diff -Nru lambda-align2-2.0.0/debian/changelog lambda-align2-2.0.0/debian/changelog --- lambda-align2-2.0.0/debian/changelog 2019-06-08 12:49:26.000000000 +0000 +++ lambda-align2-2.0.0/debian/changelog 2020-03-23 06:17:43.000000000 +0000 @@ -1,32 +1,8 @@ -lambda-align2 (2.0.0-6) unstable; urgency=medium +lambda-align2 (2.0.0-2build1) focal; urgency=medium - * Adjust reproducibility patch. - Closes: #920591 + * No-change rebuild for libgcc-s1 package name change. - -- Sascha Steinbiss Sat, 08 Jun 2019 14:49:26 +0200 - -lambda-align2 (2.0.0-5) unstable; urgency=medium - - * Team upload. - * make the build reproducible (thanks for the patch to - Chris Lamb ) - Closes: #920591 - - -- Andreas Tille Sun, 27 Jan 2019 11:18:13 +0100 - -lambda-align2 (2.0.0-4) unstable; urgency=medium - - * Skip checking md5sums in the tests as they are not currently stable. - * Post process the unix manual pages to remove errors with regards to the - subcommands. - - -- Michael R. Crusoe Wed, 23 Jan 2019 11:54:46 -0800 - -lambda-align2 (2.0.0-3) unstable; urgency=medium - - * Fix 32-bit builds. Thanks to Michael R. Crusoe for the patch. - - -- Sascha Steinbiss Tue, 22 Jan 2019 13:42:56 +0100 + -- Matthias Klose Mon, 23 Mar 2020 07:17:43 +0100 lambda-align2 (2.0.0-2) unstable; urgency=medium diff -Nru lambda-align2-2.0.0/debian/db_nucl_fm.md5sums lambda-align2-2.0.0/debian/db_nucl_fm.md5sums --- lambda-align2-2.0.0/debian/db_nucl_fm.md5sums 2019-06-08 08:59:15.000000000 +0000 +++ lambda-align2-2.0.0/debian/db_nucl_fm.md5sums 2019-01-18 09:55:39.000000000 +0000 @@ -1,23 +1,17 @@ MD5(db.fasta)= b58f6764fcdb216bbd0ad03e1d84b19b -MD5(fm.lambda/index.lf.drp)= 42a7883cc86e97e4f8c9705a06991938 -MD5(fm.lambda/index.lf.drs)= ec7f7e7bb43742ce868145f71d37b53c -MD5(fm.lambda/index.lf.drv)= 92dccb84dd3d9be8db82d4ab163bf5ff -MD5(fm.lambda/index.lf.drv.sbl)= 97938e5c5896db0141d49249ff4b8737 -MD5(fm.lambda/index.lf.drv.ubl)= fd4b38e94292e00251b9f39c47ee5710 -MD5(fm.lambda/index.lf.pst)= ff1b62533bcb52a3772f890b5ac5656d -MD5(fm.lambda/index.sa.ind)= 4b69f40b67e86836a5d550c8235863eb +MD5(fm.lambda/option:alph_translated)= 01ef0afac8c7cfc866cf812c7bb68596 MD5(fm.lambda/index.sa.len)= 7e9ddcbeb0dbe4cb0c21e8ed0a96198d -MD5(fm.lambda/index.sa.val)= bb20ec56bbf1c262b8ac223dc869af85 +MD5(fm.lambda/index.sa.ind)= 4b69f40b67e86836a5d550c8235863eb +MD5(fm.lambda/option:generation)= c4ca4238a0b923820dcc509a6f75849b +MD5(fm.lambda/index.lf.drs)= ec7f7e7bb43742ce868145f71d37b53c +MD5(fm.lambda/option:db_index_type)= c4ca4238a0b923820dcc509a6f75849b +MD5(fm.lambda/option:alph_reduced)= 01ef0afac8c7cfc866cf812c7bb68596 +MD5(fm.lambda/translated_seqs.concat)= 25d9d9b6f49e2dbf4ad50f5e90034f32 MD5(fm.lambda/index.txt.concat)= 82687a2ee200a06c72609bf095d8b15d -MD5(fm.lambda/index.txt.limits)= ec3b17c879edb71de532df257e5553ea MD5(fm.lambda/option:alph_original)= 01ef0afac8c7cfc866cf812c7bb68596 -MD5(fm.lambda/option:alph_reduced)= 01ef0afac8c7cfc866cf812c7bb68596 -MD5(fm.lambda/option:alph_translated)= 01ef0afac8c7cfc866cf812c7bb68596 -MD5(fm.lambda/option:db_index_type)= c4ca4238a0b923820dcc509a6f75849b -MD5(fm.lambda/option:generation)= c4ca4238a0b923820dcc509a6f75849b -MD5(fm.lambda/option:genetic_code)= cfcd208495d565ef66e7dff9f98764da -MD5(fm.lambda/option:subj_seq_len_bits)= 6364d3f0f495b6ab9dcf8d3b5c6e0b01 -MD5(fm.lambda/seq_ids.concat)= 922f5cce30c4a5d1cfab5b1d02d39039 MD5(fm.lambda/seq_ids.limits)= 89d74e26e6e06be6cd029d2071e5522e -MD5(fm.lambda/translated_seqs.concat)= 25d9d9b6f49e2dbf4ad50f5e90034f32 +MD5(fm.lambda/option:subj_seq_len_bits)= 6364d3f0f495b6ab9dcf8d3b5c6e0b01 MD5(fm.lambda/translated_seqs.limits)= ec3b17c879edb71de532df257e5553ea +MD5(fm.lambda/option:genetic_code)= cfcd208495d565ef66e7dff9f98764da +MD5(fm.lambda/seq_ids.concat)= 922f5cce30c4a5d1cfab5b1d02d39039 +MD5(fm.lambda/index.txt.limits)= ec3b17c879edb71de532df257e5553ea diff -Nru lambda-align2-2.0.0/debian/db_nucl_sa.md5sums lambda-align2-2.0.0/debian/db_nucl_sa.md5sums --- lambda-align2-2.0.0/debian/db_nucl_sa.md5sums 2019-06-08 08:59:15.000000000 +0000 +++ lambda-align2-2.0.0/debian/db_nucl_sa.md5sums 2019-01-18 09:55:39.000000000 +0000 @@ -1,23 +1,17 @@ MD5(db.fasta)= b58f6764fcdb216bbd0ad03e1d84b19b -MD5(sa.lambda/index.lf.drp)= 42a7883cc86e97e4f8c9705a06991938 -MD5(sa.lambda/index.lf.drs)= ec7f7e7bb43742ce868145f71d37b53c -MD5(sa.lambda/index.lf.drv)= 659e96c6203a9d784cda846f73475c51 -MD5(sa.lambda/index.lf.drv.sbl)= 97938e5c5896db0141d49249ff4b8737 -MD5(sa.lambda/index.lf.drv.ubl)= fd4b38e94292e00251b9f39c47ee5710 -MD5(sa.lambda/index.lf.pst)= ff1b62533bcb52a3772f890b5ac5656d -MD5(sa.lambda/index.sa.ind)= 4b69f40b67e86836a5d550c8235863eb +MD5(sa.lambda/option:alph_translated)= 01ef0afac8c7cfc866cf812c7bb68596 MD5(sa.lambda/index.sa.len)= 7e9ddcbeb0dbe4cb0c21e8ed0a96198d -MD5(sa.lambda/index.sa.val)= bb20ec56bbf1c262b8ac223dc869af85 +MD5(sa.lambda/index.sa.ind)= 4b69f40b67e86836a5d550c8235863eb +MD5(sa.lambda/option:generation)= c4ca4238a0b923820dcc509a6f75849b +MD5(sa.lambda/index.lf.drs)= ec7f7e7bb43742ce868145f71d37b53c +MD5(sa.lambda/option:db_index_type)= c4ca4238a0b923820dcc509a6f75849b +MD5(sa.lambda/option:alph_reduced)= 01ef0afac8c7cfc866cf812c7bb68596 +MD5(sa.lambda/translated_seqs.concat)= 25d9d9b6f49e2dbf4ad50f5e90034f32 MD5(sa.lambda/index.txt.concat)= 82687a2ee200a06c72609bf095d8b15d -MD5(sa.lambda/index.txt.limits)= ec3b17c879edb71de532df257e5553ea MD5(sa.lambda/option:alph_original)= 01ef0afac8c7cfc866cf812c7bb68596 -MD5(sa.lambda/option:alph_reduced)= 01ef0afac8c7cfc866cf812c7bb68596 -MD5(sa.lambda/option:alph_translated)= 01ef0afac8c7cfc866cf812c7bb68596 -MD5(sa.lambda/option:db_index_type)= c4ca4238a0b923820dcc509a6f75849b -MD5(sa.lambda/option:generation)= c4ca4238a0b923820dcc509a6f75849b -MD5(sa.lambda/option:genetic_code)= cfcd208495d565ef66e7dff9f98764da -MD5(sa.lambda/option:subj_seq_len_bits)= 6364d3f0f495b6ab9dcf8d3b5c6e0b01 -MD5(sa.lambda/seq_ids.concat)= 922f5cce30c4a5d1cfab5b1d02d39039 MD5(sa.lambda/seq_ids.limits)= 89d74e26e6e06be6cd029d2071e5522e -MD5(sa.lambda/translated_seqs.concat)= 25d9d9b6f49e2dbf4ad50f5e90034f32 +MD5(sa.lambda/option:subj_seq_len_bits)= 6364d3f0f495b6ab9dcf8d3b5c6e0b01 MD5(sa.lambda/translated_seqs.limits)= ec3b17c879edb71de532df257e5553ea +MD5(sa.lambda/option:genetic_code)= cfcd208495d565ef66e7dff9f98764da +MD5(sa.lambda/seq_ids.concat)= 922f5cce30c4a5d1cfab5b1d02d39039 +MD5(sa.lambda/index.txt.limits)= ec3b17c879edb71de532df257e5553ea diff -Nru lambda-align2-2.0.0/debian/db_prot_fm.md5sums lambda-align2-2.0.0/debian/db_prot_fm.md5sums --- lambda-align2-2.0.0/debian/db_prot_fm.md5sums 2019-06-08 08:59:15.000000000 +0000 +++ lambda-align2-2.0.0/debian/db_prot_fm.md5sums 2019-01-18 09:55:39.000000000 +0000 @@ -1,21 +1,15 @@ MD5(db.fasta)= b01a08d07b955fcef5fa9ea94e1f25aa -MD5(fm.lambda/index.lf.drp)= 8f4318d9a2c7dcf419df38d6ff1ba05d -MD5(fm.lambda/index.lf.drs)= 9e688c58a5487b8eaf69c9e1005ad0bf -MD5(fm.lambda/index.lf.drv)= dd9b97ec644e1335a1d2dff66316ec0b -MD5(fm.lambda/index.lf.drv.sbl)= 0cb8f0b411090455eeba5047ee758550 -MD5(fm.lambda/index.lf.drv.ubl)= bbf7c6077962a7c28114dbd10be947cd -MD5(fm.lambda/index.lf.pst)= 4a7a878c6f1c84c5ccdc11e8103e2dda -MD5(fm.lambda/index.sa.ind)= cf713e9f2a896ce8d1d6e9bdd89b4649 -MD5(fm.lambda/index.sa.len)= 8d3178082ade66084876d27bf13ee42f -MD5(fm.lambda/index.sa.val)= b5683829a51776976811ae4634429de1 -MD5(fm.lambda/option:alph_original)= 1151d962f7df03ce40c0f2126262deeb -MD5(fm.lambda/option:alph_reduced)= dd23d4ca34a76600cedbab1b29d74025 MD5(fm.lambda/option:alph_translated)= 1151d962f7df03ce40c0f2126262deeb -MD5(fm.lambda/option:db_index_type)= c4ca4238a0b923820dcc509a6f75849b +MD5(fm.lambda/index.sa.len)= 8d3178082ade66084876d27bf13ee42f +MD5(fm.lambda/index.sa.ind)= cf713e9f2a896ce8d1d6e9bdd89b4649 MD5(fm.lambda/option:generation)= c4ca4238a0b923820dcc509a6f75849b -MD5(fm.lambda/option:genetic_code)= c4ca4238a0b923820dcc509a6f75849b -MD5(fm.lambda/option:subj_seq_len_bits)= c74d97b01eae257e44aa9d5bade97baf -MD5(fm.lambda/seq_ids.concat)= 1e946a893d19945bffe18747d76ee573 -MD5(fm.lambda/seq_ids.limits)= 43c3aceb573d64bb0bbacba680c320c7 +MD5(fm.lambda/index.lf.drs)= 9e688c58a5487b8eaf69c9e1005ad0bf +MD5(fm.lambda/option:db_index_type)= c4ca4238a0b923820dcc509a6f75849b +MD5(fm.lambda/option:alph_reduced)= dd23d4ca34a76600cedbab1b29d74025 MD5(fm.lambda/translated_seqs.concat)= 854f773792dc25c957e6355db7aa2abf +MD5(fm.lambda/option:alph_original)= 1151d962f7df03ce40c0f2126262deeb +MD5(fm.lambda/seq_ids.limits)= 43c3aceb573d64bb0bbacba680c320c7 +MD5(fm.lambda/option:subj_seq_len_bits)= c74d97b01eae257e44aa9d5bade97baf MD5(fm.lambda/translated_seqs.limits)= 5a0274cc69c7db878781a4b4adf6994d +MD5(fm.lambda/option:genetic_code)= c4ca4238a0b923820dcc509a6f75849b +MD5(fm.lambda/seq_ids.concat)= 1e946a893d19945bffe18747d76ee573 diff -Nru lambda-align2-2.0.0/debian/db_prot_sa.md5sums