Steffen Möller
2015-02-10 09:47:22 UTC
Author: moeller
Date: 2015-02-10 09:47:21 +0000 (Tue, 10 Feb 2015)
New Revision: 18748
Added:
trunk/packages/fasta3/trunk/debian/fasta3.doc-base
trunk/packages/fasta3/trunk/debian/fasta3.manpages
Removed:
trunk/packages/fasta3/trunk/debian/README.Debian
trunk/packages/fasta3/trunk/debian/README.source
trunk/packages/fasta3/trunk/debian/fasta.doc-base.EX
Modified:
trunk/packages/fasta3/trunk/debian/changelog
trunk/packages/fasta3/trunk/debian/copyright
trunk/packages/fasta3/trunk/debian/docs
trunk/packages/fasta3/trunk/debian/patches/Makefile.patch
trunk/packages/fasta3/trunk/debian/rules
Log:
fasta3 - almost ready to upload
Deleted: trunk/packages/fasta3/trunk/debian/README.Debian
===================================================================
--- trunk/packages/fasta3/trunk/debian/README.Debian 2015-02-09 18:18:47 UTC (rev 18747)
+++ trunk/packages/fasta3/trunk/debian/README.Debian 2015-02-10 09:47:21 UTC (rev 18748)
@@ -1,6 +0,0 @@
-fasta for Debian
-----------------
-
-<possible notes regarding this package - if none, delete this file>
-
- -- Steffen Moeller <***@debian.org> Mon, 09 Feb 2015 15:04:28 +0100
Deleted: trunk/packages/fasta3/trunk/debian/README.source
===================================================================
--- trunk/packages/fasta3/trunk/debian/README.source 2015-02-09 18:18:47 UTC (rev 18747)
+++ trunk/packages/fasta3/trunk/debian/README.source 2015-02-10 09:47:21 UTC (rev 18748)
@@ -1,10 +0,0 @@
-fasta for Debian
-----------------
-
-<this file describes information about the source package, see Debian policy
-manual section 4.14. You WILL either need to modify or delete this file>
-
-
-
- -- Steffen Moeller <***@debian.org> Mon, 09 Feb 2015 15:04:28 +0100
-
Modified: trunk/packages/fasta3/trunk/debian/changelog
===================================================================
--- trunk/packages/fasta3/trunk/debian/changelog 2015-02-09 18:18:47 UTC (rev 18747)
+++ trunk/packages/fasta3/trunk/debian/changelog 2015-02-10 09:47:21 UTC (rev 18748)
@@ -1,5 +1,5 @@
fasta3 (36.3.7a-1) unstable; urgency=low
- * Initial release (Closes: #nnnn) <nnnn is the bug number of your ITP>
+ * Initial release (Closes: #coming)
- -- Steffen Moeller <***@debian.org> Mon, 09 Feb 2015 15:04:28 +0100
+ -- Steffen Moeller <***@debian.org> Tue, 10 Feb 2015 10:46:55 +0100
Modified: trunk/packages/fasta3/trunk/debian/copyright
===================================================================
--- trunk/packages/fasta3/trunk/debian/copyright 2015-02-09 18:18:47 UTC (rev 18747)
+++ trunk/packages/fasta3/trunk/debian/copyright 2015-02-10 09:47:21 UTC (rev 18748)
@@ -7,21 +7,29 @@
The Rector & Visitors of the University of Virginia
License: Apache-2.0
+Files: src/wm_align.c
+Copyright: William R. Pearson, University of Virginia
+ Webb Miller, Penn State University
+License: Apache-2.0
+
Files: src/karlin.c
-Copyright: 1980, 1983 Stephen Altschul
+Copyright: 1990, 1993 Stephen Altschul, NCBI
License: Apache-2.0
-Files: src/global_sse2.c
-Copyright: 2010 Michael Farrar <***@gmail.com>
-License:
- /******************************************************************
- . Copyright 2010 by Michael Farrar. All rights reserved.
