Author: osallou
Date: 2013-02-18 09:41:04 +0000 (Mon, 18 Feb 2013)
New Revision: 13026
Modified:
trunk/packages/squizz/trunk/debian/changelog
trunk/packages/squizz/trunk/debian/control
trunk/packages/squizz/trunk/debian/get-orig-source
trunk/packages/squizz/trunk/debian/libsquizz.symbols
trunk/packages/squizz/trunk/debian/patches/correct-manpages-section.patch
trunk/packages/squizz/trunk/debian/patches/disable-swissprot-test.patch
Log:
new upstream release 0.99b
Modified: trunk/packages/squizz/trunk/debian/changelog
===================================================================
--- trunk/packages/squizz/trunk/debian/changelog 2013-02-17 17:53:13 UTC
(rev 13025)
+++ trunk/packages/squizz/trunk/debian/changelog 2013-02-18 09:41:04 UTC
(rev 13026)
@@ -1,5 +1,6 @@
-squizz (0.99a+dfsg-1) UNRELEASED; urgency=low
+squizz (0.99b+dfsg-1) UNRELEASED; urgency=low
+ * New upstream release
* debian/copyright:
- DEP5
- Add Files-Excluded to document what was removed from original source
Modified: trunk/packages/squizz/trunk/debian/control
===================================================================
--- trunk/packages/squizz/trunk/debian/control 2013-02-17 17:53:13 UTC (rev
13025)
+++ trunk/packages/squizz/trunk/debian/control 2013-02-18 09:41:04 UTC (rev
13026)
@@ -15,6 +15,7 @@
Architecture: any
Section: science
Depends: ${shlibs:Depends}, ${misc:Depends}
+Breaks: squizz (<=0.99a)
Description: Converter for genetic sequences and alignments
Squizz is a sequence/alignment format checker, but it has some
conversion capabilities too.
@@ -28,6 +29,7 @@
Architecture: any
Section:libs
Depends: ${shlibs:Depends}, ${misc:Depends}
+Breaks: squizz (<=0.99a)
Description: Conversion libs used by squizz genetic sequence converter
Squizz is a sequence/alignment format checker, but it has some
conversion capabilities too.
@@ -43,6 +45,7 @@
Section: libdevel
Architecture: any
Depends: ${shlibs:Depends}, ${misc:Depends}
+Breaks: squizz (<=0.99a)
Description: development tools for squizz genetic sequence converter
Squizz is a sequence/alignment format checker, but it has some
conversion capabilities too.
Modified: trunk/packages/squizz/trunk/debian/get-orig-source
===================================================================
--- trunk/packages/squizz/trunk/debian/get-orig-source 2013-02-17 17:53:13 UTC
(rev 13025)
+++ trunk/packages/squizz/trunk/debian/get-orig-source 2013-02-18 09:41:04 UTC
(rev 13026)
@@ -11,7 +11,8 @@
mkdir -p ../tarballs
cd ../tarballs
-UTAR="${PKG}_${VERSION}.orig.tar.gz"
+#UTAR="${PKG}_${VERSION}.orig.tar.gz"
+UTAR="${PKG}-${VERSION}.tar.gz"
mv ../${UTAR} .
