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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 (112 w, 6 d)

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

Recent Activity

Thu, Jan 23

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

Thu, Jan 16

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

Tue, Jan 14

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

Sat, Jan 11

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

Sun, Dec 29

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

Sat, Dec 28

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

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

Sat, Dec 28, 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:

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

In the resulting text:

Sat, Dec 28, 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?

Sat, Dec 28, 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

Nov 17 2019

jwb committed rP517828: biology/haplohseq: Switch to distfile with example data.
biology/haplohseq: Switch to distfile with example data
Nov 17 2019, 3:00 PM

Nov 16 2019

jwb committed rP517777: devel/R-cran-optparse: Command line flag parser inspired by Python's optparse.
devel/R-cran-optparse: Command line flag parser inspired by Python's optparse
Nov 16 2019, 9:56 PM
jwb committed rP517776: Add R-cran-getopt.
Add R-cran-getopt
Nov 16 2019, 9:54 PM
jwb committed rP517763: devel/R-cran-getopt: Accept short and long flags in Rscript.
devel/R-cran-getopt: Accept short and long flags in Rscript
Nov 16 2019, 4:51 PM

Nov 8 2019

jwb committed rP517066: biology/canu: Upgrade to 1.9.
biology/canu: Upgrade to 1.9
Nov 8 2019, 2:03 PM

Nov 6 2019

jwb committed rP516853: biology/kallisto: Upgrade to 0.46.1.
biology/kallisto: Upgrade to 0.46.1
Nov 6 2019, 12:18 AM

Oct 6 2019

jwb committed rP513915: biology/star: Upgrade to 2.7.2d.
biology/star: Upgrade to 2.7.2d
Oct 6 2019, 10:18 PM
jwb committed rP513910: biology/fastahack: Upgrade to 1.0.0.
biology/fastahack: Upgrade to 1.0.0
Oct 6 2019, 9:34 PM

Sep 27 2019

jwb committed rP512997: biology/tophat: Fast splice junction mapper for RNA-Seq reads.
biology/tophat: Fast splice junction mapper for RNA-Seq reads
Sep 27 2019, 12:50 AM

Sep 23 2019

jwb committed rP512646: biology/py-multiqc: Aggregate bioinformatics analysis reports.
biology/py-multiqc: Aggregate bioinformatics analysis reports
Sep 23 2019, 4:09 PM

Sep 22 2019

jwb committed rP512600: science/packmol: Pack molecules in defined regions of space.
science/packmol: Pack molecules in defined regions of space
Sep 22 2019, 7:06 PM
jwb committed rP512591: archivers/py-lzstring: LZ-based in-memory string compression.
archivers/py-lzstring: LZ-based in-memory string compression
Sep 22 2019, 4:15 PM
jwb committed rP512590: graphics/py-spectra: Color scales and color conversion made easy for Python.
graphics/py-spectra: Color scales and color conversion made easy for Python
Sep 22 2019, 3:54 PM

Sep 21 2019

jwb committed rP512462: biology/p5-TrimGalore: Upgrade to 0.6.4.
biology/p5-TrimGalore: Upgrade to 0.6.4
Sep 21 2019, 2:51 AM
jwb committed rP512461: biology/fastqc: Upgrade to 0.11.8.
biology/fastqc: Upgrade to 0.11.8
Sep 21 2019, 2:45 AM

Sep 16 2019

jwb committed rP512137: biology/haplohseq: Identify regions of allelic imbalance.
biology/haplohseq: Identify regions of allelic imbalance
Sep 16 2019, 1:07 AM

Sep 14 2019

jwb committed rP512031: sysutils/slurm-wlm: Temporary patch to silence job accounting errors.
sysutils/slurm-wlm: Temporary patch to silence job accounting errors
Sep 14 2019, 4:02 PM
jwb committed rP512018: biology/trimmomatic: Upgrade to 0.39.
biology/trimmomatic: Upgrade to 0.39
Sep 14 2019, 2:46 PM
jwb committed rP512008: py-xopen: Upgrade to 0.8.2.
py-xopen: Upgrade to 0.8.2
Sep 14 2019, 12:25 PM

Sep 13 2019

jwb committed rP511958: biology/bedtools: Upgrade to 2.29.0.
biology/bedtools: Upgrade to 2.29.0
Sep 13 2019, 1:22 PM
jwb committed rP511957: biology/py-cutadapt: Upgrade to 2.5.
biology/py-cutadapt: Upgrade to 2.5
Sep 13 2019, 1:17 PM

Aug 17 2019

jwb committed rP509157: sysutils/desktop-installer: Upgrade to 0.6.7.
sysutils/desktop-installer: Upgrade to 0.6.7
Aug 17 2019, 3:11 PM

Aug 13 2019

jwb committed rP508832: biology/bolt-lmm: Upgrade to 2.3.4.
biology/bolt-lmm: Upgrade to 2.3.4
Aug 13 2019, 3:30 PM

