[med-svn] [Git][med-team/lagan][master] 12 commits: Upload to unstable
Andreas Tille
gitlab at salsa.debian.org
Tue Dec 4 08:04:03 GMT 2018
Andreas Tille pushed to branch master at Debian Med / lagan
Commits:
09812601 by Andreas Tille at 2018-12-02T21:40:24Z
Upload to unstable
- - - - -
71b92c2f by Andreas Tille at 2018-12-02T21:40:40Z
debhelper 11
- - - - -
3c5a27ea by Andreas Tille at 2018-12-02T21:40:42Z
Drop useless get-orig-source target
- - - - -
0dc7910c by Andreas Tille at 2018-12-02T21:40:42Z
Remove trailing whitespace in debian/changelog
- - - - -
690958f2 by Andreas Tille at 2018-12-02T21:42:25Z
Upload to unstable
- - - - -
b65e0e9f by Andreas Tille at 2018-12-04T07:35:16Z
Move /usr/bin/chaos to /usr/lib/lagan/bin
- - - - -
295d7b08 by Andreas Tille at 2018-12-04T07:35:49Z
cme formatting
- - - - -
0b1ab79a by Andreas Tille at 2018-12-04T07:43:56Z
Typo
- - - - -
271492d9 by Andreas Tille at 2018-12-04T07:49:21Z
Propagate hardening and debug options
- - - - -
d14516f7 by Andreas Tille at 2018-12-04T07:52:52Z
Fix renaming chaos -> lagan_chaos
- - - - -
290e2360 by Andreas Tille at 2018-12-04T07:54:05Z
Fix hardening patch
- - - - -
34f05f0f by Andreas Tille at 2018-12-04T07:57:12Z
DEP3
- - - - -
13 changed files:
- + debian/README.Debian
- debian/changelog
- debian/compat
- debian/control
- debian/lagan.install
- + debian/lagan.links
- debian/lagan.lintian-overrides
- debian/patches/addTest.patch
- debian/patches/adjustPerlPaths.patch
- debian/patches/ambiuousEnd.patch
- + debian/patches/hardening.patch
- debian/patches/series
- debian/rules
Changes:
=====================================
debian/README.Debian
=====================================
@@ -0,0 +1,18 @@
+lagan for Debian
+================
+
+There is a name space conflict with EMBOSS (see bug #914687). This is
+specifically unfortunate since both packages are from the field of
+bioinformatics and it should be avoided. (Remark: I even think that the
+choice of /usr/bin/chaos is a bit unfortunate in general since it is
+quite a generic name.)
+
+In Debian the package that has occupied a name first usually wins and
+the other package has to rename. In this case I also think that EMBOSS
+is quite famous and has lots of users (according to Debian popularity
+contest which is measuring the number of users of a package). Thus we
+need to choose a different name for chaos provided by lagan.
+
+For the moment this is solved by moving /usr/bin/chaos to
+/usr/lib/lagan/bin/chaos and provide a symlink /usr/bin/lagan_chaos.
+
=====================================
debian/changelog
=====================================
@@ -1,3 +1,16 @@
+lagan (2.0-3) unstable; urgency=medium
+
+ * Upload to unstable
+ * debhelper 11
+ * Drop useless get-orig-source target
+ * Remove trailing whitespace in debian/changelog
+ * Move /usr/bin/chaos to /usr/lib/lagan/bin
+ Closes: #914687
+ * debian/README.Debian: Document move of /usr/bin/chaos
+ * Propagate hardening and debug options
+
+ -- Andreas Tille <tille at debian.org> Tue, 04 Dec 2018 08:36:52 +0100
+
lagan (2.0-2) experimental; urgency=low
* Initial release to experimental to invite peer review (Closes: #908215).