tar -xzf ${UTAR}
Modified: trunk/packages/squizz/trunk/debian/libsquizz.symbols
===================================================================
--- trunk/packages/squizz/trunk/debian/libsquizz.symbols 2013-02-17
17:53:13 UTC (rev 13025)
+++ trunk/packages/squizz/trunk/debian/libsquizz.symbols 2013-02-18
09:41:04 UTC (rev 13026)
@@ -277,6 +277,44 @@
stocky_check@Base 0.99a
stocky_parse@Base 0.99a
libbioseq.so.0 libsquizz #MINVER#
+ codata_check@Base 0.99b+dfsg-1
+ codata_checksum@Base 0.99b+dfsg-1
+ codata_create_buffer@Base 0.99b+dfsg-1
+ codata_delete_buffer@Base 0.99b+dfsg-1
+ codata_flex_debug@Base 0.99b+dfsg-1
+ codata_flush_buffer@Base 0.99b+dfsg-1
+ codata_parse@Base 0.99b+dfsg-1
+ codata_print@Base 0.99b+dfsg-1
+ codata_scan_buffer@Base 0.99b+dfsg-1
+ codata_scan_bytes@Base 0.99b+dfsg-1
+ codata_scan_string@Base 0.99b+dfsg-1
+ codata_switch_to_buffer@Base 0.99b+dfsg-1
+ codataalloc@Base 0.99b+dfsg-1
+ codatafree@Base 0.99b+dfsg-1
+ codataget_debug@Base 0.99b+dfsg-1
+ codataget_in@Base 0.99b+dfsg-1
+ codataget_leng@Base 0.99b+dfsg-1
+ codataget_lineno@Base 0.99b+dfsg-1
+ codataget_out@Base 0.99b+dfsg-1
+ codataget_text@Base 0.99b+dfsg-1
+ codatain@Base 0.99b+dfsg-1
+ codataleng@Base 0.99b+dfsg-1
+ codatalex@Base 0.99b+dfsg-1
+ codatalex_destroy@Base 0.99b+dfsg-1
+ codatalineno@Base 0.99b+dfsg-1
+ codataout@Base 0.99b+dfsg-1
+ codataparse@Base 0.99b+dfsg-1
+ codatapop_buffer_state@Base 0.99b+dfsg-1
+ codatapush_buffer_state@Base 0.99b+dfsg-1
+ codatarealloc@Base 0.99b+dfsg-1
+ codatarestart@Base 0.99b+dfsg-1
+ codataset_debug@Base 0.99b+dfsg-1
+ codataset_in@Base 0.99b+dfsg-1
+ codataset_lineno@Base 0.99b+dfsg-1
+ codataset_out@Base 0.99b+dfsg-1
+ codatatext@Base 0.99b+dfsg-1
+ codatay_check@Base 0.99b+dfsg-1
+ codatay_parse@Base 0.99b+dfsg-1
embl_check@Base 0.99a
embl_create_buffer@Base 0.99a
embl_delete_buffer@Base 0.99a
@@ -314,8 +352,8 @@
embltext@Base 0.99a
embly_check@Base 0.99a
embly_parse@Base 0.99a
- error_fatal@Base 0.99a
- error_warn@Base 0.99a
+#MISSING: 0.99b+dfsg-1# error_fatal@Base 0.99a
+#MISSING: 0.99b+dfsg-1# error_warn@Base 0.99a
fasta_check@Base 0.99a
fasta_create_buffer@Base 0.99a
fasta_delete_buffer@Base 0.99a
@@ -550,44 +588,44 @@
parse_nuladd@Base 0.99a
parse_stradd@Base 0.99a
parse_veradd@Base 0.99a
- pir_check@Base 0.99a
- pir_checksum@Base 0.99a
- pir_create_buffer@Base 0.99a
- pir_delete_buffer@Base 0.99a
- pir_flex_debug@Base 0.99a
- pir_flush_buffer@Base 0.99a
- pir_parse@Base 0.99a
- pir_print@Base 0.99a
- pir_scan_buffer@Base 0.99a
- pir_scan_bytes@Base 0.99a
- pir_scan_string@Base 0.99a
- pir_switch_to_buffer@Base 0.99a
- piralloc@Base 0.99a
- pirfree@Base 0.99a
- pirget_debug@Base 0.99a
- pirget_in@Base 0.99a
- pirget_leng@Base 0.99a
