[med-svn] r6882 - trunk/packages/ncbi-blast-plus/trunk/debian/patches

[Aaron M. Ucko]

Author: ucko
Date: 2011-05-29 15:07:21 +0000 (Sun, 29 May 2011)
New Revision: 6882

Modified:
   trunk/packages/ncbi-blast-plus/trunk/debian/patches/fix_checks
Log:
Replace the old fix_checks patch (unnecessary when build-depending on time)
with a new one (freshly integrated upstream) that allows correct test
autodiscovery when unpacked under .../src/... directories.


Modified: trunk/packages/ncbi-blast-plus/trunk/debian/patches/fix_checks
===================================================================
--- trunk/packages/ncbi-blast-plus/trunk/debian/patches/fix_checks	2011-05-29 15:03:02 UTC (rev 6881)
+++ trunk/packages/ncbi-blast-plus/trunk/debian/patches/fix_checks	2011-05-29 15:07:21 UTC (rev 6882)
@@ -1,35 +1,45 @@
-Subject:  command time not found when using shell
+Subject:  checks misreported as absent when unpacked under /*/src/*
 
- * scripts/common/check/check_make_unix.sh: use bash and remove exec usage
+ * scripts/common/check/check_add.sh: accept the relative source directory
+ * src/build-system/Makefile.meta.in: supply it to check_add.sh
 
-Author: Olivier Sallou <olivier.sallou at irisa.fr>
-Last-Update: 2011-05-03
---- a/c++/scripts/common/check/check_make_unix.sh
-+++ b/c++/scripts/common/check/check_make_unix.sh
-@@ -503,8 +503,8 @@
-                         # Also, process guard works better if used after "time -p".
-                         launch_sh="/var/tmp/launch.\$\$.sh"
- cat > \$launch_sh <<EOF_launch
--#! /bin/sh
--exec time -p \$check_exec \`eval echo \$xx_run\`
-+#! /bin/bash
-+time -p \$check_exec \`eval echo \$xx_run\`
- EOF_launch
-                         chmod a+x \$launch_sh
-                         \$launch_sh >\$x_log 2>&1
---- a/c++/src/serial/datatool/datatool.sh
-+++ b/c++/src/serial/datatool/datatool.sh
-@@ -1,4 +1,4 @@
--#! /bin/sh
-+#! /bin/bash
- # $Id: datatool.sh 79502 2006-03-23 19:45:38Z gouriano $
- #
+Author: Aaron M. Ucko <ucko at debian.org>
+Last-Update: 2011-05-23
+--- a/c++/scripts/common/check/check_add.sh	2011-05-23 18:49:10.000000000 -0400
++++ b/c++/scripts/common/check/check_add.sh	2011-05-23 18:50:40.000000000 -0400
+@@ -28,14 +28,12 @@
+ x_srcdir=`(cd "$1"; pwd)`
+ x_test=$2
+ x_signature=$3
++x_srcdir_rel=$4
+ x_use_ignore_list=${CHECK_USE_IGNORE_LIST-Y}
+ x_delim=" ____ "
+ # Default timeout for check (in seconds)
+ x_timeout_default=200
  
---- a/c++/src/serial/datatool/datatool_xml.sh
-+++ b/c++/src/serial/datatool/datatool_xml.sh
-@@ -1,4 +1,4 @@
--#! /bin/sh
-+#! /bin/bash
- # $Id: datatool_xml.sh 141084 2008-09-23 19:53:09Z ivanovp $
- #
+-# Convert source dir to relative path
+-x_srcdir_rel=`echo "$x_srcdir" | perl -ne 's|^.*?/src/||; print'`
+-
+ # Check to necessity make test for this application
+ if test ! -f "$x_srcdir/Makefile.$x_test.app";  then
+    echo "Warning: File \"$x_srcdir/Makefile.$x_test.app\" not found."
+@@ -46,7 +44,7 @@
+ x_app=`grep '^ *APP[ =]' "$x_srcdir/Makefile.$x_test.app"`
+ x_app=`echo "$x_app" | sed -e 's/^.*=//' -e 's/^ *//'`
  
+-x_tpath=`echo "$x_srcdir/$x_test" | perl -ne 's|^.*?/src/||; print'`
++x_tpath=$x_srcdir_rel/$x_test
+ if grep -c '^ *CHECK_CMD' $x_srcdir/Makefile.$x_test.app > /dev/null ; then 
+    # Check ignore list
+    x_use_ignore_list=`echo $x_use_ignore_list | tr '[a-z]' '[A-Z]' | sed -e 's/^\(.\).*/\1/g'`
+--- a/c++/src/build-system/Makefile.meta.in	2011-05-23 18:48:59.000000000 -0400
++++ b/c++/src/build-system/Makefile.meta.in	2011-05-23 18:49:20.000000000 -0400
+@@ -188,7 +188,7 @@
+    expendable=false ; \
+    for i in $$x_project ; do \
+       if test "x$$i" = "x-" ; then expendable=true ; continue ; fi ; \
+-      $(check_add) $(abs_srcdir) $$i @signature@ @exe_ext@
++      $(check_add) $(abs_srcdir) $$i @signature@ $(subdir)
+ CHECK_ADD_KET = ||  exit 5 ; \
+    done ; \
+ fi