[med-svn] [Git][med-team/mcl][master] 7 commits: Add Origin to OCaml patch
Andreas Tille (@tille)
gitlab at salsa.debian.org
Wed Nov 2 12:59:34 GMT 2022
Andreas Tille pushed to branch master at Debian Med / mcl
Commits:
e8df448f by Andreas Tille at 2022-11-02T13:27:25+01:00
Add Origin to OCaml patch
- - - - -
a32f7abf by Andreas Tille at 2022-11-02T13:36:22+01:00
Deactivate OCaml patch
- - - - -
6f4a0d49 by Andreas Tille at 2022-11-02T13:38:08+01:00
There is no /usr/local we need to respect
- - - - -
9c518ddd by Andreas Tille at 2022-11-02T13:42:44+01:00
There is no minimcl doc any more, but install the script anyway
- - - - -
91ff2767 by Andreas Tille at 2022-11-02T13:54:05+01:00
Drop some doc-base files where doc was removed
- - - - -
56ee0cba by Andreas Tille at 2022-11-02T13:55:12+01:00
lintian-overrides for script-with-language-extension
- - - - -
09e39c4d by Andreas Tille at 2022-11-02T13:58:52+01:00
Upload to unstable
- - - - -
12 changed files:
- debian/changelog
- debian/control
- − debian/libmcl-ocaml-dev.install
- − debian/mcl-doc.doc-base.clmformat
- − debian/mcl-doc.doc-base.mclpipeline
- − debian/mcl-doc.doc-base.mcxassemble
- debian/mcl-doc.install
- debian/mcl.install
- + debian/mcl.lintian-overrides
- debian/patches/OCamlSupport.patch
- debian/patches/series
- debian/rules
Changes:
=====================================
debian/changelog
=====================================
@@ -1,11 +1,15 @@
-mcl (1:22-282+ds-1) UNRELEASED; urgency=medium
+mcl (1:22-282+ds-1) unstable; urgency=medium
* New upstream version
* Standards-Version: 4.6.1 (routine-update)
* Remove trailing whitespace in debian/copyright (routine-update)
* Build-Depends: libtingea-dev
+ * Deactivate OCaml patch
+ * There is no minimcl doc any more, but install the script anyway
+ * Drop some doc-base files where doc was removed
+ * lintian-overrides for script-with-language-extension
- -- Andreas Tille <tille at debian.org> Wed, 12 Oct 2022 18:03:54 +0200
+ -- Andreas Tille <tille at debian.org> Wed, 02 Nov 2022 13:57:43 +0100
mcl (1:14-137+ds-9) unstable; urgency=medium
=====================================
debian/control
=====================================
@@ -5,16 +5,10 @@ Uploaders: Andreas Tille <tille at debian.org>,
Section: math
Priority: optional
Build-Depends: debhelper-compat (= 13),
- dh-ocaml,
zoem,
tidy,
aephea,
- ocaml,
- ocamlbuild,
- ocaml-findlib,
- oasis,
bsdextrautils | bsdmainutils (<< 12.1.1~),
- dh-exec,
libtingea-dev
Standards-Version: 4.6.1
Vcs-Browser: https://salsa.debian.org/med-team/mcl
@@ -51,19 +45,3 @@ Description: documentation for mcl
.
This is documentation for mcl: the MCL FAQ, some examples as well as manpages
in HTML and PostScript format.
-
-Package: libmcl-ocaml-dev
-Architecture: any
-Section: ocaml
-Depends: ocaml-findlib,
- mcl,
- ${ocaml:Depends},
- ${shlibs:Depends},
- ${misc:Depends}
-Provides: ${ocaml:Provides}
-Description: library providing bindings between mcl and OCaml
- The MCL package is an implementation of the MCL algorithm, and offers
- utilities for manipulating sparse matrices (the essential data
- structure in the MCL algorithm) and conducting cluster experiments.
- .
- This library provides bindings between mcl and OCaml.
=====================================
debian/libmcl-ocaml-dev.install deleted
=====================================
@@ -1,4 +0,0 @@
-#!/usr/bin/dh-exec
-_build/caml/* usr/lib/ocaml
-caml/META usr/lib/ocaml/mcl
-src/*/*.a usr/lib/${DEB_HOST_MULTIARCH}
=====================================
debian/mcl-doc.doc-base.clmformat deleted
=====================================
@@ -1,12 +0,0 @@
-Document: clmformat
-Title: clmformat - display cluster results in readable form
-Author: Stijn van Dongen
-Abstract: A document describing the clmformat command line tool.
-Section: Science/Mathematics
-
-Format: PostScript
-Files: /usr/share/doc/mcl/clmformat.ps.gz
-
-Format: HTML
-Index: /usr/share/doc/mcl/html/clmformat.html
-Files: /usr/share/doc/mcl/html/clmformat.html
=====================================
debian/mcl-doc.doc-base.mclpipeline deleted
=====================================
@@ -1,13 +0,0 @@
-Document: mclpipeline
-Title: mclpipeline - a generic pipeline for generating and scrutinizing mcl
- clusterings
-Author: Stijn van Dongen
-Abstract: A document describing the mclpipeline command line tool.