- pirget_lineno@Base 0.99a
- pirget_out@Base 0.99a
- pirget_text@Base 0.99a
- pirin@Base 0.99a
- pirleng@Base 0.99a
- pirlex@Base 0.99a
- pirlex_destroy@Base 0.99a
- pirlineno@Base 0.99a
- pirout@Base 0.99a
- pirparse@Base 0.99a
- pirpop_buffer_state@Base 0.99a
- pirpush_buffer_state@Base 0.99a
- pirrealloc@Base 0.99a
- pirrestart@Base 0.99a
- pirset_debug@Base 0.99a
- pirset_in@Base 0.99a
- pirset_lineno@Base 0.99a
- pirset_out@Base 0.99a
- pirtext@Base 0.99a
- piry_check@Base 0.99a
- piry_parse@Base 0.99a
+#MISSING: 0.99b+dfsg-1# pir_check@Base 0.99a
+#MISSING: 0.99b+dfsg-1# pir_checksum@Base 0.99a
+#MISSING: 0.99b+dfsg-1# pir_create_buffer@Base 0.99a
+#MISSING: 0.99b+dfsg-1# pir_delete_buffer@Base 0.99a
+#MISSING: 0.99b+dfsg-1# pir_flex_debug@Base 0.99a
+#MISSING: 0.99b+dfsg-1# pir_flush_buffer@Base 0.99a
+#MISSING: 0.99b+dfsg-1# pir_parse@Base 0.99a
+#MISSING: 0.99b+dfsg-1# pir_print@Base 0.99a
+#MISSING: 0.99b+dfsg-1# pir_scan_buffer@Base 0.99a
+#MISSING: 0.99b+dfsg-1# pir_scan_bytes@Base 0.99a
+#MISSING: 0.99b+dfsg-1# pir_scan_string@Base 0.99a
+#MISSING: 0.99b+dfsg-1# pir_switch_to_buffer@Base 0.99a
+#MISSING: 0.99b+dfsg-1# piralloc@Base 0.99a
+#MISSING: 0.99b+dfsg-1# pirfree@Base 0.99a
+#MISSING: 0.99b+dfsg-1# pirget_debug@Base 0.99a
+#MISSING: 0.99b+dfsg-1# pirget_in@Base 0.99a
+#MISSING: 0.99b+dfsg-1# pirget_leng@Base 0.99a
+#MISSING: 0.99b+dfsg-1# pirget_lineno@Base 0.99a
+#MISSING: 0.99b+dfsg-1# pirget_out@Base 0.99a
+#MISSING: 0.99b+dfsg-1# pirget_text@Base 0.99a
+#MISSING: 0.99b+dfsg-1# pirin@Base 0.99a
+#MISSING: 0.99b+dfsg-1# pirleng@Base 0.99a
+#MISSING: 0.99b+dfsg-1# pirlex@Base 0.99a
+#MISSING: 0.99b+dfsg-1# pirlex_destroy@Base 0.99a
+#MISSING: 0.99b+dfsg-1# pirlineno@Base 0.99a
+#MISSING: 0.99b+dfsg-1# pirout@Base 0.99a
+#MISSING: 0.99b+dfsg-1# pirparse@Base 0.99a
+#MISSING: 0.99b+dfsg-1# pirpop_buffer_state@Base 0.99a
+#MISSING: 0.99b+dfsg-1# pirpush_buffer_state@Base 0.99a
+#MISSING: 0.99b+dfsg-1# pirrealloc@Base 0.99a
+#MISSING: 0.99b+dfsg-1# pirrestart@Base 0.99a
+#MISSING: 0.99b+dfsg-1# pirset_debug@Base 0.99a
+#MISSING: 0.99b+dfsg-1# pirset_in@Base 0.99a
+#MISSING: 0.99b+dfsg-1# pirset_lineno@Base 0.99a
+#MISSING: 0.99b+dfsg-1# pirset_out@Base 0.99a
+#MISSING: 0.99b+dfsg-1# pirtext@Base 0.99a
+#MISSING: 0.99b+dfsg-1# piry_check@Base 0.99a
+#MISSING: 0.99b+dfsg-1# piry_parse@Base 0.99a
protein_weight@Base 0.99a
raw_check@Base 0.99a
raw_create_buffer@Base 0.99a
Modified:
trunk/packages/squizz/trunk/debian/patches/correct-manpages-section.patch
===================================================================
--- trunk/packages/squizz/trunk/debian/patches/correct-manpages-section.patch
2013-02-17 17:53:13 UTC (rev 13025)
