jwb (jwb@freebsd.org)
HPC Systems Programmer

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User Details

User Since
Nov 27 2017, 4:37 PM (32 w, 6 d)

Systems manager and facilitator for Research Computing at the University of Wisconsin -- Milwaukee

Recent Activity

Sat, Jul 7

jwb committed rP474083: archivers/py-xopen: Upgrade to 0.3.5.
archivers/py-xopen: Upgrade to 0.3.5
Sat, Jul 7, 1:41 PM
jwb closed D16170: archivers/py-xopen: Upgrade to 0.3.5.
Sat, Jul 7, 1:41 PM
jwb created D16170: archivers/py-xopen: Upgrade to 0.3.5.
Sat, Jul 7, 2:47 AM

Wed, Jun 27

jwb added a comment to D15981: comms/cutecom: Upgrade to 0.45.0.

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

Wed, Jun 27, 12:51 PM
jwb added a comment to D16024: science/paraview: Fix protobuf conflict, upgrade to 5.5.1, modernize options.

Thanks!

Wed, Jun 27, 12:48 PM
jwb closed D16028: comms/cutecom: Fix WRKSRC name.
Wed, Jun 27, 2:18 AM
jwb committed rP473416: comms/cutecom: Fix WRKSRC name.
comms/cutecom: Fix WRKSRC name
Wed, Jun 27, 2:18 AM
jwb created D16028: comms/cutecom: Fix WRKSRC name.
Wed, Jun 27, 12:19 AM
jwb committed rP473414: science/paraview: Fix protobuf conflict, upgrade to 5.5.1, modernize options.
science/paraview: Fix protobuf conflict, upgrade to 5.5.1, modernize options
Wed, Jun 27, 12:04 AM
jwb closed D16024: science/paraview: Fix protobuf conflict, upgrade to 5.5.1, modernize options.
Wed, Jun 27, 12:04 AM

Tue, Jun 26

jwb added a comment to D16024: science/paraview: Fix protobuf conflict, upgrade to 5.5.1, modernize options.

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.

Tue, Jun 26, 11:57 PM
jwb updated the diff for D16024: science/paraview: Fix protobuf conflict, upgrade to 5.5.1, modernize options.

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.

Tue, Jun 26, 11:34 PM
jwb created D16024: science/paraview: Fix protobuf conflict, upgrade to 5.5.1, modernize options.
Tue, Jun 26, 7:05 PM
jwb closed D15981: comms/cutecom: Upgrade to 0.45.0.

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

Tue, Jun 26, 6:57 PM

Sun, Jun 24

jwb committed rP473198: comms/cutecom: Upgrade to 0.45.0.
comms/cutecom: Upgrade to 0.45.0
Sun, Jun 24, 1:18 PM
jwb added a comment to D15981: comms/cutecom: Upgrade to 0.45.0.

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.

Sun, Jun 24, 1:18 AM

Sat, Jun 23

jwb updated the diff for D15981: comms/cutecom: Upgrade to 0.45.0.

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...

Sat, Jun 23, 8:39 PM
jwb created D15981: comms/cutecom: Upgrade to 0.45.0.
Sat, Jun 23, 12:59 PM

Sat, Jun 16

jwb committed rP472560: biology/bedtools: Fix Makefile to respect PREFIX.
biology/bedtools: Fix Makefile to respect PREFIX
Sat, Jun 16, 5:55 PM
jwb closed D15851: biology/bedtools: Fix Makefile to respect PREFIX.
Sat, Jun 16, 5:55 PM
jwb added a comment to D15851: biology/bedtools: Fix Makefile to respect PREFIX.

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

Sat, Jun 16, 5:52 PM
jwb created D15851: biology/bedtools: Fix Makefile to respect PREFIX.
Sat, Jun 16, 2:58 PM

May 30 2018

jwb committed rP471151: sysutils/desktop-installer: Add KDE5 support, more default video drivers.
sysutils/desktop-installer: Add KDE5 support, more default video drivers
May 30 2018, 7:14 PM
jwb closed D15622: sysutils/desktop-installer: Add KDE5 support, more default video drivers.
May 30 2018, 7:14 PM
jwb updated the diff for D15622: sysutils/desktop-installer: Add KDE5 support, more default video drivers.