lambda-align2-2.0.0/debian/db_prot_sa.md5sums --- lambda-align2-2.0.0/debian/db_prot_sa.md5sums 2019-06-08 08:59:15.000000000 +0000 +++ lambda-align2-2.0.0/debian/db_prot_sa.md5sums 2019-01-18 09:55:39.000000000 +0000 @@ -1,21 +1,15 @@ MD5(db.fasta)= b01a08d07b955fcef5fa9ea94e1f25aa -MD5(sa.lambda/index.lf.drp)= 8f4318d9a2c7dcf419df38d6ff1ba05d -MD5(sa.lambda/index.lf.drs)= 9e688c58a5487b8eaf69c9e1005ad0bf -MD5(sa.lambda/index.lf.drv)= dd9b97ec644e1335a1d2dff66316ec0b -MD5(sa.lambda/index.lf.drv.sbl)= 0cb8f0b411090455eeba5047ee758550 -MD5(sa.lambda/index.lf.drv.ubl)= bbf7c6077962a7c28114dbd10be947cd -MD5(sa.lambda/index.lf.pst)= 4a7a878c6f1c84c5ccdc11e8103e2dda -MD5(sa.lambda/index.sa.ind)= cf713e9f2a896ce8d1d6e9bdd89b4649 -MD5(sa.lambda/index.sa.len)= 8d3178082ade66084876d27bf13ee42f -MD5(sa.lambda/index.sa.val)= b5683829a51776976811ae4634429de1 -MD5(sa.lambda/option:alph_original)= 1151d962f7df03ce40c0f2126262deeb -MD5(sa.lambda/option:alph_reduced)= dd23d4ca34a76600cedbab1b29d74025 MD5(sa.lambda/option:alph_translated)= 1151d962f7df03ce40c0f2126262deeb -MD5(sa.lambda/option:db_index_type)= c4ca4238a0b923820dcc509a6f75849b +MD5(sa.lambda/index.sa.len)= 8d3178082ade66084876d27bf13ee42f +MD5(sa.lambda/index.sa.ind)= cf713e9f2a896ce8d1d6e9bdd89b4649 MD5(sa.lambda/option:generation)= c4ca4238a0b923820dcc509a6f75849b -MD5(sa.lambda/option:genetic_code)= c4ca4238a0b923820dcc509a6f75849b -MD5(sa.lambda/option:subj_seq_len_bits)= c74d97b01eae257e44aa9d5bade97baf -MD5(sa.lambda/seq_ids.concat)= 1e946a893d19945bffe18747d76ee573 -MD5(sa.lambda/seq_ids.limits)= 43c3aceb573d64bb0bbacba680c320c7 +MD5(sa.lambda/index.lf.drs)= 9e688c58a5487b8eaf69c9e1005ad0bf +MD5(sa.lambda/option:db_index_type)= c4ca4238a0b923820dcc509a6f75849b +MD5(sa.lambda/option:alph_reduced)= dd23d4ca34a76600cedbab1b29d74025 MD5(sa.lambda/translated_seqs.concat)= 854f773792dc25c957e6355db7aa2abf +MD5(sa.lambda/option:alph_original)= 1151d962f7df03ce40c0f2126262deeb +MD5(sa.lambda/seq_ids.limits)= 43c3aceb573d64bb0bbacba680c320c7 +MD5(sa.lambda/option:subj_seq_len_bits)= c74d97b01eae257e44aa9d5bade97baf MD5(sa.lambda/translated_seqs.limits)= 5a0274cc69c7db878781a4b4adf6994d +MD5(sa.lambda/option:genetic_code)= c4ca4238a0b923820dcc509a6f75849b +MD5(sa.lambda/seq_ids.concat)= 1e946a893d19945bffe18747d76ee573 diff -Nru lambda-align2-2.0.0/debian/db_trans_fm.md5sums lambda-align2-2.0.0/debian/db_trans_fm.md5sums --- lambda-align2-2.0.0/debian/db_trans_fm.md5sums 2019-06-08 08:59:15.000000000 +0000 +++ lambda-align2-2.0.0/debian/db_trans_fm.md5sums 2019-01-18 09:55:39.000000000 +0000 @@ -1,23 +1,17 @@ MD5(db.fasta)= b58f6764fcdb216bbd0ad03e1d84b19b -MD5(fm.lambda/index.lf.drp)= 42a7883cc86e97e4f8c9705a06991938 -MD5(fm.lambda/index.lf.drs)= ec7f7e7bb43742ce868145f71d37b53c -MD5(fm.lambda/index.lf.drv)= 7e2abc90ff6c6a055378513a45f662ad -MD5(fm.lambda/index.lf.drv.sbl)= 97938e5c5896db0141d49249ff4b8737 -MD5(fm.lambda/index.lf.drv.ubl)= fd4b38e94292e00251b9f39c47ee5710 -MD5(fm.lambda/index.lf.pst)= ff1b62533bcb52a3772f890b5ac5656d -MD5(fm.lambda/index.sa.ind)= 4b69f40b67e86836a5d550c8235863eb +MD5(fm.lambda/option:alph_translated)= 01ef0afac8c7cfc866cf812c7bb68596 MD5(fm.lambda/index.sa.len)= 7e9ddcbeb0dbe4cb0c21e8ed0a96198d -MD5(fm.lambda/index.sa.val)= bb20ec56bbf1c262b8ac223dc869af85 +MD5(fm.lambda/index.sa.ind)= 4b69f40b67e86836a5d550c8235863eb +MD5(fm.lambda/option:generation)= c4ca4238a0b923820dcc509a6f75849b +MD5(fm.lambda/index.lf.drs)= ec7f7e7bb43742ce868145f71d37b53c +MD5(fm.lambda/option:db_index_type)= c4ca4238a0b923820dcc509a6f75849b +MD5(fm.lambda/option:alph_reduced)= 01ef0afac8c7cfc866cf812c7bb68596 +MD5(fm.lambda/translated_seqs.concat)= 25d9d9b6f49e2dbf4ad50f5e90034f32 MD5(fm.lambda/index.txt.concat)= 82687a2ee200a06c72609bf095d8b15d -MD5(fm.lambda/index.txt.limits)= ec3b17c879edb71de532df257e5553ea MD5(fm.lambda/option:alph_original)= 01ef0afac8c7cfc866cf812c7bb68596 -MD5(fm.lambda/option:alph_reduced)= 01ef0afac8c7cfc866cf812c7bb68596 -MD5(fm.lambda/option:alph_translated)= 01ef0afac8c7cfc866cf812c7bb68596 -MD5(fm.lambda/option:db_index_type)= c4ca4238a0b923820dcc509a6f75849b -MD5(fm.lambda/option:generation)= c4ca4238a0b923820dcc509a6f75849b -MD5(fm.lambda/option:genetic_code)= cfcd208495d565ef66e7dff9f98764da -MD5(fm.lambda/option:subj_seq_len_bits)= 6364d3f0f495b6ab9dcf8d3b5c6e0b01 -MD5(fm.lambda/seq_ids.concat)= 922f5cce30c4a5d1cfab5b1d02d39039 MD5(fm.lambda/seq_ids.limits)= 89d74e26e6e06be6cd029d2071e5522e -MD5(fm.lambda/translated_seqs.concat)= 25d9d9b6f49e2dbf4ad50f5e90034f32 +MD5(fm.lambda/option:subj_seq_len_bits)= 6364d3f0f495b6ab9dcf8d3b5c6e0b01 MD5(fm.lambda/translated_seqs.limits)= ec3b17c879edb71de532df257e5553ea +MD5(fm.lambda/option:genetic_code)= cfcd208495d565ef66e7dff9f98764da +MD5(fm.lambda/seq_ids.concat)= 922f5cce30c4a5d1cfab5b1d02d39039 +MD5(fm.lambda/index.txt.limits)= ec3b17c879edb71de532df257e5553ea diff -Nru lambda-align2-2.0.0/debian/db_trans_sa.md5sums lambda-align2-2.0.0/debian/db_trans_sa.md5sums --- lambda-align2-2.0.0/debian/db_trans_sa.md5sums 2019-06-08 08:59:15.000000000 +0000 +++ lambda-align2-2.0.0/debian/db_trans_sa.md5sums 2019-01-18 09:55:39.000000000 +0000 @@ -1,23 +1,17 @@ MD5(db.fasta)= b58f6764fcdb216bbd0ad03e1d84b19b -MD5(sa.lambda/index.lf.drp)= 42a7883cc86e97e4f8c9705a06991938 -MD5(sa.lambda/index.lf.drs)= ec7f7e7bb43742ce868145f71d37b53c -MD5(sa.lambda/index.lf.drv)= 95e0ba2cb7a95389f2a3ea0a63919672 -MD5(sa.lambda/index.lf.drv.sbl)= 97938e5c5896db0141d49249ff4b8737 -MD5(sa.lambda/index.lf.drv.ubl)= fd4b38e94292e00251b9f39c47ee5710 -MD5(sa.lambda/index.lf.pst)= ff1b62533bcb52a3772f890b5ac5656d -MD5(sa.lambda/index.sa.ind)= 4b69f40b67e86836a5d550c8235863eb +MD5(sa.lambda/option:alph_translated)= 01ef0afac8c7cfc866cf812c7bb68596 MD5(sa.lambda/index.sa.len)= 7e9ddcbeb0dbe4cb0c21e8ed0a96198d -MD5(sa.lambda/index.sa.val)= bb20ec56bbf1c262b8ac223dc869af85 +MD5(sa.lambda/index.sa.ind)= 4b69f40b67e86836a5d550c8235863eb +MD5(sa.lambda/option:generation)= c4ca4238a0b923820dcc509a6f75849b +MD5(sa.lambda/index.lf.drs)= ec7f7e7bb43742ce868145f71d37b53c +MD5(sa.lambda/option:db_index_type)= c4ca4238a0b923820dcc509a6f75849b +MD5(sa.lambda/option:alph_reduced)= 01ef0afac8c7cfc866cf812c7bb68596 +MD5(sa.lambda/translated_seqs.concat)= 25d9d9b6f49e2dbf4ad50f5e90034f32 MD5(sa.lambda/index.txt.concat)= 82687a2ee200a06c72609bf095d8b15d -MD5(sa.lambda/index.txt.limits)= ec3b17c879edb71de532df257e5553ea MD5(sa.lambda/option:alph_original)= 01ef0afac8c7cfc866cf812c7bb68596 -MD5(sa.lambda/option:alph_reduced)= 01ef0afac8c7cfc866cf812c7bb68596 -MD5(sa.lambda/option:alph_translated)= 01ef0afac8c7cfc866cf812c7bb68596 -MD5(sa.lambda/option:db_index_type)= c4ca4238a0b923820dcc509a6f75849b -MD5(sa.lambda/option:generation)= c4ca4238a0b923820dcc509a6f75849b -MD5(sa.lambda/option:genetic_code)= cfcd208495d565ef66e7dff9f98764da -MD5(sa.lambda/option:subj_seq_len_bits)= 6364d3f0f495b6ab9dcf8d3b5c6e0b01 -MD5(sa.lambda/seq_ids.concat)= 922f5cce30c4a5d1cfab5b1d02d39039 MD5(sa.lambda/seq_ids.limits)= 89d74e26e6e06be6cd029d2071e5522e -MD5(sa.lambda/translated_seqs.concat)= 25d9d9b6f49e2dbf4ad50f5e90034f32 +MD5(sa.lambda/option:subj_seq_len_bits)= 6364d3f0f495b6ab9dcf8d3b5c6e0b01 MD5(sa.lambda/translated_seqs.limits)= ec3b17c879edb71de532df257e5553ea +MD5(sa.lambda/option:genetic_code)= cfcd208495d565ef66e7dff9f98764da +MD5(sa.lambda/seq_ids.concat)= 922f5cce30c4a5d1cfab5b1d02d39039 +MD5(sa.lambda/index.txt.limits)= ec3b17c879edb71de532df257e5553ea diff -Nru lambda-align2-2.0.0/debian/patches/32bit lambda-align2-2.0.0/debian/patches/32bit --- lambda-align2-2.0.0/debian/patches/32bit 2019-06-08 08:59:15.000000000 +0000 +++ lambda-align2-2.0.0/debian/patches/32bit 1970-01-01 00:00:00.000000000 +0000 @@ -1,23 +0,0 @@ -From: Michael R. Crusoe -Subject: fix 32bit compatibility -Forwarded: https://github.com/seqan/lambda/pull/123 ---- lambda-align2.orig/src/search_algo.hpp -+++ lambda-align2/src/search_algo.hpp -@@ -1058,7 +1058,7 @@ - desiredOccs = (length(lH.matches) - oldTotalMatches) >= lH.options.maxMatches - ? minResults - : (lH.options.maxMatches - (length(lH.matches) - oldTotalMatches)) * seedHeurFactor / -- std::max((needlesSum - needlesPos - seedBegin) / lH.options.seedOffset, 1ul); -+ std::max((needlesSum - needlesPos - seedBegin) / lH.options.seedOffset, static_cast(1)); - - if (desiredOccs == 0) - desiredOccs = minResults; -@@ -1127,7 +1127,7 @@ - desiredOccs = (length(lH.matches) - oldTotalMatches) >= lH.options.maxMatches - ? minResults - : (lH.options.maxMatches - (length(lH.matches) - oldTotalMatches)) * seedHeurFactor / -- std::max((needlesSum - needlesPos - seedBegin) / lH.options.seedOffset, 1ul); -+ std::max((needlesSum - needlesPos - seedBegin) / lH.options.seedOffset, static_cast(1)); - - if (desiredOccs == 0) - desiredOccs = minResults; diff -Nru lambda-align2-2.0.0/debian/patches/enable_tests