[med-svn] r1460 - trunk/packages/primer3/trunk/debian

charles-guest at alioth.debian.org charles-guest at alioth.debian.org
Fri Feb 22 01:52:13 UTC 2008 

Author: charles-guest
Date: 2008-02-22 01:52:12 +0000 (Fri, 22 Feb 2008)
New Revision: 1460

Modified:
   trunk/packages/primer3/trunk/debian/changelog
   trunk/packages/primer3/trunk/debian/copyright
   trunk/packages/primer3/trunk/debian/ntdpal.1
   trunk/packages/primer3/trunk/debian/ntdpal.1.xml
   trunk/packages/primer3/trunk/debian/oligotm.1
   trunk/packages/primer3/trunk/debian/oligotm.1.xml
   trunk/packages/primer3/trunk/debian/primer3_core.1
   trunk/packages/primer3/trunk/debian/primer3_core.1.xml
   trunk/packages/primer3/trunk/debian/rules
Log:
New upstream version

Modified: trunk/packages/primer3/trunk/debian/changelog
===================================================================
--- trunk/packages/primer3/trunk/debian/changelog	2008-02-22 00:38:58 UTC (rev 1459)
+++ trunk/packages/primer3/trunk/debian/changelog	2008-02-22 01:52:12 UTC (rev 1460)
@@ -1,6 +1,16 @@
-primer3 (1.1.1-2) UNRELEASED; urgency=low
+primer3 (1.1.3-1) UNRELEASED; urgency=low
 
   [ Charles Plessy ]
+  * New upstream version:
+    - 1.1.3: Corrected static buffer overflow errors in
+      boulder_print_pairs() and boulder_print_oligos() in primer3_main.c.
+    - 1.1.2: Updates to dpal.c so that no error forces an exit.
+      Adpatation in primer3_main.c and ntdpal_main.c to 
+        updated error handling in dpal().
+      Arranged for primer3_main.c align() to check for
+        and circumvent local alignments to "targets" < 3 nucleotides
+        long, and added tests for this condition.
+      Comment and code readability updates in dpal.h and dpal.c
   * Moved the Homepage: field out from the package's description.
   * debian/control: updated Steffen's email address.
   * debian/*.1.xml: corrected the headers of the sources of manpages.

Modified: trunk/packages/primer3/trunk/debian/copyright
===================================================================
--- trunk/packages/primer3/trunk/debian/copyright	2008-02-22 00:38:58 UTC (rev 1459)
+++ trunk/packages/primer3/trunk/debian/copyright	2008-02-22 01:52:12 UTC (rev 1460)
@@ -13,8 +13,8 @@
  otherwise.
 
 
-Files: src/oligotm*
-Copyright: © 1996,1997,1998,1999,2000,2001,2004,2006,2007
+Files: src/oligotm*, tst/oligotm_test.pl
+Copyright: © 1996,1997,1998,1999,2000,2001,2004,2006,2007,2008
            Whitehead Institute for Biomedical Research,
            Steve Rozen (http://jura.wi.mit.edu/rozen),
 	   Helen Skaletsky
@@ -37,7 +37,7 @@
 
 
 Files: *
-Copyright: © 1996,1997,1998,1999,2000,2001,2004,2006,2007
+Copyright: © 1996,1997,1998,1999,2000,2001,2004,2006,2007,2008
            Whitehead Institute for Biomedical Research,
 	   Steve Rozen (http://jura.wi.mit.edu/rozen),
 	   Helen Skaletsky

