On Wed,  7 Nov 2018 19:56:53 +0000
Christopher Baines <mail@cbaines.net> 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."

> [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`.

> +             #t))
> +         (add-after 'use-c++14 'autoconf
>             (lambda _ (zero? (system* "autoconf")))))))

Maybe you could also update this step to use 'invoke'.

Thanks,
`~Eric