[med-svn] [Git][med-team/libvcflib][master] 3 commits: Fix build with gcc-11

[Andreas Tille (@tille)]

Andreas Tille pushed to branch master at Debian Med / libvcflib


Commits:
fb5d4266 by Andreas Tille at 2021-10-20T18:33:34+02:00
Fix build with gcc-11

- - - - -
65c3f5e4 by Andreas Tille at 2021-10-20T18:33:49+02:00
routine-update: Standards-Version: 4.6.0

- - - - -
438bafc5 by Andreas Tille at 2021-10-20T18:37:08+02:00
routine-update: Ready to upload to unstable

- - - - -


4 changed files:

- debian/changelog
- debian/control
- + debian/patches/gcc-11.patch
- debian/patches/series


Changes:

=====================================
debian/changelog
=====================================
@@ -1,3 +1,11 @@
+libvcflib (1.0.2+dfsg-3) unstable; urgency=medium
+
+  * Fix build with gcc-11
+    Closes: #984139
+  * Standards-Version: 4.6.0 (routine-update)
+
+ -- Andreas Tille <tille at debian.org>  Wed, 20 Oct 2021 18:33:54 +0200
+
 libvcflib (1.0.2+dfsg-2) unstable; urgency=medium
 
   * Team upload.


=====================================
debian/control
=====================================
@@ -9,12 +9,12 @@ Build-Depends: debhelper-compat (= 13),
                libtabixpp-dev,
                libbz2-dev,
                libdisorder-dev,
-               libsmithwaterman-dev (>= 0.0+20160702-2),
+               libsmithwaterman-dev,
                libssw-dev,
-               libfastahack-dev (>= 0.0+git20160702.bbc645f+dfsg-5~),
+               libfastahack-dev,
                pkg-config,
                libgtest-dev <!nocheck>
-Standards-Version: 4.5.1
+Standards-Version: 4.6.0
 Vcs-Browser: https://salsa.debian.org/med-team/libvcflib
 Vcs-Git: https://salsa.debian.org/med-team/libvcflib.git
 Homepage: https://github.com/vcflib/vcflib
@@ -22,8 +22,8 @@ Rules-Requires-Root: no
 
 Package: libvcflib1
 Architecture: any
-Section: libs
 Multi-Arch: same
+Section: libs
 Depends: ${shlibs:Depends},
          ${misc:Depends}
 Description: C++ library for parsing and manipulating VCF files
@@ -43,8 +43,8 @@ Description: C++ library for parsing and manipulating VCF files
 
 Package: libvcflib-dev
 Architecture: any
-Section: libdevel
 Multi-Arch: same
+Section: libdevel
 Depends: ${misc:Depends},
          libvcflib1 (= ${binary:Version}),
          libdisorder-dev,
@@ -78,9 +78,9 @@ Depends: ${shlibs:Depends},
          r-cran-plyr,
          r-cran-ggplot2,
          r-cran-gridbase
+Suggests: r-cran-pracma
 Breaks: libvcflib1 (<= 1.0.0~rc2+dfsg-3)
 Replaces: libvcflib1 (<= 1.0.0~rc2+dfsg-3)
-Suggests: r-cran-pracma
 Description: C++ library for parsing and manipulating VCF files (tools)
  The Variant Call Format (VCF) is a flat-file, tab-delimited textual format
  intended to concisely describe reference-indexed variations between


=====================================
debian/patches/gcc-11.patch
=====================================
@@ -0,0 +1,16 @@
+Description: Fix build with gcc-11
+Bug-Debian: https://bugs.debian.org/984139
+Origin: https://github.com/ekg/intervaltree/pull/32/commits/f0c4046514f41072be20da07b69d8a92220c9294
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Wed, 20 Oct 2021 18:30:53 +0200
+
+--- a/intervaltree/IntervalTree.h
++++ b/intervaltree/IntervalTree.h
+@@ -6,6 +6,7 @@
+ #include <iostream>
+ #include <memory>
+ #include <cassert>
++#include <limits>
+ 
+ template <class Scalar, typename Value>
+ class Interval {


=====================================
debian/patches/series
=====================================
@@ -8,3 +8,4 @@ pkg-config.patch
 hardening-flags
 tabix_linking
 tests
+gcc-11.patch



View it on GitLab: https://salsa.debian.org/med-team/libvcflib/-/compare/8b9b7e9b4c8d52ac2346d50a6df98670cfff4463...438bafc590d203239f59b2d513b333498418dfc5

-- 
View it on GitLab: https://salsa.debian.org/med-team/libvcflib/-/compare/8b9b7e9b4c8d52ac2346d50a6df98670cfff4463...438bafc590d203239f59b2d513b333498418dfc5
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