Modified: trunk/packages/primer3/trunk/debian/ntdpal.1
===================================================================
--- trunk/packages/primer3/trunk/debian/ntdpal.1	2008-02-22 00:38:58 UTC (rev 1459)
+++ trunk/packages/primer3/trunk/debian/ntdpal.1	2008-02-22 01:52:12 UTC (rev 1460)
@@ -1,11 +1,11 @@
 .\"     Title: NTDPAL
 .\"    Author: 
 .\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\"      Date: February 17, 2007
+.\"      Date: 02/22/2008
 .\"    Manual: Primer3 User Manuals
-.\"    Source: ntdpal 1.1.1
+.\"    Source: ntdpal 1.1.3
 .\"
-.TH "NTDPAL" "1" "February 17, 2007" "ntdpal 1.1.1" "Primer3 User Manuals"
+.TH "NTDPAL" "1" "02/22/2008" "ntdpal 1.1.3" "Primer3 User Manuals"
 .\" disable hyphenation
 .nh
 .\" disable justification (adjust text to left margin only)
@@ -96,7 +96,7 @@
 \fBprimer3_core\fR(1)
 \fBoligotm\fR(1)
 .SH "COPYRIGHT"
-Copyright \(co 1996,1997,1998,1999,2000,2001,2004,2006,2007 Whitehead Institute for Biomedical Research, Steve Rozen (http://jura.wi.mit.edu/rozen), Helen Skaletsky
+Copyright \(co 1996,1997,1998,1999,2000,2001,2004,2006,2007,2008 Whitehead Institute for Biomedical Research, Steve Rozen (http://jura.wi.mit.edu/rozen), Helen Skaletsky
 .br
 .PP
 All rights reserved\. On Debian\-based systems, please consult

Modified: trunk/packages/primer3/trunk/debian/ntdpal.1.xml
===================================================================
--- trunk/packages/primer3/trunk/debian/ntdpal.1.xml	2008-02-22 00:38:58 UTC (rev 1459)
+++ trunk/packages/primer3/trunk/debian/ntdpal.1.xml	2008-02-22 01:52:12 UTC (rev 1460)
@@ -5,14 +5,13 @@
         "http://www.oasis-open.org/docbook/xml/4.4/docbookx.dtd" [
   <!ENTITY dhfirstname "<firstname>Charles</firstname>">
   <!ENTITY dhsurname   "<surname>Plessy</surname>">
-  <!ENTITY dhdate      "<date>February 17, 2007</date>">
   <!ENTITY dhsection   "<manvolnum>1</manvolnum>">
   <!ENTITY dhemail     "<email>charles-debian-nospam at plessy.org</email>">
   <!ENTITY dhusername  "Charles Plessy">
   <!ENTITY dhtitle     "Primer3 User Manuals">
   <!ENTITY dhucpackage "<refentrytitle>NTDPAL</refentrytitle>">
   <!ENTITY dhpackage   "ntdpal">
-  <!ENTITY dhrelease   "1.1.1">
+  <!ENTITY dhrelease   "1.1.3">
   <!ENTITY debian      "<productname>Debian</productname>">
   <!ENTITY gnu         "<acronym>GNU</acronym>">
   <!ENTITY gpl         "&gnu; <acronym>GPL</acronym>">
@@ -23,7 +22,6 @@
     <title>&dhtitle;</title>
     <productname>&dhpackage;</productname>
     <releaseinfo role="version">&dhrelease;</releaseinfo>
-    &dhdate;
     <address>
       &dhemail;
     </address>
@@ -32,7 +30,7 @@
       &dhsurname;
     </author> -->
     <copyright>
-      <year>1996,1997,1998,1999,2000,2001,2004,2006,2007</year>
+      <year>1996,1997,1998,1999,2000,2001,2004,2006,2007,2008</year>
       <holder>Whitehead Institute for Biomedical Research</holder>
       <holder>Steve Rozen (http://jura.wi.mit.edu/rozen)</holder>
       <holder>Helen Skaletsky</holder>

Modified: trunk/packages/primer3/trunk/debian/oligotm.1
===================================================================
--- trunk/packages/primer3/trunk/debian/oligotm.1	2008-02-22 00:38:58 UTC (rev 1459)
+++ trunk/packages/primer3/trunk/debian/oligotm.1	2008-02-22 01:52:12 UTC (rev 1460)
@@ -1,11 +1,11 @@
 .\"     Title: OLIGOTM
 .\"    Author: 
 .\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\"      Date: February 17, 2007
+.\"      Date: 02/22/2008
 .\"    Manual: Primer3 User Manuals
-.\"    Source: oligotm 1.1.1
+.\"    Source: oligotm 1.1.3
 .\"
-.TH "OLIGOTM" "1" "February 17, 2007" "oligotm 1.1.1" "Primer3 User Manuals"
+.TH "OLIGOTM" "1" "02/22/2008" "oligotm 1.1.3" "Primer3 User Manuals"
 .\" disable hyphenation
 .nh
 .\" disable justification (adjust text to left margin only)
@@ -98,7 +98,7 @@
 \fBprimer3_core\fR(1)
 \fBntdpal\fR(1)
 .SH "COPYRIGHT"
-Copyright \(co 1996,1997,1998,1999,2000,2001,2004,2006,2007 Whitehead Institute for Biomedical Research, Steve Rozen (http://jura.wi.mit.edu/rozen), Helen Skaletsky
+Copyright \(co 1996,1997,1998,1999,2000,2001,2004,2006,2007,2008 Whitehead Institute for Biomedical Research, Steve Rozen (http://jura.wi.mit.edu/rozen), Helen Skaletsky
 .br
 .PP
 All rights reserved\. On Debian\-based systems, please consult

