[med-svn] [Git][med-team/fastdnaml][master] 8 commits: gcc-15.patch: new: fix build failure with gcc-15.
Étienne Mollier (@emollier)
gitlab at salsa.debian.org
Sun Mar 2 09:39:11 GMT 2025
Étienne Mollier pushed to branch master at Debian Med / fastdnaml
Commits:
6e7b5ba4 by Étienne Mollier at 2025-03-02T10:10:39+01:00
gcc-15.patch: new: fix build failure with gcc-15.
Closes: #1096609
- - - - -
a4b6df86 by Étienne Mollier at 2025-03-02T10:11:15+01:00
d/control: declare compliance to standards version 4.7.2.
- - - - -
a83d66e1 by Étienne Mollier at 2025-03-02T10:14:29+01:00
hardening.patch: normalise Last-Update timestamp.
- - - - -
16621d46 by Étienne Mollier at 2025-03-02T10:16:10+01:00
fixup-implicit-function-declaration.patch: dep3 header.
- - - - -
43085762 by Étienne Mollier at 2025-03-02T10:34:11+01:00
fortify.patch: new: fortify binaries hardening.
- - - - -
6f1298c5 by Étienne Mollier at 2025-03-02T10:37:22+01:00
d/*: identified new upstream source location.
- - - - -
9702712f by Étienne Mollier at 2025-03-02T10:37:40+01:00
d/watch: update watch file to new upstream location.
- - - - -
68aa6e1f by Étienne Mollier at 2025-03-02T10:38:39+01:00
d/changelog: ready for upload to unstable.
- - - - -
11 changed files:
- debian/README.source
- debian/changelog
- debian/control
- debian/copyright
- debian/patches/fixup-implicit-function-declaration.patch
- + debian/patches/fortify.patch
- + debian/patches/gcc-15.patch
- debian/patches/hardening.patch
- debian/patches/series
- debian/upstream/metadata
- debian/watch
Changes:
=====================================
debian/README.source
=====================================
@@ -1,2 +1 @@
-The package is dead upstream (=not developed any more)
-and the source is not available at the ftp server any more.
+The package is dead upstream (=not developed any more).
=====================================
debian/changelog
=====================================
@@ -1,3 +1,15 @@
+fastdnaml (1.2.2-18) unstable; urgency=medium
+
+ * gcc-15.patch: new: fix build failure with gcc-15. (Closes: #1096609)
+ * d/control: declare compliance to standards version 4.7.2.
+ * hardening.patch: normalise Last-Update timestamp.
+ * fixup-implicit-function-declaration.patch: dep3 header.
+ * fortify.patch: new: fortify binaries hardening.
+ * d/*: identified new upstream source location.
+ * d/watch: update watch file to new upstream location.
+
+ -- Étienne Mollier <emollier at debian.org> Sun, 02 Mar 2025 10:38:27 +0100
+
fastdnaml (1.2.2-17) unstable; urgency=medium
* gcc-14.patch: new: fix implicit return type for "main". (Closes: #1074947)
=====================================
debian/control
=====================================
@@ -6,10 +6,10 @@ Uploaders: Andreas Tille <tille at debian.org>,
Section: science
Priority: optional
Build-Depends: debhelper-compat (= 13)
-Standards-Version: 4.7.0
+Standards-Version: 4.7.2
Vcs-Browser: https://salsa.debian.org/med-team/fastdnaml
Vcs-Git: https://salsa.debian.org/med-team/fastdnaml.git
-Homepage: ftp://ftp.bio.indiana.edu/molbio/evolve/fastdnaml/fastDNAml.html
+Homepage: https://www.life.illinois.edu/gary/programs/fastDNAml.html
Rules-Requires-Root: no
Package: fastdnaml
=====================================
debian/copyright
=====================================
@@ -1,7 +1,7 @@
Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
Upstream-Name: fastDNAml
-Upstream-Contact: Gary J. Olsen <gary at phylo.life.uiuc.edu>
-Source: Seems not to be available any more online
+Upstream-Contact: Gary J. Olsen <gjo☮illinois.edu>
+Source: https://www.life.illinois.edu/gary/programs/fastDNAml/
Files: *
Copyright: 1998-2000 Gary J. Olsen <gary at phylo.life.uiuc.edu>,
=====================================
debian/patches/fixup-implicit-function-declaration.patch
=====================================
@@ -1,3 +1,8 @@
+Author: Nilesh Patra <nilesh at iki.fi>
+Last-Update: 2024-04-07
+Description: Add patch to fix FTBFS with implicit-function-declaration
+Bug-Debian: https://bugs.debian.org/1066709
+
--- a/source/fastDNAml.h
+++ b/source/fastDNAml.h
@@ -5,6 +5,7 @@
=====================================
debian/patches/fortify.patch
=====================================
@@ -0,0 +1,33 @@
+Description: propagate FORTIFY macro definitions.
+ This is necessary to obtain full hardening of the resulting binaries.
