notbugAs an Amazon Associate I earn from qualifying purchases.
Want a good read? Try FreeBSD Mastery: Jails (IT Mastery Book 15)
Search FreshPorts using Google
not searching src

The FreshPorts Search


Include deleted ports Case sensitive search Sort by:
Include /src tree
Output format:
HTML
Plain Text
Maximum Effort Minimal output
Branch:

Notes

  • Case sensitivity is ignored for "sounds like" and output is ordered by the soundex.
  • When searching on 'Message ID', the type of match is ignored.
  • When searching on 'Commit Message' only 'containing' is used.
  • When searching by 'Under a pathname', your path must start with something like /ports/, /doc/, or /src/. All commits under that point will be returned. The selected match type is ignored and defaults to 'Starts with'.
  • Searching for 'sounds like' is only valid for Committer, Maintainer, Package Name, and Port Name.
Number of commits: 147 (showing only 100 on this page) 1 | 2  »  
Sat, 17 Aug 2019
[ 15:11 jwb ] Original commit 
desktop-installer 0.6.7 sysutils files touched by this commit Quickly configure a FreeBSD desktop system
sysutils/desktop-installer: Upgrade to 0.6.7

Disable bsdstats install (bsdstats.org is offline)
Numerous improvements to user interface
Tue, 13 Aug 2019
[ 15:30 jwb ] Original commit 
bolt-lmm 2.3.4 biology files touched by this commit Mixed model association testing and variance component analysis
biology/bolt-lmm: Upgrade to 2.3.4

Remove previously upstreamed patches
New Makefile patch that preserves default behavior and should be palatable
to upstream
Sun, 4 Aug 2019
[ 23:48 jwb ] Original commit 
bolt-lmm 2.3.2_2 biology files touched by this commit Mixed model association testing and variance component analysis
PR:             239613
Submitted by:   pkubaj
Thu, 25 Jul 2019
[ 21:54 jwb ] Original commit 
desktop-installer 0.6.6 sysutils files touched by this commit Quickly configure a FreeBSD desktop system
sysutils/desktop-installer: Upgrade to 0.6.6

Remove obsolete qt/kde 4 references
Default to no flashplayer on all platforms
Factor out flashplayer setup to sysutils/auto-admin
Disable webcamd setup for now (interferes with uhid)
Other clean up and minor enhancements
[ 21:46 jwb ] Original commit 
auto-admin 0.4.8 sysutils files touched by this commit Portable tools for automating systems management
sysutils/auto-admin: Upgrade to 0.4.8

FreeBSD changes:

Roll auto-add-linproc-mount into auto-install-linux_base
Remove obsolete auto-amd-nfs-setup, auto-kdm3-toggle
Add scripts for installing and updating infininband kernel
Factor auto-install-linux-flash out of desktop-installer

New common scripts:

auto-idrac-passwd
auto-fetch-install-media
auto-install-media-distname
auto-lock-local-pw, auto-unlock-local-pw
auto-root-check
auto-useradd
auto-user-admin
Sun, 21 Jul 2019
[ 00:10 jwb ] Original commit 
slurm-wlm 19.05.1.2 sysutils files touched by this commit Simple Linux Utility for Resource Management
sysutils/slurm-wlm: Upgrade to 19.05.1-2

Resolves CVE-2019-12838
Add NOT_FOR_ARCHS since upstream has deprecated 32-bit architectures
Fri, 12 Jul 2019
[ 23:58 jwb ] Original commit 
ncbi-blast+ 2.9.0_2 biology files touched by this commit NCBI implementation of Basic Local Alignment Search Tool
ncbi-blast+: Unbreak build with gcc8 following gcc9 patch

GCC 8 and 9 are incompatible in handling const variables with OpenMP
default(none).  All const variables default to shared even with default(none)
present.  8 errors out if a const variable is explicitly defined as shared and
9 requires an explicit definition.

Using an upstream trunk patch for now, which checks the compiler version.
Also discussing more portable approaches to avoid future issues.

Reported by:    jrm
Thu, 11 Jul 2019
[ 13:53 jwb ] Original commit 
ncbi-blast+ 2.9.0_1 biology files touched by this commit NCBI implementation of Basic Local Alignment Search Tool
ncbi-blast+: Fix build with gcc9

GCC 9 requires OpenMP variables to be explicitly defined as shared or private
where earlier versions fell back on default.  New patch sent upstream.