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

May 30 2018, 7:10 PM
jwb created D15622: sysutils/desktop-installer: Add KDE5 support, more default video drivers.
May 30 2018, 6:59 PM
jwb added a comment to D15619: auto-admin: Add support for AD authentication, factor out pkgsrc scripts.

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

May 30 2018, 6:49 PM
jwb committed rP471149: auto-admin: Add support for AD authentication, factor out pkgsrc scripts.
auto-admin: Add support for AD authentication, factor out pkgsrc scripts
May 30 2018, 6:48 PM
jwb closed D15619: auto-admin: Add support for AD authentication, factor out pkgsrc scripts.
May 30 2018, 6:48 PM
jwb updated the diff for D15619: auto-admin: Add support for AD authentication, factor out pkgsrc scripts.

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.

May 30 2018, 6:32 PM
jwb added a comment to D15619: auto-admin: Add support for AD authentication, factor out pkgsrc scripts.

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

May 30 2018, 5:17 PM
jwb updated the diff for D15619: auto-admin: Add support for AD authentication, factor out pkgsrc scripts.

Silence mkdir

May 30 2018, 5:12 PM
jwb created D15619: auto-admin: Add support for AD authentication, factor out pkgsrc scripts.
May 30 2018, 4:47 PM

May 21 2018

jwb committed rP470582: biology/clustal-omega: Multiple alignment of nucleic acid and protein, replaces….
biology/clustal-omega: Multiple alignment of nucleic acid and protein, replaces…
May 21 2018, 10:15 PM
jwb closed D15516: biology/clustal-omega: Multiple alignment of nucleic acid and protein, replaces clustalw.
May 21 2018, 10:15 PM
jwb updated the diff for D15516: biology/clustal-omega: Multiple alignment of nucleic acid and protein, replaces clustalw.

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

May 21 2018, 10:07 PM
jwb created D15516: biology/clustal-omega: Multiple alignment of nucleic acid and protein, replaces clustalw.
May 21 2018, 9:49 PM
jwb added a comment to D15460: math/rapid: Fix build on FreeBSD 12, clean up license info, remove dead mirror.

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.

May 21 2018, 9:02 PM
jwb committed rP470575: biology/clustalx: Multiple alignment of nucleic acid and protein sequences with….
biology/clustalx: Multiple alignment of nucleic acid and protein sequences with…
May 21 2018, 8:56 PM
jwb closed D15505: biology/clustalx: Multiple alignment of nucleic acid and protein sequences with GUI.
May 21 2018, 8:56 PM
jwb updated the diff for D15505: biology/clustalx: Multiple alignment of nucleic acid and protein sequences with GUI.

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

May 21 2018, 12:26 PM
jwb added inline comments to D15505: biology/clustalx: Multiple alignment of nucleic acid and protein sequences with GUI.
May 21 2018, 1:57 AM
jwb created D15505: biology/clustalx: Multiple alignment of nucleic acid and protein sequences with GUI.
May 21 2018, 1:19 AM
jwb committed rP470494: biology/clustalw: Fix license, take maintainership.
biology/clustalw: Fix license, take maintainership
May 21 2018, 1:13 AM
jwb closed D15503: biology/clustalw: Fix license, take maintainership.
May 21 2018, 1:13 AM

May 20 2018

jwb created D15503: biology/clustalw: Fix license, take maintainership.
May 20 2018, 7:43 PM

May 19 2018

jwb committed rP470408: math/rapid: Fix build on FreeBSD 12, clean up license info, remove dead mirror.
math/rapid: Fix build on FreeBSD 12, clean up license info, remove dead mirror
May 19 2018, 2:09 PM
jwb closed D15460: math/rapid: Fix build on FreeBSD 12, clean up license info, remove dead mirror.
May 19 2018, 2:09 PM

May 18 2018

jwb updated the diff for D15460: math/rapid: Fix build on FreeBSD 12, clean up license info, remove dead mirror.

