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jwb (jwb@freebsd.org)
HPC Systems Programmer

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User Details

User Since
Nov 27 2017, 4:37 PM (156 w, 5 d)

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

Recent Activity

Mon, Nov 16

jwb committed rP555505: biology/ncbi-blast+: Upgrade to 2.11.0.
biology/ncbi-blast+: Upgrade to 2.11.0
Mon, Nov 16, 6:25 PM

Sun, Nov 15

jwb committed rP555418: biology/pooler: Optimise DNA sequencing primer-set combinations.
biology/pooler: Optimise DNA sequencing primer-set combinations
Sun, Nov 15, 6:50 PM

Mon, Nov 9

jwb committed rP554660: biology/vt: Fix build with htslib 1.11.
biology/vt: Fix build with htslib 1.11
Mon, Nov 9, 12:36 AM

Sun, Nov 8

jwb committed rP554467: biology/gcta: Switch eigen3 dep to USES framework.
biology/gcta: Switch eigen3 dep to USES framework
Sun, Nov 8, 2:48 PM

Sat, Nov 7

jwb committed rP554390: biology/bowtie2: Upgrade to 2.4.2.
biology/bowtie2: Upgrade to 2.4.2
Sat, Nov 7, 1:47 PM

Thu, Nov 5

jwb committed rP554157: biology/bcftools: Upgrade to 1.11.
biology/bcftools: Upgrade to 1.11
Thu, Nov 5, 8:34 PM
jwb committed rP554156: biology/samtools: Upgrade to 1.11.
biology/samtools: Upgrade to 1.11
Thu, Nov 5, 8:32 PM
jwb committed rP554155: biology/htslib: Upgrade to 1.11.0.
biology/htslib: Upgrade to 1.11.0
Thu, Nov 5, 8:31 PM

Tue, Nov 3

jwb committed rP554012: devel/py-srsly: Upgrade to 2.3.1.
devel/py-srsly: Upgrade to 2.3.1
Tue, Nov 3, 7:09 PM

Fri, Oct 30

jwb committed rP553694: sysutils/desktop-installer: Upgrade to 0.6.18.
sysutils/desktop-installer: Upgrade to 0.6.18
Fri, Oct 30, 2:56 PM
jwb committed rP553689: sysutils/auto-admin: Upgrade to 0.6.8.
sysutils/auto-admin: Upgrade to 0.6.8
Fri, Oct 30, 1:34 PM

Oct 16 2020

jwb committed rP552519: biology/py-biopython: Upgrade to 1.78.
biology/py-biopython: Upgrade to 1.78
Oct 16 2020, 7:13 PM

Oct 1 2020

jwb committed rP550854: sysutils/ganglia-monitor-core: Upgrade to 3.7.2, disable python modules.
sysutils/ganglia-monitor-core: Upgrade to 3.7.2, disable python modules
Oct 1 2020, 6:01 PM

Sep 22 2020

jwb committed rP549546: biology/gmap: Upgrade to 2020.09.12.
biology/gmap: Upgrade to 2020.09.12
Sep 22 2020, 12:56 AM

Sep 18 2020

jwb committed rP548871: biology/subread: Add -fcommon for clang 11.
biology/subread: Add -fcommon for clang 11
Sep 18 2020, 12:57 AM

Sep 14 2020

jwb committed rP548685: biology/canu: Upgrade to 2.1.
biology/canu: Upgrade to 2.1
Sep 14 2020, 10:27 PM

Aug 30 2020

jwb committed rP547056: biology/picard-tools: Remove extraneous file.
biology/picard-tools: Remove extraneous file
Aug 30 2020, 2:07 PM

Aug 11 2020

jwb committed rP544688: MFH: r544687.
MFH: r544687
Aug 11 2020, 3:34 PM
jwb committed rP544687: sysutils/auto-admin: Upgrade to 0.6.7 bugfix release.
sysutils/auto-admin: Upgrade to 0.6.7 bugfix release
Aug 11 2020, 3:02 PM