PR:             238471
Reported by:    gerald
Tue, 18 Jun 2019
[ 19:00 jwb ] Original commit 
afni 19.1.20 science files touched by this commit Advanced Functional Neuro Imaging
science/afni: Upgrade to 19.1.20

Upstreamed FreeBSD patches, other minor fixes and enhancements

Reported by:    portscout, Rick Reynolds (NIH)
Fri, 14 Jun 2019
[ 00:37 jwb ] Original commit 
ncbi-blast+ 2.9.0 biology files touched by this commit NCBI implementation of Basic Local Alignment Search Tool
biology/ncbi-blast+: Fix build on powerpc64, add run dep for update_blastdb.pl
[ 00:21 jwb ] Original commit 
slurm-wlm 18.08.7 sysutils files touched by this commit Simple Linux Utility for Resource Management
sysutils/slurm-wlm: Revert previous change enabling Linux option by default

Option is not actually necessary anymore to enable linproc parsing code.
It merely adds a linux_base dependency now.
Thu, 13 Jun 2019
[ 23:53 jwb ] Original commit 
slurm-wlm 18.08.7 sysutils files touched by this commit Simple Linux Utility for Resource Management
sysutils/slurm-wlm: Enable jobacct_gather/linux by default

Currently required to terminate jobs exceeding their memory allocation
(until jobacct_gather/freebsd is implemented)
Wed, 12 Jun 2019
[ 23:53 jwb ] Original commit 
ncbi-blast+ 2.9.0 biology files touched by this commit NCBI implementation of Basic Local Alignment Search Tool
biology/ncbi-blast+: Upgrade to 2.9.0

Fixes build issue with gcc9

PR:             238471
Reported by:    gerald
[ 15:24 jwb ] Original commit 
kallisto 0.46.0 biology files touched by this commit Quantify abundances of transcripts from RNA-Seq data
biology/kallisto: Upgrade to 0.46.0

Reported by:    portscout
Sat, 8 Jun 2019
[ 19:14 jwb ] Original commit 
afni 19.1.18 science files touched by this commit Advanced Functional Neuro Imaging
science/afni: Upgrade to 19.1.18

Minor bugfixes/enhancements
Sat, 1 Jun 2019
[ 12:59 jwb ] Original commit 
afni 19.1.14 science files touched by this commit Advanced Functional Neuro Imaging
science/afni: Upgrade to 19.1.14

Minor bug fixes and enhancements, some FreeBSD patches upstreamed
Sun, 26 May 2019
[ 03:36 jwb ] Original commit 
bolt-lmm 2.3.2 biology files touched by this commit Mixed model association testing and variance component analysis
biology/bolt-lmm: Mixed model association testing and variance component
analysis

The BOLT-LMM software package currently consists of two main algorithms, the
BOLT-LMM algorithm for mixed model association testing, and the BOLT-REML
algorithm for variance components analysis (i.e., partitioning of
SNP-heritability and estimation of genetic correlations).
Wed, 22 May 2019
[ 12:44 jwb ] Original commit 
afni 19.1.10 science files touched by this commit Advanced Functional Neuro Imaging
science/afni: Upgrade to 19.1.10

Rapid response from upstream on reported issue.  Additional patches to be
upstreamed in next release.
Mon, 20 May 2019
[ 23:46 jwb ] Original commit 
slurm-wlm 18.08.7 sysutils files touched by this commit Simple Linux Utility for Resource Management
sysutils/slurm-wlm: Remove redundant USE_GCC

Reported by:    tobik
[ 23:41 jwb ] Original commit 
fastp 0.20.0 biology files touched by this commit Ultra-fast all-in-one FASTQ preprocessor
biology/fastp: Remove redundant USE_GCC
[ 19:35 jwb ] Original commit 
afni 19.1.08 science files touched by this commit Advanced Functional Neuro Imaging
science/afni: Upgrade to 19.1.08

