Étienne Mollier pushed to branch master at Debian Med / librostlab-blast
Commits: bc827835 by Étienne Mollier at 2022-09-29T12:07:53+02:00 initialize changelog. - - - - - 53b1f65c by Étienne Mollier at 2022-09-29T12:17:41+02:00 gcc-12.patch: added; fix ftbfs with gcc-12. Closes: #1012990 - - - - - 2b2cc118 by Étienne Mollier at 2022-09-29T13:04:24+02:00 update changelog. - - - - - 66d08920 by Étienne Mollier at 2022-09-29T13:18:50+02:00 routine-update: Standards-Version: 4.6.1 - - - - - 5f516cc4 by Étienne Mollier at 2022-09-29T14:06:34+02:00 d/rules: filter librostlab-blast.tag to remove build path. The idea is to attempt to improve build reproducibility. - - - - - 565ab450 by Étienne Mollier at 2022-09-29T14:07:57+02:00 ready to upload to unstable - - - - - 5 changed files: - debian/changelog - debian/control - + debian/patches/gcc-12.patch - debian/patches/series - debian/rules Changes: ===================================== debian/changelog ===================================== @@ -1,3 +1,13 @@ +librostlab-blast (1.0.1-13) unstable; urgency=medium + + * Team upload. + * gcc-12.patch: added; fix ftbfs with gcc-12. (Closes: #1012990) + * Standards-Version: 4.6.1 (routine-update) + * d/rules: filter librostlab-blast.tag to remove build path; attempt to + improve build reproducibility. + + -- Étienne Mollier <[email protected]> Thu, 29 Sep 2022 14:07:24 +0200 + librostlab-blast (1.0.1-12) unstable; urgency=medium [ Aaron M. Ucko ] ===================================== debian/control ===================================== @@ -14,7 +14,7 @@ Build-Depends: debhelper-compat (= 13), librostlab-dev, texlive-fonts-recommended, texlive-latex-extra -Standards-Version: 4.6.0 +Standards-Version: 4.6.1 Vcs-Browser: https://salsa.debian.org/med-team/librostlab-blast Vcs-Git: https://salsa.debian.org/med-team/librostlab-blast.git Homepage: https://rostlab.org/ ===================================== debian/patches/gcc-12.patch ===================================== @@ -0,0 +1,44 @@ +Description: resolve template scoping for operator<< past gcc-12 + Since gcc-12, and also recent clang versions[1], the template scoping is more + picky about having proper declaration of the necessary methods before their + definition. The fact that some of the templates have to be resolved in the + librostlab aux_functions.h header makes the result a bit confusing, so may be + more of a workaround than a real fix. This patch fixes failure to build from + source with gcc-12. + . + [1]: https://clang.llvm.org/compatibility.html#dep_lookup +Author: Étienne Mollier <[email protected]> +Bug-Debian: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1012990 +Forwarded: no +Last-Update: 2022-09-29 +--- +This patch header follows DEP-3: http://dep.debian.net/deps/dep3/ +--- librostlab-blast.orig/lib/rostlab/blast-result.h ++++ librostlab-blast/lib/rostlab/blast-result.h +@@ -22,7 +22,6 @@ + #include <sstream> + #include <string> + #include <vector> +-#include <rostlab/aux_functions.h> + + namespace rostlab { + +@@ -203,6 +202,18 @@ + + } // namespace blast + ++// methods declaration - needs to be done before aux_funtions inclusion in ++// order to properly resolve template scoping with gcc-12. ++inline std::ostream& operator<<(std::ostream&, const rostlab::blast::round&); ++inline std::ostream& operator<<(std::ostream&, const rostlab::blast::oneline&); ++inline std::ostream& operator<<(std::ostream&, const rostlab::blast::hsp&); ++inline std::ostream& operator<<(std::ostream&, const rostlab::blast::hit&); ++inline std::ostream& operator<<(std::ostream&, const rostlab::blast::result&); ++} // namespace rostlab ++ ++#include <rostlab/aux_functions.h> ++ ++namespace rostlab { + /// Stream output operator for blast::round. + inline + std::ostream& operator<<( std::ostream& __os, const rostlab::blast::round& __r ) ===================================== debian/patches/series ===================================== @@ -1,2 +1,3 @@ reproducible.patch modernize_c++.patch +gcc-12.patch ===================================== debian/rules ===================================== @@ -23,9 +23,13 @@ override_dh_auto_build: dh_auto_build $(MAKE) -C lib doxygen-doc +DINSTALLDOC = debian/librostlab-blast-doc/usr/share/doc/librostlab-blast-doc +FAKEBUILDPATH = /fakebuildpath/lib/rostlab/ override_dh_installdocs: dh_installdocs find debian -name "*.md5" -delete + sed -i 's@<path>/.*/lib/rostlab/</path>@$(FAKEBUILDPATH)</path>@' \ + $(DINSTALLDOC)/librostlab-blast.tag override_dh_link: find debian -name jquery.js -delete View it on GitLab: https://salsa.debian.org/med-team/librostlab-blast/-/compare/38509c9f285584a4cd21b8be8457ef64a71ea776...565ab4509ddc4922c2883e4eb45245a5112fbe77 -- View it on GitLab: https://salsa.debian.org/med-team/librostlab-blast/-/compare/38509c9f285584a4cd21b8be8457ef64a71ea776...565ab4509ddc4922c2883e4eb45245a5112fbe77 You're receiving this email because of your account on salsa.debian.org.
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