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jwb (jwb@freebsd.org)
Scientific computing instructor, bioinformatics consultant

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User Details

User Since
Nov 27 2017, 4:37 PM (410 w, 2 d)

Instructor for Research Computing, etc. at the University of Wisconsin -- Milwaukee

Recent Activity

Sun, Oct 5

jwb committed R11:f07bc6e23dc6: biology/vsearch: Update to 2.30.1 (authored by jwb).
biology/vsearch: Update to 2.30.1
Sun, Oct 5, 6:28 PM

Fri, Oct 3

jwb committed R11:e4b0269fe7a7: math/rapid: Deprecate (authored by jwb).
math/rapid: Deprecate
Fri, Oct 3, 12:32 PM

Wed, Oct 1

jwb committed R11:380ec0827846: net/py-google-cloud-pubsub: Python interface to Google pubsub (authored by jwb).
net/py-google-cloud-pubsub: Python interface to Google pubsub
Wed, Oct 1, 2:25 AM

Tue, Sep 30

jwb committed R11:b21bd86a1be5: sysutils/auto-admin: Update to 0.8.3.28 (authored by jwb).
sysutils/auto-admin: Update to 0.8.3.28
Tue, Sep 30, 8:29 PM

Sun, Sep 21

jwb committed R11:ef680967ddb6: devel/mongo-c-driver: Enable SRV option by default (authored by jwb).
devel/mongo-c-driver: Enable SRV option by default
Sun, Sep 21, 11:25 PM
jwb committed R11:613bcfe053d3: sysutils/desktop-installer: Update to 1.1.1.4 (authored by jwb).
sysutils/desktop-installer: Update to 1.1.1.4
Sun, Sep 21, 2:20 PM
jwb committed R11:39cc1c08f8a1: sysutils/auto-admin: Update to 0.8.3.27 (authored by jwb).
sysutils/auto-admin: Update to 0.8.3.27
Sun, Sep 21, 2:17 PM

Fri, Sep 19

jwb committed R11:d94c7a1a9ee3: devel/cppcodec: Update to 0.2-11 (authored by jwb).
devel/cppcodec: Update to 0.2-11
Fri, Sep 19, 3:14 PM

Tue, Sep 16

jwb committed R11:4cbdaf82ef44: x11/coreterminal: Update to 5.0.0 (authored by jwb).
x11/coreterminal: Update to 5.0.0
Tue, Sep 16, 1:44 PM
jwb committed R11:aca2d57f1b19: deskutils/coregarage: Update to 5.0.0 (authored by jwb).
deskutils/coregarage: Update to 5.0.0
Tue, Sep 16, 1:44 PM
jwb committed R11:57f1bc675fa6: deskutils/libcprime: Update to 5.0.0 (authored by jwb).
deskutils/libcprime: Update to 5.0.0
Tue, Sep 16, 1:35 PM
jwb committed R11:1c2ccb4be11c: archivers/libarchive-qt: Update to 2.0.8 (authored by jwb).
archivers/libarchive-qt: Update to 2.0.8
Tue, Sep 16, 1:35 PM

Sun, Sep 14

jwb committed R11:a706669299c2: comms/cutecom: Update to 0.60.0-RC1 (authored by jwb).
comms/cutecom: Update to 0.60.0-RC1
Sun, Sep 14, 8:04 PM

Wed, Sep 10

jwb committed R11:4ea563b952a6: sysutils/desktop-installer: Update to 1.1.1.3 (authored by jwb).
sysutils/desktop-installer: Update to 1.1.1.3
Wed, Sep 10, 4:06 PM

Sep 7 2025

jwb committed R11:3841f8ba550a: sysutils/auto-admin: Update to 0.8.3.25 (authored by jwb).
sysutils/auto-admin: Update to 0.8.3.25
Sep 7 2025, 8:35 PM

Sep 6 2025

jwb committed R11:c209be0887f1: devel/Makefile: cpp-codec -> cppcodec (authored by jwb).
devel/Makefile: cpp-codec -> cppcodec
Sep 6 2025, 7:48 PM

Sep 5 2025

jwb committed R11:092acfc2ac18: devel/mongo-cxx-driver: MongoDB C++ driver (authored by jwb).
devel/mongo-cxx-driver: MongoDB C++ driver
Sep 5 2025, 11:52 PM
jwb committed R11:5679cabff6b1: devel/cppcodec: Library to encode/decode base64, base64url, etc. (authored by jwb).
devel/cppcodec: Library to encode/decode base64, base64url, etc.
Sep 5 2025, 11:30 PM

