Aaron M. Ucko pushed to branch master at Debian Med / sra-sdk
Commits: 648f0b0d by Aaron M. Ucko at 2021-10-14T16:23:45-04:00 fix_libngs_linkage.patch (new): Substitute ngs-c++ for absent ngs. - - - - - 8b630244 by Aaron M. Ucko at 2021-10-14T16:27:48-04:00 debian/rules: Stop renaming kget now that it's retired altogether. The historical rename addressed a file conflict, #851219. - - - - - 4 changed files: - debian/changelog - + debian/patches/fix_libngs_linkage.patch - debian/patches/series - debian/rules Changes: ===================================== debian/changelog ===================================== @@ -1,11 +1,18 @@ sra-sdk (2.11.2+dfsg-1) UNRELEASED; urgency=medium + [ Andreas Tille ] * Fix watchfile to detect new versions on github * New upstream version * Standards-Version: 4.6.0 (routine-update) * Bump versioned Build-Depends: libngs-sdk-dev (>= 2.11.2) - -- Andreas Tille <[email protected]> Wed, 13 Oct 2021 15:54:35 +0200 + [ Aaron M. Ucko ] + * d/p/fix_libngs_linkage.patch (new): Substitute ngs-c++ library for + absent ngs library. + * debian/rules: Stop renaming kget (to avoid a file conflict, #851219) + now that it's retired altogether. + + -- Aaron M. Ucko <[email protected]> Thu, 14 Oct 2021 16:27:47 -0400 sra-sdk (2.10.9+dfsg-2) unstable; urgency=medium ===================================== debian/patches/fix_libngs_linkage.patch ===================================== @@ -0,0 +1,38 @@ +Author: Aaron M. Ucko <[email protected]> +Last-Changed: Thu, 14 Oct 2021 16:23:45 -0400 +Description: Substitute ngs-c++ library for absent ngs library. + +Index: b/tools/vdb-sql/Makefile +=================================================================== +--- a/tools/vdb-sql/Makefile ++++ b/tools/vdb-sql/Makefile +@@ -80,7 +80,7 @@ VDB_SQL_SRC = \ + + VDB_SQL_LIB = \ + -svdb-sqlite \ +- -sngs \ ++ -sngs-c++ \ + -sncbi-vdb \ + -lm \ + -lpthread +@@ -100,7 +100,7 @@ FASTCONV_LIB = \ + -skapp \ + -stk-version \ + -svdb-sqlite \ +- -sngs \ ++ -sngs-c++ \ + -sncbi-vdb \ + -lm \ + -lpthread +Index: b/tools/ngs-pileup/Makefile +=================================================================== +--- a/tools/ngs-pileup/Makefile ++++ b/tools/ngs-pileup/Makefile +@@ -73,7 +73,6 @@ NGS_PILEUP_OBJ = \ + NGS_PILEUP_LIBS = \ + -sncbi-ngs-c++ \ + -sngs-c++ \ +- -sngs \ + -sncbi-vdb \ + -skapp \ + -stk-version \ ===================================== debian/patches/series ===================================== @@ -20,3 +20,4 @@ python3 use_exposed_headers.patch #reenable_legacy_schema_in_sra_load.patch skip_broken_loaders.patch +fix_libngs_linkage.patch ===================================== debian/rules ===================================== @@ -68,8 +68,6 @@ override_dh_install: dh_install # remove susipcious file which is not executable and conflicts with package magic rm -f debian/*/usr/bin/magic - # rename kget which conflicts with kget download manager (see #851219) - mv debian/$(pkg)/usr/bin/kget debian/$(pkg)/usr/bin/vdb-get # Formally supply a standard installation ID to satisfy sratools echo '/LIBS/GUID = "$(DEBIAN_GUID)"' >debian/$(pkg)/etc/ncbi/debian.kfg View it on GitLab: https://salsa.debian.org/med-team/sra-sdk/-/compare/dc201cc5cb985642eed919d69867b80feb7b9ce9...8b630244e7e1071868df80ea76b80b9a14bb6db1 -- View it on GitLab: https://salsa.debian.org/med-team/sra-sdk/-/compare/dc201cc5cb985642eed919d69867b80feb7b9ce9...8b630244e7e1071868df80ea76b80b9a14bb6db1 You're receiving this email because of your account on salsa.debian.org.
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