jwb (jwb@freebsd.org)
HPC Systems Programmer

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User Since
Nov 27 2017, 4:37 PM (7 w, 5 d)

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

Recent Activity

Wed, Jan 17

jwb added a comment to D13400: [new port] biology/p5-trimgalore: Wrapper around Cutadapt and FastQC for adapter and quality trimming.

Apparently this *is* by design:

Wed, Jan 17, 3:06 PM
jwb added a comment to D13400: [new port] biology/p5-trimgalore: Wrapper around Cutadapt and FastQC for adapter and quality trimming.

I think you've discovered a BSD make bug. Using -j should not change the results of the build no matter how the makefile is coded.

Wed, Jan 17, 1:54 PM

Thu, Dec 28

jwb committed rP457479: sysutils/desktop-installer: Add gnome3 support, numerous bug fixes.
sysutils/desktop-installer: Add gnome3 support, numerous bug fixes
Thu, Dec 28, 9:06 PM
jwb closed D13669: sysutils/desktop-installer: Add gnome3 support, numerous bug fixes.
Thu, Dec 28, 9:06 PM
jwb created D13669: sysutils/desktop-installer: Add gnome3 support, numerous bug fixes.
Thu, Dec 28, 7:52 PM
jwb added a comment to D13668: sysutils/auto-admin: Update to auto-xdm-toggle critical to desktop-installer.

Yeah, I realize I forgot (mentor) right after I hit enter..

Thu, Dec 28, 7:42 PM
jwb committed rP457473: sysutils/auto-admin: Update to auto-xdm-toggle critical to desktop-installer.
sysutils/auto-admin: Update to auto-xdm-toggle critical to desktop-installer
Thu, Dec 28, 7:40 PM
jwb closed D13668: sysutils/auto-admin: Update to auto-xdm-toggle critical to desktop-installer.
Thu, Dec 28, 7:40 PM
jwb created D13668: sysutils/auto-admin: Update to auto-xdm-toggle critical to desktop-installer.
Thu, Dec 28, 6:51 PM

Fri, Dec 22

jwb committed rP456982: biology/canu: Replace += with = for depends.
biology/canu: Replace += with = for depends
Fri, Dec 22, 2:14 PM
jwb closed D13574: [new port] biology/canu: Single molecule sequence assembler.
Fri, Dec 22, 2:14 PM
jwb updated the diff for D13574: [new port] biology/canu: Single molecule sequence assembler.

Good catch on the +=, that was an oversight.

Fri, Dec 22, 1:45 PM
jwb reopened D13574: [new port] biology/canu: Single molecule sequence assembler.
Fri, Dec 22, 1:42 PM

Dec 22 2017

jwb committed rP456950: [new port] biology/canu: Single molecule sequence assembler.
[new port] biology/canu: Single molecule sequence assembler
Dec 22 2017, 1:30 AM
jwb closed D13574: [new port] biology/canu: Single molecule sequence assembler.
Dec 22 2017, 1:30 AM
jwb updated the diff for D13574: [new port] biology/canu: Single molecule sequence assembler.

Added that to my checklist

Dec 22 2017, 1:27 AM
jwb updated the test plan for D13574: [new port] biology/canu: Single molecule sequence assembler.
Dec 22 2017, 12:09 AM

Dec 21 2017

jwb created D13574: [new port] biology/canu: Single molecule sequence assembler.
Dec 21 2017, 4:53 PM

Dec 18 2017

jwb added a comment to D13463: [new port] x11/lilyterm: Lightweight, but functional terminal emulator.

So I got an email at 8:46pm stating that the revision was accepted, but the commit message stated that it was in a needs review state. Guessing that's because I restored the svn tag line to match the previous commit and forgot to do an arc update after. My working copy contained $FreeBSD$ and I was afraid the commit might have problems if this line differed from the previous commit. Based on what I've seen tonight, I'm thinking the old content is ignored and the new tag is inserted in its place.