Aug 26 2025

jwb committed R11:81ad72065ddc: biology/salmon: Update to tag 1.10.3 (authored by jwb).
biology/salmon: Update to tag 1.10.3
Aug 26 2025, 11:33 AM
jwb committed R11:ef86e09b7e3a: biology/ncbi-blast+: Update to 2.17.0 (authored by jwb).
biology/ncbi-blast+: Update to 2.17.0
Aug 26 2025, 11:28 AM

Aug 24 2025

jwb committed R11:9890f0cfefbe: sysutils/auto-admin: Update to 0.8.3.25 (authored by jwb).
sysutils/auto-admin: Update to 0.8.3.25
Aug 24 2025, 11:25 AM

Aug 21 2025

jwb committed R11:5d8f84ce55c7: biology/bbmap: Update to 39.34 (authored by jwb).
biology/bbmap: Update to 39.34
Aug 21 2025, 8:33 PM

Aug 14 2025

jwb committed R11:486b568db0d0: sysutils/auto-admin: Update to 0.8.3.24 (authored by jwb).
sysutils/auto-admin: Update to 0.8.3.24
Aug 14 2025, 7:09 PM

Aug 5 2025

jwb added a comment to D51702: kernel: Allow unprivileged chroot by default.

It occurred to me that it might be good to set NO_NEW_PRIVS automatically when chroot is not invoked by root, rather than error out and make the user specify -n.

Aug 5 2025, 3:00 PM

Aug 3 2025

jwb added a comment to D51702: kernel: Allow unprivileged chroot by default.

For chroot(8), it seems a little cryptic to only mention security.bsd.unprivileged_chroot in the -n flag section. Might I suggest adding a paragraph like the following up-top, before the options descriptions:

Aug 3 2025, 12:20 AM

Jul 27 2025

jwb committed R11:ace12788b0db: biology/salmon: Update to tag 1.10.3 (authored by jwb).
biology/salmon: Update to tag 1.10.3
Jul 27 2025, 9:13 PM

Jul 24 2025

jwb committed R11:c850bf3a31c1: biology/ncbi-blast+: Update to 2.17.0 (authored by jwb).
biology/ncbi-blast+: Update to 2.17.0
Jul 24 2025, 9:06 PM

Jun 28 2025

jwb committed R11:538a8718e2ff: biology/py-pydeseq2: Update to 0.5.2 (authored by jwb).
biology/py-pydeseq2: Update to 0.5.2
Jun 28 2025, 11:48 AM

Jun 21 2025

jwb committed R11:890b1c25be4d: biology/bcf-score: Use latest versions of hstlib and bcftools (authored by jwb).
biology/bcf-score: Use latest versions of hstlib and bcftools
Jun 21 2025, 10:18 PM
jwb committed R11:49752ef6cd89: biology/bio-mocha: Use latest versions of htslib and bcftools (authored by jwb).
biology/bio-mocha: Use latest versions of htslib and bcftools
Jun 21 2025, 10:09 PM
jwb committed R11:14102a0178f9: biology/minimap2: Remove extraneous file that snuck in the last commit (authored by jwb).
biology/minimap2: Remove extraneous file that snuck in the last commit
Jun 21 2025, 9:48 PM

Jun 16 2025

jwb committed R11:027b959425c8: biology/minimap2: Update to 2.30 (authored by jwb).
biology/minimap2: Update to 2.30
Jun 16 2025, 1:10 PM

Jun 14 2025

jwb committed R11:ec7391b149b9: devel/isa-l: Enable build on aarch64 (authored by jwb).
devel/isa-l: Enable build on aarch64
Jun 14 2025, 12:18 PM

Jun 11 2025

jwb committed R11:e91e2f54bddb: biology/py-pydeseq2: Python reimplementation of the DESeq2 R package (authored by jwb).
biology/py-pydeseq2: Python reimplementation of the DESeq2 R package
Jun 11 2025, 2:25 PM
jwb committed R11:cfe792f0ddf0: math/py-formulaic-contrasts: Build arbitrary contrasts formulaic models (authored by jwb).
math/py-formulaic-contrasts: Build arbitrary contrasts formulaic models
Jun 11 2025, 2:21 PM
jwb committed R11:0b1ab7cf4c4d: devel/py-joblib: Unbreak build (authored by jwb).
devel/py-joblib: Unbreak build
Jun 11 2025, 2:11 PM

Jun 7 2025

jwb committed R11:b902f8f425a4: biology/fastp: Update to 0.26.0 (authored by jwb).
biology/fastp: Update to 0.26.0
Jun 7 2025, 12:32 PM

