Andreas Tille pushed to branch master at Debian Med / bcalm
Commits: a3fe863a by Andreas Tille at 2019-09-27T06:46:57Z Build-Depends: cmake - - - - - e829cacf by Andreas Tille at 2019-09-27T06:48:32Z Enhance description - - - - - 575677e2 by Andreas Tille at 2019-09-27T06:49:21Z Standards-Version: 4.4.0 - - - - - a890c94f by Andreas Tille at 2019-09-27T06:49:21Z Remove trailing whitespace in debian/copyright - - - - - cb8c4ab6 by Andreas Tille at 2019-09-27T06:55:22Z Cleanup after `routine-update --force` - - - - - 351f9bdf by Andreas Tille at 2019-09-27T07:07:01Z Force export LC_ALL=C.UTF-8 ... which does not help - - - - - 4 changed files: - debian/changelog - debian/control - debian/copyright - debian/tests/run-unit-test Changes: ===================================== debian/changelog ===================================== @@ -2,4 +2,4 @@ bcalm (2.2.1-1) UNRELEASED; urgency=medium * Initial release (Closes: #<bug>) - -- Shayan Doust <[email protected]> Mon, 23 Sep 2019 05:48:54 +0100 + -- Shayan Doust <[email protected]> Fri, 27 Sep 2019 08:49:22 +0200 ===================================== debian/control ===================================== @@ -4,11 +4,12 @@ Uploaders: Shayan Doust <[email protected]> Section: science Priority: optional Build-Depends: debhelper-compat (= 12), - libgatbcore-dev, - libboost-dev, - libhdf5-dev, - zlib1g-dev -Standards-Version: 4.3.0 + libgatbcore-dev, + libboost-dev, + libhdf5-dev, + zlib1g-dev, + cmake +Standards-Version: 4.4.0 Vcs-Browser: https://salsa.debian.org/med-team/bcalm Vcs-Git: https://salsa.debian.org/med-team/bcalm.git Homepage: https://github.com/GATB/bcalm @@ -17,7 +18,10 @@ Package: bcalm Architecture: any Depends: ${shlibs:Depends}, ${misc:Depends}, - libgatbcore2 + libgatbcore2 Description: de Bruijn compaction in low memory A bioinformatics tool for constructing the compacted de Bruijn graph from sequencing data. + . + This is the parallel version of the BCALM software using gatb-core + library. ===================================== debian/copyright ===================================== @@ -7,10 +7,10 @@ Copyright: 2014 INRIA <https://inria.fr/> 2018 Rayan Chikhi, Antoine Limasset, Paul Medvedev License: Expat -Files: thirdparty/concurrentqueue.h +Files: thirdparty/concurrentqueue.h thirdparty/lockbasedqueue.h thirdparty/lockstdqueue.h - thirdparty/lockstdvector.h + thirdparty/lockstdvector.h Copyright: 2013-2014 Cameron Desrochers License: BSD-2-Clause @@ -23,24 +23,24 @@ Copyright: 2019 Shayan Doust <[email protected]> License: Expat License: BSD-2-Clause - Redistribution and use in source and binary forms, with or without modification, + Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: . - 1. Redistributions of source code must retain the above copyright notice, this list + 1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. . - 2. Redistributions in binary form must reproduce the above copyright notice, this - list of conditions and the following disclaimer in the documentation and/or other + 2. Redistributions in binary form must reproduce the above copyright notice, this + list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. . - THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY - EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES - OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT - SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, - SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT - OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) - HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, - OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF + THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY + EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES + OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT + SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, + SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT + OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) + HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, + OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. License: zlib/libpng @@ -64,19 +64,19 @@ License: zlib/libpng distribution. License: Expat - Permission is hereby granted, free of charge, to any person obtaining a copy of - this software and associated documentation files (the "Software"), to deal in the - Software without restriction, including without limitation the rights to use, - copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the - Software, and to permit persons to whom the Software is furnished to do so, subject + Permission is hereby granted, free of charge, to any person obtaining a copy of + this software and associated documentation files (the "Software"), to deal in the + Software without restriction, including without limitation the rights to use, + copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the + Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: . - The above copyright notice and this permission notice shall be included in all + The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. . - THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, - INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A - PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT - HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF - CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE - OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. + THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, + INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A + PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT + HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF + CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE + OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. ===================================== debian/tests/run-unit-test ===================================== @@ -3,6 +3,7 @@ set -e pkg=bcalm +export LC_ALL=C.UTF-8 if [ "${AUTOPKGTEST_TMP}" = "" ] ; then AUTOPKGTEST_TMP=$(mktemp -d /tmp/${pkg}-test.XXXXXX) # shellcheck disable=SC2064 View it on GitLab: https://salsa.debian.org/med-team/bcalm/compare/534b1255b0bcc28a89e18dbc0ad50daa657fae00...351f9bdfa72d02f6e4be6c1fb997b7d60097f16b -- View it on GitLab: https://salsa.debian.org/med-team/bcalm/compare/534b1255b0bcc28a89e18dbc0ad50daa657fae00...351f9bdfa72d02f6e4be6c1fb997b7d60097f16b You're receiving this email because of your account on salsa.debian.org.
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