Dec 18 2017, 4:07 AM
jwb committed rP456586: x11/lilyterm: Add DOCS option, remove redundant config file, patch man page.
x11/lilyterm: Add DOCS option, remove redundant config file, patch man page
Dec 18 2017, 3:55 AM
This revision was not accepted when it landed; it landed in state Needs Review.
Dec 18 2017, 3:55 AM
jwb closed D13526: sysutils/desktop-installer: Update to 0.5.5.
Dec 18 2017, 3:50 AM
jwb committed rP456585: sysutils/desktop-installer: Update to 0.5.5.
sysutils/desktop-installer: Update to 0.5.5
Dec 18 2017, 3:50 AM
jwb added a comment to D13526: sysutils/desktop-installer: Update to 0.5.5.

Got it, thanks.

Dec 18 2017, 3:49 AM
jwb added a comment to D13526: sysutils/desktop-installer: Update to 0.5.5.

Oh, that line... I thought you were referring to $FreeBSD$ not showing the svn tag. I apparently misinterpreted our earlier discussion as a call to remove the "Created by" comments. I'll leave it in for this commit, pending clarification.

Dec 18 2017, 3:40 AM
jwb added a comment to D13526: sysutils/desktop-installer: Update to 0.5.5.

I'm not clear on what you mean, but apparently "svn diff" does not include the tag in its output if that's what you're getting at. I never noticed this before, though. I just home in on the changes.

Dec 18 2017, 3:31 AM
jwb updated the summary of D13526: sysutils/desktop-installer: Update to 0.5.5.
Dec 18 2017, 3:22 AM
jwb added reviewers for D13526: sysutils/desktop-installer: Update to 0.5.5: jrm, wen.
Dec 18 2017, 3:17 AM
jwb updated the summary of D13526: sysutils/desktop-installer: Update to 0.5.5.
Dec 18 2017, 3:17 AM
jwb created D13526: sysutils/desktop-installer: Update to 0.5.5.
Dec 18 2017, 3:13 AM
jwb committed rP456581: auto-admin: Update to 0.4.1.
auto-admin: Update to 0.4.1
Dec 18 2017, 3:08 AM
jwb closed D13523: auto-admin: Update to 0.4.1.
Dec 18 2017, 3:08 AM

Dec 17 2017

jwb created D13523: auto-admin: Update to 0.4.1.
Dec 17 2017, 11:37 PM

Dec 15 2017

jwb added a comment to D13463: [new port] x11/lilyterm: Lightweight, but functional terminal emulator.
In D13463#282213, @jrm wrote:

Oh, but since the package will change, bumping PORTREVISION is necessary.

Dec 15 2017, 2:54 PM
jwb updated the diff for D13463: [new port] x11/lilyterm: Lightweight, but functional terminal emulator.

Add PORTREVISION, silence RM

Dec 15 2017, 2:51 PM
jwb added a comment to D13463: [new port] x11/lilyterm: Lightweight, but functional terminal emulator.

I'd lean toward echoing STRIP_CMD, so I'd amend that to

Dec 15 2017, 2:47 PM
jwb added a comment to D13463: [new port] x11/lilyterm: Lightweight, but functional terminal emulator.

Perhaps there could be agreement on a general principal regarding what should be echoed?

Dec 15 2017, 2:38 PM
jwb added a comment to D13463: [new port] x11/lilyterm: Lightweight, but functional terminal emulator.

No hurry on my end, especially since we have a working port already committed. Let's use this as an opportunity to learn and maybe improve the docs before it's committed.

Dec 15 2017, 2:12 AM
jwb added a comment to D13463: [new port] x11/lilyterm: Lightweight, but functional terminal emulator.

Yeah, feels like the same revision since I reopened the differential. Too much to keep track of for my worn-out brain...

Dec 15 2017, 12:51 AM
jwb updated the diff for D13463: [new port] x11/lilyterm: Lightweight, but functional terminal emulator.

Remove redundant conf file from EXAMPLES_DIR

Dec 15 2017, 12:27 AM
jwb added a comment to D13463: [new port] x11/lilyterm: Lightweight, but functional terminal emulator.

My instinct said to stick with the canonical method (STRIP_CMD), now I know why. Thanks...

Dec 15 2017, 12:01 AM

Dec 14 2017

jwb added a comment to D13463: [new port] x11/lilyterm: Lightweight, but functional terminal emulator.

