[med-svn] samtools 01/01: Reduce per-thread memory limit of sort tests, upload to unstable

[Graham Inggs]

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commit 931933e085e8a0d61fd17c1c7e4654a3c9eaffb9
Author: Graham Inggs <ginggs at debian.org>
Date:   Sat Dec 23 09:05:16 2017 +0200

    Reduce per-thread memory limit of sort tests, upload to unstable
---
 debian/changelog                             |  6 +++++
 debian/patches/series                        |  1 +
 debian/patches/sort-tests-memory-limit.patch | 37 ++++++++++++++++++++++++++++
 3 files changed, 44 insertions(+)

diff --git a/debian/changelog b/debian/changelog
index b128290..d732a71 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,9 @@
+samtools (1.6-4) unstable; urgency=medium
+
+  * Reduce per-thread memory limit of sort tests
+
+ -- Graham Inggs <ginggs at debian.org>  Sat, 23 Dec 2017 07:03:20 +0000
+
 samtools (1.6-3) unstable; urgency=medium
 
   * Upload to unstable
diff --git a/debian/patches/series b/debian/patches/series
index d87adb1..e1149f7 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,2 +1,3 @@
 spelling.patch
 mayhem.patch
+sort-tests-memory-limit.patch
diff --git a/debian/patches/sort-tests-memory-limit.patch b/debian/patches/sort-tests-memory-limit.patch
new file mode 100644
index 0000000..1b48b83
--- /dev/null
+++ b/debian/patches/sort-tests-memory-limit.patch
@@ -0,0 +1,37 @@
+Description: Reduce per-thread memory limit of sort tests
+ Fixes FTBFS on mips and mipsel, and autopkgtest failures
+ occurring on most architectures in Ubuntu
+Author: Graham Inggs <ginggs at debian.org>
+Last-Update: 2017-12-22
+
+--- a/test/test.pl
++++ b/test/test.pl
+@@ -2465,22 +2465,22 @@
+ 
+ 
+     # Pos sort
+-    test_cmd($opts, out=>"sort/pos.sort.expected.sam", cmd=>"$$opts{bin}/samtools sort${threads}  $$opts{path}/dat/test_input_1_a.bam -O SAM -o -");
++    test_cmd($opts, out=>"sort/pos.sort.expected.sam", cmd=>"$$opts{bin}/samtools sort${threads} -m 192M  $$opts{path}/dat/test_input_1_a.bam -O SAM -o -");
+ 
+     # Name sort
+-    test_cmd($opts, out=>"sort/name.sort.expected.sam", cmd=>"$$opts{bin}/samtools sort${threads} -n  $$opts{path}/dat/test_input_1_a.bam -O SAM -o -");
++    test_cmd($opts, out=>"sort/name.sort.expected.sam", cmd=>"$$opts{bin}/samtools sort${threads} -m 192M -n  $$opts{path}/dat/test_input_1_a.bam -O SAM -o -");
+ 
+     # Tag sort (RG)
+-    test_cmd($opts, out=>"sort/tag.rg.sort.expected.sam", cmd=>"$$opts{bin}/samtools sort${threads} -t RG  $$opts{path}/dat/test_input_1_a.bam -O SAM -o -");
++    test_cmd($opts, out=>"sort/tag.rg.sort.expected.sam", cmd=>"$$opts{bin}/samtools sort${threads} -m 192M -t RG  $$opts{path}/dat/test_input_1_a.bam -O SAM -o -");
+ 
+     # Tag sort (RG); secondary by name
+-    test_cmd($opts, out=>"sort/tag.rg.n.sort.expected.sam", cmd=>"$$opts{bin}/samtools sort${threads} -n -t RG  $$opts{path}/dat/test_input_1_a.bam -O SAM -o -");
++    test_cmd($opts, out=>"sort/tag.rg.n.sort.expected.sam", cmd=>"$$opts{bin}/samtools sort${threads} -m 192M -n -t RG  $$opts{path}/dat/test_input_1_a.bam -O SAM -o -");
+ 
+     # Tag sort (AS)
+-    test_cmd($opts, out=>"sort/tag.as.sort.expected.sam", cmd=>"$$opts{bin}/samtools sort${threads} -t AS $$opts{path}/dat/test_input_1_d.sam -O SAM -o -");
++    test_cmd($opts, out=>"sort/tag.as.sort.expected.sam", cmd=>"$$opts{bin}/samtools sort${threads} -m 192M -t AS $$opts{path}/dat/test_input_1_d.sam -O SAM -o -");
+ 
+     # Tag sort (FI)
+-    test_cmd($opts, out=>"sort/tag.fi.sort.expected.sam", cmd=>"$$opts{bin}/samtools sort${threads} -t FI $$opts{path}/dat/test_input_1_d.sam -O SAM -o -");
++    test_cmd($opts, out=>"sort/tag.fi.sort.expected.sam", cmd=>"$$opts{bin}/samtools sort${threads} -m 192M -t FI $$opts{path}/dat/test_input_1_d.sam -O SAM -o -");
+ }
+ 
+ sub test_fixmate

-- 
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