Thanks for clarifying, I've updated my checklist...

Thanks!

Yeah, I got that, but now I'm uncertain about exactly which OPTIONS features require it. The handbook isn't clear and the mk file is too big to study in detail. I'll just try without it and add when needed, I guess.

Apparently so. Never would have thought of it. The handbook is vague about
this, but it seems to work fine. I ran a make clean rmconfig configure
with 3 different options combos and got expected results.

I put the wrong revision URL in the commit, so it did not close automatically.

Thanks for digging up the old link. I already did change PORTNAME back to cutecom, as @mat's comment would seem to suggest. Also I recall the conversation going to email and getting a little heated, but @mat's take seemed reasonable to me so I've been trying to follow it.

I recall the conversation, but I think it ended with a lack of consensus
even among senior developers. The handbook still doesn't clarify this.
I'm agnostic...

I think that's a good idea and certainly won't hurt. I'll add it to the commit. Thanks...

Another distracted error. The good news is, I'll have fewer distractions once this is committed. ;-)

Yeah, I knew about the done box. Sorry, just distracted today.

Better yet, I'm just going to stop generating manpages for undocumented
scripts. I need to catch up on the documentation as well as separate it out.
I'd like to autogenerate man pages for each script, but haven't found a good
tool yet. Doxygen is nice for HTML but stinks at man pages.

Yes, it's correct. Currently there is one man page covering all scripts (at least the ones that are documented).

Silence mkdir

Actually works with or without :ldflags, so I'll have the project 64 bits.
Added special mention to my checklist.

I think the license perms section is clear enough. Maybe we should add notes where RESTRICTED, NO_CDROM, etc. are introduced stating that they've been superseded, with a link to the license section.

That's what happens when I don't follow my checklist...

Thanks, Mat. There doesn't seem to be much info in the handbook about RESTRICTED. Maybe this should be enhanced.

Kinda doubt I'm going to hear from them given how long the project has been
idle. Also silenced a compiler warning I got tired of looking at.

I'm going to wait for a response from UNC just to be safe. If I don't hear back from them, I'll restore the RESTRICTED entry.

The author told me personally many years ago that it was OK to reditribute, at least in source form. I sent a message to the mailto link on their site asking for clarification. The software hasn't been touched since I ported it maybe 14 years ago. The author finished his PhD and moved on...

Thanks, I'm actually agnostic about things like this (and disagree with any argument that one way should *always* be preferred). I just use whichever syntax is more readable in a given situation. In this case, I think `` is cleaner, because it stands out against the other $ chars in the string. Where there are quotes, I tend to prefer $(). As for nesting output capture, I just avoid it. I'll break it into two commands, the first being a variable assignment. As I've aged, I've shifted toward a preference for readability over hyper-efficiency and cleverness. ( More referring to C syntax regarding efficiency, it's a non-issue in shell commands). ;-)

Yep, 'been using this for years, at least in my wip ports. Very handy for persnickety genomics ports.

No worries, I managed to find something else to do while I waited. ;-)

Good catch. I deliberately left it out because it's a compiled language,
but forgot that it's only installing headers.

Don't stop making suggestions until I stop making mistakes. ;-)

I think biology/Makefile should match the directory name, not PKGBASE.

Well that's interesting... A couple days ago SeqLib was behaving like vcflib, ending up empty except for the subdirectories. I only noticed it after the vcflib patch failed and I realized that these are the two submodules with submodules. I don't think I trust this new development, so I'll leave the hack in until we get to the bottom of this.

What were you saying about the vcflib contents? Here's what I'm seeing:

I don't know why it was added originally, but I've built the new version
at least a dozen times without it and run it through poudriere testport
twice on all platforms, so I'm pretty confident.

Yeah, I get the same problem with SeqLib and vcflib, as both of them have submodules. If I list them directly in GH_TUPLE, they get blanked when their submodules are moved into place. I didn't notice it at first with SeqLib, because there are no patches in that directory. patch-vcflib_Makefile failed when I added ekg:fastahack:c68cebb:fastahack/vcflib/fastahack, which is what tipped me off to the problem.

Yeah, I didn't bother testing this one as I'm hoping for some discussion
before I commit. Should have done so anyway. I'm going to script the
import process to remove the wip category, run port-check, and open
category/Makefile so I won't miss anything in the future.