+Author: Étienne Mollier <emollier at debian.org>
+Forwarded: not-needed
+Last-Update: 2025-03-02
+---
+This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
+--- fastdnaml.orig/source/Makefile
++++ fastdnaml/source/Makefile
+@@ -9,10 +9,10 @@
+ all : fastDNAml
+
+ fastDNAml : fastDNAml.o
+- $(CC) $(CFLAGS) -o fastDNAml fastDNAml.o $(LDFLAGS)
++ $(CC) $(CPPFLAGS) $(CFLAGS) -o fastDNAml fastDNAml.o $(LDFLAGS)
+
+ fastDNAml.o : fastDNAml.c fastDNAml.h
+- $(CC) $(CFLAGS) -c fastDNAml.c
++ $(CC) $(CPPFLAGS) $(CFLAGS) -c fastDNAml.c
+
+ clean :
+ $(RM) fastDNAml.o
+--- fastdnaml.orig/Makefile
++++ fastdnaml/Makefile
+@@ -1,7 +1,7 @@
+ all: fastDNAml
+
+ fastDNAml:
+- cd source && $(CC) ${CFLAGS} fastDNAml.c -o fastDNAml -lm ${LDFLAGS}
++ cd source && $(CC) $(CPPFLAGS) ${CFLAGS} fastDNAml.c -o fastDNAml -lm ${LDFLAGS}
+
+ install:
+ install -m0755 source/fastDNAml debian/fastDNAml-util ${DESTDIR}/usr/bin
=====================================
debian/patches/gcc-15.patch
=====================================
@@ -0,0 +1,69 @@
+Description: fix build failure with gcc-15.
+ This patch completes multiple function prototypes for compliance with
+ standard C 2023.
+Author: Étienne Mollier <emollier at debian.org>
+Bug-Debian: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1096609
+Forwarded: no
+Last-Update: 2025-03-02
+---
+This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
+--- fastdnaml.orig/source/fastDNAml.h
++++ fastdnaml/source/fastDNAml.h
+@@ -215,7 +215,7 @@
+ int tipy;
+ } drawdata;
+
+-void exit();
++void exit(int);
+
+ #if ANSI || MALLOC_VOID
+ void *malloc();
+--- fastdnaml.orig/source/fastDNAml.c
++++ fastdnaml/source/fastDNAml.c
+@@ -500,8 +500,8 @@
+
+ boolean restoreTree (topol *tpl, tree *tr)
+ { /* restoreTree */
+- void hookup();
+- boolean initrav();
++ void hookup(nodeptr, nodeptr, double);
++ boolean initrav(tree*, nodeptr);
+
+ connptr r;
+ nodeptr p, p0;
+@@ -677,7 +677,7 @@
+ * position into which it should be inserted.
+ */
+
+-int findInList (void *item, void *list[], int n, int (* cmpFunc)())
++int findInList (void *item, void *list[], int n, int (* cmpFunc)(void*, void*))
+ { /* findInList */
+ int mid, hi, lo, cmp;
+
+@@ -1771,7 +1771,7 @@
+ void makeboot (analdef *adef, rawdata *rdta, cruncheddata *cdta)
+ { /* makeboot */
+ int i, j, nonzero;
+- double randum();
++ double randum(long*);
+
+ nonzero = 0;
+ for (i = 1; i <= rdta->sites; i++) if (rdta->wgt[i] > 0) nonzero++;
+@@ -3224,7 +3224,7 @@
+ { /* writeCheckpoint */
+ char filename[128];
+ FILE *checkpointf;
+- void treeOut();
++ void treeOut(FILE*, tree*, int);
+
+ checkpointf = fopen_pid(checkpointname, "a", filename);
+ if (checkpointf) {
+@@ -4618,7 +4618,7 @@
+ int *enterorder; /* random entry order */
+ int i, j, k, nextsp, newsp, maxtrav, tested;
+
+- double randum();
++ double randum(long*);
+
+
+ enterorder = (int *) Malloc(sizeof(int) * (tr->mxtips + 1));
=====================================
debian/patches/hardening.patch
=====================================
@@ -1,5 +1,5 @@
Author: Andreas Tille <tille at debian.org>
-Last-Update: Wed, 27 Sep 2017 13:55:51 +0200
+Last-Update: 2017-09-27
Description: Propagate hardening options
--- a/source/Makefile
=====================================
debian/patches/series
=====================================
@@ -4,3 +4,5 @@ hardening.patch
cross.patch
fixup-implicit-function-declaration.patch
gcc-14.patch
+gcc-15.patch
+fortify.patch
=====================================
debian/upstream/metadata
=====================================
@@ -17,3 +17,5 @@ Registry:
Entry: OMICS_15837
- Name: bio.tools
Entry: NA
+Repository: https://www.life.illinois.edu/gary/programs/fastDNAml/
+Bug-Submit: Gary J. Olsen <gjo☮illinois.edu>
=====================================
debian/watch
=====================================
@@ -1,3 +1,3 @@
version=4
-opts=dversionmangle=s/.*/0.No-Site/ \
- https://people.debian.org/~eriberto/ FakeWatchNoUpstreamSiteForThisPackage-(\d\S+)\.gz
+https://www.life.illinois.edu/gary/programs/fastDNAml/ \
+fastDNAml_ at ANY_VERSION@@ARCHIVE_EXT@
View it on GitLab: https://salsa.debian.org/med-team/fastdnaml/-/compare/328cd4712d4cb334811b03ec24535a6a8fc61d94...68aa6e1ff7d9cd3b8157dfb1b5aa586c12d0e4d2
--
View it on GitLab: https://salsa.debian.org/med-team/fastdnaml/-/compare/328cd4712d4cb334811b03ec24535a6a8fc61d94...68aa6e1ff7d9cd3b8157dfb1b5aa586c12d0e4d2
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