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URL: https://reviews.freebsd.org/p/jwb/

⇱ ♟ jwb

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

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User Details

User Since
Nov 27 2017, 4:37 PM (436 w, 4 d)

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

Recent Activity

Sun, Mar 29

biology/samtools: Update to 1.23.1
biology/bcftools: Update to 1.23.1
biology/htslib: Update to 1.23.1

Sat, Mar 28

science/orthanc: Use unversioned dcmtk DATADIR
biology/vsearch: Update to 2.30.6
graphics/dcmtk: Add unversioned link to DATADIR

Thu, Mar 26

biology/sra-tools: Unbreak distfile
biology/sra-tools: Update to 3.4.1

Mon, Mar 23

biology/wfa2-lib: Update to 2.3.6

Sun, Mar 22

biology/fastp: Update to 1.2.0

Mar 11 2026

biology/vsearch: Update to 2.30.5

Mar 10 2026

biology/salmon: Unbreak: Relax libgff version requirement

Mar 7 2026

biology/libgff: Update to 2.0.1

Mar 5 2026

biology/py-macs3: Update to 3.0.4
biology/atac-seq: Update to 0.3.0
biology/bowtie2: Update to 2.5.5

Mar 4 2026

biology/rna-seq: Update to 0.2.0
biology/kallisto: Update to 0.52.0,1
sysutils/auto-admin: Update to 0.8.4.24

Feb 4 2026

sysutils/desktop-installer: Update to 1.1.1.31
sysutils/auto-admin: Update to 0.8.4.22

Feb 1 2026

biology/hisat2: Update to 2.2.2
devel/py-rich-click: Update to 1.9.7

Jan 31 2026

sysutils/auto-admin: Update to 0.8.4.14

Jan 30 2026

devel/py-rich-click: Update to 1.9.6

Jan 21 2026

biology/vsearch: Update to 2.30.4

Jan 14 2026

biology/vsearch: Update to 2.30.3

Jan 11 2026

biology/sra-tools: Unbreak with extra JDK present

Dec 21 2025

sysutils/desktop-installer: Update to 1.1.1.13
sysutils/auto-admin: Update to 0.8.4.6

Dec 20 2025

biology/vsearch: Add patch for FreeBSD 16

Dec 18 2025

biology/vsearch: Update to 2.30.2
science/csvtk: Update to 0.36.0
biology/biostar-tools: Update to 2.1
biology/R-cran-BiocManager: Update to 1.30.27

Dec 17 2025

science/orthanc-postgresql: Update to 10.0
biology/sra-tools: Update to 3.3.0

Dec 16 2025

devel/libxtend: Update to 0.2.1.10

Dec 11 2025

sysutils/auto-admin: Update to 0.8.4.2

Dec 7 2025

sysutils/auto-admin: Update to 0.8.4

Nov 28 2025

science/orthanc-mysql: Bump orthanc version to 1.12.10
science/orthanc-postgresql: Bump orthanc version to 1.12.10
science/orthanc-dicomweb: Bump orthanc version to 1.12.10
science/orthanc: Update to 1.12.10

Nov 26 2025

sysutils/diskimage-tools: Update to 0.3.1.5

Nov 13 2025

math/rapid: DEPRECATED -> BROKEN

Oct 30 2025

net/py-google-cloud-pubsub: Update to 2.32.0

Oct 29 2025

science/csvtk: Update to 0.35.0

Oct 27 2025

science/orthanc-postgresql: Update to 9.0
science/orthanc-mysql: Update to 5.2
science/orthanc-dicomweb: Update to 1.21
science/orthanc-webviewer: Update to 2.10
science/orthanc: Take maintainership

Oct 26 2025

sysutils/auto-admin: Update to 0.8.3.30
sysutils/auto-admin: Update to 0.8.3.30

Oct 25 2025

science/orthanc: Update to 1.12.9 and unbreak

Oct 5 2025

biology/vsearch: Update to 2.30.1

Oct 3 2025

math/rapid: Deprecate

Oct 1 2025

net/py-google-cloud-pubsub: Python interface to Google pubsub

Sep 30 2025

sysutils/auto-admin: Update to 0.8.3.28

Sep 21 2025

devel/mongo-c-driver: Enable SRV option by default
sysutils/desktop-installer: Update to 1.1.1.4
sysutils/auto-admin: Update to 0.8.3.27

Sep 19 2025

devel/cppcodec: Update to 0.2-11

Sep 16 2025

x11/coreterminal: Update to 5.0.0
deskutils/coregarage: Update to 5.0.0
deskutils/libcprime: Update to 5.0.0
archivers/libarchive-qt: Update to 2.0.8

Sep 14 2025

comms/cutecom: Update to 0.60.0-RC1

Sep 10 2025

sysutils/desktop-installer: Update to 1.1.1.3

Sep 7 2025

sysutils/auto-admin: Update to 0.8.3.25

Sep 6 2025

devel/Makefile: cpp-codec -> cppcodec

Sep 5 2025

devel/mongo-cxx-driver: MongoDB C++ driver
devel/cppcodec: Library to encode/decode base64, base64url, etc.

Aug 26 2025

biology/salmon: Update to tag 1.10.3
biology/ncbi-blast+: Update to 2.17.0

Aug 24 2025

sysutils/auto-admin: Update to 0.8.3.25

Aug 21 2025

biology/bbmap: Update to 39.34

Aug 14 2025

sysutils/auto-admin: Update to 0.8.3.24

Aug 5 2025

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 3 2025

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:

Jul 27 2025

biology/salmon: Update to tag 1.10.3

Jul 24 2025

biology/ncbi-blast+: Update to 2.17.0

Jun 28 2025

biology/py-pydeseq2: Update to 0.5.2

Jun 21 2025

biology/bcf-score: Use latest versions of hstlib and bcftools
biology/bio-mocha: Use latest versions of htslib and bcftools
biology/minimap2: Remove extraneous file that snuck in the last commit

Jun 16 2025

biology/minimap2: Update to 2.30

Jun 14 2025

devel/isa-l: Enable build on aarch64

Jun 11 2025

biology/py-pydeseq2: Python reimplementation of the DESeq2 R package
math/py-formulaic-contrasts: Build arbitrary contrasts formulaic models
devel/py-joblib: Unbreak build

Jun 7 2025

biology/fastp: Update to 0.26.0

Jun 5 2025

sysutils/auto-admin: Update to 0.8.3.7

Jun 4 2025

biology/seqtk: Update to 1.5
biology/bcftools: Update to 1.22
biology/samtools: Update to 1.22
biology/htslib: Update to 1.22

Jun 1 2025

biology/fastp: Update to 0.25.0

May 30 2025

biology/fastp: Update to 0.24.3