[med-svn] [Git][med-team/wise][master] 5 commits: routine-update: Packaging update
Lance Lin (@linqigang)
gitlab at salsa.debian.org
Thu Mar 14 15:54:51 GMT 2024
Lance Lin pushed to branch master at Debian Med / wise
Commits:
41432d6a by Lance Lin at 2024-03-14T21:47:01+07:00
routine-update: Packaging update
- - - - -
a7608cc8 by Lance Lin at 2024-03-14T21:47:17+07:00
routine-update: Standards-Version: 4.6.2
- - - - -
3a33e49d by Lance Lin at 2024-03-14T21:47:35+07:00
routine-update: debhelper-compat 13
- - - - -
4a81ecbb by Lance Lin at 2024-03-14T21:47:53+07:00
routine-update: watch file standard 4
- - - - -
db6df704 by Lance Lin at 2024-03-14T22:52:02+07:00
d/patches: Fix implicit-function-declaration errors (Closes: #1066705)
- - - - -
6 changed files:
- debian/changelog
- debian/control
- debian/patches/cross.patch
- + debian/patches/implicit-function-declaration.patch
- debian/patches/series
- debian/watch
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,13 @@
+wise (2.4.1-24) UNRELEASED; urgency=medium
+
+ * Team upload.
+ * Standards-Version: 4.6.2 (routine-update)
+ * debhelper-compat 13 (routine-update)
+ * watch file standard 4 (routine-update)
+ * d/patches: Fix implicit-function-declaration errors (Closes: #1066705)
+
+ -- Lance Lin <lq27267 at gmail.com> Thu, 14 Mar 2024 21:41:46 +0700
+
wise (2.4.1-23) unstable; urgency=medium
* Team upload.
=====================================
debian/control
=====================================
@@ -5,13 +5,13 @@ Uploaders: Steffen Moeller <moeller at debian.org>,
Andreas Tille <tille at debian.org>
Section: science
Priority: optional
-Build-Depends: debhelper-compat (= 12),
+Build-Depends: debhelper-compat (= 13),
texlive-latex-base,
texlive-extra-utils,
hevea,
docbook-to-man,
libglib2.0-dev
-Standards-Version: 4.5.0
+Standards-Version: 4.6.2
Vcs-Browser: https://salsa.debian.org/med-team/wise
Vcs-Git: https://salsa.debian.org/med-team/wise.git
Homepage: https://www.ebi.ac.uk/~birney/wise2/
=====================================
debian/patches/cross.patch
=====================================
@@ -17,7 +17,7 @@ Description: Do not hard code the build architecture pkg-config
CFLAGS += $(CPPFLAGS) -pthread -c -DUNIX -I../base/ -I../dynlibsrc `orbit-config --cflags client`
LDFLAGS += -L../base/ -lm -lpthread
AR_OPTIONS = ru
-@@ -14,18 +15,18 @@ hspscan_corba.c : hspscan_corba.idl
+@@ -14,18 +15,18 @@
orbit-idl hspscan_corba.idl
test_server : test_server.o hspscan_server_impl.o hspscan_corba-common.o hspscan_corba-skels.o hspscan_corba-stubs.o corba_singleton.o
@@ -42,7 +42,7 @@ Description: Do not hard code the build architecture pkg-config
$(CC) $(CFLAGS) $(INCFLAGS) $?