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

May 18 2018, 2:09 PM

May 17 2018

jwb updated the diff for D15460: math/rapid: Fix build on FreeBSD 12, clean up license info, remove dead mirror.

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.

May 17 2018, 11:14 PM
jwb added a comment to D15460: math/rapid: Fix build on FreeBSD 12, clean up license info, remove dead mirror.

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.

May 17 2018, 2:35 PM
jwb added a comment to D15460: math/rapid: Fix build on FreeBSD 12, clean up license info, remove dead mirror.

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...

May 17 2018, 2:02 AM

May 16 2018

jwb created D15460: math/rapid: Fix build on FreeBSD 12, clean up license info, remove dead mirror.
May 16 2018, 10:06 PM
jwb committed rP470124: biology/fastx-toolkit: Fix build on FreeBSD 12.
biology/fastx-toolkit: Fix build on FreeBSD 12
May 16 2018, 3:14 PM
jwb closed D15451: biology/fastx-toolkit: Fix build on FreeBSD 12.
May 16 2018, 3:14 PM
jwb created D15451: biology/fastx-toolkit: Fix build on FreeBSD 12.
May 16 2018, 3:08 PM

Apr 26 2018

jwb committed rP468321: biology/canu: Upgrade to 1.7 release.
biology/canu: Upgrade to 1.7 release
Apr 26 2018, 4:16 AM
jwb closed D15201: biology/canu: Upgrade to 1.7 release.
Apr 26 2018, 4:16 AM
jwb added a comment to D15201: biology/canu: Upgrade to 1.7 release.

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). ;-)

Apr 26 2018, 2:27 AM

Apr 25 2018

jwb created D15201: biology/canu: Upgrade to 1.7 release.
Apr 25 2018, 6:39 PM

Apr 24 2018

jwb committed rP468214: biology/unanimity: Pacific Biosciences consensus library and applications.
biology/unanimity: Pacific Biosciences consensus library and applications
Apr 24 2018, 2:17 PM
jwb closed D15172: biology/unanimity: Pacific Biosciences consensus library and applications.
Apr 24 2018, 2:16 PM
jwb added a comment to D15172: biology/unanimity: Pacific Biosciences consensus library and applications.

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

Apr 24 2018, 4:35 AM

Apr 23 2018

jwb created D15172: biology/unanimity: Pacific Biosciences consensus library and applications.
Apr 23 2018, 5:19 PM
jwb committed rP468101: biology/pbcopper: Core C++ library for Pacific Biosciences tools.
biology/pbcopper: Core C++ library for Pacific Biosciences tools
Apr 23 2018, 4:24 PM
jwb closed D15171: biology/pbcopper: Core C++ library for Pacific Biosciences tools.
Apr 23 2018, 4:24 PM
jwb added a comment to D15154: biology/pbbam: PacBio BAM C++ library, with SWIG bindings.

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

Apr 23 2018, 4:18 PM
jwb created D15171: biology/pbcopper: Core C++ library for Pacific Biosciences tools.
Apr 23 2018, 4:17 PM
jwb committed rP468100: biology/pbbam: PacBio BAM C++ library, with SWIG bindings.
biology/pbbam: PacBio BAM C++ library, with SWIG bindings
Apr 23 2018, 4:08 PM
jwb closed D15154: biology/pbbam: PacBio BAM C++ library, with SWIG bindings.
Apr 23 2018, 4:08 PM

Apr 21 2018

jwb created D15154: biology/pbbam: PacBio BAM C++ library, with SWIG bindings.
Apr 21 2018, 9:08 PM
jwb committed rP467901: biology/pbseqan: Pacific Biosciences patched and stripped down SeqAn.
biology/pbseqan: Pacific Biosciences patched and stripped down SeqAn
Apr 21 2018, 5:21 PM
jwb closed D15152: biology/pbseqan: Pacific Biosciences patched and stripped down SeqAn.
Apr 21 2018, 5:21 PM
jwb updated the diff for D15152: biology/pbseqan: Pacific Biosciences patched and stripped down SeqAn.

