Re: [PATCH] Add Blast+.

[Ricardo Wurmus]

Mark H Weaver <address@hidden> 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 +            ;; files are out of date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