@@ -21,7 +34,7 @@ lagan (2.0-1) UNRELEASED; urgency=low
- permissions
- hardening
- testing
-
+
* Moved packaging from SVN to Git
-- Andreas Tille <tille at debian.org> Fri, 15 Nov 2013 10:31:20 +0100
=====================================
debian/compat
=====================================
@@ -1 +1 @@
-10
+11
=====================================
debian/control
=====================================
@@ -1,9 +1,10 @@
Source: lagan
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
-Uploaders: Andreas Tille <tille at debian.org>, Steffen Moeller <moeller at debian.org>
+Uploaders: Andreas Tille <tille at debian.org>,
+ Steffen Moeller <moeller at debian.org>
Section: science
Priority: optional
-Build-Depends: debhelper (>= 10),
+Build-Depends: debhelper (>= 11~),
libboost-dev
Standards-Version: 4.2.1
Vcs-Browser: https://salsa.debian.org/med-team/lagan
=====================================
debian/lagan.install
=====================================
@@ -1,5 +1,5 @@
anchors usr/bin
-chaos usr/bin
+chaos usr/lib/lagan/bin
glocal usr/bin
mlagan usr/bin
prolagan usr/bin
=====================================
debian/lagan.links
=====================================
@@ -0,0 +1 @@
+usr/lib/lagan/bin/chaos usr/bin/lagan_chaos
=====================================
debian/lagan.lintian-overrides
=====================================
@@ -9,7 +9,7 @@ lagan: script-with-language-extension usr/bin/supermap.pl
lagan: script-with-language-extension usr/bin/xmfa2mfa.pl
lagan: binary-without-manpage usr/bin/anal_gloc.pl
lagan: binary-without-manpage usr/bin/anchors
-lagan: binary-without-manpage usr/bin/chaos
+lagan: binary-without-manpage usr/bin/lagan_chaos
lagan: binary-without-manpage usr/bin/glocal
lagan: binary-without-manpage usr/bin/lagan.pl
lagan: binary-without-manpage usr/bin/order
=====================================
debian/patches/addTest.patch
=====================================
@@ -1,3 +1,7 @@
+Author: Steffen Moeller
+Last-Update: 2018-09-07 15:08:19 +0200
+Description: Add primitive build time test
+
Index: lagan/Makefile
===================================================================
--- lagan.orig/Makefile
=====================================
debian/patches/adjustPerlPaths.patch
=====================================
@@ -1,3 +1,7 @@
+Author: Steffen Moeller
+Last-Update: 2018-09-07 15:08:19 +0200
+Description: Adjust Perl path
+
Index: lagan/anal_gloc.pl
===================================================================
--- lagan.orig/anal_gloc.pl
=====================================
debian/patches/ambiuousEnd.patch
=====================================
@@ -1,3 +1,7 @@
+Author: Steffen Moeller
+Last-Update: 2018-09-07 15:08:19 +0200
+Description: Fix build issue
+
Index: lagan/src/glocal/rightinfluence.cpp
===================================================================
--- lagan.orig/src/glocal/rightinfluence.cpp
=====================================
debian/patches/hardening.patch
=====================================
@@ -0,0 +1,83 @@
+Description: Propagate hardening options
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Tue, 04 Dec 2018 08:36:52 +0100
+
+--- a/src/Makefile
++++ b/src/Makefile
+@@ -1,6 +1,6 @@
+ CC = gcc $(CFLAGS)
+ CPP = g++ $(CFLAGS)
+-CFLAGS = -O3 # -Wall -W
++CFLAGS += -O3 # -Wall -W
+ TRGT_DIR = ..
