[med-svn] [Git][med-team/amos][master] Outdated c++, needs considerable work
Steffen Möller
gitlab at salsa.debian.org
Wed May 2 20:18:47 BST 2018
Steffen Möller pushed to branch master at Debian Med / amos
Commits:
169d23fe by Steffen Moeller at 2018-05-02T21:18:35+02:00
Outdated c++, needs considerable work
- - - - -
6 changed files:
- debian/changelog
- debian/control
- debian/copyright
- + debian/patches/narrowing.patch
- + debian/patches/series
- debian/rules
Changes:
=====================================
debian/changelog
=====================================
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,9 +1,16 @@
amos (3.1.0-1) UNRELEASED; urgency=low
+ * Initial release (Closes: #897191).
+
[Andreas Tille]
* Draft packaging
[Afif Elghraoui]
* Finalized packaging
+ [Steffen Moeller]
+ * Added license text to d/copyright
+ * (mostly) fixed narrowing build problem in src/AMOS
+ * Does not build because of hash_multimap issue
+
-- Afif Elghraoui <afif at ghraoui.name> Wed, 12 Aug 2015 00:52:14 -0700
=====================================
debian/control
=====================================
--- a/debian/control
+++ b/debian/control
@@ -11,10 +11,10 @@ Build-Depends: debhelper (>= 9),
zlib1g,
python,
perl
-Standards-Version: 3.9.6
+Standards-Version: 4.1.3
Homepage: http://amos.sourceforge.net/
-Vcs-Browser: http://anonscm.debian.org/cgit/debian-med/amos.git
-Vcs-Svn: git://anonscm.debian.org/debian-med/amos.git
+Vcs-Browser: https://salsa.debian.org/med-team/amos
+Vcs-Git: https://salsa.debian.org/med-team/amos.git
Package: amos-assembler
Architecture: any
=====================================
debian/copyright
=====================================
--- a/debian/copyright
+++ b/debian/copyright
@@ -9,3 +9,14 @@ License: Artistic
Files: debian/*
Copyright: © 2012 Andreas Tille <tille at debian.org>
License: Artistic
+
+License: Artistic
+ This program is free software; you can redistribute it and/or modify it
+ under the terms of the "Artistic License" which comes with Debian.
+ .
+ THIS PACKAGE IS PROVIDED "AS IS" AND WITHOUT ANY EXPRESS OR IMPLIED
+ WARRANTIES, INCLUDING, WITHOUT LIMITATION, THE IMPLIED WARRANTIES
+ OF MERCHANTIBILITY AND FITNESS FOR A PARTICULAR PURPOSE.
+ .
+ On Debian systems, the complete text of the Artistic License
+ can be found in "/usr/share/common-licenses/Artistic".
=====================================
debian/patches/narrowing.patch
=====================================
--- /dev/null
+++ b/debian/patches/narrowing.patch
@@ -0,0 +1,50 @@
+Index: amos/src/AMOS/utility_AMOS.cc
+===================================================================
+--- amos.orig/src/AMOS/utility_AMOS.cc
++++ amos/src/AMOS/utility_AMOS.cc
+@@ -24,6 +24,8 @@ const char COMPLEMENT_DNA[256] =
+ 80, 81,'Y','S','A', 85,'B','W','X','R', 90, 91, 92, 93, 94, 95,
+ 96,'t','v','g','h',101,102,'c','d',105,106,'m',108,'k','n',111,
+ 112,113,'y','s','a',117,'b','w','x','r',122,123,124,125,126,127,
++/*
++ these are not char values
+ 128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,
+ 144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,
+ 160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,
+@@ -32,6 +34,17 @@ const char COMPLEMENT_DNA[256] =
+ 208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,
+ 224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,
+ 240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255
++*/
++ -128, -127, -126, -125, -124, -123, -122, -121, -120, -119, -118,
++ -117, -116, -115, -114, -113, -112, -111, -110, -109, -108, -107,
++ -106, -105, -104, -103, -102, -101, -100, -99, -98, -97, -96, -95,
++ -94, -93, -92, -91, -90, -89, -88, -87, -86, -85, -84, -83, -82,
++ -81, -80, -79, -78, -77, -76, -75, -74, -73, -72, -71, -70, -69,
++ -68, -67, -66, -65, -64, -63, -62, -61, -60, -59, -58, -57, -56,
++ -55, -54, -53, -52, -51, -50, -49, -48, -47, -46, -45, -44, -43,
++ -42, -41, -40, -39, -38, -37, -36, -35, -34, -33, -32, -31, -30,
++ -29, -28, -27, -26, -25, -24, -23, -22, -21, -20, -19, -18, -17,
++ -16, -15, -14, -13, -12, -11, -10, -9, -8, -7, -6, -5, -4, -3, -2, -1
+ };
+
+
+Index: amos/src/AMOS/inttypes_AMOS.hh
+===================================================================
+--- amos.orig/src/AMOS/inttypes_AMOS.hh
++++ amos/src/AMOS/inttypes_AMOS.hh
+@@ -75,8 +75,12 @@ inline uint8_t Char2Qual (char qual)
+ //!
+ inline std::string Decode (NCode_t ncode)
+ {
+- char buff[4] = {ncode & CHAR_MAX, ncode >> CHAR_BIT & CHAR_MAX,
+- ncode >> CHAR_BIT >> CHAR_BIT & CHAR_MAX, '\0'};
++ // this is buggy
++ char buff[4];
++ buff[0] = ncode%128;
++ buff[1] = (ncode/256)%128;
++ buff[2] = (ncode/256/256)%128;
++ buff[3] = '\0';
+ return buff;
+ }
+
=====================================
debian/patches/series
=====================================
--- /dev/null
+++ b/debian/patches/series
@@ -0,0 +1 @@
+narrowing.patch
=====================================
debian/rules
=====================================
--- a/debian/rules
+++ b/debian/rules
@@ -1,8 +1,12 @@
#!/usr/bin/make -f
#DH_VERBOSE = 1
-DPKG_EXPORT_BUILDFLAGS = 1
-include /usr/share/dpkg/default.mk
+#DPKG_EXPORT_BUILDFLAGS = 1
+#include /usr/share/dpkg/default.mk
%:
dh $@
+
+#override_dh_auto_configure:
+# ./configure --prefix=$(CURDIR)/debian/tmp --enable-AMOScmp=yes --enable-all=no
+
View it on GitLab: https://salsa.debian.org/med-team/amos/commit/169d23fee9b8c994d90a3b3cfd98d7cd49f3804b
---
View it on GitLab: https://salsa.debian.org/med-team/amos/commit/169d23fee9b8c994d90a3b3cfd98d7cd49f3804b
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