lambda-align2-2.0.0/debian/patches/enable_tests --- lambda-align2-2.0.0/debian/patches/enable_tests 2019-06-08 08:59:15.000000000 +0000 +++ lambda-align2-2.0.0/debian/patches/enable_tests 2019-01-18 09:55:39.000000000 +0000 @@ -1,12 +1,10 @@ From: Michael R. Crusoe Subject: Enable and update tests for lambda2 -Skip checking the md5sums as they are not currently stable - Only the first 10 tests pass with this patch ---- lambda-align2.orig/CMakeLists.txt -+++ lambda-align2/CMakeLists.txt +--- lambda-align.orig/CMakeLists.txt ++++ lambda-align/CMakeLists.txt @@ -60,5 +60,5 @@ # Add Tests # ---------------------------------------------------------------------------- @@ -15,8 +13,8 @@ -# add_subdirectory(tests) +message ("\n${ColourBold}Setting up unit tests${ColourReset}") +add_subdirectory(tests) ---- lambda-align2.orig/tests/maintests.sh -+++ lambda-align2/tests/maintests.sh +--- lambda-align.orig/tests/maintests.sh ++++ lambda-align/tests/maintests.sh @@ -1,5 +1,7 @@ #!/bin/sh @@ -50,7 +48,7 @@ SALPH=trans QALPHIN=nucl SALPHIN=nucl -@@ -53,16 +61,18 @@ +@@ -53,10 +61,10 @@ gunzip < "${SRCDIR}/tests/db_${SALPHIN}.fasta.gz" > db.fasta [ $? -eq 0 ] || errorout "Could not unzip database file" @@ -59,22 +57,11 @@ [ $? -eq 0 ] || errorout "Could not run the indexer" -openssl md5 * > md5sums -+openssl md5 $(find * -type f | sort) > db_${SALPH}_${DI}.md5sums ++openssl md5 $(find * -type f) > md5sums [ $? -eq 0 ] || errorout "Could not run md5 or md5sums" -+#openssl md5 $(find * -type f | sort | grep -v md5sums) > ${SRCDIR}/tests/db_${SALPH}_${DI}.md5sums -+#gzip -f ${SRCDIR}/tests/db_${SALPH}_${DI}.md5sums --gunzip < "${SRCDIR}/tests/db_${SALPH}_${DI}.md5sums.gz" > md5sums.orig --[ $? -eq 0 ] || errorout "Could not unzip md5sums.orig" -+gunzip < "${SRCDIR}/tests/db_${SALPH}_${DI}.md5sums.gz" > db_${SALPH}_${DI}.md5sums.orig -+[ $? -eq 0 ] || errorout "Could not unzip tests/db_${SALPH}_${DI}.md5sums.gz" - --[ "$(cat md5sums)" = "$(cat md5sums.orig)" ] || errorout "$(diff -u md5sums md5sums.orig)" -+#[ "$(cat db_${SALPH}_${DI}.md5sums)" = "$(cat db_${SALPH}_${DI}.md5sums.orig)" ] || errorout "$(diff -u db_${SALPH}_${DI}.md5sums db_${SALPH}_${DI}.md5sums.orig)" - - ## INDEXER tests end here - if [ "$MODE" = "MKINDEX" ]; then -@@ -73,7 +83,7 @@ + gunzip < "${SRCDIR}/tests/db_${SALPH}_${DI}.md5sums.gz" > md5sums.orig +@@ -73,7 +81,7 @@ gunzip < "${SRCDIR}/tests/queries_${QALPHIN}.fasta.gz" > queries.fasta [ $? -eq 0 ] || errorout "Could not unzip queries.fasta" diff -Nru lambda-align2-2.0.0/debian/patches/series lambda-align2-2.0.0/debian/patches/series --- lambda-align2-2.0.0/debian/patches/series 2019-06-08 08:59:15.000000000 +0000 +++ lambda-align2-2.0.0/debian/patches/series 2019-01-18 09:55:39.000000000 +0000 @@ -1,4 +1,3 @@ enable_tests -32bit set-seqan-cmake-dir.patch force-link-rt-pthread.patch diff -Nru lambda-align2-2.0.0/debian/patches/set-seqan-cmake-dir.patch