Switch from personal dist snapshots to Github releases
Improve staging procedure to preserve results of build phase
Temporarily use bundled GLw pending fix of libglw port
Sat, 18 May 2019
[ 22:41 jwb ] Original commit 
gemma 0.98.1 biology files touched by this commit Genome-wide Efficient Mixed Model Association
biology/gemma: Lowercase PORTNAME, remove unnecesary USE_GCC

Reported by:    danfe, Gerald Pfeifer
Fri, 17 May 2019
[ 14:45 jwb ] Original commit 
gemma 0.98.1 biology files touched by this commit Genome-wide Efficient Mixed Model Association
biology/gemma: Genome-wide Efficient Mixed Model Association

GEMMA is a software toolkit for fast application of linear mixed models (LMMs)
and related models to genome-wide association studies (GWAS) and other
large-scale data sets.
Wed, 15 May 2019
[ 01:34 jwb ] Original commit 
slurm-wlm 18.08.7 sysutils files touched by this commit Simple Linux Utility for Resource Management
sysutils/slurm-wlm: Upgrade to 18.08.7

Improve default settings for FreeBSD

Reviewed by:    jrm
Mon, 13 May 2019
[ 16:23 jwb ] Original commit 
jellyfish 2.2.10_5 biology files touched by this commit Fast, memory-efficient counting of k-mers in DNA
biology/jellyfish: Upgrade to 2.2.10, patch for powerpc64

PR:             237868
Submitted by:   pkubaj
Sat, 11 May 2019
[ 13:42 jwb ] Original commit 
vsearch 2.13.4 biology files touched by this commit Versatile open-source tool for metagenomics
biology/vsearch: Update to 2.13.4

FreeBSD patches incorporated into new upstream release

Reported by:    portscout
[ 00:18 jwb ] Original commit 
trimadap 0.1.3 biology files touched by this commit Trim adapter sequences from Illumina data using heuristic rules
biology/trimadap: Mark only for amd64 and i386

Contains hard-coded SSE instructions
Fri, 10 May 2019
[ 21:15 jwb ] Original commit 
stacks 2.4 biology files touched by this commit Software pipeline for building loci from short-read sequences
biology/stacks: Remove obsolete pkg-message regarding web interface

PHP code no longer included in dist as of v2.4
[ 21:04 jwb ] Original commit 
stacks 2.4 biology files touched by this commit Software pipeline for building loci from short-read sequences
biology/stacks: Upgrade to 2.4

Improve check to avoid outdated GCC on 2nd tier platforms

Reported by:    portscout
Thu, 9 May 2019
[ 22:12 jwb ] Original commit 
vsearch 2.13.3 biology files touched by this commit Versatile open-source tool for metagenomics
biology/vsearch: Remove powerpc64 support

Requires little endian mode and FreeBSD currently does not support it
[ 21:28 jwb ] Original commit 
vsearch 2.13.3 biology files touched by this commit Versatile open-source tool for metagenomics
biology/vsearch: Versatile open-source tool for metagenomics

VSEARCH supports de novo and reference based chimera detection, clustering,
full-length and prefix dereplication, rereplication, reverse complementation,
masking, all-vs-all pairwise global alignment, exact and global alignment
searching, shuffling, subsampling and sorting. It also supports FASTQ file
analysis, filtering, conversion and merging of paired-end reads.

The aim of this project is to create an alternative to the USEARCH tool
developed by Robert C. Edgar (2010).
Sun, 5 May 2019
[ 14:56 jwb ] Original commit 
minimap2 2.17 biology files touched by this commit Pairwise aligner for genomic and spliced nucleotide sequences
biology/minimap2: Upgrade to 2.17

Reported by:    portscout
Sat, 4 May 2019
[ 15:09 jwb ] Original commit 
ddocent 2.7.8 biology files touched by this commit Bash pipeline for RAD sequencing
biology/ddocent: Upgrade to 2.7.8

