[med-svn] r15568 - in trunk/packages/primer3/trunk/debian: . patches
Andreas Tille
tille at moszumanska.debian.org
Thu Dec 19 09:56:49 UTC 2013
Author: tille
Date: 2013-12-19 09:56:49 +0000 (Thu, 19 Dec 2013)
New Revision: 15568
Added:
trunk/packages/primer3/trunk/debian/patches/primer_thermodynamic_parameters_path_2_etc.patch
Modified:
trunk/packages/primer3/trunk/debian/changelog
trunk/packages/primer3/trunk/debian/patches/series
Log:
Make sure config files will be searched for in /etc/primer3_config/ instead of /opt/primer3_config/
Modified: trunk/packages/primer3/trunk/debian/changelog
===================================================================
--- trunk/packages/primer3/trunk/debian/changelog 2013-12-19 09:44:22 UTC (rev 15567)
+++ trunk/packages/primer3/trunk/debian/changelog 2013-12-19 09:56:49 UTC (rev 15568)
@@ -2,7 +2,7 @@
[ Charles Plessy ]
* New upstream release.
- * Install configuration files in /etc (first step to fix #702693).
+ * Install configuration files in /etc (first step to fix bug 702693).
* Normalised debian/control with config-model-edit.
* Use canonical VCS URLs.
@@ -11,6 +11,10 @@
* replace cdbs by dh
* debian/patches/hardening.patch: Propagate hardening options
* Standards-Version: 3.9.5 (no changes needed)
+ * debian/patches/primer_thermodynamic_parameters_path_2_etc.patch:
+ Make sure config files will be searched for in /etc/primer3_config/
+ instead of /opt/primer3_config/
+ Closes: #702693
-- Andreas Tille <tille at debian.org> Thu, 19 Dec 2013 09:58:19 +0100
Added: trunk/packages/primer3/trunk/debian/patches/primer_thermodynamic_parameters_path_2_etc.patch
===================================================================
--- trunk/packages/primer3/trunk/debian/patches/primer_thermodynamic_parameters_path_2_etc.patch (rev 0)
+++ trunk/packages/primer3/trunk/debian/patches/primer_thermodynamic_parameters_path_2_etc.patch 2013-12-19 09:56:49 UTC (rev 15568)
@@ -0,0 +1,83 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Changed: Thu, 19 Dec 2013 09:58:19 +0100
+Bug-Debian: http://bugs.debian.org/702693
+Description: Configuration in /etc
+ Make sure config files will be searched for in /etc/primer3_config/
+ instead of /opt/primer3_config/
+
+
+--- a/src/primer3_boulder_main.c
++++ b/src/primer3_boulder_main.c
+@@ -505,18 +505,18 @@ read_thermodynamic_parameters()
+ return;
+ }
+ #else
+- /* in linux, check for ./primer3_config and /opt/primer3_config */
++ /* in Debian, check for ./primer3_config and /etc/primer3_config */
+ struct stat st;
+ if ((stat("./primer3_config", &st) == 0) && S_ISDIR(st.st_mode)) {
+ thermodynamic_params_path =
+ (char*) malloc(strlen("./primer3_config/") * sizeof(char) + 1);
+ if (NULL == thermodynamic_params_path) exit (-2); /* Out of memory */
+ strcpy(thermodynamic_params_path, "./primer3_config/");
+- } else if ((stat("/opt/primer3_config", &st) == 0) && S_ISDIR(st.st_mode)) {
++ } else if ((stat("/etc/primer3_config", &st) == 0) && S_ISDIR(st.st_mode)) {
+ thermodynamic_params_path =
+- (char*) malloc(strlen("/opt/primer3_config/") * sizeof(char) + 1);
++ (char*) malloc(strlen("/etc/primer3_config/") * sizeof(char) + 1);
+ if (NULL == thermodynamic_params_path) exit (-2); /* Out of memory */
+- strcpy(thermodynamic_params_path, "/opt/primer3_config/");
++ strcpy(thermodynamic_params_path, "/etc/primer3_config/");
+ } else {
+ /* no default directory found */
+ return;
+--- a/src/thal_main.c
