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jwb (jwb@freebsd.org)
HPC Systems Programmer

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User Since
Nov 27 2017, 4:37 PM (46 w, 5 d)

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

Recent Activity

Sun, Sep 30

jwb committed rP480985: science/fsom: Fix build on GCC-based architectures.
science/fsom: Fix build on GCC-based architectures
Sun, Sep 30, 9:41 PM
jwb closed D17366: science/fsom: Fix build on GCC-based architectures.
Sun, Sep 30, 9:41 PM
jwb created D17366: science/fsom: Fix build on GCC-based architectures.
Sun, Sep 30, 4:37 PM

Fri, Sep 21

jwb committed rP480273: sysutils/ganglia-webfrontend: Fix known display bug in cluster view.
sysutils/ganglia-webfrontend: Fix known display bug in cluster view
Fri, Sep 21, 2:57 PM
jwb closed D17264: sysutils/ganglia-webfrontend: Fix known display bug in cluster view.
Fri, Sep 21, 2:57 PM

Sep 20 2018

jwb created D17264: sysutils/ganglia-webfrontend: Fix known display bug in cluster view.
Sep 20 2018, 11:03 PM
jwb committed rP480173: biology/py-cutadapt: Upgrade to 1.18.
biology/py-cutadapt: Upgrade to 1.18
Sep 20 2018, 2:11 PM
jwb closed D17099: biology/py-cutadapt: Upgrade to 1.18.
Sep 20 2018, 2:10 PM

Sep 18 2018

jwb updated the diff for D17099: biology/py-cutadapt: Upgrade to 1.18.

Cripes, I have no memory of removing that. I hope it's good now.
Let's get this one tied up and then you won't hear from me again until
I restore some order to my life... ;-)

Sep 18 2018, 11:24 PM

Sep 17 2018

jwb updated the diff for D17099: biology/py-cutadapt: Upgrade to 1.18.

Hopefully final patch for this upgrade. Added one overlooked runtime dep.

Sep 17 2018, 4:19 PM
jwb added a comment to D17099: biology/py-cutadapt: Upgrade to 1.18.

Yeah, that might be a good idea. I took this as more of a future reference tip than something urgent for this port, and I've added a note to my checklist.

Sep 17 2018, 2:09 PM
jwb added a comment to D17099: biology/py-cutadapt: Upgrade to 1.18.

The do-test target is proving a little squirrely. I'll have to come back to this when I'm not so slammed...

Sep 17 2018, 1:34 PM

Sep 10 2018

jwb updated the diff for D17099: biology/py-cutadapt: Upgrade to 1.18.

Ooops, made changes to wip instead of biology the first time.

Sep 10 2018, 1:52 PM
jwb updated the diff for D17099: biology/py-cutadapt: Upgrade to 1.18.

Good stuff, thanks guys! I added these tips to my checklist.

Sep 10 2018, 1:42 PM

Sep 9 2018

jwb created D17099: biology/py-cutadapt: Upgrade to 1.18.
Sep 9 2018, 7:15 PM

Sep 1 2018

jwb committed rP478697: biology/stacks: Enable OpenMP (oversight in previous commit).
biology/stacks: Enable OpenMP (oversight in previous commit)
Sep 1 2018, 2:14 PM
jwb closed D16973: biology/stacks: Enable OpenMP (oversight in previous commit).
Sep 1 2018, 2:14 PM
jwb updated the diff for D16973: biology/stacks: Enable OpenMP (oversight in previous commit).

Ugh, slow down Jason...

Sep 1 2018, 1:36 PM

Aug 31 2018

jwb created D16973: biology/stacks: Enable OpenMP (oversight in previous commit).
Aug 31 2018, 2:11 PM

Aug 25 2018

jwb committed rP478089: biology/unanimity: Upgrade to latest release, soften dep version requirements.
biology/unanimity: Upgrade to latest release, soften dep version requirements
Aug 25 2018, 10:55 PM
jwb closed D16902: biology/unanimity: Upgrade to latest release, soften dep version requirements.
Aug 25 2018, 10:55 PM
jwb created D16902: biology/unanimity: Upgrade to latest release, soften dep version requirements.
Aug 25 2018, 9:15 PM

Aug 4 2018

jwb committed rP476330: biology/vcftools: Update to 0.1.16, a security release.
biology/vcftools: Update to 0.1.16, a security release
Aug 4 2018, 1:29 AM
jwb closed D16587: biology/vcftools: Update to 0.1.16, a security release.
Aug 4 2018, 1:29 AM

Aug 3 2018

jwb created D16587: biology/vcftools: Update to 0.1.16, a security release.
Aug 3 2018, 9:14 PM

Jul 7 2018

jwb committed rP474083: archivers/py-xopen: Upgrade to 0.3.5.
archivers/py-xopen: Upgrade to 0.3.5
Jul 7 2018, 1:41 PM
jwb closed D16170: archivers/py-xopen: Upgrade to 0.3.5.
Jul 7 2018, 1:41 PM
jwb created D16170: archivers/py-xopen: Upgrade to 0.3.5.
Jul 7 2018, 2:47 AM

Jun 27 2018

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

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

Jun 27 2018, 12:51 PM
jwb added a comment to D16024: science/paraview: Fix protobuf conflict, upgrade to 5.5.1, modernize options.

Thanks!

Jun 27 2018, 12:48 PM
jwb closed D16028: comms/cutecom: Fix WRKSRC name.
Jun 27 2018, 2:18 AM
jwb committed rP473416: comms/cutecom: Fix WRKSRC name.
comms/cutecom: Fix WRKSRC name
Jun 27 2018, 2:18 AM
jwb created D16028: comms/cutecom: Fix WRKSRC name.
Jun 27 2018, 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
Jun 27 2018, 12:04 AM
jwb closed D16024: science/paraview: Fix protobuf conflict, upgrade to 5.5.1, modernize options.
Jun 27 2018, 12:04 AM

Jun 26 2018

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.

Jun 26 2018, 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.

Jun 26 2018, 11:34 PM
jwb created D16024: science/paraview: Fix protobuf conflict, upgrade to 5.5.1, modernize options.
Jun 26 2018, 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.

Jun 26 2018, 6:57 PM

Jun 24 2018

jwb committed rP473198: comms/cutecom: Upgrade to 0.45.0.
comms/cutecom: Upgrade to 0.45.0
Jun 24 2018, 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.

Jun 24 2018, 1:18 AM

Jun 23 2018

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...

Jun 23 2018, 8:39 PM
jwb created D15981: comms/cutecom: Upgrade to 0.45.0.
Jun 23 2018, 12:59 PM

Jun 16 2018

jwb committed rP472560: biology/bedtools: Fix Makefile to respect PREFIX.
biology/bedtools: Fix Makefile to respect PREFIX
Jun 16 2018, 5:55 PM
jwb closed D15851: biology/bedtools: Fix Makefile to respect PREFIX.
Jun 16 2018, 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...

Jun 16 2018, 5:52 PM
jwb created D15851: biology/bedtools: Fix Makefile to respect PREFIX.
Jun 16 2018, 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