[PATCH] Fix subread on non-x86_64

[PATCH] Fix subread on non-x86_64

[Ricardo Wurmus]

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Hi Guix,

the attached patch should fix the build of subread on non-x86_64 by
overriding the CC and CCFLAGS variables, which by default are set to
contain a lot of x86_64 optimisations.

~~ Ricardo


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From 71a37b56d0962f0db4009bdb6a88c22025278a00 Mon Sep 17 00:00:00 2001
From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
Date: Fri, 23 Oct 2015 14:16:27 +0200
Subject: [PATCH] gnu: subread: Use SSE optimizations on x86_64 only.

* gnu/packages/bioinformatics.scm (subread)[arguments]: Override CC and
  CCFLAGS conditionally dependent on target system.
---
 gnu/packages/bioinformatics.scm | 16 +++++++++++++++-
 1 file changed, 15 insertions(+), 1 deletion(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 8a81150..ddaffd8 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -2814,7 +2814,21 @@ sequences.")
     (build-system gnu-build-system)
     (arguments
      `(#:tests? #f ;no "check" target
-       #:make-flags '("-f" "Makefile.Linux")
+       #:make-flags
+       (list (let ((system ,(or (%current-target-system)
+                                (%current-system)))
+                   (flags '("-ggdb" "-fomit-frame-pointer"
+                            "-ffast-math" "-funroll-loops"
+                            "-fmessage-length=0"
+                            "-O9" "-Wall" "-DMAKE_FOR_EXON"
+                            "-DMAKE_STANDALONE"
+                            "-DSUBREAD_VERSION=\\\"${SUBREAD_VERSION}\\\""))
+                   (flags64 '("-mmmx" "-msse" "-msse2" "-msse3")))
+               (if (string-prefix? "x86_64" system)
+                   (string-append "CCFLAGS=" (string-join (append flags flags64) " "))
+                   (string-append "CCFLAGS=" (string-join flags " "))))
+             "-f" "Makefile.Linux"
+             "CC=gcc ${CCFLAGS}")
        #:phases
        (alist-cons-after
         'unpack 'enter-dir
-- 
2.1.0

Re: [PATCH] Fix subread on non-x86_64

[Ludovic Courtès]

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

> the attached patch should fix the build of subread on non-x86_64 by
> overriding the CC and CCFLAGS variables, which by default are set to
> contain a lot of x86_64 optimisations.

Nice!  Could you add a comment explaining that?

> From 71a37b56d0962f0db4009bdb6a88c22025278a00 Mon Sep 17 00:00:00 2001
> From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
> Date: Fri, 23 Oct 2015 14:16:27 +0200
> Subject: [PATCH] gnu: subread: Use SSE optimizations on x86_64 only.
>
> * gnu/packages/bioinformatics.scm (subread)[arguments]: Override CC and
>   CCFLAGS conditionally dependent on target system.

[...]

> +               (if (string-prefix? "x86_64" system)
> +                   (string-append "CCFLAGS=" (string-join (append flags flags64) " "))
> +                   (string-append "CCFLAGS=" (string-join flags " "))))

The last argument to ‘string-join’ can be omitted here.

OK with these two changes.

It may be a good case for ‘guix challenge’ here: If things like
-mtune=native or FDO creep in, ‘guix challenge’ is likely to flag them.

Thanks,
Ludo’.

Re: [PATCH] Fix subread on non-x86_64

[Ricardo Wurmus]

Ludovic Courtès <ludo@gnu.org> writes:

> Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de> skribis:
>
>> the attached patch should fix the build of subread on non-x86_64 by
>> overriding the CC and CCFLAGS variables, which by default are set to
>> contain a lot of x86_64 optimisations.
>
> Nice!  Could you add a comment explaining that?

Sure.

>> From 71a37b56d0962f0db4009bdb6a88c22025278a00 Mon Sep 17 00:00:00 2001
>> From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
>> Date: Fri, 23 Oct 2015 14:16:27 +0200
>> Subject: [PATCH] gnu: subread: Use SSE optimizations on x86_64 only.
>>
>> * gnu/packages/bioinformatics.scm (subread)[arguments]: Override CC and
>>   CCFLAGS conditionally dependent on target system.
>
> [...]
>
>> +               (if (string-prefix? "x86_64" system)
>> +                   (string-append "CCFLAGS=" (string-join (append flags flags64) " "))
>> +                   (string-append "CCFLAGS=" (string-join flags " "))))
>
> The last argument to ‘string-join’ can be omitted here.

Okay.  Pushed with the above changes.
Thanks!

~~ Ricardo