Aug 3 2020

jwb committed rP544098: biology/samtools: Upgrade to 1.10.
biology/samtools: Upgrade to 1.10
Aug 3 2020, 6:22 PM
jwb committed rP544096: biology/bcftools: Upgrade to 1.10.2.
biology/bcftools: Upgrade to 1.10.2
Aug 3 2020, 6:17 PM
jwb committed rP544091: biology/vt: Patch to work with htslib 1.10.2.
biology/vt: Patch to work with htslib 1.10.2
Aug 3 2020, 5:42 PM
jwb committed rP544090: biology/htslib: Upgrade to 1.10.2.
biology/htslib: Upgrade to 1.10.2
Aug 3 2020, 5:40 PM
jwb committed rP544077: biology/kallisto: Revert to 0.46.1.
biology/kallisto: Revert to 0.46.1
Aug 3 2020, 3:45 PM

Aug 2 2020

jwb committed rP544005: devel/py-pathlib: Allow building with python3.
devel/py-pathlib: Allow building with python3
Aug 2 2020, 10:44 PM

Jul 19 2020

jwb committed rP542588: MFH: r542587.
MFH: r542587
Jul 19 2020, 4:15 PM
jwb committed rP542587: desktop-installer: Upgrade to 0.6.17 bugfix release.
desktop-installer: Upgrade to 0.6.17 bugfix release
Jul 19 2020, 4:10 PM

Jul 13 2020

jwb committed rP542146: MFH: r542001.
MFH: r542001
Jul 13 2020, 3:41 PM

Jul 11 2020

jwb committed rP542001: sysutils/auto-admin: Upgrade to 0.6.6.
sysutils/auto-admin: Upgrade to 0.6.6
Jul 11 2020, 5:52 PM

Jul 3 2020

jwb committed rP541135: devel/py-srsly: Add missing python version requirement.
devel/py-srsly: Add missing python version requirement
Jul 3 2020, 9:15 PM

Jun 29 2020

jwb committed rP540781: devel/py-srsly: Modern high-performance serialization utilities for Python.
devel/py-srsly: Modern high-performance serialization utilities for Python
Jun 29 2020, 3:38 PM

Jun 20 2020

jwb committed rP539742: biology/vsearch: Update to 2.15.0.
biology/vsearch: Update to 2.15.0
Jun 20 2020, 2:32 PM

Jun 13 2020

jwb committed rP538672: biology/picard-tools: CLI tools for manipulating sequencing data.
biology/picard-tools: CLI tools for manipulating sequencing data
Jun 13 2020, 1:54 PM
jwb committed rP538671: biology/py-biopython: Set python requirement to 3.6+.
biology/py-biopython: Set python requirement to 3.6+
Jun 13 2020, 1:42 PM

Jun 11 2020

jwb committed rP538508: sysutils/desktop-installer: Update to 0.6.16.
sysutils/desktop-installer: Update to 0.6.16
Jun 11 2020, 4:41 PM
jwb committed rP538504: auto-admin: Greatly improved auto-gpu-setup.
auto-admin: Greatly improved auto-gpu-setup
Jun 11 2020, 4:14 PM

Jun 5 2020

jwb committed rP537983: biology/bioawk: BWK awk modified for biological data.
biology/bioawk: BWK awk modified for biological data
Jun 5 2020, 2:45 AM

Jun 4 2020

jwb committed rP537926: bioloty/vt: Discovers short variants from Next Generation Sequencing data.
bioloty/vt: Discovers short variants from Next Generation Sequencing data
Jun 4 2020, 6:28 PM

Jun 2 2020

jwb committed rP537566: sysutils/desktop-installer: Upgrade to 0.6.15.
sysutils/desktop-installer: Upgrade to 0.6.15
Jun 2 2020, 6:13 PM
jwb committed rP537564: sysutils/auto-admin: Upgrade to 0.6.4.
sysutils/auto-admin: Upgrade to 0.6.4
Jun 2 2020, 6:11 PM

May 29 2020

jwb committed rP536875: biology/py-biopython: Upgrade to 1.77.
biology/py-biopython: Upgrade to 1.77
May 29 2020, 2:03 AM