Jun 5 2025

jwb committed R11:45095055298e: sysutils/auto-admin: Update to 0.8.3.7 (authored by jwb).
sysutils/auto-admin: Update to 0.8.3.7
Jun 5 2025, 12:45 PM

Jun 4 2025

jwb committed R11:cb80427150ce: biology/seqtk: Update to 1.5 (authored by jwb).
biology/seqtk: Update to 1.5
Jun 4 2025, 2:21 PM
jwb committed R11:3a7978fed606: biology/bcftools: Update to 1.22 (authored by jwb).
biology/bcftools: Update to 1.22
Jun 4 2025, 1:26 PM
jwb committed R11:3c62a6836854: biology/samtools: Update to 1.22 (authored by jwb).
biology/samtools: Update to 1.22
Jun 4 2025, 1:26 PM
jwb committed R11:c8a79b9a3b12: biology/htslib: Update to 1.22 (authored by jwb).
biology/htslib: Update to 1.22
Jun 4 2025, 1:26 PM

Jun 1 2025

jwb committed R11:78e546084e93: biology/fastp: Update to 0.25.0 (authored by jwb).
biology/fastp: Update to 0.25.0
Jun 1 2025, 1:28 PM

May 30 2025

jwb committed R11:b3918a5e6eea: biology/fastp: Update to 0.24.3 (authored by jwb).
biology/fastp: Update to 0.24.3
May 30 2025, 1:07 PM

May 27 2025

jwb committed R11:b15df322b48c: biology/kallisto: Remove USE_GCC, fix build with clang19 (authored by jwb).
biology/kallisto: Remove USE_GCC, fix build with clang19
May 27 2025, 2:20 PM
jwb committed R11:bba37490f132: biology/bifrost: Remove USE_GCC, fix build with clang19 (authored by jwb).
biology/bifrost: Remove USE_GCC, fix build with clang19
May 27 2025, 2:09 PM

May 25 2025

jwb committed R11:7611c373bf8f: biology/fasda: Update to 0.2.0.1 (authored by jwb).
biology/fasda: Update to 0.2.0.1
May 25 2025, 2:27 PM

May 23 2025

jwb committed R11:b3b1a391c149: biology/megahit: Update to 1.2.9.20 (authored by jwb).
biology/megahit: Update to 1.2.9.20
May 23 2025, 12:34 PM

May 20 2025

jwb committed R11:51c1f17ce70a: biology/haplohseq: Update to 0.1.2.3 (authored by jwb).
biology/haplohseq: Update to 0.1.2.3
May 20 2025, 11:33 PM
jwb committed R11:bd2f753fe114: biology/lamarc: New maintainer hayzam@alchemilla.io (authored by jwb).
biology/lamarc: New maintainer hayzam@alchemilla.io
May 20 2025, 11:17 PM
jwb committed R11:ba0d68b692fc: biology/lamarc: Unbreak build on 14.x (authored by jwb).
biology/lamarc: Unbreak build on 14.x
May 20 2025, 11:32 AM

May 19 2025

jwb committed R11:101f13edbc07: biology/bamtools: Update to 2.5.3 (authored by jwb).
biology/bamtools: Update to 2.5.3
May 19 2025, 9:23 PM

May 15 2025

jwb committed R11:3ae8b09ca041: biology/vcftools: Update to 0.1.17 (authored by jwb).
biology/vcftools: Update to 0.1.17
May 15 2025, 12:29 PM
jwb committed R11:18cabe581ff1: biology/kallisto: Unbreak build on 15-CURRENT (authored by jwb).
biology/kallisto: Unbreak build on 15-CURRENT
May 15 2025, 11:46 AM
jwb committed R11:40478d7acd2a: biology/bifrost: Unbreak build on 15-CURRENT (authored by jwb).
biology/bifrost: Unbreak build on 15-CURRENT
May 15 2025, 11:39 AM

May 8 2025

jwb committed R11:c3626a7f1664: sysutils/desktop-installer: Update to 1.1.1 (authored by jwb).
sysutils/desktop-installer: Update to 1.1.1
May 8 2025, 9:44 PM
jwb committed R11:a654249b48c6: sysutils/auto-admin: Update to 0.8.3 (authored by jwb).
sysutils/auto-admin: Update to 0.8.3
May 8 2025, 9:43 PM

May 5 2025

jwb committed R11:9a23beadaa33: biology/fasda-utils: Update to 0.1.0.2 (authored by jwb).
biology/fasda-utils: Update to 0.1.0.2
May 5 2025, 9:46 PM

