[med-svn] [Git][med-team/paml][master] 4 commits: d/control: add myself to uploaders.
Étienne Mollier (@emollier)
gitlab at salsa.debian.org
Mon Jul 15 21:52:31 BST 2024
Étienne Mollier pushed to branch master at Debian Med / paml
Commits:
9d43d5d4 by Étienne Mollier at 2024-07-15T21:14:54+02:00
d/control: add myself to uploaders.
- - - - -
43d36275 by Étienne Mollier at 2024-07-15T21:15:09+02:00
d/control: declare compliance to standards version 4.7.0.
- - - - -
b361d4fa by Étienne Mollier at 2024-07-15T22:45:52+02:00
gcc14.patch: new: fix incompatible pointer type conversions.
Closes: #1075359
- - - - -
99582ce9 by Étienne Mollier at 2024-07-15T22:51:54+02:00
ready to upload to unstable.
- - - - -
4 changed files:
- debian/changelog
- debian/control
- + debian/patches/gcc14.patch
- debian/patches/series
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,12 @@
+paml (4.9j+dfsg-5) unstable; urgency=medium
+
+ * d/control: add myself to uploaders.
+ * d/control: declare compliance to standards version 4.7.0.
+ * gcc14.patch: new: fix incompatible pointer type conversions.
+ (Closes: #1075359)
+
+ -- Étienne Mollier <emollier at debian.org> Mon, 15 Jul 2024 22:46:05 +0200
+
paml (4.9j+dfsg-4) unstable; urgency=medium
* Team upload.
=====================================
debian/control
=====================================
@@ -2,11 +2,12 @@ Source: paml
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
Uploaders: Pjotr Prins <pjotr.debian at thebird.nl>,
Steffen Moeller <moeller at debian.org>,
- Andreas Tille <tille at debian.org>
+ Andreas Tille <tille at debian.org>,
+ Étienne Mollier <emollier at debian.org>
Section: science
Priority: optional
Build-Depends: debhelper-compat (= 13)
-Standards-Version: 4.6.2
+Standards-Version: 4.7.0
Vcs-Browser: https://salsa.debian.org/med-team/paml
Vcs-Git: https://salsa.debian.org/med-team/paml.git
Homepage: http://abacus.gene.ucl.ac.uk/software/paml.html
=====================================
debian/patches/gcc14.patch
=====================================
@@ -0,0 +1,81 @@
+Description: fix incompatible pointer types with gcc 14.
+ This patch fixes a number of build failures caused by incompatible
+ pointer types, now fatal with gcc 14. Typical symptom looks like:
+ .
+ In file included from baseml.c:131:
+ treesub.c: In function ‘IdenticalSeqs’:
+ In file included from codeml.c:238:
+ treesub.c: In function ‘IdenticalSeqs’:
+ treesub.c:1310:33: error: passing argument 3 of ‘printSeqs’ from incompatible pointer type [-Wincompatible-pointer-types]
+ 1310 | printSeqs(ftmp, com.z, com.spname, com.ns, com.ls, com.npatt, com.fpatt, NULL, keep, 1);
+ | ~~~^~~~~~~
+ | |
+ | char **
+ In file included from baseml.c:11:
+ paml.h:150:63: note: expected ‘unsigned char **’ but argument is of type ‘char **’
+ 150 | void printSeqs(FILE *fout, unsigned char *z[], unsigned char *spnames[], int ns, int ls, int npatt, double fpatt[], int *pose, char keep[], int format);
+ | ~~~~~~~~~~~~~~~^~~~~~~~~
+ treesub.c:1310:33: error: passing argument 3 of ‘printSeqs’ from incompatible pointer type [-Wincompatible-pointer-types]
+ 1310 | printSeqs(ftmp, com.z, com.spname, com.ns, com.ls, com.npatt, com.fpatt, NULL, keep, 1);
+ | ~~~^~~~~~~
+ | |
+ | char **
+ .
+ Every time when a change was needed, the plain "char" type was favored
+ over the "unsigned char" type. This is to allow the compiler to set
+ the optimum char signature depending on the target CPU architecture
+ (e.g. signed char for x86_64, unsigned char for Aarch64).
+
+Author: Étienne Mollier <emollier at debian.org>
+Bug-Debian: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1075359
+Forwarded: no
+Last-Update: 2024-07-15
+---
+This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
+--- paml.orig/src/paml.h
++++ paml/src/paml.h
+@@ -147,7 +147,7 @@
+ int PickExtreme (FILE *fout, char z[], int ls, int iring, int lfrag, int ffrag[]);
+
+ int print1seq (FILE*fout, unsigned char *z, int ls, int pose[]);
+-void printSeqs(FILE *fout, unsigned char *z[], unsigned char *spnames[], int ns, int ls, int npatt, double fpatt[], int *pose, char keep[], int format);
++void printSeqs(FILE *fout, unsigned char *z[], char *spnames[], int ns, int ls, int npatt, double fpatt[], int *pose, char keep[], int format);
+ int printPatterns(FILE *fout);
+ void printSeqsMgenes (void);
+ int printsma (FILE*fout, char*spname[], unsigned char*z[], int ns, int l, int lline, int gap, int seqtype,
+--- paml.orig/src/basemlg.c
++++ paml/src/basemlg.c
+@@ -40,7 +40,9 @@
+ int lfunG_dd (double x[], double *lnL, double dl[], double ddl[], int np);
+
+ struct CommonInfo {
+- unsigned char *z[NS], *spname[NS], seqf[2048],outf[2048],treef[2048];
++ unsigned char *z[NS];
++ char *spname[NS];
++ unsigned char seqf[2048],outf[2048],treef[2048];
+ int seqtype, ns, ls, ngene, posG[NGENE+1],lgene[NGENE],*pose,npatt, readpattern;
+ int clock,fix_alpha,fix_kappa,fix_rgene,Malpha,print,verbose;
+ int model, runmode, cleandata, ndata;
+--- paml.orig/src/treesub.c
++++ paml/src/treesub.c
+@@ -1881,7 +1881,7 @@
+ return(0);
+ }
+
+-void printSeqs(FILE *fout, unsigned char *z[], unsigned char *spnames[], int ns, int ls, int npatt, double fpatt[], int *pose, char keep[], int format)
++void printSeqs(FILE *fout, unsigned char *z[], char *spnames[], int ns, int ls, int npatt, double fpatt[], int *pose, char keep[], int format)
+ {
+ /* Print sequences into fout, using paml (format=0 or 1) or NEXUS (format=2)
+ formats.
+--- paml.orig/src/evolver.c
++++ paml/src/evolver.c
+@@ -36,7 +36,8 @@
+
+ struct CommonInfo {
+ unsigned char *z[2 * NS - 1];
+- unsigned char *spname[NS], daafile[512], cleandata, readpattern;
++ char *spname[NS];
++ unsigned char daafile[512], cleandata, readpattern;
+ int ns, ls, npatt, np, ntime, ncode, clock, rooted, model, icode;
+ int seqtype, *pose, ncatG, NSsites;
+ int ngene, lgene[1], posG[1 + 1]; /* not used */
=====================================
debian/patches/series
=====================================
@@ -1,3 +1,4 @@
gcc10.patch
hardening.patch
add_clean_target.patch
+gcc14.patch
View it on GitLab: https://salsa.debian.org/med-team/paml/-/compare/08c44059474c874022bdd1061feb0a04162d4e2e...99582ce9e8505df06553d8db05d923b1e4d5e83d
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