May 24 2020

jwb committed rP536409: biology/py-dnaio: Upgrade to 0.4.2.
biology/py-dnaio: Upgrade to 0.4.2
May 24 2020, 3:23 PM
jwb committed rP536407: R-cran-optparse: Upgrade to 1.6.6.
R-cran-optparse: Upgrade to 1.6.6
May 24 2020, 3:20 PM

May 9 2020

jwb committed rP534741: sysutils/desktop-installer: Upgrade to 0.6.13.
sysutils/desktop-installer: Upgrade to 0.6.13
May 9 2020, 1:37 PM

May 4 2020

jwb committed rP533993: biology/plink: Whole genome association analysis toolset.
biology/plink: Whole genome association analysis toolset
May 4 2020, 11:02 PM
jwb added a comment to D24572: math/R: Update to version 4.0.0.
In D24572#543344, @jrm wrote:

I build tested everything and it all looks fine. Unless you have concrete objections, I am going to go ahead and commit this. @rhurlin_gwdg.de, I think the library versions we are making up are somewhat arbitrary in this case, since, after a long discussion with upstream, they do not really intend for them to be share libraries, but dynamically loaded. We are bumping dependencies manually, so I think things are fine. If you have other reasons that I am missing, we can always adapt later.

May 4 2020, 2:14 PM

May 1 2020

jwb committed rP533548: sysutils/desktop-installer: Upgrade to 0.6.12.
sysutils/desktop-installer: Upgrade to 0.6.12
May 1 2020, 2:31 PM
jwb committed rP533547: sysutils/auto-admin: Upgrade to 0.6.2.
sysutils/auto-admin: Upgrade to 0.6.2
May 1 2020, 2:26 PM

Apr 30 2020

jwb committed rP533470: sysutils/automount: Upgrade to 1.7.2.
sysutils/automount: Upgrade to 1.7.2
Apr 30 2020, 7:33 PM

Apr 24 2020

jwb committed rP532890: audio/praat: Upgrade to 6.1.13.
audio/praat: Upgrade to 6.1.13
Apr 24 2020, 7:22 PM

Apr 20 2020

jwb committed rP532202: science/afni: Upgrade to 20.1.02.
science/afni: Upgrade to 20.1.02
Apr 20 2020, 12:21 PM

Apr 15 2020

jwb committed rP531770: biology/gcta: Genome-wide Complex Trait Analysis.
biology/gcta: Genome-wide Complex Trait Analysis
Apr 15 2020, 3:22 PM
jwb committed rP531764: sysutils/slurm-wlm: Revert error file to stderr when redirect no longer needed.
sysutils/slurm-wlm: Revert error file to stderr when redirect no longer needed
Apr 15 2020, 12:50 PM

Apr 14 2020

jwb committed rP531674: biology/py-macs2: Upgrade to 2.2.7.1.
biology/py-macs2: Upgrade to 2.2.7.1
Apr 14 2020, 12:14 PM

Apr 12 2020

jwb committed rP531521: science/dlpoly-classic: Change dependency to openmpi3.
science/dlpoly-classic: Change dependency to openmpi3
Apr 12 2020, 2:31 PM
jwb committed rP531468: sysutils/slurm-wlm: Upgrade to 20.02.1.
sysutils/slurm-wlm: Upgrade to 20.02.1
Apr 12 2020, 12:57 AM

Apr 9 2020

jwb committed rP531215: biology/fastp: Upgrade to 0.20.1.
biology/fastp: Upgrade to 0.20.1
Apr 9 2020, 4:17 PM
jwb committed rP531206: biology/star: Upgrade to 2.7.3a.
biology/star: Upgrade to 2.7.3a
Apr 9 2020, 12:43 PM

Apr 2 2020

jwb committed rP530371: MFH: r530250.
MFH: r530250
Apr 2 2020, 1:41 PM

Apr 1 2020

jwb committed rP530250: kallisto: Patch for build with GCC.
kallisto: Patch for build with GCC
Apr 1 2020, 11:35 PM

