[med-svn] r20494 - in trunk/packages/vsearch/trunk/debian: . patches

[Andreas Tille]

Author: tille
Date: 2015-11-13 23:45:35 +0000 (Fri, 13 Nov 2015)
New Revision: 20494

Removed:
   trunk/packages/vsearch/trunk/debian/vsearch-data.install
   trunk/packages/vsearch/trunk/debian/vsearch-data.lintian-overrides
Modified:
   trunk/packages/vsearch/trunk/debian/changelog
   trunk/packages/vsearch/trunk/debian/control
   trunk/packages/vsearch/trunk/debian/patches/sysconf_memory_sizing.patch
   trunk/packages/vsearch/trunk/debian/rules
Log:
Adapt packaging to separate vsearch test data package


Modified: trunk/packages/vsearch/trunk/debian/changelog
===================================================================
--- trunk/packages/vsearch/trunk/debian/changelog	2015-11-13 23:41:49 UTC (rev 20493)
+++ trunk/packages/vsearch/trunk/debian/changelog	2015-11-13 23:45:35 UTC (rev 20494)
@@ -1,6 +1,7 @@
-vsearch (1.4.0-1) UNRELEASED; urgency=medium
+vsearch (1.9.1-1) UNRELEASED; urgency=medium
 
   * New upstream version (no need to exclude files any more)
+  * Test data are in separate package now
 
  -- Andreas Tille <tille at debian.org>  Mon, 28 Sep 2015 18:05:27 +0200
 

Modified: trunk/packages/vsearch/trunk/debian/control
===================================================================
--- trunk/packages/vsearch/trunk/debian/control	2015-11-13 23:41:49 UTC (rev 20493)
+++ trunk/packages/vsearch/trunk/debian/control	2015-11-13 23:45:35 UTC (rev 20494)
@@ -35,24 +35,3 @@
     than 4GB of memory
   - be as accurate or more accurate than usearch
   - be as fast or faster than usearch
-
-Package: vsearch-data
-Architecture: all
-Depends: ${shlibs:Depends},
-         ${misc:Depends}
-Description: example data for vsearch tool for processing metagenomic sequences
- Open and free 64-bit multithreaded tool for processing metagenomic sequences,
- including searching, clustering, chimera detection, dereplication, sorting,
- masking and shuffling
- .
- The aim of this project is to create an alternative to the USEARCH tool
- developed by Robert C. Edgar (2010). The new tool should:
- .
-  - have open source code with an appropriate open source license
-  - be free of charge, gratis
-  - have a 64-bit design that handles very large databases and much more
-    than 4GB of memory
-  - be as accurate or more accurate than usearch
-  - be as fast or faster than usearch
- .
- This package only contains data to run the vsearch test suite.

Modified: trunk/packages/vsearch/trunk/debian/patches/sysconf_memory_sizing.patch
===================================================================
--- trunk/packages/vsearch/trunk/debian/patches/sysconf_memory_sizing.patch	2015-11-13 23:41:49 UTC (rev 20493)
+++ trunk/packages/vsearch/trunk/debian/patches/sysconf_memory_sizing.patch	2015-11-13 23:45:35 UTC (rev 20494)
@@ -18,20 +18,3 @@
  unsigned long arch_get_memused()
  {
    struct rusage r_usage;
-@@ -92,7 +94,15 @@ unsigned long arch_get_memtotal()
-   if(sysctl(mib, 2, &ram, &length, NULL, 0) == -1)
-     fatal("Cannot determine amount of RAM");
-   return ram;
--
-+#elif defined(_SC_PHYS_PAGES) && defined(_SC_PAGESIZE)
-+  long phys_pages = sysconf(_SC_PHYS_PAGES),
-+       pagesize = sysconf(_SC_PAGESIZE);
-+  // sysconf(3) notes that pagesize * phys_pages can overflow, such as
-+  // when long is 32-bits and there's more than 4GB RAM.  Since vsearch
-+  // apparently targets LP64 systems like x86_64 linux, this will not
-+  // arise in practice on the intended platform.
-+  if( pagesize > LONG_MAX / phys_pages )  return LONG_MAX;
-+  return pagesize * phys_pages;
- #else
- 
-   struct sysinfo si;

Modified: trunk/packages/vsearch/trunk/debian/rules
===================================================================
--- trunk/packages/vsearch/trunk/debian/rules	2015-11-13 23:41:49 UTC (rev 20493)
+++ trunk/packages/vsearch/trunk/debian/rules	2015-11-13 23:45:35 UTC (rev 20494)
@@ -27,10 +27,14 @@
 
 ifeq (,$(findstring nocheck,$(DEB_BUILD_OPTIONS)))
 override_dh_auto_test:
-	cd test && \
-	for t in *.sh ; do \
-	    bash $$t v ; \
-	done
+	if [ -d /usr/share/vsearch/data ] ; then \
+	    ln -s /usr/share/vsearch/data ../vsearch-data && \
+	    cd test && \
+	    for t in *.sh ; do \
+	        bash $$t v ; \
+	    done ; \
+	    rm ../vsearch-data ; \
+	fi
 endif
 
 override_dh_clean:

Deleted: trunk/packages/vsearch/trunk/debian/vsearch-data.install
===================================================================
--- trunk/packages/vsearch/trunk/debian/vsearch-data.install	2015-11-13 23:41:49 UTC (rev 20493)
+++ trunk/packages/vsearch/trunk/debian/vsearch-data.install	2015-11-13 23:45:35 UTC (rev 20494)
@@ -1,2 +0,0 @@
-eval/*.pl		usr/share/doc/vsearch/tests/eval
-eval/*.txt		usr/share/doc/vsearch/tests/eval

Deleted: trunk/packages/vsearch/trunk/debian/vsearch-data.lintian-overrides
===================================================================
--- trunk/packages/vsearch/trunk/debian/vsearch-data.lintian-overrides	2015-11-13 23:41:49 UTC (rev 20493)
+++ trunk/packages/vsearch/trunk/debian/vsearch-data.lintian-overrides	2015-11-13 23:45:35 UTC (rev 20494)
@@ -1,4 +0,0 @@
-# vsearch is dueal licensed GPL-3+ or BSD-2-clause
-# since it is linked against openssl we choose BSD-2-clause license and thus
-# these lintian errors are void
-vsearch-data: copyright-should-refer-to-common-license-file-for-gpl