[med-svn] [Git][med-team/altree][master] 9 commits: d/watch: bump to v5 and git mode.
Étienne Mollier (@emollier)
gitlab at salsa.debian.org
Tue Sep 16 21:58:54 BST 2025
Étienne Mollier pushed to branch master at Debian Med / altree
Commits:
5de15dc8 by Étienne Mollier at 2025-09-16T19:48:18+02:00
d/watch: bump to v5 and git mode.
The gitlab instance looks to be running on top of an older version
which is not yet supported by uscan's gitlab template. Therefore,
let's move to plain git ls-remote itself.
- - - - -
dbd23bdf by Étienne Mollier at 2025-09-16T19:51:21+02:00
d/control: build depends on perl-xs-dev.
Closes: #1102872
- - - - -
81d8cf53 by Étienne Mollier at 2025-09-16T20:11:23+02:00
gcc-15.patch: new: fix ftbfs with GCC-15.
Closes: #1096300
- - - - -
7dee8c24 by Étienne Mollier at 2025-09-16T20:15:48+02:00
typo.patch: new: fix "allows to" typo caught by lintian.
- - - - -
b8c69545 by Étienne Mollier at 2025-09-16T20:55:14+02:00
d/rules: isolate documentation specific rules.
- - - - -
b7575a38 by Étienne Mollier at 2025-09-16T20:55:48+02:00
d/control: adjust build-dependencies for cross-compilation.
- - - - -
11fc5f7d by Étienne Mollier at 2025-09-16T20:56:42+02:00
d/rules: convert various Perl scripts to UTF-8.
- - - - -
374680b2 by Étienne Mollier at 2025-09-16T22:55:35+02:00
d/control: declare compliance to standards version 4.7.2.
- - - - -
1ba12652 by Étienne Mollier at 2025-09-16T22:58:09+02:00
d/changelog: ready for upload to unstable.
- - - - -
7 changed files:
- debian/changelog
- debian/control
- + debian/patches/gcc-15.patch
- + debian/patches/series
- + debian/patches/typo.patch
- debian/rules
- debian/watch
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,20 @@
+altree (1.3.2-3) unstable; urgency=medium
+
+ * Team upload.
+ * gcc-15.patch: new: fix ftbfs with GCC-15. (Closes: #1096300)
+ * d/control: build depends on perl-xs-dev. (Closes: #1102872)
+ * d/control: adjust build-dependencies for cross-compilation.
+ * d/rules: isolate documentation specific rules.
+ * typo.patch: new: fix "allows to" typo caught by lintian.
+ * d/rules: convert various Perl scripts to UTF-8.
+ * d/control: declare compliance to standards version 4.7.2.
+ * d/watch: bump to v5 and git mode.
+ The gitlab instance looks to be running on top of an older version
+ which is not yet supported by uscan's gitlab template. Therefore,
+ let's move to plain git ls-remote itself.
+
+ -- Étienne Mollier <emollier at debian.org> Tue, 16 Sep 2025 22:55:54 +0200
+
altree (1.3.2-2) unstable; urgency=medium
* Alternative to libblas-dev | libblas.so
=====================================
debian/control
=====================================
@@ -7,18 +7,20 @@ Section: science
Priority: optional
Build-Depends: bash-completion,
debhelper-compat (= 13),
- latex-make,
- ghostscript,
- texlive-lang-french,
- texlive-latex-extra,
- texlive-latex-recommended,
- texlive-fonts-recommended,
- libmath-tamuanova-perl,
+ perl:native,
+ perl-xs-dev,
+ latex-make <!nodoc>,
+ ghostscript <!nodoc>,
+ texlive-lang-french <!nodoc>,
+ texlive-latex-extra <!nodoc>,
+ texlive-latex-recommended <!nodoc>,
+ texlive-fonts-recommended <!nodoc>,
+ libmath-tamuanova-perl <!nocheck>,
libgsl-dev,
libblas-dev | libblas.so,
- libtest-deep-perl,
- fig2dev
-Standards-Version: 4.6.2
+ libtest-deep-perl <!nocheck>,
+ fig2dev <!nodoc>
+Standards-Version: 4.7.2
Vcs-Browser: https://salsa.debian.org/med-team/altree
Vcs-Git: https://salsa.debian.org/med-team/altree.git
Homepage: https://gitlab.inria.fr/NGS/ALTree
=====================================
debian/patches/gcc-15.patch
=====================================
@@ -0,0 +1,40 @@
+Description: fix build failures with gcc-15.
