Liubov Chuprikova pushed to branch master at Debian Med / t-coffee
Commits: c95d597d by Liubov Chuprikova at 2019-02-04T09:48:44Z A patch to fix autopkgtest COREDUMP - - - - - 8282ba9a by Liubov Chuprikova at 2019-02-04T09:50:17Z Standards-Version: 4.3.0 - - - - - 4 changed files: - debian/changelog - debian/control - + debian/patches/fix_tempfile_name_sharing.patch - debian/patches/series Changes: ===================================== debian/changelog ===================================== @@ -1,3 +1,13 @@ +t-coffee (12.00.7fb08c2-2) UNRELEASED; urgency=medium + + * Team upload. + * Fix "t-coffee breaks libbio-tools-run-alignment-tcoffee-perl + autopkgtest: COREDUMP" fix_tempfile_name_sharing.patch + (Closes: #917143) + * Standards-Version: 4.3.0 + + -- Liubov Chuprikova <[email protected]> Mon, 04 Feb 2019 10:37:01 +0100 + t-coffee (12.00.7fb08c2-1) unstable; urgency=medium * New upstream version ===================================== debian/control ===================================== @@ -5,7 +5,7 @@ Uploaders: Steffen Moeller <[email protected]>, Section: science Priority: optional Build-Depends: debhelper (>= 11~) -Standards-Version: 4.2.1 +Standards-Version: 4.3.0 Vcs-Browser: https://salsa.debian.org/med-team/t-coffee Vcs-Git: https://salsa.debian.org/med-team/t-coffee.git Homepage: http://www.tcoffee.org/Projects_home_page/t_coffee_home_page.html ===================================== debian/patches/fix_tempfile_name_sharing.patch ===================================== @@ -0,0 +1,29 @@ +Author: Liubov Chuprikova <[email protected]> +Bug-Debian: https://bugs.debian.org/917143 +Last-Update: Sun, 03 Feb 2019 23:42:41 +0100 +Description: Delete static for tempfile names so that +different processes do not use the same file. + + +--- a/t_coffee_source/util_lib/reformat.c ++++ b/t_coffee_source/util_lib/reformat.c +@@ -1524,8 +1524,8 @@ + } + else if (format && (strm(format, "saga_aln" ) ||strm(format, "clustal_aln")||strm(format, "t_coffee_aln" ) || strm (format, "msf_aln"))) + { +- static char*tmp_name1=vtmpnam (NULL); +- static char*tmp_name2=vtmpnam (NULL); ++ char*tmp_name1=vtmpnam (NULL); ++ char*tmp_name2=vtmpnam (NULL); + + printf_system ( "seq2name_seq.pl %s > %s",name, tmp_name1); + printf_system ( "nameseq2fasta.pl %s > %s",tmp_name1, tmp_name2); +@@ -1534,6 +1534,8 @@ + A=seq2aln (S, A, 0); + //read_aln ( name, A); + ++ vfree(tmp_name1); ++ vfree(tmp_name2); + } + + else if (format && strm (format, "conc_aln"))A=input_conc_aln (name,NULL); ===================================== debian/patches/series ===================================== @@ -6,3 +6,4 @@ set_proper_dir_permissions.patch mayhem.patch stable-linking-inputs.patch clustalw2.patch +fix_tempfile_name_sharing.patch View it on GitLab: https://salsa.debian.org/med-team/t-coffee/compare/b9d1db114cd4f8cc1586d125f577fb55b175ad6f...8282ba9a71902a1a84e34b1fcf0a6d7fe0bb9773 -- View it on GitLab: https://salsa.debian.org/med-team/t-coffee/compare/b9d1db114cd4f8cc1586d125f577fb55b175ad6f...8282ba9a71902a1a84e34b1fcf0a6d7fe0bb9773 You're receiving this email because of your account on salsa.debian.org.
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