- . This program may not be sold or incorporated into a commercial product,
- . in whole or in part, without written consent of Michael Farrar. For
- . further information regarding permission for use or reproduction, please
- . contact: Michael Farrar at ***@gmail.com.
- .******************************************************************/
+Files: src/smith_waterman_altivec.c
+Copyright: 2004, Erik Lindahl <***@sbc.su.se>
+ Stockholm Bioinformatics Center, 2004
+License: Apache-2.0
+Files: src/glo[bc]al_sse2.[ch]
+ src/smith_waterman_sse2.c
+Copyright: 2006,2010 Michael Farrar <***@gmail.com>
+License: Academics-only
+ This program may not be sold or incorporated into a commercial product,
+ in whole or in part, without written consent of Michael Farrar. For
+ further information regarding permission for use or reproduction, please
+ contact: Michael Farrar at ***@gmail.com.
+
Files: debian/*
Copyright: 2015 Steffen Moeller <***@debian.org>
License: Apache-2.0
Modified: trunk/packages/fasta3/trunk/debian/docs
===================================================================
--- trunk/packages/fasta3/trunk/debian/docs 2015-02-09 18:18:47 UTC (rev 18747)
+++ trunk/packages/fasta3/trunk/debian/docs 2015-02-10 09:47:21 UTC (rev 18748)
@@ -1,2 +1,5 @@
README
-doc/*
+doc/readme*
+doc/README*
+doc/changes*
+doc/fasta_guide.pdf
Deleted: trunk/packages/fasta3/trunk/debian/fasta.doc-base.EX
===================================================================
--- trunk/packages/fasta3/trunk/debian/fasta.doc-base.EX 2015-02-09 18:18:47 UTC (rev 18747)
+++ trunk/packages/fasta3/trunk/debian/fasta.doc-base.EX 2015-02-10 09:47:21 UTC (rev 18748)
@@ -1,20 +0,0 @@
-Document: fasta
-Title: Debian fasta Manual
-Author: <insert document author here>
-Abstract: This manual describes what fasta is
- and how it can be used to
- manage online manuals on Debian systems.
-Section: unknown
-
-Format: debiandoc-sgml
-Files: /usr/share/doc/fasta/fasta.sgml.gz
-
-Format: postscript
-Files: /usr/share/doc/fasta/fasta.ps.gz
-
-Format: text
-Files: /usr/share/doc/fasta/fasta.text.gz
-
-Format: HTML
-Index: /usr/share/doc/fasta/html/index.html
-Files: /usr/share/doc/fasta/html/*.html
Copied: trunk/packages/fasta3/trunk/debian/fasta3.doc-base (from rev 18744, trunk/packages/fasta3/trunk/debian/fasta.doc-base.EX)
===================================================================
--- trunk/packages/fasta3/trunk/debian/fasta3.doc-base (rev 0)
+++ trunk/packages/fasta3/trunk/debian/fasta3.doc-base 2015-02-10 09:47:21 UTC (rev 18748)
@@ -0,0 +1,15 @@
+Document: fasta3
+Title: The FASTA program package
+Author: William R. Pearson
+Abstract: This documentation describes the version 36 of the FASTA program
+ package (see W. R. Pearson and D. J. Lipman (1988), "Improved Tools for
+ Biological Sequence Analysis", PNAS 85:2444-2448. W. R. Pearson (1996)
+ "Effective protein sequence comparison" Meth. Enzymol. 266:227-258;
+ and Pearson et. al. (1997) Genomics 46:24-36 [18]. Version 3 of the
+ FASTA packages contains many programs for searching DNA and protein
+ databases and for evaluating statistical significance from randomly
+ shuffled sequences.