Reported by:    portscout
[ 02:07 jwb ] Original commit 
fastp 0.20.0 biology files touched by this commit Ultra-fast all-in-one FASTQ preprocessor
biology/fastp: Respect WITH_DEBUG - do not strip binary
Fri, 3 May 2019
[ 14:41 jwb ] Original commit 
fastp 0.20.0 biology files touched by this commit Ultra-fast all-in-one FASTQ preprocessor
biology/fastp: Ultra-fast all-in-one FASTQ preprocessor

fastp is a tool designed to provide fast all-in-one preprocessing for FastQ
files. This tool is developed in C++ with multithreading supported to afford
high performance.
Thu, 2 May 2019
[ 00:39 jwb ] Original commit 
star 2.7.0.f biology files touched by this commit Spliced Transcripts Alignment to a Reference
biology/star: Force newer GCC on platforms with GCC 4.2 base

PR:             237700
Submitted by:   pkubaj
Sat, 27 Apr 2019
[ 01:26 jwb ] Original commit 
py-cutadapt 2.3 biology files touched by this commit Trim adapters from high-throughput sequencing reads
biology/py-cutadapt: Upgrade to 2.3

Numerous bugfixes and enhancements since 2.1
[ 01:22 jwb ] Original commit 
py-xopen 0.5.1 archivers files touched by this commit Open compressed files transparently
archivers/py-xopen: Upgrade to 0.5.1

Minor bugfix release
Wed, 24 Apr 2019
[ 18:03 jwb ] Original commit 
minimap2 2.16 biology files touched by this commit Pairwise aligner for genomic and spliced nucleotide sequences
biology/minimap2: Pairwise aligner for genomic and spliced nucleotide sequences

Minimap2 is a versatile sequence alignment program that aligns DNA or mRNA
sequences against a large reference database.
[ 17:41 jwb ] Original commit 
bowtie2 2.3.5.1 biology files touched by this commit Ultrafast, memory-efficient short read aligner
biology/bowtie2: Clarify CPU-specificity
Tue, 23 Apr 2019
[ 15:03 jwb ] Original commit 
star 2.7.0.f biology files touched by this commit Spliced Transcripts Alignment to a Reference
biology/star: Modify PKGBASE to avoid conflict with archivers/star
Sun, 21 Apr 2019
[ 20:30 jwb ] Original commit 
star 2.7.0.f biology files touched by this commit Spliced Transcripts Alignment to a Reference
biology/star: Spliced Transcripts Alignment to a Reference

STAR is an extremely fast RNA-seq aligner, an alternative to tophat2,
hisat2, bowtie, subread, etc.
[ 15:23 jwb ] Original commit 
bowtie2 2.3.5.1 biology files touched by this commit Ultrafast, memory-efficient short read aligner
biology/bowtie2: Upgrade to 2.3.5.1

Disable aarch64.  Upstream support has changed and I lack the resources
to develop new patches.
Thu, 18 Apr 2019
[ 12:15 jwb ] Original commit 
canu 1.8_3 biology files touched by this commit Single molecule sequence assembler
biology/canu: Fix build on powerpc64 and aarch64

Should also work on powerpc and arm*, but unable to test

PR:             237105
Reported by:    pkubaj
Sun, 24 Mar 2019
[ 21:44 jwb ] Original commit 
p5-TrimGalore 0.6.1 biology files touched by this commit Wrapper around Cutadapt and FastQC for adapter and quality trimming
biology/p5-TrimGalore: Upgrade to 0.6.1

Add test script
[ 21:20 jwb ] Original commit 
py-cutadapt 2.1 biology files touched by this commit Trim adapters from high-throughput sequencing reads
biology/py-cutadapt: Upgrade to 2.1

Add do-test target
[ 20:05 jwb ] Original commit 
py-xopen 0.5.0 archivers files touched by this commit Open compressed files transparently
archivers/py-xopen: Upgrade to 0.5.0

Add do-test target
[ 19:40 jwb ] Original commit 
py-dnaio 0.3 biology files touched by this commit Read and write FASTQ and FASTA
biology/py-dnaio: Read and write FASTQ and FASTA

Factored out of py-cutadapt

Reviewed by:    jrm
Mon, 18 Mar 2019
[ 17:30 jwb ] Original commit 
bowtie2 2.3.5 biology files touched by this commit Ultrafast, memory-efficient short read aligner
biology/bowtie2: Upgrade to 2.3.5