Mar 30 2020

jwb committed rP529850: auto-admin: Upgrade to 0.6.1.
auto-admin: Upgrade to 0.6.1
Mar 30 2020, 12:30 AM

Mar 28 2020

jwb committed rP529747: auto-admin: Upgrade to 0.6.0.
auto-admin: Upgrade to 0.6.0
Mar 28 2020, 5:37 PM

Mar 20 2020

jwb committed rP528792: biology/canu: Upgrade to 2.0.
biology/canu: Upgrade to 2.0
Mar 20 2020, 6:14 PM

Mar 15 2020

jwb committed rP528511: sysutils/slurm-wlm: Remove obsolete and broken REINPLACE.
sysutils/slurm-wlm: Remove obsolete and broken REINPLACE
Mar 15 2020, 11:19 PM
jwb committed rP528464: sysutils/slurm-wlm: Patch build system for clang/lld 10.
sysutils/slurm-wlm: Patch build system for clang/lld 10
Mar 15 2020, 1:34 AM

Mar 7 2020

jwb committed rP527971: biology/jellyfish: Patch for clang 10.
biology/jellyfish: Patch for clang 10
Mar 7 2020, 7:26 PM

Mar 1 2020

jwb committed rP527560: biology/bowtie2: Upgrade to 2.4.1.
biology/bowtie2: Upgrade to 2.4.1
Mar 1 2020, 4:01 PM

Feb 19 2020

jwb committed rP526534: biology/vsearch: Upgrade to 2.14.2.
biology/vsearch: Upgrade to 2.14.2
Feb 19 2020, 10:34 PM

Feb 15 2020

jwb committed rP526244: biology/kallisto: Upgrade to 0.46.2.
biology/kallisto: Upgrade to 0.46.2
Feb 15 2020, 11:09 PM

Feb 9 2020

jwb committed rP525659: biology/py-macs2: Bump revision for previous run dep addition.
biology/py-macs2: Bump revision for previous run dep addition
Feb 9 2020, 2:24 PM
jwb committed rP525658: biology/py-macs2: Add missing numpy run depend.
biology/py-macs2: Add missing numpy run depend
Feb 9 2020, 2:21 PM

Jan 23 2020

jwb committed rP523858: sysutils/slurm-wlm: Upgrade to 19.05.5.
sysutils/slurm-wlm: Upgrade to 19.05.5
Jan 23 2020, 1:52 AM
jwb committed rP523857: sysutils/desktop-installer: Upgrade to 0.6.11.
sysutils/desktop-installer: Upgrade to 0.6.11
Jan 23 2020, 1:32 AM
jwb committed rP523856: sysutils/auto-admin: Upgrade to 0.5.1.
sysutils/auto-admin: Upgrade to 0.5.1
Jan 23 2020, 1:28 AM

Jan 16 2020

jwb committed rP523237: sysutils/desktop-installer: Upgrade to 0.6.10.
sysutils/desktop-installer: Upgrade to 0.6.10
Jan 16 2020, 2:55 PM
jwb committed rP523233: sysutils/autoadmin: Upgrade to 0.5.0.
sysutils/autoadmin: Upgrade to 0.5.0
Jan 16 2020, 2:05 PM

Jan 14 2020

jwb committed rP523074: biology/gemma: Unbreak build.
biology/gemma: Unbreak build
Jan 14 2020, 10:35 PM

Jan 11 2020

jwb committed rP522687: biology/py-macs2: Upgrade to 2.2.6.
biology/py-macs2: Upgrade to 2.2.6
Jan 11 2020, 2:20 PM

Dec 29 2019

jwb closed D22708: Fix the Ethernet+WiFi example.
Dec 29 2019, 3:13 PM
jwb committed rD53718: Update WiFi failover example in advanced-networking..
Update WiFi failover example in advanced-networking.
Dec 29 2019, 3:13 PM

Dec 28 2019

jwb added a comment to D22708: Fix the Ethernet+WiFi example.