+Section: Science/Biology
+
+Format: pdf
+Files: /usr/share/doc/fasta3/fasta_guide.pdf
Added: trunk/packages/fasta3/trunk/debian/fasta3.manpages
===================================================================
--- trunk/packages/fasta3/trunk/debian/fasta3.manpages (rev 0)
+++ trunk/packages/fasta3/trunk/debian/fasta3.manpages 2015-02-10 09:47:21 UTC (rev 18748)
@@ -0,0 +1,6 @@
+doc/fasta36.1
+doc/fastf3.1
+doc/fasts3.1
+doc/map_db.1
+doc/prss3.1
+doc/ps_lav.1
Modified: trunk/packages/fasta3/trunk/debian/patches/Makefile.patch
===================================================================
--- trunk/packages/fasta3/trunk/debian/patches/Makefile.patch 2015-02-09 18:18:47 UTC (rev 18747)
+++ trunk/packages/fasta3/trunk/debian/patches/Makefile.patch 2015-02-10 09:47:21 UTC (rev 18748)
@@ -10,3 +10,38 @@
XDIR = /seqprg/bin
DROPGSW_NA_O = dropgsw2.o wm_align.o calcons_sw.o
+Index: fasta3-36.3.7a/make/Makefile.linux64_sse2
+===================================================================
+--- fasta3-36.3.7a.orig/make/Makefile.linux64_sse2
++++ fasta3-36.3.7a/make/Makefile.linux64_sse2
+@@ -12,7 +12,7 @@
+
+ SHELL=/bin/bash
+
+-CC = gcc -g -O -msse2
++CC = gcc -g -O -msse2 $(CPPFLAGS)
+ #CC= gcc -pg -g -O -msse2 -ffast-math
+ #CC = gcc -g -DDEBUG -msse2
+
+@@ -25,7 +25,7 @@
+
+ # standard options
+
+-CFLAGS= -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DPROGRESS -DM10_CONS -DFASTA_HOST='"your_fasta_host_here"' -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64
++CFLAGS+= -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DPROGRESS -DM10_CONS -DFASTA_HOST='"your_fasta_host_here"' -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64
+ # -I/usr/include/mysql -DMYSQL_DB
+ # -DSUPERFAMNUM -DSFCHAR="'|'"
+
+Index: fasta3-36.3.7a/make/Makefile36m.common
+===================================================================
+--- fasta3-36.3.7a.orig/make/Makefile36m.common
++++ fasta3-36.3.7a/make/Makefile36m.common
+@@ -34,7 +34,7 @@
+ # and "-L/usr/lib64/mysql -lmysqlclient -lz" in LIB_M
+ # some systems may also require a LD_LIBRARY_PATH change
+
+-LIB_M= -lm -lz
++LIB_M= $(LDFLAGS) -lm -lz
+ #LIB_M= -L/usr/lib64/mysql -lmysqlclient -lz -lm
+ NCBL_LIB=ncbl2_mlib.o
+ #NCBL_LIB=ncbl2_mlib.o mysql_lib.o
Modified: trunk/packages/fasta3/trunk/debian/rules
===================================================================
--- trunk/packages/fasta3/trunk/debian/rules 2015-02-09 18:18:47 UTC (rev 18747)
+++ trunk/packages/fasta3/trunk/debian/rules 2015-02-10 09:47:21 UTC (rev 18748)
@@ -12,7 +12,9 @@
MAKEFILE="../make/Makefile.linux64"
#endif
-#export DEB_BUILD_MAINT_OPTIONS = hardening=+all
+export DEB_BUILD_MAINT_OPTIONS = hardening=+all
+CFLAGS+=-flto
+LDFLAGS+=-flto
# package maintainers to append CFLAGS
#export DEB_CFLAGS_MAINT_APPEND = -Wall -pedantic
@@ -26,7 +28,8 @@
cd src && $(MAKE) -f $(MAKEFILE)
override_dh_auto_clean:
- cd src && $(MAKE) -f $(MAKEFILE) clean-up
+ if [ -d src ]; then cd src && $(MAKE) -f $(MAKEFILE) clean-up; fi
+override_dh_compress:
+ dh_compress --exclude=.pdf
-
Date: 2015-02-10 09:47:21 +0000 (Tue, 10 Feb 2015)
New Revision: 18748
Added:
trunk/packages/fasta3/trunk/debian/fasta3.doc-base
trunk/packages/fasta3/trunk/debian/fasta3.manpages
Removed:
trunk/packages/fasta3/trunk/debian/README.Debian
trunk/packages/fasta3/trunk/debian/README.source
trunk/packages/fasta3/trunk/debian/fasta.doc-base.EX
Modified:
trunk/packages/fasta3/trunk/debian/changelog
trunk/packages/fasta3/trunk/debian/copyright
trunk/packages/fasta3/trunk/debian/docs
trunk/packages/fasta3/trunk/debian/patches/Makefile.patch
trunk/packages/fasta3/trunk/debian/rules
Log:
fasta3 - almost ready to upload
Deleted: trunk/packages/fasta3/trunk/debian/README.Debian
===================================================================
--- trunk/packages/fasta3/trunk/debian/README.Debian 2015-02-09 18:18:47 UTC (rev 18747)
+++ trunk/packages/fasta3/trunk/debian/README.Debian 2015-02-10 09:47:21 UTC (rev 18748)
@@ -1,6 +0,0 @@
-fasta for Debian
-----------------
-
-<possible notes regarding this package - if none, delete this file>
-
- -- Steffen Moeller <***@debian.org> Mon, 09 Feb 2015 15:04:28 +0100
Deleted: trunk/packages/fasta3/trunk/debian/README.source
===================================================================
--- trunk/packages/fasta3/trunk/debian/README.source 2015-02-09 18:18:47 UTC (rev 18747)
+++ trunk/packages/fasta3/trunk/debian/README.source 2015-02-10 09:47:21 UTC (rev 18748)
@@ -1,10 +0,0 @@
-fasta for Debian
-----------------
-
-<this file describes information about the source package, see Debian policy
-manual section 4.14. You WILL either need to modify or delete this file>
-
-
-
- -- Steffen Moeller <***@debian.org> Mon, 09 Feb 2015 15:04:28 +0100
-
Modified: trunk/packages/fasta3/trunk/debian/changelog
===================================================================
--- trunk/packages/fasta3/trunk/debian/changelog 2015-02-09 18:18:47 UTC (rev 18747)
+++ trunk/packages/fasta3/trunk/debian/changelog 2015-02-10 09:47:21 UTC (rev 18748)
@@ -1,5 +1,5 @@
fasta3 (36.3.7a-1) unstable; urgency=low
- * Initial release (Closes: #nnnn) <nnnn is the bug number of your ITP>
+ * Initial release (Closes: #coming)
- -- Steffen Moeller <***@debian.org> Mon, 09 Feb 2015 15:04:28 +0100
+ -- Steffen Moeller <***@debian.org> Tue, 10 Feb 2015 10:46:55 +0100
Modified: trunk/packages/fasta3/trunk/debian/copyright
===================================================================
--- trunk/packages/fasta3/trunk/debian/copyright 2015-02-09 18:18:47 UTC (rev 18747)
+++ trunk/packages/fasta3/trunk/debian/copyright 2015-02-10 09:47:21 UTC (rev 18748)
@@ -7,21 +7,29 @@
The Rector & Visitors of the University of Virginia
License: Apache-2.0
+Files: src/wm_align.c
+Copyright: William R. Pearson, University of Virginia
+ Webb Miller, Penn State University
+License: Apache-2.0
+
Files: src/karlin.c
-Copyright: 1980, 1983 Stephen Altschul
+Copyright: 1990, 1993 Stephen Altschul, NCBI
License: Apache-2.0
-Files: src/global_sse2.c
-Copyright: 2010 Michael Farrar <***@gmail.com>
-License:
- /******************************************************************
- . Copyright 2010 by Michael Farrar. All rights reserved.
- . This program may not be sold or incorporated into a commercial product,
- . in whole or in part, without written consent of Michael Farrar. For
- . further information regarding permission for use or reproduction, please
- . contact: Michael Farrar at ***@gmail.com.