-Section: Science/Mathematics
-
-Format: PostScript
-Files: /usr/share/doc/mcl/mclpipeline.ps.gz
-
-Format: HTML
-Index: /usr/share/doc/mcl/html/mclpipeline.html
-Files: /usr/share/doc/mcl/html/mclpipeline.html
=====================================
debian/mcl-doc.doc-base.mcxassemble deleted
=====================================
@@ -1,12 +0,0 @@
-Document: mcxassemble
-Title: mcxassemble - transform raw cooccurrence data to mcl matrix format
-Author: Stijn van Dongen
-Abstract: A document describing the mcxassemble command line tool.
-Section: Science/Mathematics
-
-Format: PostScript
-Files: /usr/share/doc/mcl/mcxassemble.ps.gz
-
-Format: HTML
-Index: /usr/share/doc/mcl/html/mcxassemble.html
-Files: /usr/share/doc/mcl/html/mcxassemble.html
=====================================
debian/mcl-doc.install
=====================================
@@ -1,5 +1,4 @@
usr/share/doc/mcl/*.html usr/share/doc/mcl/html
usr/share/doc/mcl/*.ps usr/share/doc/mcl/
-usr/share/doc/mcl/minimcl usr/share/doc/mcl/
debian/tests/run-unit-tests usr/share/doc/mcl/
debian/tests/data/* usr/share/doc/mcl/test
=====================================
debian/mcl.install
=====================================
@@ -1,2 +1,3 @@
usr/bin
scripts/clx* usr/share/doc/mcl/scripts
+scripts/minimcl usr/share/doc/mcl/scripts
=====================================
debian/mcl.lintian-overrides
=====================================
@@ -0,0 +1,2 @@
+# see https://lists.debian.org/debian-med/2018/06/msg00043.html
+mcl: script-with-language-extension
=====================================
debian/patches/OCamlSupport.patch
=====================================
@@ -1,7 +1,14 @@
Description: add OCaml support
- Add OCaml support. This patch has been generated by taking the diff of an mcl clone that has implemented OCaml support and upstream's version of mcl 12-068, stripping out unnecessary changes and refreshing it over the Debian mcl packed version 14-137.
+ Add OCaml support. This patch has been generated by taking the diff of an mcl
+ clone that has implemented OCaml support and upstream's version of mcl 12-068,
+ stripping out unnecessary changes and refreshing it over the Debian mcl packed
+ version 14-137.
+ .
+ This patch is deactivated since it does not work any more.
Author: Shayan Doust <hello at shayandoust.me>
Last-Update: 2020-06-02
+Origin: https://github.com/fhcrc/mcl
+
---
--- /dev/null
+++ b/_oasis
=====================================
debian/patches/series
=====================================
@@ -1,4 +1,4 @@
-OCamlSupport.patch
+# OCamlSupport.patch
02-wrong-interpreter-path.patch
05-manual-what-is.patch
spelling.patch
=====================================
debian/rules
=====================================
@@ -60,7 +60,7 @@ confflags += --enable-blast
docbackupdir:=$(CURDIR)/debian/doc.bak
%:
- dh $@ --with ocaml
+ dh $@
override_dh_clean:
dh_clean
@@ -69,18 +69,10 @@ override_dh_clean:
rm -rf doc/*.1 doc/*.html doc/*-html doc/*.ps
rm -rf src/alien/oxygen/doc/*.1 src/alien/oxygen/doc/*.html src/alien/oxygen/doc/*.ps
-override_dh_auto_build:
- #dh_auto_build
- autoreconf --install
- oasis setup
- ocaml setup.ml -all
-
override_dh_auto_configure:
dh_auto_configure -- $(confflags)
override_dh_install:
- mv debian/tmp/usr/local/* debian/tmp/usr
- rm -rf debian/tmp/usr/local
dh_install
for pl in `grep -Rl '#![[:space:]]*/usr/bin/env[[:space:]]\+perl' debian/*/usr/*` ; do \
sed -i '1s?^#![[:space:]]*/usr/bin/env[[:space:]]\+perl?#!/usr/bin/perl?' $${pl} ; \
View it on GitLab: https://salsa.debian.org/med-team/mcl/-/compare/0320df3bbb155ae086d49222a5b28bdf5305aaa7...09e39c4da245e588aaa2b17c03b64bfff9a904c1
--
View it on GitLab: https://salsa.debian.org/med-team/mcl/-/compare/0320df3bbb155ae086d49222a5b28bdf5305aaa7...09e39c4da245e588aaa2b17c03b64bfff9a904c1
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