lambda-align2-2.0.0/debian/patches/set-seqan-cmake-dir.patch --- lambda-align2-2.0.0/debian/patches/set-seqan-cmake-dir.patch 2019-06-08 08:59:15.000000000 +0000 +++ lambda-align2-2.0.0/debian/patches/set-seqan-cmake-dir.patch 2019-01-18 09:55:39.000000000 +0000 @@ -1,8 +1,8 @@ Description: set SeqAn_DIR to find CMake modules Author: Sascha Steinbiss ---- lambda-align2.orig/src/CMakeLists.txt -+++ lambda-align2/src/CMakeLists.txt -@@ -25,6 +25,8 @@ +--- a/src/CMakeLists.txt ++++ b/src/CMakeLists.txt +@@ -22,6 +22,8 @@ # Dependencies (continued) # ---------------------------------------------------------------------------- diff -Nru lambda-align2-2.0.0/debian/rules lambda-align2-2.0.0/debian/rules --- lambda-align2-2.0.0/debian/rules 2019-06-08 12:03:30.000000000 +0000 +++ lambda-align2-2.0.0/debian/rules 2019-01-19 22:19:15.000000000 +0000 @@ -17,19 +17,6 @@ %: dh $@ --builddirectory=build -override_dh_installman: - sed -i -e 's@\(defaults to working directory\.\).*@\1@g' ./debian/lambda-align2/usr/share/man/man1/*.1 - sed -i -e 's@\(number of threads to run concurrently\).*@\1. Default: autodetected.@g' ./debian/lambda-align2/usr/share/man/man1/*.1 - sed -i 's/LAMBDA2 MKINDEXN/LAMBDA2_MKINDEXN/' ./debian/lambda-align2/usr/share/man/man1/lambda2-mkindexn.1 - sed -i 's/^lambda2 mkindexn /lambda2_mkindexn /' ./debian/lambda-align2/usr/share/man/man1/lambda2-mkindexn.1 - sed -i 's/LAMBDA2 MKINDEXP/LAMBDA2_MKINDEXP/' ./debian/lambda-align2/usr/share/man/man1/lambda2-mkindexp.1 - sed -i 's/^lambda2 mkindexp /lambda2_mkindexp /' ./debian/lambda-align2/usr/share/man/man1/lambda2-mkindexp.1 - sed -i 's/LAMBDA2 SEARCHN/LAMBDA2_SEARCHN/' ./debian/lambda-align2/usr/share/man/man1/lambda2-searchn.1 - sed -i 's/^lambda2 searchn /lambda2_searchn /' ./debian/lambda-align2/usr/share/man/man1/lambda2-searchn.1 - sed -i 's/LAMBDA2 SEARCHP/LAMBDA2_SEARCHP/' ./debian/lambda-align2/usr/share/man/man1/lambda2-searchp.1 - sed -i 's/^lambda2 searchp /lambda2_searchp /' ./debian/lambda-align2/usr/share/man/man1/lambda2-searchp.1 - dh_installman - override_dh_install: dh_install find debian -name "LICENSE*.rst" -delete diff -Nru lambda-align2-2.0.0/debian/tests/run-tests lambda-align2-2.0.0/debian/tests/run-tests --- lambda-align2-2.0.0/debian/tests/run-tests 2019-06-08 08:59:15.000000000 +0000 +++ lambda-align2-2.0.0/debian/tests/run-tests 2019-01-18 23:48:22.000000000 +0000 @@ -9,11 +9,9 @@ cmake -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON \ -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON ../ for binary in $(dpkg -L lambda-align2 | grep bin/); do ln -s ${binary} bin/; done -mkdir -p libexec -for binary in $(dpkg -L lambda-align2 | grep libexec/); do ln -s ${binary} libexec/; done cd tests set +e -ctest --parallel $(nproc) -I 1,10 --output-on-failure; RESULT=$? +ctest --parallel $(nproc) -I 1,10 && RESULT=$? if ls tests/*~ 1> /dev/null 2>&1; then \ for backup in tests/*~; do mv $${backup} $${backup%\~}; done; \ fi