- .******************************************************************/
+Files: src/smith_waterman_altivec.c
+Copyright: 2004, Erik Lindahl <***@sbc.su.se>
+ Stockholm Bioinformatics Center, 2004
+License: Apache-2.0
+Files: src/glo[bc]al_sse2.[ch]
+ src/smith_waterman_sse2.c
+Copyright: 2006,2010 Michael Farrar <***@gmail.com>
+License: Academics-only
+ This program may not be sold or incorporated into a commercial product,
+ in whole or in part, without written consent of Michael Farrar. For
+ further information regarding permission for use or reproduction, please
+ contact: Michael Farrar at ***@gmail.com.
+
Files: debian/*
Copyright: 2015 Steffen Moeller <***@debian.org>
License: Apache-2.0
Modified: trunk/packages/fasta3/trunk/debian/docs
===================================================================
--- trunk/packages/fasta3/trunk/debian/docs 2015-02-09 18:18:47 UTC (rev 18747)
+++ trunk/packages/fasta3/trunk/debian/docs 2015-02-10 09:47:21 UTC (rev 18748)
@@ -1,2 +1,5 @@
README
-doc/*
+doc/readme*
+doc/README*
+doc/changes*
+doc/fasta_guide.pdf
Deleted: trunk/packages/fasta3/trunk/debian/fasta.doc-base.EX
===================================================================
--- trunk/packages/fasta3/trunk/debian/fasta.doc-base.EX 2015-02-09 18:18:47 UTC (rev 18747)
+++ trunk/packages/fasta3/trunk/debian/fasta.doc-base.EX 2015-02-10 09:47:21 UTC (rev 18748)
@@ -1,20 +0,0 @@
-Document: fasta
-Title: Debian fasta Manual
-Author: <insert document author here>
-Abstract: This manual describes what fasta is
- and how it can be used to
- manage online manuals on Debian systems.
-Section: unknown
-
-Format: debiandoc-sgml
-Files: /usr/share/doc/fasta/fasta.sgml.gz
-
-Format: postscript
-Files: /usr/share/doc/fasta/fasta.ps.gz
-
-Format: text
-Files: /usr/share/doc/fasta/fasta.text.gz
-
-Format: HTML
-Index: /usr/share/doc/fasta/html/index.html
-Files: /usr/share/doc/fasta/html/*.html
Copied: trunk/packages/fasta3/trunk/debian/fasta3.doc-base (from rev 18744, trunk/packages/fasta3/trunk/debian/fasta.doc-base.EX)
===================================================================
--- trunk/packages/fasta3/trunk/debian/fasta3.doc-base (rev 0)
+++ trunk/packages/fasta3/trunk/debian/fasta3.doc-base 2015-02-10 09:47:21 UTC (rev 18748)
@@ -0,0 +1,15 @@
+Document: fasta3
+Title: The FASTA program package
+Author: William R. Pearson
+Abstract: This documentation describes the version 36 of the FASTA program
+ package (see W. R. Pearson and D. J. Lipman (1988), "Improved Tools for
+ Biological Sequence Analysis", PNAS 85:2444-2448. W. R. Pearson (1996)
+ "Effective protein sequence comparison" Meth. Enzymol. 266:227-258;
+ and Pearson et. al. (1997) Genomics 46:24-36 [18]. Version 3 of the
+ FASTA packages contains many programs for searching DNA and protein
+ databases and for evaluating statistical significance from randomly
+ shuffled sequences.
