[PATCH] Attempt to fix build of sra-tools on i686.

[PATCH] Attempt to fix build of sra-tools on i686.

[Ricardo Wurmus]

[-- Attachment #1: Type: text/plain, Size: 304 bytes --]

Currently sra-tools fails to build on i686 because the custom
configuration system cannot find the "ilib" directory for "ncbi-vdb".
Turns out that "ncbi-vdb" had a broken "install-interfaces" phase on
i686.

The attached patch fixes the phase on i686 and should thus fix the build
of sra-tools on i686.


[-- Warning: decoded text below may be mangled, UTF-8 assumed --]
[-- Attachment #2: 0001-gnu-ncbi-vdb-Use-i386-instead-of-i686-in-directory-n.patch --]
[-- Type: text/x-patch, Size: 1653 bytes --]

From 6d3e22354c767f76711e3f73a2e26d7d7783f57a Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Mon, 1 Jun 2015 11:31:29 +0200
Subject: [PATCH] gnu: ncbi-vdb: Use "i386" instead of "i686" in directory
 name.

* gnu/packages/bioinformatics.scm (ncbi-vdb)[arguments]: Copy libraries from
  "linux/gcc/i386" directory instead of "linux/gcc/i686" when building on
  i686.
---
 gnu/packages/bioinformatics.scm | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 71055d1..9f6d75a 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -1506,11 +1506,13 @@ simultaneously.")
                                    (assoc-ref inputs "hdf5"))))))
         (alist-cons-after
          'install 'install-interfaces
-         (lambda* (#:key system outputs #:allow-other-keys)
+         (lambda* (#:key outputs #:allow-other-keys)
            ;; Install interface libraries
            (mkdir (string-append (assoc-ref outputs "out") "/ilib"))
            (copy-recursively (string-append "build/ncbi-vdb/linux/gcc/"
-                                            (car (string-split system #\-))
+                                            ,(system->linux-architecture
+                                              (or (%current-target-system)
+                                                  (%current-system)))
                                             "/rel/ilib")
                              (string-append (assoc-ref outputs "out")
                                             "/ilib"))
-- 
2.1.0

Re: [PATCH] Attempt to fix build of sra-tools on i686.

[Ludovic Courtès]

Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de> skribis:

> From 6d3e22354c767f76711e3f73a2e26d7d7783f57a Mon Sep 17 00:00:00 2001
> From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
> Date: Mon, 1 Jun 2015 11:31:29 +0200
> Subject: [PATCH] gnu: ncbi-vdb: Use "i386" instead of "i686" in directory
>  name.
>
> * gnu/packages/bioinformatics.scm (ncbi-vdb)[arguments]: Copy libraries from
>   "linux/gcc/i386" directory instead of "linux/gcc/i686" when building on
>   i686.

This is terrible!  :-)  Could you make the explanation a comment in the source?

Otherwise LGTM!

Ludo’.