It *is* staged, so the build system need not worry about it, but the ports install target works from the plist and ignores whatever is commented out.

Dec 14 2017, 11:57 PM
jwb added a comment to D13463: [new port] x11/lilyterm: Lightweight, but functional terminal emulator.

Yes, they are the same.

Dec 14 2017, 11:45 PM
jwb updated the diff for D13463: [new port] x11/lilyterm: Lightweight, but functional terminal emulator.

Add DOCS and EXAMPLES to OPTIONS

Dec 14 2017, 4:32 PM
jwb reopened D13463: [new port] x11/lilyterm: Lightweight, but functional terminal emulator.

One more patch needed

Dec 14 2017, 4:31 PM
jwb added a comment to D13463: [new port] x11/lilyterm: Lightweight, but functional terminal emulator.

What's the traditional approach when arc diff --update produces this?

Dec 14 2017, 2:20 PM
jwb added a comment to D13463: [new port] x11/lilyterm: Lightweight, but functional terminal emulator.

The first time you mentioned it, I suggested removing PORTDOCS and PORTEXAMPLES from options because they only install 4 very small files. I did not see a response to that suggestion.

Dec 14 2017, 2:05 PM
jwb added a comment to D13463: [new port] x11/lilyterm: Lightweight, but functional terminal emulator.

I removed them from the Makefile, which I thought was the issue. Are you referring to the %%PORTDOCS%% and %%PORTEXAMPLES%% in pkg-plist? If so, I can remove them as well. They were generated by makeplist.

Dec 14 2017, 1:44 PM

Dec 13 2017

jwb committed rP456225: [new port] x11/lilyterm: Lightweight, but functional terminal emulator.
[new port] x11/lilyterm: Lightweight, but functional terminal emulator
Dec 13 2017, 6:43 PM
This revision was not accepted when it landed; it landed in state Needs Review.
Dec 13 2017, 6:43 PM
jwb added a comment to D13463: [new port] x11/lilyterm: Lightweight, but functional terminal emulator.

Thanks for all the feedback, guys. This one is out of my usual realm as well. Most of my ports are scientific apps running on headless servers...

Dec 13 2017, 6:40 PM
jwb updated the diff for D13463: [new port] x11/lilyterm: Lightweight, but functional terminal emulator.

Removed NLS_DESC.

Dec 13 2017, 5:37 PM
jwb updated the diff for D13463: [new port] x11/lilyterm: Lightweight, but functional terminal emulator.

Fix config file issue. Awaiting feedback on other items...

Dec 13 2017, 4:56 PM
jwb added a comment to D13463: [new port] x11/lilyterm: Lightweight, but functional terminal emulator.
  1. Porter's Handbook section 5.13.1.2. Syntax has this:
Dec 13 2017, 4:53 PM
jwb updated the diff for D13463: [new port] x11/lilyterm: Lightweight, but functional terminal emulator.

Think I've got it now...

Dec 13 2017, 3:41 PM
jwb committed rP456189: science/paraview: Unbreak build with clang 4.0.
science/paraview: Unbreak build with clang 4.0
Dec 13 2017, 3:34 AM
jwb closed D13462: science/paraview: Unbreak build.
Dec 13 2017, 3:34 AM

Dec 12 2017

jwb added a comment to D13462: science/paraview: Unbreak build.

I think 4 months without a response to Tobias is enough. Just wanted to know if there are any strict rules about this situation. I'm going to let the last of 4 poudriere builds finish and then I'll do the commit assuming it succeeds.

Dec 12 2017, 11:14 PM
jwb added a comment to D13462: science/paraview: Unbreak build.

Haven't heard from the maintainer yet. He submitted part of the patch on Aprll 6th and that's the last anyone heard from him. Should I try to reach out to him in case he didn't see the bugtracker updates?

Dec 12 2017, 10:18 PM
jwb updated the diff for D13462: science/paraview: Unbreak build.

Add python flavor to RUN_DEPENDS

Dec 12 2017, 9:45 PM
jwb added a comment to D13462: science/paraview: Unbreak build.

I'm getting swamped again this morning, so I'll get back to these later when I can focus again...