-   Add bowtie2-test script
-   Separate Makefile patches into a static patch for upstream and reinplace
    for ports-specifics
-   Allow aarch64 per upstream Makefile (untested)
Thu, 14 Mar 2019
[ 23:59 jwb ] Original commit 
cd-hit 4.8.1 biology files touched by this commit Clustering and comparing protein or nucleotide sequences
biology/cd-hit: Upgrade to 4.8.1

Convert Makefile REINPLACE to patch for sending upstream
Tue, 26 Feb 2019
[ 02:13 jwb ] Original commit 
desktop-installer 0.6.5 sysutils files touched by this commit Quickly configure a FreeBSD desktop system
sysutils/desktop-installer: PPC64 fixes, user guidance for drm-kmod

Hoping to better automate drm-kmod selection, but some sort of guidance
was sorely needed, so this is a stop-gap solution.
[ 02:04 jwb ] Original commit 
auto-admin 0.4.7 sysutils files touched by this commit Portable tools for automating systems management
sysutils/auto-admin: Factor code out of desktop-installer and cluster-admin

desktop-installer: auto-detect-gpu, auto-detect-laptops
cluster-admin: nfs and user management tools
Sun, 24 Feb 2019
[ 20:32 jwb ] Original commit 
kallisto 0.45.1 biology files touched by this commit Quantify abundances of transcripts from RNA-Seq data
kallisto: Upgrade to 0.45.1, unbundle hstlib
[ 16:04 jwb ] Original commit 
unanimity 3.4.1 biology files touched by this commit Pacific Biosciences consensus library and applications
biology/unanimity: Upgrade to 3.4.1

Minor fixes and enhancements upstream.
Wed, 20 Feb 2019
[ 01:53 jwb ] Original commit 
pbseqan g20171011 biology  Deprecated files touched by this commit Pacific Biosciences patched and stripped down SeqAn
biology/pbseqan: Mark deprecated

Upstream was merged into the SeqAn project represented by biology/seqan.
[ 01:36 jwb ] Original commit 
unanimity 3.4.0 biology files touched by this commit Pacific Biosciences consensus library and applications
biology/unanimity: Upgrade to 3.4.0

Switch from cmake to new meson build system
Tests disabled for now pending work on unbundling googletest
Tue, 19 Feb 2019
[ 23:03 jwb ] Original commit 
pbbam 0.18.0 biology files touched by this commit PacBio BAM C++ library, with SWIG bindings
biology/pbbam: Upgrade to 0.18.0 release

In preparation for unanimity upgrade
[ 22:20 jwb ] Original commit 
pbcopper 0.4.1 biology files touched by this commit Core C++ library for Pacific Biosciences tools
biology/pbcopper: Upgrade to 0.4.1 release

In preparation for biology/unanimity upgrade
Sun, 17 Feb 2019
[ 19:31 jwb ] Original commit 
pbseqan g20171011 biology  Deprecated files touched by this commit Pacific Biosciences patched and stripped down SeqAn
biology/pbseqan: Minor upgrade to latest commit

In preparation for biology/unanimity upgrade
Mon, 21 Jan 2019
[ 13:18 jwb ] Original commit 
cutecom 0.51.0 comms files touched by this commit Graphical serial terminal for embedded programming
comms/cutecom: Update pkg-descr to reflect new home

Reported by:    swills
Sun, 20 Jan 2019
[ 14:00 jwb ] Original commit 
cutecom 0.51.0 comms files touched by this commit Graphical serial terminal for embedded programming
comms/cutecom: Add c++11-lang for GCC-based platforms, upgrade to 0.51.0

Upstream has moved to Gitlab

PR:             235043
Reported by:    Piotr Kubaj
Sat, 12 Jan 2019
[ 15:53 jwb ] Original commit 
stacks 2.3 biology files touched by this commit Software pipeline for building loci from short-read sequences
biology/stacks: Upgrade to 2.3

Approved by:    jrm (mentor, implicit)
Fri, 11 Jan 2019
[ 16:02 jwb ] Original commit 
hisat2 2.1.0.23 biology files touched by this commit Alignment program for mapping next-generation sequencing reads
New port: biology/hisat2: Program for mapping next-generation sequencing reads

Approved by:    jrm (mentor, implicit)
Tue, 1 Jan 2019
[ 19:55 jwb ] Original commit 
ncbi-blast+ 2.8.1 biology files touched by this commit NCBI implementation of Basic Local Alignment Search Tool
biology/ncbi-blast+: Upgrade to 2.8.1

