe843e3b90b54277db4b63722276bb6 921258 t-coffee_11.00.8cbe486-1_amd64.deb 70f6bb18b407cf11335d19309d94a849b631c4fe3f82741309c8d823d9822f60 525856 t-coffee-examples_11.00.8cbe486-1_all.deb Files: bbedfb4bb70033437045f398a6551f43 921258 science optional t-coffee_11.00.8cbe486-1_amd64.deb ac836d23debd73dde3ad2395e384f52b 525856 science optional t-coffee-examples_11.00.8cbe486-1_all.deb a709c81ffa076fa58c861fbc1ddf1261 2155 science optional t-coffee_11.00.8cbe486-1.dsc bd91485c06eda4f2ffcb61542d3ce302 3526354 science optional t-coffee_11.00.8cbe486.orig.tar.gz 5b16100497016001a250320b06fdda6e 10312 science optional t-coffee_11.00.8cbe486-1.debian.tar.xz -----BEGIN PGP SIGNATURE----- Version: GnuPG v1 iQIcBAEBCAAGBQJT81BPAAoJEFeKBJTRxkbR0sUP/j/HjIE/TJxIJ1l4h/B8Qinh tdU6SQmeIIzuJmieiYpto0/3SCNZKpbKip3Gq28hgCnrl2vCH50ib8B/5uN+3CB1 H0qoKqm842TdI4/F3IbPRvIe0IpNrUjkfR9xsU6s6m0jPZTO5DN/Ti96bL+rtMFp 3AwNAafbzTOTvxU8d6RFl0HjElwHyRjGr5hnmQnIZk4tdxBCELO7qErjdjt75mn4 DFAAg3SARNBT/Tz2EG77D1bk5rMgvqhEiDKTH9kBk3w/pDWj0xAjwuuVLYxoanHG J5BIL44X109m27ULrgrawEaGL/eaWXeLP1RmjOgZULlk9XfCJgJIO85ypEGepy2v u3uYEb9m9V79l21cX43T0lXwveCIljA22FLUahmZRyiMVII10s1b/sfLJVcec9eH uVOgztPgG0EvnphwaO3hkje4gvmPzZnCmh5n8IwuUpjhG8XwESD70bha5SOk7dmY 9KYo0uuUwyp/jRQBLHZFbbW2Afg05V7zGsCWOHDN38WSStVd7V1nwL3HR2zjItAf L4W5k8mTLEacZRshR8B9IUYKTfIHSc65air6zinevuD9elvEbkzBpWGF49N4kD7E 56l/JSg6zkzk7s7se1CqkBam8OaD+CVBBtOseDgeKStrMezLDVfpKxtfVrjGhmQy 4MpccyinN76nZ58U0Gvg =6pEJ -----END PGP SIGNATURE-----
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