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| author | George Hartzell <hartzell@alerce.com> | 2020-04-09 09:53:34 -0700 |
|---|---|---|
| committer | GitHub <noreply@github.com> | 2020-04-09 11:53:34 -0500 |
| commit | 1b2638c9b15638600da92a350b15ec32523059cf (patch) | |
| tree | fd72c3538c13756599392e3459c157b8300a496c | |
| parent | 05a80523c84eb2a696441762728bebf6fc2d8404 (diff) | |
| download | spack-1b2638c9b15638600da92a350b15ec32523059cf.tar.gz spack-1b2638c9b15638600da92a350b15ec32523059cf.tar.bz2 spack-1b2638c9b15638600da92a350b15ec32523059cf.tar.xz spack-1b2638c9b15638600da92a350b15ec32523059cf.zip | |
primer3: move to github, add 2.5.0, fix 2.3.7 (#15958)
* primer3: move to github, add 2.5.0, fix 2.3.7
- The Primer3 project moved to GitHub.
- update the URL
- compare the tarballs 2.3.7 from Sourceforge and github, no
significant differences (e.g. the Sourceforge tarball contained a
couple of "tmp" files).
- update the signature for the 2.3.7 tarball.
- @2.3.7 doesn't build with gcc@8.4.0, there's a dubious pointer/int
comparison that causes an error. It was fixed upstream in newer
versions, apply simple patch to this version so that it continues to
be build-able with newer compilers. See:
- https://github.com/primer3-org/primer3/issues/2
- https://github.com/primer3-org/primer3/issues/3
- Add info for @2.5.0, which builds cleanly.
* Flake8 cleanup
| -rw-r--r-- | var/spack/repos/builtin/packages/primer3/package.py | 18 |
1 files changed, 15 insertions, 3 deletions
diff --git a/var/spack/repos/builtin/packages/primer3/package.py b/var/spack/repos/builtin/packages/primer3/package.py index f54d1d6828..b4f2ad849b 100644 --- a/var/spack/repos/builtin/packages/primer3/package.py +++ b/var/spack/repos/builtin/packages/primer3/package.py @@ -12,13 +12,25 @@ class Primer3(MakefilePackage): ubiquitous tool in genetics and molecular biology. Primer3 can also design hybridization probes and sequencing primers.""" - homepage = "http://primer3.sourceforge.net/" - url = "https://sourceforge.net/projects/primer3/files/primer3/2.3.7/primer3-2.3.7.tar.gz/download" + homepage = "https://primer3.org/" + url = "https://github.com/primer3-org/primer3/archive/v2.3.7.tar.gz" - version('2.3.7', sha256='9e37a301d2ca9e5034c9a9d4afcb3e90041f6cc44c658b63598d0ccfcb176e5e') + version('2.5.0', sha256='7581e2fa3228ef0ee1ffa427b2aa0a18fc635d561208327471daf59d1b804da0') + version('2.3.7', sha256='f7ac3e64dc89b7c80882bf0f52c2c0a58572f5fdafd178680d4a7ae91b6c465b') build_directory = 'src' + # Prior to May 15, 2018, the code contained invalid pointer/int + # comparisons, leading to compilers that default to strict mode + # failing to compile thal.c. + # This prevents building 2.3.7 w/ gcc@8.4.0. Details here: + # https://github.com/primer3-org/primer3/issues/2 + # https://github.com/primer3-org/primer3/issues/3 + def patch(self): + if self.spec.version == Version('2.3.7'): + filter_file(r'^(CC_OPTS.*)', r'\1 -fpermissive', + join_path('src', 'Makefile')) + def install(self, spec, prefix): with working_dir(self.build_directory): mkdirp(prefix.bin) |