Remove hacks that are no longer needed
New patch for endian.h location

Approved by:    jrm (mentor, implicit)
Fri, 28 Dec 2018
[ 14:57 jwb ] Original commit 
desktop-installer 0.6.4 sysutils files touched by this commit Quickly configure a FreeBSD desktop system
sysutils/desktop-installer: Add nVidia GPU detection

Auto-configure commercial nVidia driver with user input
Factor out linux_base install to auto-admin

Approved by:    jrm (mentor, implicit)
[ 14:06 jwb ] Original commit 
auto-admin 0.4.6 sysutils files touched by this commit Portable tools for automating systems management
sysutils/auto-admin: New scripts to support of desktop-installer, cluster-admin

Highlights:

auto-detect-nvidia-gpu: Assist with commercial nvidia driver setup
auto-install-linux_base: Install and configure c6 or c7 linux_base

Approved by:    jrm (mentor, implicit)
Mon, 10 Dec 2018
[ 21:40 jwb ] Original commit 
condor 8.4.12_3 sysutils files touched by this commit High-throughput computing on distributively owned resources
sysutils/condor: Permanent fix for FreeBSD 13 and all future versions

Previous HTCondor code checks for each FreeBSD version individually.
Add a generic patch to cover all current and future FreeBSD versions.

Approved by:    jrm (mentor, implicit)
Sat, 17 Nov 2018
[ 20:40 jwb ] Original commit 
desktop-installer 0.6.3 sysutils files touched by this commit Quickly configure a FreeBSD desktop system
sysutils/desktop-installer: Necessary maintenance updates

Add drm-kmod support to unbreak x11 setup on some systems
Update supported wifi drivers
Install battery_shutdown.sh via port for proper updating

Approved by:    jrm (mentor, implicit)
[ 20:33 jwb ] Original commit 
auto-admin 0.4.5 sysutils files touched by this commit Portable tools for automating systems management
auto-admin: Add several scripts to support wip/cluster-admin

Approved by:    jrm (mentor, implicit)
Sun, 4 Nov 2018
[ 15:52 jwb ] Original commit 
voro++ 0.4.6_1 science files touched by this commit Three-dimensional computations of the Voronoi tessellation
science/voro++: Add shared library

Consolidated build changes into patch files.

Kept static lib as well as some dependencies may specify it explicitly
(this is common in scientific software for better or worse) and the library
is very small.

PR:             232876
Reported by:    yuri
Approved by:    jrm (mentor, implicit)
[ 14:29 jwb ] Original commit 
canu 1.8 biology files touched by this commit Single molecule sequence assembler
biology/canu: Upgrade to 1.8, add experimental SLURM integration

Solves build issue with gcc8.

PR:             232930
Reported by:    gerald
Approved by:    jrm (mentor, implicit)
Sat, 3 Nov 2018
[ 23:24 jwb ] Original commit 
bowtie 1.1.2_7 biology files touched by this commit Ultrafast, memory-efficient short read aligner
biology/bowtie: Patch for gcc8 and clean up

PR:             232929
Reported by:    gerald
Approved by:    jrm (mentor, implicit)
[ 23:16 jwb ] Original commit 
bowtie 1.1.2_6 biology files touched by this commit Ultrafast, memory-efficient short read aligner
biology/bowtie: Revert previous commit with missing log message
[ 21:10 jwb ] Original commit 
bowtie 1.1.2_7 biology files touched by this commit Ultrafast, memory-efficient short read aligner
biology/bowtie: Patch
Tue, 23 Oct 2018
[ 12:51 jwb ] Original commit 
p5-transdecoder 5.4.0 biology files touched by this commit Identify candidate coding regions within transcript sequences
biology/p5-transdecoder: Upgrade to 5.4.0

Minor clean up to silence portlint
Approved by:    jrm (mentor, implicit)
Mon, 22 Oct 2018
[ 02:29 jwb ] Original commit 
desktop-installer 0.6.2 sysutils files touched by this commit Quickly configure a FreeBSD desktop system
sysutils/desktop-installer: Fix battery monitor, install audio/lame

