From: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
To: Mark H Weaver <mhw@netris.org>
Cc: guix-devel <guix-devel@gnu.org>
Subject: Re: [PATCH] Add Blast+.
Date: Mon, 29 Jun 2015 16:15:39 +0200 [thread overview]
Message-ID: <idjpp4eios4.fsf@bimsb-sys02.mdc-berlin.net> (raw)
In-Reply-To: <87egkxf1je.fsf@netris.org>
Mark H Weaver <mhw@netris.org> writes:
>> + (snippet
>> + '(begin
>> + ;; Remove bundled bzip2 and zlib
>> + (delete-file-recursively "c++/src/util/compress/bzip2")
>> + (delete-file-recursively "c++/src/util/compress/zlib")
>> + (substitute* "c++/src/util/compress/Makefile.in"
>> + (("bzip2 zlib api") "api"))
>> + ;; Remove useless msbuild directory
>> + (delete-file-recursively
>> + "c++/src/build-system/project_tree_builder/msbuild")))))
>
> As with phase procedures, the snippet should return a boolean, so please
> add #t here.
Done.
>> + ;; Proceed even though the weird build system says that generated
>> + ;; files are out of date
>> + (setenv "NCBICXX_RECONF_POLICY" "warn")
>> +
>> + ;; Rewrite hardcoded paths to various tools
>> + (substitute* (append (find-files "scripts/common/check" "\\.sh$")
>> + '("scripts/common/impl/if_diff.sh"
>> + "scripts/common/impl/run_with_lock.sh"
>> + "src/build-system/Makefile.configurables.real"
>> + "src/build-system/Makefile.in.top"
>> + "src/build-system/Makefile.meta.gmake=no"
>> + "src/build-system/Makefile.meta.in"
>> + "src/build-system/Makefile.meta_l"
>> + "src/build-system/Makefile.meta_p"
>> + "src/build-system/Makefile.meta_r"
>> + "src/build-system/Makefile.mk.in"
>> + "src/build-system/Makefile.requirements"
>> + "src/build-system/Makefile.rules_with_autodep.in"
>> + "src/build-system/configure"
>> + "src/build-system/configure.ac"))
>> + (("(/usr/bin/|/bin/)([a-z][-_.a-z]*)" all dir cmd)
>> + (or (which* cmd) all)))
>
> It would be better to patch configure.ac first, and then configure, and
> then the others. As you have it here, the modification times will
> indicate that 'configure' is older than 'configure.ac' and thus out of
> date. Perhaps this is why you needed to setenv NCBICXX_RECONF_POLICY?
You were right. I reordered the patching and could remove the
variable. Thank you for the review and sharing your insights!
I updated to Blast 2.2.31, built successfully and just pushed.
~~ Ricardo
prev parent reply other threads:[~2015-06-29 14:15 UTC|newest]
Thread overview: 8+ messages / expand[flat|nested] mbox.gz Atom feed top
2015-06-16 14:26 [PATCH] Add Blast+ Ricardo Wurmus
2015-06-16 21:37 ` Mark H Weaver
2015-06-23 8:06 ` Ricardo Wurmus
2015-06-27 10:14 ` Ludovic Courtès
2015-06-27 13:10 ` Ben Woodcroft
2015-06-27 14:09 ` Ricardo Wurmus
2015-06-27 18:29 ` Mark H Weaver
2015-06-29 14:15 ` Ricardo Wurmus [this message]
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