+++ trunk/packages/squizz/trunk/debian/patches/correct-manpages-section.patch
2013-02-18 09:41:04 UTC (rev 13026)
@@ -1,4 +1,8 @@
-Debian packaging patch, 21/03/2011 Olivier Sallou <[email protected]>
+Subject: Fix man page section
+Description: wrong section used
+Author: Olivier Sallou <[email protected]>
+Last-Updated: 2013-02-18
+Forwarded: Yes
--- a/doc/alifmt.man
+++ b/doc/alifmt.man
@@ -128,8 +128,8 @@
@@ -14,14 +18,14 @@
.IX Item "alifmt - Aligned sequences formats"
--- a/doc/seqfmt.man
+++ b/doc/seqfmt.man
-@@ -128,8 +128,8 @@
+@@ -123,8 +123,8 @@
.rm #[ #] #H #V #F C
.\" ========================================================================
.\"
-.IX Title "SEQFMT 1"
--.TH SEQFMT 1 "2009-05-19" "Unix" "User Manuals"
+-.TH SEQFMT 1 "2013-02-08" "Unix" "User Manuals"
+.IX Title "SEQFMT 5"
-+.TH SEQFMT 5 "2009-05-19" "Unix" "User Manuals"
- .SH "NAME"
- .IP "\fBseqfmt\fR \- Sequences formats" 4
- .IX Item "seqfmt - Sequences formats"
++.TH SEQFMT 5 "2013-02-08" "Unix" "User Manuals"
+ .\" For nroff, turn off justification. Always turn off hyphenation; it makes
+ .\" way too many mistakes in technical documents.
+ .if n .ad l
Modified:
trunk/packages/squizz/trunk/debian/patches/disable-swissprot-test.patch
===================================================================
--- trunk/packages/squizz/trunk/debian/patches/disable-swissprot-test.patch
2013-02-17 17:53:13 UTC (rev 13025)
+++ trunk/packages/squizz/trunk/debian/patches/disable-swissprot-test.patch
2013-02-18 09:41:04 UTC (rev 13026)
@@ -1,38 +1,44 @@
-Debian packaging patch, 21/03/2011 Olivier Sallou <[email protected]>
+Subject: Disable tests using copyrigthed seq
+Description: upstream constains copyrighted sequence,
+ removed form packaged. This patch removes tests using this
+ sequence
+Author: Olivier Sallou <[email protected]>
+Last-Updated: 2013-02-18
+Forwarded: No
--- a/test/Makefile.am
+++ b/test/Makefile.am
-@@ -4,7 +4,7 @@
+@@ -6,7 +6,7 @@
- TESTS_ALIS = clustal.sh mega.sh msf.sh nexus.sh phylipi.sh phylips.sh \
+ TESTS_ALIS = clustal.sh mega.sh msf.sh nexusi.sh phylipi.sh phylips.sh \
stockholm.sh
--TESTS_SEQS = embl.sh genbank.sh ig.sh raw.sh sprot.sh
-+TESTS_SEQS = embl.sh genbank.sh ig.sh raw.sh
+-TESTS_SEQS = embl.sh genbank.sh ig.sh nbrf.sh raw.sh sprot.sh
++TESTS_SEQS = embl.sh genbank.sh ig.sh nbrf.sh raw.sh
XFAIL_TESTS =
-@@ -16,6 +16,6 @@
+@@ -18,6 +18,6 @@
SEQS = sequence/embl.seq sequence/fasta.seq sequence/gde.seq \
sequence/genbank.seq sequence/genpept.seq sequence/gcg.seq \
- sequence/ig.seq sequence/nbrf.seq sequence/pir.seq sequence/raw.seq \
+ sequence/ig.seq sequence/nbrf.seq sequence/codata.seq sequence/raw.seq \
- sequence/refseqn.seq sequence/refseqp.seq sequence/sprot.seq
+ sequence/refseqn.seq sequence/refseqp.seq