Approved by:    jrm (mentor)
Differential Revision:  https://reviews.freebsd.org/D17643
[ 01:12 jwb ] Original commit 
auto-admin 0.4.4 sysutils files touched by this commit Portable tools for automating systems management
sysutils/auto-admin: Improved support for desktop-installer, cluster-admin

Approved by:    jrm (mentor)
Differential Revision:  https://reviews.freebsd.org/D17638
Sun, 30 Sep 2018
[ 21:41 jwb ] Original commit 
fsom g20151117 science files touched by this commit Tiny C library for managing SOM (Self-Organizing Maps) neural networks
science/fsom: Fix build on GCC-based architectures

PR:             231693
Submitted by:   Piotr Kubaj <pkubaj@anongoth.pl>
Approved by:    jrm (mentor)
Differential Revision:  https://reviews.freebsd.org/D17366
Fri, 21 Sep 2018
[ 14:57 jwb ] Original commit 
ganglia-webfrontend 3.7.2_2 sysutils files touched by this commit Ganglia cluster monitor, web frontend
sysutils/ganglia-webfrontend: Fix known display bug in cluster view

This is an emergency fix for a serious bug that wrecks the main page.
I will upgrade to 3.7.4 after working out different issues with that release.

Approved by:    jrm (mentor)
Differential Revision:  https://reviews.freebsd.org/D17264
Thu, 20 Sep 2018
[ 14:10 jwb ] Original commit 
py-cutadapt 1.18 biology files touched by this commit Trim adapters from high-throughput sequencing reads
biology/py-cutadapt: Upgrade to 1.18

Approved by:    jrm (mentor)
Differential Revision:  https://reviews.freebsd.org/D17099
Sat, 1 Sep 2018
[ 14:14 jwb ] Original commit 
stacks 1.48_2 biology files touched by this commit Software pipeline for building loci from short-read sequences
biology/stacks: Enable OpenMP (oversight in previous commit)

Upgrade to latest release will follow, after testing

Approved by:    jrm (mentor)
Differential Revision:  https://reviews.freebsd.org/D16973
Sat, 25 Aug 2018
[ 22:54 jwb ] Original commit 
unanimity 3.1.0 biology files touched by this commit Pacific Biosciences consensus library and applications
biology/unanimity: Upgrade to latest release, soften dep version requirements

Approved by:    jrm (mentor)
Differential Revision:  https://reviews.freebsd.org/D16902
Sat, 4 Aug 2018
[ 01:29 jwb ] Original commit 
vcftools 0.1.16 biology files touched by this commit Tools for working with VCF genomics files
biology/vcftools: Update to 0.1.16, a security release

Approved by:    jrm (mentor)
Differential Revision:  https://reviews.freebsd.org/D16587
Sat, 7 Jul 2018
[ 13:41 jwb ] Original commit 
py-xopen 0.3.5 archivers files touched by this commit Open compressed files transparently
archivers/py-xopen: Upgrade to 0.3.5

Approved by:    jrm (mentor)
Differential Revision:  https://reviews.freebsd.org/D16170
Wed, 27 Jun 2018
[ 02:18 jwb ] Original commit 
cutecom 0.45.0 comms files touched by this commit Graphical serial terminal for embedded programming
comms/cutecom: Fix WRKSRC name

Approved by:    jrm (mentor)
Differential Revision:  https://reviews.freebsd.org/D16028
[ 00:04 jwb ] Original commit 
paraview 5.5.1 science files touched by this commit Powerful scientific data visualization application
science/paraview: Fix protobuf conflict, upgrade to 5.5.1, modernize options

PR:             229116
Reported by:    jwb
Approved by:    jrm (mentor)
Differential Revision:  https://reviews.freebsd.org/D16024
Sun, 24 Jun 2018
[ 13:18 jwb ] Original commit 
cutecom 0.45.0 comms files touched by this commit Graphical serial terminal for embedded programming
comms/cutecom: Upgrade to 0.45.0

PR:             229094
Submitted by:   yuri
Approved by:    jrm (mentor)
Differential Revision:  https://bugs.freebsd.org/bugzilla/show_bug.cgi?id=229094
Sat, 16 Jun 2018
[ 17:55 jwb ] Original commit 
bedtools 2.27.1_1 biology files touched by this commit Toolset for genome set arithmetic such as intersect, union
biology/bedtools: Fix Makefile to respect PREFIX

Approved by:    jrm (mentor)
Differential Revision:  https://reviews.freebsd.org/D15851
Wed, 30 May 2018
[ 19:14 jwb ] Original commit 
desktop-installer 0.6.1 sysutils files touched by this commit Quickly configure a FreeBSD desktop system
sysutils/desktop-installer: Add KDE5 support, more default video drivers
Various other bug fixes, updates, and minor enhancements.

