[med-svn] [Git][med-team/librostlab-blast][master] 6 commits: initialize changelog.

[Étienne Mollier (@emollier)]

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 <emollier at debian.org>  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 <emollier at debian.org>
+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
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