ncbi/ngs

Please don't assume that only macos uses clang

yurivict opened this issue · 6 comments

yurivict commented

This line my $versionMin = '-mmacosx-version-min=10.6'; adds the flag that BSD systems using clang don't understand. Please either remove it, or adjust it.

kwrodarmer commented

Please notice that if you are building for BSD, then you are creating a new port: we only have (and support) builds for Linux, Mac and Windows. You are more than welcome to build for BSD, but your demands give the impression that you think we support BSD, and we don't.

yurivict commented

This is a bug report, not a demand.

kwrodarmer commented

Perhaps I misunderstood. If you are trying to create a new port, we would be happy to talk with you and work with you, but we lack the ability to test changes under BSD.

yurivict commented

I am about to create a port for FreeBSD. There are a few patches that I added for the port to build.

One of them is this issue, I had to add this patch:

-    my $versionMin = '-mmacosx-version-min=10.6';
+    my $versionMin = '';

You might want to only use this key (-mmacosx-version-min) on MacOS. Currently it is used for clang in general.

yurivict commented

FYI: I've added the port: https://svnweb.freebsd.org/ports/head/biology/ngs-sdk/
It works, you don't need to verify anything.

Few patches can be upstreamed:

  • This one with mmacosx-version-min which is MacOS-specific
  • Library suffix (lib64) is platform-specific. BSDs don't add $BITS to lib
  • Soname is probably MacOS-specific.
klymenko commented

ngs was moved into sra-tools.
Please check use of clang there.