EXTRA_DIST = $(TESTS) $(DATAS)
--- a/test/Makefile.in
+++ b/test/Makefile.in
-@@ -178,7 +178,7 @@
- TESTS_ALIS = clustal.sh mega.sh msf.sh nexus.sh phylipi.sh phylips.sh \
+@@ -417,7 +417,7 @@
+ TESTS_ALIS = clustal.sh mega.sh msf.sh nexusi.sh phylipi.sh phylips.sh \
stockholm.sh
--TESTS_SEQS = embl.sh genbank.sh ig.sh raw.sh sprot.sh
-+TESTS_SEQS = embl.sh genbank.sh ig.sh raw.sh
+-TESTS_SEQS = embl.sh genbank.sh ig.sh nbrf.sh raw.sh sprot.sh
++TESTS_SEQS = embl.sh genbank.sh ig.sh nbrf.sh raw.sh
DATAS = $(ALIS) $(SEQS)
ALIS = align/clustal.seq align/fasta.seq align/mega.seq align/msf.seq \
align/nexusi.seq align/phylipi.seq align/phylips.seq align/stock.seq
-@@ -186,7 +186,7 @@
+@@ -425,7 +425,7 @@
SEQS = sequence/embl.seq sequence/fasta.seq sequence/gde.seq \
sequence/genbank.seq sequence/genpept.seq sequence/gcg.seq \
- sequence/ig.seq sequence/nbrf.seq sequence/pir.seq sequence/raw.seq \
+ sequence/ig.seq sequence/nbrf.seq sequence/codata.seq sequence/raw.seq \
- sequence/refseqn.seq sequence/refseqp.seq sequence/sprot.seq
+ sequence/refseqn.seq sequence/refseqp.seq
@@ -44,22 +50,40 @@
## Sequence files location
seqdir=$srcdir/sequence
--seqlist='embl.seq fasta.seq gcg.seq gde.seq genbank.seq genpept.seq ig.seq
nbrf.seq pir.seq raw.seq refseqn.seq refseqp.seq sprot.seq'
-+seqlist='embl.seq fasta.seq gcg.seq gde.seq genbank.seq genpept.seq ig.seq
nbrf.seq pir.seq raw.seq refseqn.seq refseqp.seq'
+-seqlist='codata.seq embl.seq fasta.seq gcg.seq gde.seq genbank.seq
genpept.seq ig.seq nbrf.seq raw.seq refseqn.seq refseqp.seq sprot.seq'
++seqlist='codata.seq embl.seq fasta.seq gcg.seq gde.seq genbank.seq
genpept.seq ig.seq nbrf.seq raw.seq refseqn.seq refseqp.seq'
- ## Checks EMBL-like sequence
+ ## Checks CODATA-like sequence
for f in $seqlist; do
+@@ -64,10 +64,10 @@
+ done
+
+ ## Checks SWISSPROT-like sequence
+-for f in $seqlist; do
+- ../src/squizz -c swissprot $seqdir/$f >$tmpseq 2>/dev/null
+- (../src/squizz $tmpseq 2>&1 | grep -v SWISSPROT) && exit 1
+-done
++#for f in $seqlist; do
++# ../src/squizz -c swissprot $seqdir/$f >$tmpseq 2>/dev/null
++# (../src/squizz $tmpseq 2>&1 | grep -v SWISSPROT) && exit 1
++#done
+
+ ## Clean temp files
+ rm -f $tmpseq
--- a/test/fmtseq.sh
+++ b/test/fmtseq.sh
-@@ -60,11 +60,6 @@
- (../src/squizz $srcdir/$f 2>&1 | grep -v RAW) && exit 1
+@@ -61,10 +61,10 @@
done
--## Checks SWISSPROT-like sequence
+ ## Checks SWISSPROT-like sequence
-seqlist='sprot.seq'
-for f in $seqlist; do
- (../src/squizz $srcdir/$f 2>&1 | grep -v SWISSPROT) && exit 1
-done
++#seqlist='sprot.seq'
++#for f in $seqlist; do
++# (../src/squizz $srcdir/$f 2>&1 | grep -v SWISSPROT) && exit 1
++#done
exit 0
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