Dec 12 2017, 3:38 PM
jwb added a comment to D13463: [new port] x11/lilyterm: Lightweight, but functional terminal emulator.

NLS is on by default, so I'm thinking we need to explicitly disable it for the option to have any effect:

Dec 12 2017, 2:47 PM
jwb updated the diff for D13462: science/paraview: Unbreak build.

Add Python flavor and silence REINPLACE_CMD.

Dec 12 2017, 2:41 PM
jwb created D13463: [new port] x11/lilyterm: Lightweight, but functional terminal emulator.
Dec 12 2017, 2:15 PM
jwb created D13462: science/paraview: Unbreak build.
Dec 12 2017, 1:49 PM

Dec 9 2017

jwb committed rP455857: [new port] biology/p5-TrimGalore: Wrapper around Cutadapt and FastQC for….
[new port] biology/p5-TrimGalore: Wrapper around Cutadapt and FastQC for…
Dec 9 2017, 1:23 PM
jwb closed D13400: [new port] biology/p5-trimgalore: Wrapper around Cutadapt and FastQC for adapter and quality trimming.
Dec 9 2017, 1:23 PM
jwb updated the diff for D13400: [new port] biology/p5-trimgalore: Wrapper around Cutadapt and FastQC for adapter and quality trimming.

Rename with caps to match PORTNAME.

Dec 9 2017, 3:11 AM

Dec 8 2017

jwb added a comment to D13400: [new port] biology/p5-trimgalore: Wrapper around Cutadapt and FastQC for adapter and quality trimming.

Alrighty, so I have a powerful ally...

Dec 8 2017, 3:59 AM

Dec 7 2017

jwb added a comment to D13400: [new port] biology/p5-trimgalore: Wrapper around Cutadapt and FastQC for adapter and quality trimming.

I think mat's comment about python was confirming that USES=python:env is correct, but python:run wouldn't do any harm in this case. Since this port doesn't use python, but needs PYTHON_PKGNAMEPREFIX and PY_FLAVOR, I think python:env is the best pick.

Dec 7 2017, 6:54 PM
jwb added a comment to D13400: [new port] biology/p5-trimgalore: Wrapper around Cutadapt and FastQC for adapter and quality trimming.

Good stuff, thanks! I reran it through poudriere just to be safe.

Dec 7 2017, 3:13 PM
jwb updated the diff for D13400: [new port] biology/p5-trimgalore: Wrapper around Cutadapt and FastQC for adapter and quality trimming.

Change PORTNAME to match upstream dist

Dec 7 2017, 3:05 PM
jwb added a comment to D13400: [new port] biology/p5-trimgalore: Wrapper around Cutadapt and FastQC for adapter and quality trimming.

Thanks for clarifying the python dependency issue. I wasn't sure about that one... I updated my checklist accordingly.

Dec 7 2017, 2:22 PM
jwb added a comment to D13400: [new port] biology/p5-trimgalore: Wrapper around Cutadapt and FastQC for adapter and quality trimming.

Actually, parens would have no effect in this case. The cd only affects other commands on the same line anyway, since each line is executed under a new shell process that's a direct child of the make process. The Makefile below will show the different shell processes for each line and different output from pwd:

Dec 7 2017, 5:00 AM
jwb updated the diff for D13400: [new port] biology/p5-trimgalore: Wrapper around Cutadapt and FastQC for adapter and quality trimming.

Fix issues noted by mentors

Dec 7 2017, 1:50 AM
jwb added a comment to D13400: [new port] biology/p5-trimgalore: Wrapper around Cutadapt and FastQC for adapter and quality trimming.

Thanks for the tips. Can't believe I missed DISTVERSION... ;-)

Dec 7 2017, 1:49 AM

Dec 6 2017

jwb updated the diff for D13400: [new port] biology/p5-trimgalore: Wrapper around Cutadapt and FastQC for adapter and quality trimming.