--- a/src/dnaindex/assembly/makefile
+++ b/src/dnaindex/assembly/makefile
-@@ -26,10 +26,11 @@ arraymatcher : arraymatcher.o assemblygr
+@@ -26,10 +26,11 @@
CC = cc
@@ -58,7 +58,7 @@ Description: Do not hard code the build architecture pkg-config
.c.o :
--- a/src/dnaindex/makefile
+++ b/src/dnaindex/makefile
-@@ -27,14 +27,14 @@ all: $(ASSEMBLY_OBJ)
+@@ -27,14 +27,14 @@
kwise : kwise.o $(ASSEMBLY_OBJ)
@@ -76,7 +76,7 @@ Description: Do not hard code the build architecture pkg-config
make_shotgun : make_shotgun.o shotgun.o
$(CC) -o make_shotgun make_shotgun.o shotgun.o -ldyna -lwisebase $(LDFLAGS)
-@@ -70,10 +70,11 @@ show_euler : show_euler.o eulerindex.o s
+@@ -70,10 +70,11 @@
$(CC) -o show_euler show_euler.o eulerindex.o singleseqspace.o -ldyna -lwisebase $(LDFLAGS)
CC = cc
@@ -92,7 +92,7 @@ Description: Do not hard code the build architecture pkg-config
.c.o :
--- a/src/dynlibsrc/makefile
+++ b/src/dynlibsrc/makefile
-@@ -82,11 +82,12 @@ DYNHELPEROBJ = packaln.o \
+@@ -82,11 +82,12 @@
CC = cc
@@ -108,7 +108,7 @@ Description: Do not hard code the build architecture pkg-config
#CFLAGS = -O -c -DUNIX -DNOERROR -I../base/
LDFLAGS += -g -L../base/ -lm
AR_OPTIONS = ru
-@@ -148,13 +149,13 @@ test_shadowindex : test_shadowindex.o sh
+@@ -148,13 +149,13 @@
$(CC) $(LDFLAGS) -g -o test_shadowindex test_shadowindex.o shadowseqindex.o shadowseq.o ./libdyna.a ../base/libwisebase.a -lm
test_seqhash : test_seqhash.o subseqhash.o hsp.o hitlist.o hspscaninterface.o hsplookupscan.o libdyna.a
@@ -135,7 +135,7 @@ Description: Do not hard code the build architecture pkg-config
# These are the CFLAGS to use. These days Wise2 is inherently
# pthreaded, and everything is compiled with threads. However
-@@ -31,13 +32,13 @@ CC = cc
+@@ -31,13 +32,13 @@
# Intel icc flags
@@ -154,7 +154,7 @@ Description: Do not hard code the build architecture pkg-config
EXTRALIBS = -lm
--- a/src/models/makefile
+++ b/src/models/makefile
-@@ -192,10 +192,10 @@ psw : psw.o seqaligndisplay.o proteinsw.
+@@ -192,10 +192,10 @@
$(CC) -o psw psw.o sw_wrap.o seqaligndisplay.o proteinsw.o abc.o pba.o $(LDFLAGS) -ldyna_glib -ldyna -lwisebase $(EXTRALIBS)
scanwisep.o : scanwisep.c
@@ -167,7 +167,7 @@ Description: Do not hard code the build architecture pkg-config
scanwisep_mysql.o : scanwisep.c
$(CC) $(CFLAGS) -DSCAN_MYSQL -I../corba -I../external/mott -I../mysql/protein_index/ -I/usr/local/mysql/include scanwisep.c
-@@ -226,25 +226,25 @@ scanwisep_compress : scanwisep_compress.
+@@ -226,25 +226,25 @@
scanwisep : scanwisep.o seqaligndisplay.o proteinsw.o sw_wrap.o abc.o pba.o hsp2aln_sw.o
@@ -200,7 +200,7 @@ Description: Do not hard code the build architecture pkg-config
dnawise : dnawise.o dnahmm.o dnahmmdp.o seqaligndisplay.o
$(CC) -o dnawise dnawise.o dnahmm.o dnahmmdp.o seqaligndisplay.o $(LDFLAGS) -ldyna_glib -ldyna -lwisebase -lpthread
-@@ -343,13 +343,14 @@ HMMER_DEFINE =
+@@ -343,13 +343,14 @@
CC = cc
=====================================
debian/patches/implicit-function-declaration.patch
=====================================
@@ -0,0 +1,25 @@
+Description: Fix implicit-function-declaration build errors
+Author: Lance Lin <lq27267 at gmail.com>
+Last-Update: 14 Mar 2024
+
+--- a/src/HMMer2/prior.c
++++ b/src/HMMer2/prior.c
+@@ -4,6 +4,7 @@
+ * Support for Dirichlet prior data structure, p7prior_s.
+ */
+
++#include <string.h>
+ #include "config.h"
+ #include "structs.h"
+ #include "funcs.h"
+--- a/src/external/mott/mott_api.c
++++ b/src/external/mott/mott_api.c
+@@ -1,6 +1,8 @@
+ #include<stdio.h>
++#include<stdlib.h>
+ #include<limits.h>
+ #include<math.h>
++#include<ctype.h>
+ #include"gapstat.h"
+
+ double default_lambda0, default_K0, default_Kplus, default_H, default_r, default_s, default_alpha;
=====================================
debian/patches/series
=====================================
@@ -11,3 +11,4 @@
11_consistent_manual_dates.patch
spelling.patch
cross.patch
+implicit-function-declaration.patch
=====================================
debian/watch
=====================================
@@ -1,4 +1,4 @@
-version=3
+version=4
http://www.ebi.ac.uk/~birney/wise2/ (?:./)?wise(.*)\.tar\.gz \
debian uupdate
View it on GitLab: https://salsa.debian.org/med-team/wise/-/compare/25ef29b5302971df7fe4b02e176557c05cabf070...db6df7047ece158a76184da0fc8e12544c314ead
--
View it on GitLab: https://salsa.debian.org/med-team/wise/-/compare/25ef29b5302971df7fe4b02e176557c05cabf070...db6df7047ece158a76184da0fc8e12544c314ead
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