Modified: trunk/packages/primer3/trunk/debian/oligotm.1.xml
===================================================================
--- trunk/packages/primer3/trunk/debian/oligotm.1.xml	2008-02-22 00:38:58 UTC (rev 1459)
+++ trunk/packages/primer3/trunk/debian/oligotm.1.xml	2008-02-22 01:52:12 UTC (rev 1460)
@@ -3,17 +3,15 @@
         href="http://docbook.sourceforge.net/release/xsl/current/manpages/docbook.xsl"?>
 <!DOCTYPE refentry PUBLIC "-//OASIS//DTD DocBook XML V4.4//EN"
         "http://www.oasis-open.org/docbook/xml/4.4/docbookx.dtd" [
-"/usr/share/xml/docbook/schema/dtd/4.4/docbookx.dtd" [
   <!ENTITY dhfirstname "<firstname>Charles</firstname>">
   <!ENTITY dhsurname   "<surname>Plessy</surname>">
-  <!ENTITY dhdate      "<date>February 17, 2007</date>">
   <!ENTITY dhsection   "<manvolnum>1</manvolnum>">
   <!ENTITY dhemail     "<email>charles-debian-nospam at plessy.org</email>">
   <!ENTITY dhusername  "Charles Plessy">
   <!ENTITY dhucpackage "<refentrytitle>OLIGOTM</refentrytitle>">
   <!ENTITY dhtitle     "Primer3 User Manuals">
   <!ENTITY dhpackage   "oligotm">
-  <!ENTITY dhrelease   "1.1.1">
+  <!ENTITY dhrelease   "1.1.3">
   <!ENTITY debian      "<productname>Debian</productname>">
   <!ENTITY gnu         "<acronym>GNU</acronym>">
   <!ENTITY gpl         "&gnu; <acronym>GPL</acronym>">
@@ -24,7 +22,6 @@
     <title>&dhtitle;</title>
     <productname>&dhpackage;</productname>
     <releaseinfo role="version">&dhrelease;</releaseinfo>
-    &dhdate;
     <address>
       &dhemail;
     </address>
@@ -33,7 +30,7 @@
       &dhsurname;
     </author> -->
     <copyright>
-      <year>1996,1997,1998,1999,2000,2001,2004,2006,2007</year>
+      <year>1996,1997,1998,1999,2000,2001,2004,2006,2007,2008</year>
       <holder>Whitehead Institute for Biomedical Research</holder>
       <holder>Steve Rozen (http://jura.wi.mit.edu/rozen)</holder>
       <holder>Helen Skaletsky</holder>
@@ -49,7 +46,6 @@
       granted to copy, distribute and/or modify this document under
       the same terms as oligotm itself.<!-- This also applies to this source document --></para>
     </legalnotice>
-    &dhdate;
   </refentryinfo>
 