+Author: Étienne Mollier <emollier at debian.org>
+Bug-Debian: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1096300
+Forwarded: no
+Last-Update: 2025-09-16
+---
+This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
+--- altree.orig/CUtils/c_sources/chisq.c
++++ altree/CUtils/c_sources/chisq.c
+@@ -23,8 +23,8 @@
+ #define BIGX 20.0 /* max value to represent exp (x) */
+ #define ex(x) (((x) < -BIGX) ? 0.0 : exp (x))
+
+-double pochisq ();
+-double critchi ();
++double pochisq (double, int);
++double critchi (double, int);
+
+ #ifdef CHISQTEST
+ double Prob[] = { .10, .05, .01, .005, .001, -1.0 };
+@@ -80,7 +80,7 @@
+ {
+ double a, y, s;
+ double e, c, z;
+- double poz (); /* computes probability of normal z score */
++ double poz (double); /* computes probability of normal z score */
+ int even; /* true if df is an even number */
+
+ if (x <= 0.0 || df < 1)
+--- altree.orig/CUtils/c_sources/z.c
++++ altree/CUtils/c_sources/z.c
+@@ -94,7 +94,7 @@
+ double minz = -Z_MAX; /* minimum of range of z */
+ double maxz = Z_MAX; /* maximum of range of z */
+ double zval = 0.0; /* computed/returned z value */
+- double poz (), pval; /* prob (z) function, pval := poz (zval) */
++ double poz (double), pval; /* prob (z) function, pval := poz (zval) */
+
+ if (p <= 0.0 || p >= 1.0)
+ return (0.0);
=====================================
debian/patches/series
=====================================
@@ -0,0 +1,2 @@
+gcc-15.patch
+typo.patch
=====================================
debian/patches/typo.patch
=====================================
@@ -0,0 +1,17 @@
+Description: fix an "allows to" typo caught by lintian.
+Author: Étienne Mollier <emollier at debian.org>
+Forwarded: no
+Last-Update: 2025-09-16
+---
+This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
+--- altree.orig/progs/altree
++++ altree/progs/altree
+@@ -1920,7 +1920,7 @@
+
+ (a) an association test between a candidate gene and disease or a quantitative trait
+
+-(b) a localsation tests: it allows to detect which SNP is involved in the determinism of the disease or the quantitative trait
++(b) a localsation tests: it detects which SNP is involved in the determinism of the disease or the quantitative trait
+
+ These two tests are based on the analysis of haplotype phylogenetic trees.
+
=====================================
debian/rules
=====================================
@@ -7,13 +7,24 @@
%:
dh $@
-override_dh_auto_clean:
+ifeq (,$(filter nodoc,$(DEB_BUILD_OPTIONS)))
+execute_before_dh_auto_clean:
$(MAKE) -C Documentation distclean || true
- dh_auto_clean
-override_dh_auto_build:
+execute_before_dh_auto_build:
$(MAKE) -C Documentation pdf
- dh_auto_build
override_dh_compress:
dh_compress --exclude=.pdf
+endif # !nodoc
+
+INSTALL_DIR != echo debian/altree/usr/lib/*/perl*/*/ALTree/
+NATIONAL_ENCODING = Chi2.pm Import.pm Input.pm Node.pm SitePerForet.pm
+NATIONAL_ENCODING+= SiteSensPerTree.pm Tree.pm to_rewrite.pm
+execute_after_dh_install:
+ set -e \
+ ; cd $(INSTALL_DIR) \
+ ; for file in $(NATIONAL_ENCODING) \
+ ; do iconv -f ISO-8859-1 -t UTF-8 < "$${file}" > "$${file}.conv" \
+ ; mv -v "$${file}.conv" "$${file}" \
+ ; done
=====================================
debian/watch
=====================================
@@ -1,5 +1,5 @@
-version=4
+Version: 5
-https://gitlab.inria.fr/NGS/ALTree/tags .*/v[0-9.]*/ALTree-v at ANY_VERSION@\.tar\.gz
-
-# https://gitlab.inria.fr/NGS/ALTree/repository/v1.3.1/archive.tar.gz
+Source: https://gitlab.inria.fr/NGS/ALTree.git
+Mode: git
+Matching-Pattern: refs/tags/@ANY_VERSION@
View it on GitLab: https://salsa.debian.org/med-team/altree/-/compare/a8c999afa36ed30426b3f9f878cb6463c8152d2d...1ba126525f1968a237e203b175f62fea669dfd27
--
View it on GitLab: https://salsa.debian.org/med-team/altree/-/compare/a8c999afa36ed30426b3f9f878cb6463c8152d2d...1ba126525f1968a237e203b175f62fea669dfd27
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