May 4 2025

jwb committed R11:1a7bd4d40277: sysutils/linux-miniconda-installer: Update to 0.1.0.6 (authored by jwb).
sysutils/linux-miniconda-installer: Update to 0.1.0.6
May 4 2025, 12:35 PM
jwb committed R11:3a58d96ad5ab: sysutils/linux-miniconda-installer: Update to 0.1.0.4 (authored by jwb).
sysutils/linux-miniconda-installer: Update to 0.1.0.4
May 4 2025, 12:27 PM

Apr 30 2025

jwb committed R11:f34a8493a4c4: sysutils/auto-admin: Update to 0.8.2 (authored by jwb).
sysutils/auto-admin: Update to 0.8.2
Apr 30 2025, 11:15 AM
jwb committed R11:b5fed385507c: biology/fastq-trim: Update to 0.1.4 (authored by jwb).
biology/fastq-trim: Update to 0.1.4
Apr 30 2025, 11:12 AM

Apr 28 2025

jwb committed R11:6034a63dcea9: biology/fasda-utils: Update to 0.1.0.1 (authored by jwb).
biology/fasda-utils: Update to 0.1.0.1
Apr 28 2025, 3:43 PM
jwb committed R11:39b2e62d29fa: biology/vcflib: Update to 1.0.13 (authored by jwb).
biology/vcflib: Update to 1.0.13
Apr 28 2025, 11:43 AM

Apr 26 2025

jwb committed R11:0bef7dda8ca9: biology/biolibc-tools: Update to 0.1.5 (authored by jwb).
biology/biolibc-tools: Update to 0.1.5
Apr 26 2025, 8:41 PM
jwb committed R11:aa9df88f1c31: biology/fasda: Update to 0.2.0 (authored by jwb).
biology/fasda: Update to 0.2.0
Apr 26 2025, 8:39 PM
jwb committed R11:f680350d5ef9: biology/biolibc: Update to 0.2.7 (authored by jwb).
biology/biolibc: Update to 0.2.7
Apr 26 2025, 8:37 PM
jwb committed R11:cff47c67ef95: devel/libxtend: Update to 0.2.1 (authored by jwb).
devel/libxtend: Update to 0.2.1
Apr 26 2025, 8:35 PM

Apr 20 2025

jwb committed R11:cdd5a51ea04a: biology/minimap2: Update to 2.29 (authored by jwb).
biology/minimap2: Update to 2.29
Apr 20 2025, 1:19 PM

Apr 17 2025

jwb committed R11:b3f6f8596df4: biology/fastp: Update to 0.24.1 (authored by jwb).
biology/fastp: Update to 0.24.1
Apr 17 2025, 12:52 PM

Apr 16 2025

jwb committed R11:6d74c851a644: sysutils/diskimage-tools: Unbreak build (authored by jwb).
sysutils/diskimage-tools: Unbreak build
Apr 16 2025, 4:42 PM

Apr 6 2025

jwb committed R11:cc15cab2da4c: biology/fasda-utils: Fast and simple differential analysis extras (authored by jwb).
biology/fasda-utils: Fast and simple differential analysis extras
Apr 6 2025, 11:28 AM

Mar 27 2025

jwb committed R11:888c0b0e32d3: biology/subread: Update to 2.1.0 (authored by jwb).
biology/subread: Update to 2.1.0
Mar 27 2025, 10:06 PM

Mar 21 2025

jwb committed R11:a57f4b8deadd: biology/sra-tools: Update to 3.2.1 (authored by jwb).
biology/sra-tools: Update to 3.2.1
Mar 21 2025, 11:29 AM

Mar 19 2025

jwb committed R11:da25ff8f31cd: biology/py-macs3: Unbreak package build (authored by jwb).
biology/py-macs3: Unbreak package build
Mar 19 2025, 1:46 PM

Mar 13 2025

jwb committed R11:2e67831b3ea0: sysutils/desktop-installer: Update to 1.1.0.6 (authored by jwb).
sysutils/desktop-installer: Update to 1.1.0.6
Mar 13 2025, 4:36 PM
jwb committed R11:655c50cfc53d: science/csvtk: Update to 0.33.0 (authored by jwb).
science/csvtk: Update to 0.33.0
Mar 13 2025, 12:37 PM

Mar 11 2025

jwb committed R11:a7c9cc2b093f: math/py-hmmlearn: Unbreak poudriere build (authored by jwb).
math/py-hmmlearn: Unbreak poudriere build
Mar 11 2025, 2:56 PM

Mar 7 2025

jwb committed R11:c2d10be9f215: biology/py-macs3: Update to 3.0.3 (authored by jwb).
biology/py-macs3: Update to 3.0.3
Mar 7 2025, 2:30 PM