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

Apr 21 2018, 5:08 PM
jwb created D15152: biology/pbseqan: Pacific Biosciences patched and stripped down SeqAn.
Apr 21 2018, 4:20 PM

Apr 20 2018

jwb closed D15139: biology/ddocent: Bash pipeline for RAD sequencing.
Apr 20 2018, 1:34 AM
jwb committed rP467808: biology/ddocent: Bash pipeline for RAD sequencing.
biology/ddocent: Bash pipeline for RAD sequencing
Apr 20 2018, 1:34 AM
jwb added a comment to D15139: biology/ddocent: Bash pipeline for RAD sequencing.

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

Apr 20 2018, 1:30 AM
jwb updated the diff for D15139: biology/ddocent: Bash pipeline for RAD sequencing.

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

Apr 20 2018, 1:16 AM
jwb created D15139: biology/ddocent: Bash pipeline for RAD sequencing.
Apr 20 2018, 12:32 AM
jwb committed rP467806: biology/freebayes: Bayesian haplotype-based polymorphism discovery and….
biology/freebayes: Bayesian haplotype-based polymorphism discovery and…
Apr 20 2018, 12:07 AM
jwb closed D15116: Bayesian haplotype-based polymorphism discovery and genotyping.
Apr 20 2018, 12:07 AM
jwb added a comment to D15116: Bayesian haplotype-based polymorphism discovery and genotyping.

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.

Apr 20 2018, 12:03 AM

Apr 19 2018

jwb added a comment to D15116: Bayesian haplotype-based polymorphism discovery and genotyping.

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

Apr 19 2018, 11:03 PM
jwb committed rP467783: biology/bedtools: Upgrade to 2.27.1.
biology/bedtools: Upgrade to 2.27.1
Apr 19 2018, 4:45 PM
jwb closed D15137: biology/bedtools: Upgrade to 2.27.1.
Apr 19 2018, 4:45 PM
jwb updated the diff for D15137: biology/bedtools: Upgrade to 2.27.1.

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.

Apr 19 2018, 4:22 PM
jwb created D15137: biology/bedtools: Upgrade to 2.27.1.
Apr 19 2018, 3:51 PM

Apr 18 2018

jwb added a comment to D15116: Bayesian haplotype-based polymorphism discovery and genotyping.

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.

Apr 18 2018, 6:04 AM

Apr 17 2018

jwb updated the diff for D15116: Bayesian haplotype-based polymorphism discovery and genotyping.

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.

Apr 17 2018, 6:05 PM
jwb created D15116: Bayesian haplotype-based polymorphism discovery and genotyping.
Apr 17 2018, 3:05 PM
jwb committed rP467553: biology/vcflib: C++ library and CLI tools for parsing and manipulating VCF files.
biology/vcflib: C++ library and CLI tools for parsing and manipulating VCF files
Apr 17 2018, 3:11 AM
jwb closed D15109: C++ library and CLI tools for parsing and manipulating VCF files.
Apr 17 2018, 3:11 AM

Apr 16 2018

jwb created D15109: C++ library and CLI tools for parsing and manipulating VCF files.
Apr 16 2018, 10:39 PM
jwb committed rP467529: math/intervaltree: Remove invalid category.
math/intervaltree: Remove invalid category
Apr 16 2018, 7:18 PM
jwb committed rP467527: math/intervaltree: Minimal C++ interval tree implementation.
math/intervaltree: Minimal C++ interval tree implementation
Apr 16 2018, 6:56 PM
jwb closed D15105: math/intervaltree: Minimal C++ interval tree implementation.
Apr 16 2018, 6:56 PM
jwb created D15105: math/intervaltree: Minimal C++ interval tree implementation.
Apr 16 2018, 6:43 PM
jwb committed rP467502: math/multichoose: Generate multiset combinations (n multichoose k).
math/multichoose: Generate multiset combinations (n multichoose k)
Apr 16 2018, 6:32 PM
jwb closed D15104: math/multichoose: Generate multiset combinations (n multichoose k).
Apr 16 2018, 6:32 PM