++++ b/src/thal_main.c
+@@ -303,8 +303,8 @@ if(a.debug == 0) {
+ #else
+ if ((stat("./primer3_config", &st) == 0) && S_ISDIR(st.st_mode)) {
+ tmp_ret = get_thermodynamic_values("./primer3_config/", &o);
+- } else if ((stat("/opt/primer3_config", &st) == 0) && S_ISDIR(st.st_mode)) {
+- tmp_ret = get_thermodynamic_values("/opt/primer3_config/", &o);
++ } else if ((stat("/etc/primer3_config", &st) == 0) && S_ISDIR(st.st_mode)) {
++ tmp_ret = get_thermodynamic_values("/etc/primer3_config/", &o);
+ } else {
+ /* no default directory found, error */
+ fprintf(stderr, "Error: thermodynamic approach chosen, but path to thermodynamic parameters not specified\n");
+--- a/src/release_notes.txt
++++ b/src/release_notes.txt
+@@ -151,9 +151,9 @@ defaults. The default is --default_vers
+ 1.5 IMPORTANT: because PRIMER_THERMODYNAMIC_ALIGNMENT=1,
+ PRIMER_THERMODYNAMIC_PARAMETERS_PATH must point to the right location.
+ This tag specifies the path to the directory that contains all the
+-parameter files used by the thermodynamic approach. In Linux, there
++parameter files used by the thermodynamic approach. In Debian, there
+ are two *default* locations that are tested if this tag is not
+-defined: ./primer3_config/ and /opt/primer3_config/. For Windows,
++defined: ./primer3_config/ and /etc/primer3_config/. For Windows,
+ there is only one default location: .\primer3_config\. If the the
+ parameter files are not in one these locations, be sure to set
+ PRIMER_THERMODYNAMIC_PARAMETERS_PATH
+--- a/primer3_manual.htm
++++ b/primer3_manual.htm
+@@ -229,9 +229,9 @@ defaults. The default is --default_vers
+ 2.5. IMPORTANT: because <a href="#PRIMER_THERMODYNAMIC_OLIGO_ALIGNMENT">PRIMER_THERMODYNAMIC_OLIGO_ALIGNMENT</a>=1,
+ <a href="#PRIMER_THERMODYNAMIC_PARAMETERS_PATH">PRIMER_THERMODYNAMIC_PARAMETERS_PATH</a> must point to the right location.
+ This tag specifies the path to the directory that contains all the
+-parameter files used by the thermodynamic approach. In Linux, there
++parameter files used by the thermodynamic approach. In Debian, there
+ are two *default* locations that are tested if this tag is not
+-defined: ./primer3_config/ and /opt/primer3_config/. For Windows,
++defined: ./primer3_config/ and /etc/primer3_config/. For Windows,
+ there is only one default location: .\primer3_config\. If the the
+ parameter files are not in one these locations, be sure to set
+ <a href="#PRIMER_THERMODYNAMIC_PARAMETERS_PATH">PRIMER_THERMODYNAMIC_PARAMETERS_PATH</a>.<br>
+@@ -2452,7 +2452,7 @@ the propensity of oligos to anneal to un
+ <p>This tag specifies the path to the directory that contains all the
+ parameter files used by the thermodynamic approach. In Linux, there are two
+ default locations that are tested if this tag is not defined:
+-<i>./primer3_config/</i> and <i>/opt/primer3_config/</i>.
++<i>./primer3_config/</i> and <i>/etc/primer3_config/</i>.
+ For Windows, there is only one default location: <i>.\primer3_config\</i>.</p>
+
+
Modified: trunk/packages/primer3/trunk/debian/patches/series
===================================================================
--- trunk/packages/primer3/trunk/debian/patches/series 2013-12-19 09:44:22 UTC (rev 15567)
+++ trunk/packages/primer3/trunk/debian/patches/series 2013-12-19 09:56:49 UTC (rev 15568)
@@ -1 +1,2 @@
hardening.patch
+primer_thermodynamic_parameters_path_2_etc.patch
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