Étienne Mollier pushed to branch master at Debian Med / sweed
Commits: 2596f2b5 by Etienne Mollier at 2020-07-22T12:03:15+02:00 added gcc10.patch to fix FTBFS with gcc 10 - - - - - 86924645 by Etienne Mollier at 2020-07-22T12:10:58+02:00 routine-update: Standards-Version: 4.5.0 - - - - - 71f21d44 by Etienne Mollier at 2020-07-22T12:10:58+02:00 routine-update: debhelper-compat 13 - - - - - 7b454c65 by Etienne Mollier at 2020-07-22T12:10:59+02:00 routine-update: Add salsa-ci file - - - - - b6bdd530 by Etienne Mollier at 2020-07-22T12:10:59+02:00 routine-update: Rules-Requires-Root: no - - - - - e3b18bec by Etienne Mollier at 2020-07-22T12:49:39+02:00 d/u/metadata: added repository information This addresses lintian tag upstream-metadata-missing-repository. - - - - - 16765a3c by Etienne Mollier at 2020-07-22T12:52:21+02:00 routine-update: Ready to upload to unstable - - - - - 7 changed files: - debian/changelog - − debian/compat - debian/control - + debian/patches/gcc10.patch - debian/patches/series - + debian/salsa-ci.yml - debian/upstream/metadata Changes: ===================================== debian/changelog ===================================== @@ -1,3 +1,16 @@ +sweed (3.2.1+dfsg-2) unstable; urgency=medium + + * Team upload. + * Added gcc10.patch to fix compilation issues related with the move to GCC 10 + in Debian Bullseye. (Closes: #957851) + * Standards-Version: 4.5.0 (routine-update) + * debhelper-compat 13 (routine-update) + * Add salsa-ci file (routine-update) + * Rules-Requires-Root: no (routine-update) + * Added repository informations in debian/upstream/metadata + + -- Étienne Mollier <[email protected]> Wed, 22 Jul 2020 12:51:56 +0200 + sweed (3.2.1+dfsg-1) unstable; urgency=medium * Initial release (Closes: #902960) ===================================== debian/compat deleted ===================================== @@ -1 +0,0 @@ -11 ===================================== debian/control ===================================== @@ -3,11 +3,12 @@ Maintainer: Debian Med Packaging Team <[email protected]. Uploaders: Steffen Moeller <[email protected]> Section: science Priority: optional -Build-Depends: debhelper (>= 11) -Standards-Version: 4.1.5 +Build-Depends: debhelper-compat (= 13) +Standards-Version: 4.5.0 Vcs-Browser: https://salsa.debian.org/med-team/sweed Vcs-Git: https://salsa.debian.org/med-team/sweed.git Homepage: https://sco.h-its.org/exelixis/web/software/sweed/ +Rules-Requires-Root: no Package: sweed Architecture: any ===================================== debian/patches/gcc10.patch ===================================== @@ -0,0 +1,95 @@ +Description: fix FTBFS with GCC 10 +Author: Étienne Mollier <[email protected]> +Bug-Debian: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=957851 +Forwarded: no +Last-Update: 2020-07-22 +--- +This patch header follows DEP-3: http://dep.debian.net/deps/dep3/ +--- sweed.orig/SweeD.h ++++ sweed/SweeD.h +@@ -114,18 +114,18 @@ + #define MAXINT 2147483647 + + +-char bits_in_16bits [0x1u << 16]; ++extern char bits_in_16bits [0x1u << 16]; + +-int linkage_disequilibrium; ++extern int linkage_disequilibrium; + +-int borderTol; ++extern int borderTol; + +-int VCF_header_lines; +-char VCF_alignment_name [MAX_CHROM_NAME_VCF]; +-int VCF_first_SNP; +-int nxtVCFalignment; ++__attribute__((__common__)) int VCF_header_lines; ++__attribute__((__common__)) char VCF_alignment_name [MAX_CHROM_NAME_VCF]; ++__attribute__((__common__)) int VCF_first_SNP; ++__attribute__((__common__)) int nxtVCFalignment; + +-char runName[INFILENAMESIZE]; ++__attribute__((__common__)) char runName[INFILENAMESIZE]; + + typedef float cor_t; + +@@ -133,13 +133,13 @@ + + cor_t ABS (cor_t input); + +-double mainTime0; ++__attribute__((__common__)) double mainTime0; + +-int map[INTOKS]; ++extern int map[INTOKS]; + +-int nofTokens; ++extern int nofTokens; + +-int nofSamples; ++extern int nofSamples; + + typedef int al_t; + typedef double t_sfs; +@@ -222,17 +222,17 @@ + + } alignment_struct; + +-alignment_struct * alignment; ++__attribute__((__common__)) alignment_struct * alignment; + +-double * rv; +-double ** rvLUT; +-double ** rvLUT2; ++extern double * rv; ++__attribute__((__common__)) double ** rvLUT; ++extern double ** rvLUT2; + + + #define GRIDSIZE 300 + #define LOCALGRIDSIZE 100 + +-double div6; ++__attribute__((__common__)) double div6; + + + typedef struct +@@ -242,7 +242,7 @@ + + } factorial_LUT; + +-factorial_LUT * factLUT; ++__attribute__((__common__)) factorial_LUT * factLUT; + + + typedef struct +@@ -254,7 +254,7 @@ + + } clr_struct; + +-clr_struct * clr; ++__attribute__((__common__)) clr_struct * clr; + + #ifdef _ANALYTICAL_SFS + typedef struct ===================================== debian/patches/series ===================================== @@ -1 +1,2 @@ +gcc10.patch hardening.patch ===================================== debian/salsa-ci.yml ===================================== @@ -0,0 +1,4 @@ +--- +include: + - https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/salsa-ci.yml + - https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/pipeline-jobs.yml ===================================== debian/upstream/metadata ===================================== @@ -1,3 +1,5 @@ +Repository: https://git.assembla.com/sweed.git +Repository-Browse: https://app.assembla.com/spaces/sweed/git/source Reference: - Author: > Pavlos Pavlidis and Daniel Živković and Alexandros Stamatakis and View it on GitLab: https://salsa.debian.org/med-team/sweed/-/compare/04fb9d905e22cbed4e9f2869bc16ff9b44f2be47...16765a3c476beffae3c3d4c9b8c2132900c54f5e -- View it on GitLab: https://salsa.debian.org/med-team/sweed/-/compare/04fb9d905e22cbed4e9f2869bc16ff9b44f2be47...16765a3c476beffae3c3d4c9b8c2132900c54f5e You're receiving this email because of your account on salsa.debian.org.
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