+Section: Science/Biology
+
+Format: pdf
+Files: /usr/share/doc/fasta3/fasta_guide.pdf
Added: trunk/packages/fasta3/trunk/debian/fasta3.manpages
===================================================================
--- trunk/packages/fasta3/trunk/debian/fasta3.manpages (rev 0)
+++ trunk/packages/fasta3/trunk/debian/fasta3.manpages 2015-02-10 09:47:21 UTC (rev 18748)
@@ -0,0 +1,6 @@
+doc/fasta36.1
+doc/fastf3.1
+doc/fasts3.1
+doc/map_db.1
+doc/prss3.1
+doc/ps_lav.1
Modified: trunk/packages/fasta3/trunk/debian/patches/Makefile.patch
===================================================================
--- trunk/packages/fasta3/trunk/debian/patches/Makefile.patch 2015-02-09 18:18:47 UTC (rev 18747)
+++ trunk/packages/fasta3/trunk/debian/patches/Makefile.patch 2015-02-10 09:47:21 UTC (rev 18748)
@@ -10,3 +10,38 @@
XDIR = /seqprg/bin
DROPGSW_NA_O = dropgsw2.o wm_align.o calcons_sw.o
+Index: fasta3-36.3.7a/make/Makefile.linux64_sse2
+===================================================================
+--- fasta3-36.3.7a.orig/make/Makefile.linux64_sse2
++++ fasta3-36.3.7a/make/Makefile.linux64_sse2
+@@ -12,7 +12,7 @@
+
+ SHELL=/bin/bash
+
+-CC = gcc -g -O -msse2
++CC = gcc -g -O -msse2 $(CPPFLAGS)
+ #CC= gcc -pg -g -O -msse2 -ffast-math
+ #CC = gcc -g -DDEBUG -msse2
+
+@@ -25,7 +25,7 @@
+
+ # standard options
+
+-CFLAGS= -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DPROGRESS -DM10_CONS -DFASTA_HOST='"your_fasta_host_here"' -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64
++CFLAGS+= -DSHOW_HELP -DSHOWSIM -DUNIX -DTIMES -DHZ=100 -DMAX_WORKERS=8 -DTHR_EXIT=pthread_exit -DPROGRESS -DM10_CONS -DFASTA_HOST='"your_fasta_host_here"' -D_REENTRANT -DHAS_INTTYPES -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -DUSE_FSEEKO -DSAMP_STATS -DPGM_DOC -DUSE_MMAP -D_LARGEFILE64_SOURCE -DBIG_LIB64
+ # -I/usr/include/mysql -DMYSQL_DB
+ # -DSUPERFAMNUM -DSFCHAR="'|'"
+
+Index: fasta3-36.3.7a/make/Makefile36m.common
+===================================================================
+--- fasta3-36.3.7a.orig/make/Makefile36m.common
++++ fasta3-36.3.7a/make/Makefile36m.common
+@@ -34,7 +34,7 @@
+ # and "-L/usr/lib64/mysql -lmysqlclient -lz" in LIB_M
+ # some systems may also require a LD_LIBRARY_PATH change
+
+-LIB_M= -lm -lz
++LIB_M= $(LDFLAGS) -lm -lz
+ #LIB_M= -L/usr/lib64/mysql -lmysqlclient -lz -lm
+ NCBL_LIB=ncbl2_mlib.o
+ #NCBL_LIB=ncbl2_mlib.o mysql_lib.o
Modified: trunk/packages/fasta3/trunk/debian/rules
===================================================================
--- trunk/packages/fasta3/trunk/debian/rules 2015-02-09 18:18:47 UTC (rev 18747)
+++ trunk/packages/fasta3/trunk/debian/rules 2015-02-10 09:47:21 UTC (rev 18748)
@@ -12,7 +12,9 @@
MAKEFILE="../make/Makefile.linux64"
#endif
-#export DEB_BUILD_MAINT_OPTIONS = hardening=+all
+export DEB_BUILD_MAINT_OPTIONS = hardening=+all
+CFLAGS+=-flto
+LDFLAGS+=-flto
# package maintainers to append CFLAGS
#export DEB_CFLAGS_MAINT_APPEND = -Wall -pedantic
@@ -26,7 +28,8 @@
cd src && $(MAKE) -f $(MAKEFILE)
override_dh_auto_clean:
- cd src && $(MAKE) -f $(MAKEFILE) clean-up
+ if [ -d src ]; then cd src && $(MAKE) -f $(MAKEFILE) clean-up; fi
+override_dh_compress:
+ dh_compress --exclude=.pdf
-