[med-svn] [Git][med-team/canu][master] 3 commits: Add patch to fix FTBFS with new glibc (Closes: #997215)

[Nilesh Patra (@nilesh)]

Nilesh Patra pushed to branch master at Debian Med / canu


Commits:
7b542b7f by Nilesh Patra at 2021-10-29T01:56:44+05:30
Add patch to fix FTBFS with new glibc (Closes: #997215)

- - - - -
7b465482 by Nilesh Patra at 2021-10-29T01:57:30+05:30
Run cme

- - - - -
cb18223c by Nilesh Patra at 2021-10-29T02:05:11+05:30
Upload to unstable

- - - - -


6 changed files:

- debian/changelog
- debian/control
- debian/install
- debian/patches/canu_version.patch
- + debian/patches/remove-deprecated-sysctl.patch
- debian/patches/series


Changes:

=====================================
debian/changelog
=====================================
@@ -1,3 +1,11 @@
+canu (2.0+dfsg-2) unstable; urgency=medium
+
+  * Team Upload.
+  * Add patch to fix FTBFS with new glibc (Closes: #997215)
+  * Run cme
+
+ -- Nilesh Patra <nilesh at debian.org>  Fri, 29 Oct 2021 01:57:43 +0530
+
 canu (2.0+dfsg-1) unstable; urgency=medium
 
   * Team upload.


=====================================
debian/control
=====================================
@@ -2,13 +2,13 @@ Source: canu
 Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
 Section: science
 Priority: optional
-Build-Depends: debhelper-compat (= 12),
+Build-Depends: debhelper-compat (= 13),
                libboost-dev,
                libmeryl-dev,
 # For File::Path
                libfilesys-df-perl,
-               mhap (>= 2.1.3)
-Standards-Version: 4.5.0
+               mhap
+Standards-Version: 4.6.0
 Vcs-Browser: https://salsa.debian.org/med-team/canu
 Vcs-Git: https://salsa.debian.org/med-team/canu.git
 Homepage: http://canu.readthedocs.org/en/latest/
@@ -19,7 +19,7 @@ Depends: ${shlibs:Depends},
          ${misc:Depends},
          ${perl:Depends},
          libfilesys-df-perl,
-         mhap (>= 2.1.3),
+         mhap,
          gnuplot
 Suggests: pbgenomicconsensus,
           nanopolish


=====================================
debian/install
=====================================
@@ -1,3 +1,3 @@
 *-*/bin	usr/lib/canu/
 *-*/lib usr/lib/canu/
-debian/bin/canu	/usr/bin/
+debian/bin/canu	usr/bin/


=====================================
debian/patches/canu_version.patch
=====================================
@@ -1,3 +1,4 @@
+Description: Canu_version
 Index: canu/src/canu_version_update.pl
 ===================================================================
 --- canu.orig/src/canu_version_update.pl


=====================================
debian/patches/remove-deprecated-sysctl.patch
=====================================
@@ -0,0 +1,18 @@
+Description: sysctl.h has been removed with latest glibc, do not include it
+Bug-Debian: https://bugs.debian.org/997215
+Author: Nilesh Patra <nilesh at debian.org>
+Last-Update: 2021-10-29
+--- a/src/utility/system.C
++++ b/src/utility/system.C
+@@ -42,11 +42,6 @@
+ #include "jemalloc/jemalloc.h"
+ #endif
+ 
+-#if !defined(__CYGWIN__) && !defined(_WIN32)
+-#include <sys/sysctl.h>
+-#endif
+-
+-
+ 
+ double
+ getTime(void) {


=====================================
debian/patches/series
=====================================
@@ -1,3 +1,4 @@
 use-debian-mhap-at-runtime.patch
 external-mhap.patch
 canu_version.patch
+remove-deprecated-sysctl.patch



View it on GitLab: https://salsa.debian.org/med-team/canu/-/compare/5d1934b4bf09daddd794f2c466d8a86631a92801...cb18223c245fc94bfa933e8fe09a85d98b991219

-- 
View it on GitLab: https://salsa.debian.org/med-team/canu/-/compare/5d1934b4bf09daddd794f2c466d8a86631a92801...cb18223c245fc94bfa933e8fe09a85d98b991219
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