Re: [PATCH] gnu: Add samtools

[Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>]

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>>>> Can we disable the test suite for certain architectures?  Or would they
>>>> have to be disabled completely?
>>
>> Since it fails the same way on mips64el, I suggest this instead:
>>
>>    #:tests? (string=? (or (%current-system) (%current-target-system))
>>                           "x86_64-linux")
>
> Oops, we forgot to mention that there should be a comma before that
> first open paren, like this:
>
>     #:tests? ,(string=? (or (%current-system) (%current-target-system))
>                             "x86_64-linux")

Attached is a patch that disables the tests on all systems but
x86_64-linux.  I'm unsure about the indentation, though.  Should the
compared string really be aligned with the arguments of `(or' (as shown
above), or rather aligned with `(or', the argument to `(string=?' (as in
the attached patch)?

-- rekado


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From c9846248c28f2c22660c156d4275326fe8afac80 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Mon, 15 Dec 2014 12:23:01 +0100
Subject: [PATCH] gnu: samtools: disable tests for non-64-bit systems

* gnu/packages/bioinformatics.scm (samtools): disable tests for all non-64-bit
  systems because of an upstream bug in the test data.
---
 gnu/packages/bioinformatics.scm | 9 ++++++++-
 1 file changed, 8 insertions(+), 1 deletion(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index bcc5d43..1f323eb 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -111,7 +111,14 @@ BED, GFF/GTF, VCF.")
          "1y5p2hs4gif891b4ik20275a8xf3qrr1zh9wpysp4g8m0g1jckf2"))))
     (build-system gnu-build-system)
     (arguments
-     '(#:make-flags (list (string-append "prefix=" (assoc-ref %outputs "out")))
+     `(;; There are 87 test failures when building on non-64-bit architectures
+       ;; due to invalid test data.  This has since been fixed upstream (see
+       ;; <https://github.com/samtools/samtools/pull/307>), but as there has
+       ;; not been a new release we disable the tests for all non-64-bit
+       ;; systems.
+       #:tests? ,(string=? (or (%current-system) (%current-target-system))
+                           "x86_64-linux")
+       #:make-flags (list (string-append "prefix=" (assoc-ref %outputs "out")))
        #:phases
        (alist-cons-after
         'unpack
-- 
1.9.3