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

[Étienne Mollier (@emollier)]

Étienne Mollier pushed to branch master at Debian Med / pirs


Commits:
7d57ce0f by Étienne Mollier at 2023-12-18T14:05:57+01:00
initialize changelog.

- - - - -
b179950d by Étienne Mollier at 2023-12-18T14:22:11+01:00
d/rules: define BOOST_TIMER_ENABLE_DEPRECATED.

This flag is passed to C preprocessor options to fix failure to build
from source with boost 1.83.

Closes: #1056023

- - - - -
00aed64f by Étienne Mollier at 2023-12-18T14:24:25+01:00
d/control: gnuplot-qt as default gnuplot dependency.

- - - - -
1ffed4c4 by Étienne Mollier at 2023-12-18T14:25:25+01:00
d/control: declare compliance to standars version 4.6.2.

- - - - -
754a9e6c by Étienne Mollier at 2023-12-18T14:38:51+01:00
typos.patch: new: fix typos caught by lintian.

- - - - -
b797bb73 by Étienne Mollier at 2023-12-18T14:42:06+01:00
ready to upload to unstable.

- - - - -


5 changed files:

- debian/changelog
- debian/control
- debian/patches/series
- + debian/patches/typos.patch
- debian/rules


Changes:

=====================================
debian/changelog
=====================================
@@ -1,3 +1,20 @@
+pirs (2.0.2+dfsg-12) unstable; urgency=medium
+
+  * Team upload.
+
+  [ Andreas Tille ]
+  * Forward patch
+
+  [ Étienne Mollier ]
+  * d/rules: define BOOST_TIMER_ENABLE_DEPRECATED.
+    This flag is passed to C preprocessor options to fix failure to build
+    from source with boost 1.83. (Closes: #1056023)
+  * d/control: gnuplot-qt as default gnuplot dependency.
+  * d/control: declare compliance to standars version 4.6.2.
+  * typos.patch: new: fix typos caught by lintian.
+
+ -- Étienne Mollier <emollier at debian.org>  Mon, 18 Dec 2023 14:39:21 +0100
+
 pirs (2.0.2+dfsg-11) unstable; urgency=medium
 
   * Standards-Version: 4.6.1 (routine-update)


=====================================
debian/control
=====================================
@@ -7,7 +7,7 @@ Build-Depends: debhelper-compat (= 13),
                libboost-dev,
                zlib1g-dev,
                libgzstream-dev
-Standards-Version: 4.6.1
+Standards-Version: 4.6.2
 Vcs-Browser: https://salsa.debian.org/med-team/pirs
 Vcs-Git: https://salsa.debian.org/med-team/pirs.git
 Homepage: https://github.com/galaxy001/pirs
@@ -19,7 +19,7 @@ Depends: ${shlibs:Depends},
          ${misc:Depends},
          pirs-profiles,
          fonts-liberation,
-         gnuplot
+         gnuplot-qt | gnuplot
 Description: Profile based Illumina pair-end Reads Simulator
  The program pIRS can be used for simulating Illumina PE reads, with a
  series of characters generated by Illumina sequencing platform, such as


=====================================
debian/patches/series
=====================================
@@ -3,3 +3,4 @@ Fix-spelling-of-sse2-option.patch
 do_not_seek_for_arial.ttf.patch
 Remove-mtune-compiler-flag.patch
 gcc-12.patch
+typos.patch


=====================================
debian/patches/typos.patch
=====================================
@@ -0,0 +1,28 @@
+Description: fix typos caught by lintian.
+Author: Étienne Mollier <emollier at debian.org>
+Forwarded: https://github.com/galaxy001/pirs/pull/16
+Last-Update: 2023-12-18
+---
+This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
+--- pirs.orig/README
++++ pirs/README
+@@ -244,7 +244,7 @@
+ 			 several parameters, it is very difficult to determine exactly
+ 			 what needs to be done to make the error rate be a given
+ 			 value.  We try to adjust the probabilities of getting each
+-			 quality score in order to accomodate the user-supplied error
++			 quality score in order to accommodate the user-supplied error
+ 			 rate.  However, depending on your input sequences, the actual
+ 			 error rate simulated by pIRS could be off by 20% or more.
+ 			 Please check the informational output to see the final error
+--- pirs.orig/src/pirs/pirs_simulate.cpp
++++ pirs/src/pirs/pirs_simulate.cpp
+@@ -194,7 +194,7 @@
+ "                 several parameters, it is very difficult to determine exactly\n"
+ "                 what needs to be done to make the error rate be a given\n"
+ "                 value.  We try to adjust the probabilities of getting each\n"
+-"                 quality score in order to accomodate the user-supplied error\n"
++"                 quality score in order to accommodate the user-supplied error\n"
+ "                 rate.  However, depending on your input sequences, the actual\n"
+ "                 error rate simulated by pIRS could be off by 20% or more.\n"
+ "                 Please check the informational output to see the final error\n"


=====================================
debian/rules
=====================================
@@ -3,6 +3,7 @@
 # DH_VERBOSE := 1
 
 export DEB_BUILD_MAINT_OPTIONS = hardening=+all
+export DEB_CPPFLAGS_MAINT_APPEND = -DBOOST_TIMER_ENABLE_DEPRECATED
 
 include /usr/share/dpkg/default.mk
 



View it on GitLab: https://salsa.debian.org/med-team/pirs/-/compare/8cbe37c5e821d1a4a3efaa528cb06724a7115443...b797bb7372f03937ace2d1220056d5ace16b8bcf

-- 
View it on GitLab: https://salsa.debian.org/med-team/pirs/-/compare/8cbe37c5e821d1a4a3efaa528cb06724a7115443...b797bb7372f03937ace2d1220056d5ace16b8bcf
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