+
+ all: ../anchors ../chaos ../order ../mlagan ../prolagan ../utils/bin2mf ../utils/bin2bl ../utils/cextract ../utils/cstat ../utils/contigorder ../utils/getbounds ../utils/getlength ../utils/getoverlap ../utils/rc ../utils/seqmerge ../utils/scorealign ../utils/scorecontigs ../utils/getcontigpos ../utils/fa2xfa ../utils/Glue ../utils/dotplot ../utils/overlay
+@@ -9,46 +9,46 @@ clean:
+ rm -f *.o *~ utils/*~ mlagan.purify core
+ (cd glocal; $(MAKE) clean)
+ ../anchors: anchors.c skiplist.c
+- $(CC) -o $(TRGT_DIR)/anchors anchors.c skiplist.c
++ $(CC) -o $(TRGT_DIR)/anchors anchors.c skiplist.c $(LDFLAGS)
+ ../chaos: fchaos.c thrtrie.c skiplist.c global.c translate.c mempage.c filebuffer.c
+- $(CC) -o $(TRGT_DIR)/chaos fchaos.c thrtrie.c skiplist.c global.c translate.c filebuffer.c -lm -DCHAOS__FLAG
++ $(CC) -o $(TRGT_DIR)/chaos fchaos.c thrtrie.c skiplist.c global.c translate.c filebuffer.c -lm -DCHAOS__FLAG $(LDFLAGS)
+ ../order: order.c diagmatrix.c filebuffer.c
+- $(CC) -o $(TRGT_DIR)/order order.c diagmatrix.c filebuffer.c
++ $(CC) -o $(TRGT_DIR)/order order.c diagmatrix.c filebuffer.c $(LDFLAGS)
+ ../mlagan: mlagan.c diagmatrix.c multial.c skiplist.c filebuffer.c
+- $(CC) -o $(TRGT_DIR)/mlagan mlagan.c multial.c diagmatrix.c skiplist.c filebuffer.c -lm -DMULTIAL__FLAG
++ $(CC) -o $(TRGT_DIR)/mlagan mlagan.c multial.c diagmatrix.c skiplist.c filebuffer.c -lm -DMULTIAL__FLAG $(LDFLAGS)
+ ../prolagan: prolagan.c diagmatrix.c multial.c skiplist.c filebuffer.c
+- $(CC) -o $(TRGT_DIR)/prolagan prolagan.c multial.c diagmatrix.c skiplist.c filebuffer.c -lm -DMULTIAL__FLAG
++ $(CC) -o $(TRGT_DIR)/prolagan prolagan.c multial.c diagmatrix.c skiplist.c filebuffer.c -lm -DMULTIAL__FLAG $(LDFLAGS)
+ ../utils/bin2mf: utils/bin2mf.c
+- $(CC) -o $(TRGT_DIR)/utils/bin2mf utils/bin2mf.c
++ $(CC) -o $(TRGT_DIR)/utils/bin2mf utils/bin2mf.c $(LDFLAGS)
+ ../utils/bin2bl: utils/bin2bl.c
+- $(CC) -o $(TRGT_DIR)/utils/bin2bl utils/bin2bl.c
++ $(CC) -o $(TRGT_DIR)/utils/bin2bl utils/bin2bl.c $(LDFLAGS)
+ ../utils/cextract: utils/cextract.c
+- $(CC) -o $(TRGT_DIR)/utils/cextract utils/cextract.c
++ $(CC) -o $(TRGT_DIR)/utils/cextract utils/cextract.c $(LDFLAGS)
+ ../utils/cstat: utils/cstat.c
+- $(CC) -o $(TRGT_DIR)/utils/cstat utils/cstat.c
++ $(CC) -o $(TRGT_DIR)/utils/cstat utils/cstat.c $(LDFLAGS)
+ ../utils/contigorder: utils/contigorder.c
+- $(CC) -o $(TRGT_DIR)/utils/contigorder utils/contigorder.c
++ $(CC) -o $(TRGT_DIR)/utils/contigorder utils/contigorder.c $(LDFLAGS)
+ ../utils/getbounds: utils/getbounds.c
+- $(CC) -o $(TRGT_DIR)/utils/getbounds utils/getbounds.c
++ $(CC) -o $(TRGT_DIR)/utils/getbounds utils/getbounds.c $(LDFLAGS)
