[bug#33308] [PATCH 1/2] gnu: mash: Update to 2.1.

[Christopher Baines]

Eric Bavier <address@hidden> writes:

> On Wed,  7 Nov 2018 19:56:53 +0000
> Christopher Baines <address@hidden> wrote:
>
>
>> * gnu/packages/bioinformatics.scm (mash)[version]: Change to 2.1.
>> [source]: Update sha256 hash.
>
> I think here we typically just say "(mash)[source]: Upgrade to 2.1."

Ok, I've sent a new set of patches now, and updated the commit messages.

>> [arguments]: Add new use-c++14 phase, to patch source to build using c++14.
>> ---
>>  gnu/packages/bioinformatics.scm | 14 +++++++++++---
>>  1 file changed, 11 insertions(+), 3 deletions(-)
>>
>> diff --git a/gnu/packages/bioinformatics.scm 
>> b/gnu/packages/bioinformatics.scm
>> index 9f0b8025da..93503d82b8 100644
>> --- a/gnu/packages/bioinformatics.scm
>> +++ b/gnu/packages/bioinformatics.scm
>> @@ -4012,7 +4012,15 @@ sequences).")
>>                 (("^#include \"kseq\\.h\"")
>>                  "#include \"htslib/kseq.h\""))
>>               #t))
>> -         (add-after 'fix-includes 'autoconf
>> +         (add-after 'fix-includes 'use-c++14
>> +           (lambda _
>> +             ;; capnproto 0.7 requires c++14 to build
>> +             (substitute* "configure.ac"
>> +               (("c\\+\\+11") "c++14"))
>> +             (substitute* "Makefile.in"
>> +               (("c\\+\\+11") "c++14"))
>
> I believe the configure.ac patch is sufficient for us here, since the
> compile steps will pick up the CPPFLAGS set there.  Too bad the
> configure.ac is written so poorly... :(  one should be able to just
> pass "CPPFLAGS=-std=c++14" to `make`.

I tried removing the Makefile.in change, but it didn't work for some
reason.

>> +             #t))
>> +         (add-after 'use-c++14 'autoconf
>>             (lambda _ (zero? (system* "autoconf")))))))
>
> Maybe you could also update this step to use 'invoke'.

This patch has now turned in to just fixing the package for the newer
version of capnproto, as Ricardo did the upgrade a few weeks ago. This
particular stage was removed in
e35dce017090685d07aedf10c9899c0cdcc70d9e.

Thanks for your comments Eric :)

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