   <refmeta>

Modified: trunk/packages/primer3/trunk/debian/primer3_core.1
===================================================================
--- trunk/packages/primer3/trunk/debian/primer3_core.1	2008-02-22 00:38:58 UTC (rev 1459)
+++ trunk/packages/primer3/trunk/debian/primer3_core.1	2008-02-22 01:52:12 UTC (rev 1460)
@@ -1,11 +1,11 @@
 .\"     Title: PRIMER3_CORE
 .\"    Author: 
 .\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\"      Date: February 17, 2007
+.\"      Date: 02/22/2008
 .\"    Manual: Primer3 User Manuals
-.\"    Source: primer3_core 1.1.1
+.\"    Source: primer3_core 1.1.3
 .\"
-.TH "PRIMER3_CORE" "1" "February 17, 2007" "primer3_core 1.1.1" "Primer3 User Manuals"
+.TH "PRIMER3_CORE" "1" "02/22/2008" "primer3_core 1.1.3" "Primer3 User Manuals"
 .\" disable hyphenation
 .nh
 .\" disable justification (adjust text to left margin only)
@@ -74,7 +74,7 @@
 \fBntdpal\fR(1)
 \fBoligotm\fR(1)
 .SH "COPYRIGHT"
-Copyright \(co 1996,1997,1998,1999,2000,2001,2004,2006,2007 Whitehead Institute for Biomedical Research, Steve Rozen (http://jura.wi.mit.edu/rozen), Helen Skaletsky
+Copyright \(co 1996,1997,1998,1999,2000,2001,2004,2006,2007,2008 Whitehead Institute for Biomedical Research, Steve Rozen (http://jura.wi.mit.edu/rozen), Helen Skaletsky
 .br
 .PP
 All rights reserved\. On Debian\-based systems, please consult

Modified: trunk/packages/primer3/trunk/debian/primer3_core.1.xml
===================================================================
--- trunk/packages/primer3/trunk/debian/primer3_core.1.xml	2008-02-22 00:38:58 UTC (rev 1459)
+++ trunk/packages/primer3/trunk/debian/primer3_core.1.xml	2008-02-22 01:52:12 UTC (rev 1460)
@@ -6,14 +6,13 @@
   <!ENTITY dhfirstname "<firstname>Steffen</firstname>">
   <!ENTITY dhsurname   "<surname>Moeller</surname>">
   <!-- Please adjust the date whenever revising the manpage. -->
-  <!ENTITY dhdate      "<date>February 17, 2007</date>">
   <!ENTITY dhtitle     "Primer3 User Manuals">
   <!ENTITY dhsection   "<manvolnum>1</manvolnum>">
   <!ENTITY dhemail     "<email>steffen_moeller at gmx.de</email>">
   <!ENTITY dhusername  "Steffen Moeller">
   <!ENTITY dhucpackage "<refentrytitle>PRIMER3_CORE</refentrytitle>">
   <!ENTITY dhpackage   "primer3_core">
-  <!ENTITY dhrelease   "1.1.1">
+  <!ENTITY dhrelease   "1.1.3">
   <!ENTITY debian      "<productname>Debian</productname>">
   <!ENTITY gnu         "<acronym>GNU</acronym>">
   <!ENTITY gpl         "&gnu; <acronym>GPL</acronym>">
@@ -24,7 +23,6 @@
     <title>&dhtitle;</title>
     <productname>&dhpackage;</productname>
     <releaseinfo role="version">&dhrelease;</releaseinfo>
-      &dhdate;
     <address>
       &dhemail;
     </address>
@@ -33,7 +31,7 @@
       &dhsurname;
     </author> -->
     <copyright>
-      <year>1996,1997,1998,1999,2000,2001,2004,2006,2007</year>
+      <year>1996,1997,1998,1999,2000,2001,2004,2006,2007,2008</year>
       <holder>Whitehead Institute for Biomedical Research</holder>
       <holder>Steve Rozen (http://jura.wi.mit.edu/rozen)</holder>
       <holder>Helen Skaletsky</holder>

Modified: trunk/packages/primer3/trunk/debian/rules
===================================================================
--- trunk/packages/primer3/trunk/debian/rules	2008-02-22 00:38:58 UTC (rev 1459)
+++ trunk/packages/primer3/trunk/debian/rules	2008-02-22 01:52:12 UTC (rev 1460)
@@ -1,17 +1,9 @@
 #!/usr/bin/make -f
 
-DEB_HOST_ARCH_CPU ?= $(shell dpkg-architecture -qDEB_HOST_ARCH_CPU)
-SKIP_TEST_CPUS := arm m68k s390 mips mipsel hppa
-
 include /usr/share/cdbs/1/class/makefile.mk
 include /usr/share/cdbs/1/rules/debhelper.mk
 
-ifeq (,$(filter $(DEB_HOST_ARCH_CPU),$(SKIP_TEST_CPUS)))
 DEB_MAKE_CHECK_TARGET   = -C test test
-else
-DEB_MAKE_CHECK_TARGET   =
-endif
-
 DEB_MAKE_CLEAN_TARGET   = -C src clean
 DEB_MAKE_BUILD_TARGET   = -C src all

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