Mar 6 2025

jwb committed R11:8de761e7d400: biology/ncbi-blast+: Update to 2.16.0_3 (authored by jwb).
biology/ncbi-blast+: Update to 2.16.0_3
Mar 6 2025, 12:44 PM

Mar 4 2025

jwb committed R11:886844b5ecf8: biology/py-crossmap: Update to 0.7.3 (authored by jwb).
biology/py-crossmap: Update to 0.7.3
Mar 4 2025, 1:15 PM

Mar 2 2025

jwb committed R11:84399cefee34: biology/vsearch: Update to 2.30.0 (authored by jwb).
biology/vsearch: Update to 2.30.0
Mar 2 2025, 12:38 PM

Feb 21 2025

jwb committed R11:d758b1caa19e: Multiple biology ports: Replace pypi homepage with github (authored by jwb).
Multiple biology ports: Replace pypi homepage with github
Feb 21 2025, 1:05 PM

Feb 18 2025

jwb committed R11:bac90e855c13: biology/freebayes: Update to 1.3.9 (authored by jwb).
biology/freebayes: Update to 1.3.9
Feb 18 2025, 8:47 PM
jwb committed R11:813f71aa155a: biology/tabixpp: Undeprecate and update to 1.1.2 (authored by jwb).
biology/tabixpp: Undeprecate and update to 1.1.2
Feb 18 2025, 3:40 PM
jwb committed R11:38e86db59cdc: biology/tabixpp: Update to 1.1.2 (authored by jwb).
biology/tabixpp: Update to 1.1.2
Feb 18 2025, 3:40 PM
jwb committed R11:03b4820d4c5b: devel/intervaltree: Minimal C++ interval tree implementation (authored by jwb).
devel/intervaltree: Minimal C++ interval tree implementation
Feb 18 2025, 2:57 PM

Feb 16 2025

jwb committed R11:4bbc35807790: biology/vsearch: Update to 2.29.4 (authored by jwb).
biology/vsearch: Update to 2.29.4
Feb 16 2025, 2:21 PM
jwb committed R11:ef08ef1262c3: archivers/vbz-compression: Update to 1.0.13 (authored by jwb).
archivers/vbz-compression: Update to 1.0.13
Feb 16 2025, 1:18 PM

Feb 12 2025

jwb committed R11:ac235c50dc8f: sysutils/desktop-installer: Update to 1.1.0.5 (authored by jwb).
sysutils/desktop-installer: Update to 1.1.0.5
Feb 12 2025, 7:24 PM

Feb 8 2025

jwb committed R11:f0a998aad6e9: sysutils/desktop-installer: Update to 1.1.0.2 (authored by jwb).
sysutils/desktop-installer: Update to 1.1.0.2
Feb 8 2025, 5:59 PM

Feb 4 2025

jwb committed R11:222db315a10a: sysutils/desktop-installer: Update to 1.1.0 (authored by jwb).
sysutils/desktop-installer: Update to 1.1.0
Feb 4 2025, 4:05 PM
jwb committed R11:fa1e2038c23b: sysutils/auto-admin: Update to 0.8.1 (authored by jwb).
sysutils/auto-admin: Update to 0.8.1
Feb 4 2025, 4:05 PM
jwb committed R11:be795d728897: textproc/xml-format: Add missing dep (authored by jwb).
textproc/xml-format: Add missing dep
Feb 4 2025, 12:49 PM

Feb 3 2025

jwb committed R11:d426cea9b31c: textproc/xml-format: Update to 0.2.0.3 (authored by jwb).
textproc/xml-format: Update to 0.2.0.3
Feb 3 2025, 11:17 PM
jwb committed R11:aa76d692b293: sysutils/mcweject: Deprecate (authored by jwb).
sysutils/mcweject: Deprecate
Feb 3 2025, 11:10 PM
jwb committed R11:4c7ab59d2705: sysutils/endian: Update to 1.1.6 (authored by jwb).
sysutils/endian: Update to 1.1.6
Feb 3 2025, 11:08 PM
jwb committed R11:97b7e676be66: sysutils/diskimage-tools: Update to 0.3.1.1 (authored by jwb).
sysutils/diskimage-tools: Update to 0.3.1.1
Feb 3 2025, 10:26 PM
jwb committed R11:10a5ec03125f: math/matlab-installer: Deprecate (authored by jwb).
math/matlab-installer: Deprecate
Feb 3 2025, 10:08 PM
jwb committed R11:4a351aa5583d: math/matlab-installer: Deprecate (authored by jwb).
math/matlab-installer: Deprecate
Feb 3 2025, 9:27 PM