I actually put the note right after the statement it's clarifying:

Dec 28 2019, 10:35 PM
jwb added a comment to D22708: Fix the Ethernet+WiFi example.

Only the PDF output is screwy and I can verify using the HTML, so I'll go ahead with the commit shortly. I made one small change, adding a note to inform the reader why we should change the Ethernet MAC rather than the WiFi:

Dec 28 2019, 8:27 PM
jwb added a comment to D22708: Fix the Ethernet+WiFi example.

In the resulting text:

Dec 28 2019, 3:51 PM
jwb added a comment to D22708: Fix the Ethernet+WiFi example.

I'm trying to build-test per https://www.freebsd.org/doc/en_US.ISO8859-1/books/fdp-primer/overview.html and I'm getting nothing but '#' symbols for the text. Anybody seen this issue before?

Dec 28 2019, 3:01 PM

Dec 26 2019

jwb committed rP520932: biology/ncbi-blast+: Upgrade to 2.10.0.
biology/ncbi-blast+: Upgrade to 2.10.0
Dec 26 2019, 4:21 PM

Dec 19 2019

jwb committed rP520414: biology/bedtools: Upgrade to 2.29.2.
biology/bedtools: Upgrade to 2.29.2
Dec 19 2019, 1:04 AM

Dec 17 2019

jwb added a comment to D22708: Fix the Ethernet+WiFi example.

Didn't know that was possible. I'm going to be swamped for the next week or two, but I'll look into it ASAP after that.

Dec 17 2019, 1:52 AM

Dec 15 2019

jwb added a comment to D22708: Fix the Ethernet+WiFi example.

I'm currently only a ports committer, so this will have to fall on someone else.

Dec 15 2019, 6:51 PM
jwb accepted D22708: Fix the Ethernet+WiFi example.

Barring any typos that escaped my notice, looks fine to me. Thanks for your work on this!

Dec 15 2019, 3:18 PM

Dec 11 2019

jwb committed rP519810: biology/bedtools: Upgrade to 2.29.1.
biology/bedtools: Upgrade to 2.29.1
Dec 11 2019, 3:13 PM

Nov 28 2019

jwb committed rP518557: biology/unanimity: Remove erroneous BROKEN.
biology/unanimity: Remove erroneous BROKEN
Nov 28 2019, 5:46 AM

Nov 27 2019

jwb committed rP518515: sysutils/desktop-installer: Upgrade to 0.6.9.
sysutils/desktop-installer: Upgrade to 0.6.9
Nov 27 2019, 6:18 PM

Nov 26 2019

jwb committed rP518470: biology/py-multiqc: Upgrade to 1.8.
biology/py-multiqc: Upgrade to 1.8
Nov 26 2019, 4:25 PM
jwb committed rP518469: biology/p5-TrimGalore: Upgrade to 0.6.5.
biology/p5-TrimGalore: Upgrade to 0.6.5
Nov 26 2019, 4:20 PM

Nov 24 2019

jwb committed rP518334: biology/unanimity and dependencies: Flag as no longer open source.
biology/unanimity and dependencies: Flag as no longer open source
Nov 24 2019, 3:53 PM

Nov 23 2019

jwb committed rP518264: sysutils/desktop-installer: Upgrade to 0.6.8.
sysutils/desktop-installer: Upgrade to 0.6.8
Nov 23 2019, 6:10 PM
jwb committed rP518262: sysutils/auto-admin: Upgrade to 0.4.9.
sysutils/auto-admin: Upgrade to 0.4.9
Nov 23 2019, 6:05 PM
jwb committed rP518242: biology/py-cutadapt: Upgrade to 2.7.
biology/py-cutadapt: Upgrade to 2.7
Nov 23 2019, 2:46 PM
jwb committed rP518241: archivers/py-xopen: Upgrade to 0.8.4.
archivers/py-xopen: Upgrade to 0.8.4
Nov 23 2019, 2:41 PM
jwb committed rP518240: biology/py-dnaio: Upgrade to 0.4.1.
biology/py-dnaio: Upgrade to 0.4.1
Nov 23 2019, 2:40 PM