Add missing USES=python arg

Dec 6 2017, 9:43 PM
jwb created D13400: [new port] biology/p5-trimgalore: Wrapper around Cutadapt and FastQC for adapter and quality trimming.
Dec 6 2017, 9:35 PM

Dec 5 2017

jwb committed rP455562: biology/fasttree: update to version 2.1.10.
biology/fasttree: update to version 2.1.10
Dec 5 2017, 3:03 AM
jwb closed D8187: biology/fasttree: update to version 2.1.9.
Dec 5 2017, 3:03 AM
jwb committed rP455561: biology/py-macs2: Restrict to python 2.7..
biology/py-macs2: Restrict to python 2.7.
Dec 5 2017, 2:59 AM
jwb closed D13350: biology/py-macs2: Restrict to python 2.7.
Dec 5 2017, 2:59 AM
jwb added a comment to D8187: biology/fasttree: update to version 2.1.9.

Thanks, I hadn't given it a full review since commandeering...

Dec 5 2017, 2:51 AM
jwb updated the diff for D8187: biology/fasttree: update to version 2.1.9.

Clean up

Dec 5 2017, 2:47 AM
jwb added a comment to D13322: [new port] biology/py-macs2: Analysis of chromatin immunoprecipitation (ChIP) sequences.

Thanks for the tips. I hadn't thought to use bulk -t instead of testport. My plan was to manually run testport again with @py36 when needed. I see that numpy gets the VIP treatment in python.mk. I'll keep an eye on that section for additions in the future...

Dec 5 2017, 2:13 AM

Dec 4 2017

jwb updated the diff for D8187: biology/fasttree: update to version 2.1.9.

Add Makefile. Will send upstream along with malloc patch.

Dec 4 2017, 3:55 PM
jwb updated the diff for D8187: biology/fasttree: update to version 2.1.9.

Fix core dump issue. Code was assuming malloc() aligns to 16 byte boundaries. May be a Linuxism.

Dec 4 2017, 3:39 PM
jwb updated the diff for D8187: biology/fasttree: update to version 2.1.9.

Remove wip category

Dec 4 2017, 2:26 PM
jwb commandeered D8187: biology/fasttree: update to version 2.1.9.
Dec 4 2017, 1:29 PM
jwb updated the diff for D8187: biology/fasttree: update to version 2.1.9.

Update to new release 2.1.10.

Dec 4 2017, 1:25 PM

Dec 3 2017

jwb added a comment to D8187: biology/fasttree: update to version 2.1.9.

I don't think we have anyone using fasttree presently, but if you send me a test case that produces the core dump, I'll try and reproduce it.

Dec 3 2017, 4:27 PM
jwb created D13350: biology/py-macs2: Restrict to python 2.7.
Dec 3 2017, 1:04 PM

Dec 2 2017

jwb committed rP455384: Fill out block comment.
Fill out block comment
Dec 2 2017, 8:50 PM
jwb committed rP455383: [new port] biology/py-macs2: Analysis of chromatin immunoprecipitation (ChIP)….
[new port] biology/py-macs2: Analysis of chromatin immunoprecipitation (ChIP)…
Dec 2 2017, 8:46 PM
jwb closed D13322: [new port] biology/py-macs2: Analysis of chromatin immunoprecipitation (ChIP) sequences.
Dec 2 2017, 8:46 PM
jwb committed rP455382: [new port] biology/kallisto: Quantify abundances of transcripts from RNA-Seq….
[new port] biology/kallisto: Quantify abundances of transcripts from RNA-Seq…
Dec 2 2017, 8:44 PM
jwb closed D13328: [new port] biology/kallisto: Quantify abundances of transcripts from RNA-Seq data.
Dec 2 2017, 8:44 PM
jwb updated the diff for D13322: [new port] biology/py-macs2: Analysis of chromatin immunoprecipitation (ChIP) sequences.

Settled on a usable PORTVERSION

Dec 2 2017, 7:23 PM
jwb added a comment to D13322: [new port] biology/py-macs2: Analysis of chromatin immunoprecipitation (ChIP) sequences.

I agree with PORTVERSION=2.1.0.p20170505. That would have been the next thing I came up with myself, all seemingly reasonable alternatives eliminated.

Dec 2 2017, 7:22 PM
jwb added a comment to D13322: [new port] biology/py-macs2: Analysis of chromatin immunoprecipitation (ChIP) sequences.

Or maybe

Dec 2 2017, 5:07 PM