Aug 4 2019

jwb committed rP508135: PR: 239613.
PR: 239613
Aug 4 2019, 11:48 PM

Jul 25 2019

jwb committed rP507331: sysutils/desktop-installer: Upgrade to 0.6.6.
sysutils/desktop-installer: Upgrade to 0.6.6
Jul 25 2019, 9:54 PM
jwb committed rP507330: sysutils/auto-admin: Upgrade to 0.4.8.
sysutils/auto-admin: Upgrade to 0.4.8
Jul 25 2019, 9:46 PM

Jul 21 2019

jwb committed rP507030: sysutils/slurm-wlm: Upgrade to 19.05.1-2.
sysutils/slurm-wlm: Upgrade to 19.05.1-2
Jul 21 2019, 12:10 AM

Jul 12 2019

jwb committed rP506497: ncbi-blast+: Unbreak build with gcc8 following gcc9 patch.
ncbi-blast+: Unbreak build with gcc8 following gcc9 patch
Jul 12 2019, 11:58 PM

Jul 11 2019

jwb committed rP506409: ncbi-blast+: Fix build with gcc9.
ncbi-blast+: Fix build with gcc9
Jul 11 2019, 1:53 PM

Jun 18 2019

jwb committed rP504496: science/afni: Upgrade to 19.1.20.
science/afni: Upgrade to 19.1.20
Jun 18 2019, 7:01 PM

Jun 14 2019

jwb committed rP504153: biology/ncbi-blast+: Fix build on powerpc64, add run dep for update_blastdb.pl.
biology/ncbi-blast+: Fix build on powerpc64, add run dep for update_blastdb.pl
Jun 14 2019, 12:38 AM
jwb committed rP504151: sysutils/slurm-wlm: Revert previous change enabling Linux option by default.
sysutils/slurm-wlm: Revert previous change enabling Linux option by default
Jun 14 2019, 12:21 AM

Jun 13 2019

jwb committed rP504147: sysutils/slurm-wlm: Enable jobacct_gather/linux by default.
sysutils/slurm-wlm: Enable jobacct_gather/linux by default
Jun 13 2019, 11:53 PM

Jun 12 2019

jwb committed rP504047: biology/ncbi-blast+: Upgrade to 2.9.0.
biology/ncbi-blast+: Upgrade to 2.9.0
Jun 12 2019, 11:53 PM
jwb committed rP504011: biology/kallisto: Upgrade to 0.46.0.
biology/kallisto: Upgrade to 0.46.0
Jun 12 2019, 3:25 PM

Jun 8 2019

jwb committed rP503747: science/afni: Upgrade to 19.1.18.
science/afni: Upgrade to 19.1.18
Jun 8 2019, 7:14 PM

Jun 1 2019

jwb committed rP503233: science/afni: Upgrade to 19.1.14.
science/afni: Upgrade to 19.1.14
Jun 1 2019, 1:00 PM

May 26 2019

jwb committed rP502673: biology/bolt-lmm: Mixed model association testing and variance component….
biology/bolt-lmm: Mixed model association testing and variance component…
May 26 2019, 3:37 AM

May 22 2019

jwb committed rP502266: science/afni: Upgrade to 19.1.10.
science/afni: Upgrade to 19.1.10
May 22 2019, 12:44 PM

May 20 2019

jwb committed rP502179: sysutils/slurm-wlm: Remove redundant USE_GCC.
sysutils/slurm-wlm: Remove redundant USE_GCC
May 20 2019, 11:47 PM
jwb committed rP502178: biology/fastp: Remove redundant USE_GCC.
biology/fastp: Remove redundant USE_GCC
May 20 2019, 11:41 PM
jwb committed rP502158: science/afni: Upgrade to 19.1.08.
science/afni: Upgrade to 19.1.08
May 20 2019, 7:36 PM

May 18 2019

jwb committed rP501990: biology/gemma: Lowercase PORTNAME, remove unnecesary USE_GCC.
biology/gemma: Lowercase PORTNAME, remove unnecesary USE_GCC
May 18 2019, 10:41 PM

May 17 2019

jwb committed rP501873: biology/gemma: Genome-wide Efficient Mixed Model Association.
biology/gemma: Genome-wide Efficient Mixed Model Association
May 17 2019, 2:45 PM

May 15 2019

jwb committed rP501674: sysutils/slurm-wlm: Upgrade to 18.08.7.
sysutils/slurm-wlm: Upgrade to 18.08.7
May 15 2019, 1:34 AM

May 13 2019

jwb committed rP501578: biology/jellyfish: Upgrade to 2.2.10, patch for powerpc64.
biology/jellyfish: Upgrade to 2.2.10, patch for powerpc64
May 13 2019, 4:23 PM