+ ../utils/getcontigpos: utils/getcontigpos.c
+- $(CC) -o $(TRGT_DIR)/utils/getcontigpos utils/getcontigpos.c
++ $(CC) -o $(TRGT_DIR)/utils/getcontigpos utils/getcontigpos.c $(LDFLAGS)
+ ../utils/getlength: utils/getlength.c
+- $(CC) -o $(TRGT_DIR)/utils/getlength utils/getlength.c
++ $(CC) -o $(TRGT_DIR)/utils/getlength utils/getlength.c $(LDFLAGS)
+ ../utils/getoverlap: utils/getoverlap.c
+- $(CC) -o $(TRGT_DIR)/utils/getoverlap utils/getoverlap.c
++ $(CC) -o $(TRGT_DIR)/utils/getoverlap utils/getoverlap.c $(LDFLAGS)
+ ../utils/rc: utils/rc.c
+- $(CC) -o $(TRGT_DIR)/utils/rc utils/rc.c
++ $(CC) -o $(TRGT_DIR)/utils/rc utils/rc.c $(LDFLAGS)
+ ../utils/seqmerge: utils/seqmerge.c
+- $(CC) -o $(TRGT_DIR)/utils/seqmerge utils/seqmerge.c
++ $(CC) -o $(TRGT_DIR)/utils/seqmerge utils/seqmerge.c $(LDFLAGS)
+ ../utils/scorealign: utils/scorealign.c
+- $(CC) -o $(TRGT_DIR)/utils/scorealign utils/scorealign.c -lm
++ $(CC) -o $(TRGT_DIR)/utils/scorealign utils/scorealign.c -lm $(LDFLAGS)
+ ../utils/scorecontigs: utils/scorecontigs.c
+- $(CC) -o $(TRGT_DIR)/utils/scorecontigs utils/scorecontigs.c -lm
++ $(CC) -o $(TRGT_DIR)/utils/scorecontigs utils/scorecontigs.c -lm $(LDFLAGS)
+ ../utils/fa2xfa: utils/fa2xfa.c
+- $(CC) -o $(TRGT_DIR)/utils/fa2xfa utils/fa2xfa.c
++ $(CC) -o $(TRGT_DIR)/utils/fa2xfa utils/fa2xfa.c $(LDFLAGS)
+ ../utils/overlay: utils/overlay.c
+- $(CC) -o $(TRGT_DIR)/utils/overlay utils/overlay.c
++ $(CC) -o $(TRGT_DIR)/utils/overlay utils/overlay.c $(LDFLAGS)
+ ../utils/Glue: utils/Glue.cpp
+- $(CPP) -o $(TRGT_DIR)/utils/Glue utils/Glue.cpp
++ $(CPP) -o $(TRGT_DIR)/utils/Glue utils/Glue.cpp $(LDFLAGS)
+ ../utils/dotplot: utils/dotplot.cpp
+- $(CPP) -o $(TRGT_DIR)/utils/dotplot utils/dotplot.cpp
++ $(CPP) -o $(TRGT_DIR)/utils/dotplot utils/dotplot.cpp $(LDFLAGS)
=====================================
debian/patches/series
=====================================
@@ -3,3 +3,4 @@ gcc-4.8.patch
ambiuousEnd.patch
addTest.patch
adjustPerlPaths.patch
+hardening.patch
=====================================
debian/rules
=====================================
@@ -5,9 +5,8 @@
%:
dh $@
-get-orig-source:
- mkdir -p ../tarballs
- uscan --verbose --force-download --repack-compression xz --destdir=../tarballs
+override_dh_auto_build:
+ dh_auto_build --sourcedirectory=src
override_dh_auto_clean:
dh_auto_clean
View it on GitLab: https://salsa.debian.org/med-team/lagan/compare/690c74bd2f44de1a70375de1107789db15357798...34f05f0f3291c4b5e06b71770a619a26c9fb2601
--
View it on GitLab: https://salsa.debian.org/med-team/lagan/compare/690c74bd2f44de1a70375de1107789db15357798...34f05f0f3291c4b5e06b71770a619a26c9fb2601
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