May 11 2019

jwb committed rP501259: biology/vsearch: Update to 2.13.4.
biology/vsearch: Update to 2.13.4
May 11 2019, 1:42 PM
jwb committed rP501207: biology/trimadap: Mark only for amd64 and i386.
biology/trimadap: Mark only for amd64 and i386
May 11 2019, 12:18 AM

May 10 2019

jwb committed rP501200: biology/stacks: Remove obsolete pkg-message regarding web interface.
biology/stacks: Remove obsolete pkg-message regarding web interface
May 10 2019, 9:16 PM
jwb committed rP501199: biology/stacks: Upgrade to 2.4.
biology/stacks: Upgrade to 2.4
May 10 2019, 9:04 PM

May 9 2019

jwb committed rP501148: biology/vsearch: Remove powerpc64 support.
biology/vsearch: Remove powerpc64 support
May 9 2019, 10:12 PM
jwb committed rP501147: biology/vsearch: Versatile open-source tool for metagenomics.
biology/vsearch: Versatile open-source tool for metagenomics
May 9 2019, 9:29 PM

May 5 2019

jwb committed rP500860: biology/minimap2: Upgrade to 2.17.
biology/minimap2: Upgrade to 2.17
May 5 2019, 2:56 PM

May 4 2019

jwb committed rP500812: biology/ddocent: Upgrade to 2.7.8.
biology/ddocent: Upgrade to 2.7.8
May 4 2019, 3:09 PM
jwb committed rP500770: biology/fastp: Respect WITH_DEBUG - do not strip binary.
biology/fastp: Respect WITH_DEBUG - do not strip binary
May 4 2019, 2:07 AM

May 3 2019

jwb committed rP500737: biology/fastp: Ultra-fast all-in-one FASTQ preprocessor.
biology/fastp: Ultra-fast all-in-one FASTQ preprocessor
May 3 2019, 2:42 PM

May 2 2019

jwb committed rP500629: biology/star: Force newer GCC on platforms with GCC 4.2 base.
biology/star: Force newer GCC on platforms with GCC 4.2 base
May 2 2019, 12:40 AM

Apr 27 2019

jwb committed rP500187: biology/py-cutadapt: Upgrade to 2.3.
biology/py-cutadapt: Upgrade to 2.3
Apr 27 2019, 1:26 AM
jwb committed rP500186: archivers/py-xopen: Upgrade to 0.5.1.
archivers/py-xopen: Upgrade to 0.5.1
Apr 27 2019, 1:22 AM

Apr 24 2019

jwb committed rP499895: biology/minimap2: Pairwise aligner for genomic and spliced nucleotide sequences.
biology/minimap2: Pairwise aligner for genomic and spliced nucleotide sequences
Apr 24 2019, 6:04 PM
jwb committed rP499873: biology/bowtie2: Clarify CPU-specificity.
biology/bowtie2: Clarify CPU-specificity
Apr 24 2019, 5:41 PM

Apr 23 2019

jwb committed rP499763: biology/star: Modify PKGBASE to avoid conflict with archivers/star.
biology/star: Modify PKGBASE to avoid conflict with archivers/star
Apr 23 2019, 3:03 PM

Apr 21 2019

jwb committed rP499592: biology/star: Spliced Transcripts Alignment to a Reference.
biology/star: Spliced Transcripts Alignment to a Reference
Apr 21 2019, 8:31 PM
jwb committed rP499544: biology/bowtie2: Upgrade to 2.3.5.1.
biology/bowtie2: Upgrade to 2.3.5.1
Apr 21 2019, 3:23 PM

Apr 18 2019

jwb committed rP499251: biology/canu: Fix build on powerpc64 and aarch64.
biology/canu: Fix build on powerpc64 and aarch64
Apr 18 2019, 12:16 PM

Mar 24 2019

jwb committed rP496785: biology/p5-TrimGalore: Upgrade to 0.6.1.
biology/p5-TrimGalore: Upgrade to 0.6.1
Mar 24 2019, 9:44 PM
jwb committed rP496783: biology/py-cutadapt: Upgrade to 2.1.
biology/py-cutadapt: Upgrade to 2.1
Mar 24 2019, 9:20 PM
jwb abandoned D19693: biology/py-dnaio: Read and write FASTQ and FASTA.

Answered my own question + received some feedback.

Mar 24 2019, 8:46 PM
jwb committed rP496774: archivers/py-xopen: Upgrade to 0.5.0.
archivers/py-xopen: Upgrade to 0.5.0
Mar 24 2019, 8:05 PM
jwb committed rP496770: biology/py-dnaio: Read and write FASTQ and FASTA.
biology/py-dnaio: Read and write FASTQ and FASTA
Mar 24 2019, 7:40 PM
jwb updated the diff for D19693: biology/py-dnaio: Read and write FASTQ and FASTA.

Thanks, checksubdirs is not mentioned in the FAQ. It just says to make
sure you don't want a repocopy instead, and use Tools/scripts/addport.

Mar 24 2019, 3:09 PM