Approved by:    jrm (mentor)
Differential Revision:  https://reviews.freebsd.org/D15622
[ 18:48 jwb ] Original commit 
auto-admin 0.4.3 sysutils files touched by this commit Portable tools for automating systems management
auto-admin: Add support for AD authentication, factor out pkgsrc scripts

Reviewed by:    mat
Approved by:    jrm
Differential Revision:  https://reviews.freebsd.org/D15619
Mon, 21 May 2018
[ 22:15 jwb ] Original commit 
clustal-omega 1.2.4 biology files touched by this commit Multiple alignment of nucleic acid and protein, replaces clustalw
biology/clustal-omega: Multiple alignment of nucleic acid and protein, replaces
clustalw

Approved by:    jrm
Differential Revision:  https://reviews.freebsd.org/D15516
[ 20:56 jwb ] Original commit 
clustalx 2.1 biology  Deleted Deprecated Expired files touched by this commit Multiple alignment of nucleic acid and protein sequences with GUI
biology/clustalx: Multiple alignment of nucleic acid and protein sequences with
GUI

Approved by:    jrm
Differential Revision:  https://reviews.freebsd.org/D15505
[ 01:13 jwb ] Original commit 
clustalw 2.1_2 biology files touched by this commit Multiple alignment program for DNA or proteins
biology/clustalw: Fix license, take maintainership

Approved by:    jrm (mentor)
Differential Revision:  https://reviews.freebsd.org/D15503
Sat, 19 May 2018
[ 14:09 jwb ] Original commit 
rapid 2.01 math files touched by this commit Robust and Accurate Polygon Interference Detection
math/rapid: Fix build on FreeBSD 12, clean up license info, remove dead mirror

Approved by:    jrm (mentor)
Differential Revision:  https://reviews.freebsd.org/D15460
Wed, 16 May 2018
[ 15:13 jwb ] Original commit 
fastx-toolkit 0.0.14 biology files touched by this commit CLI tools for Short-Reads FASTA/FASTQ files preprocessing
biology/fastx-toolkit: Fix build on FreeBSD 12

Approved by:    jrm (mentor)
Differential Revision:  https://reviews.freebsd.org/D15451
Thu, 26 Apr 2018
[ 04:16 jwb ] Original commit 
canu 1.7 biology files touched by this commit Single molecule sequence assembler
biology/canu: Upgrade to 1.7 release

Approved by:    jrm (mentor)
Differential Revision:  https://reviews.freebsd.org/D15201
Tue, 24 Apr 2018
[ 14:16 jwb ] Original commit 
unanimity g20180307 biology files touched by this commit Pacific Biosciences consensus library and applications
biology/unanimity: Pacific Biosciences consensus library and applications

Reviewed by:    jrm
Differential Revision:  https://reviews.freebsd.org/D15172
Mon, 23 Apr 2018
[ 16:23 jwb ] Original commit 
pbcopper g20180413 biology files touched by this commit Core C++ library for Pacific Biosciences tools
biology/pbcopper: Core C++ library for Pacific Biosciences tools

Approved by:    jrm (mentor)
Differential Revision:  https://reviews.freebsd.org/D15171
[ 16:08 jwb ] Original commit 
pbbam g20180416 biology files touched by this commit PacBio BAM C++ library, with SWIG bindings
biology/pbbam: PacBio BAM C++ library, with SWIG bindings

Approved by:    jrm (mentor)
Differential Revision:  https://reviews.freebsd.org/D15154
Sat, 21 Apr 2018
[ 17:21 jwb ] Original commit 
pbseqan g20171002 biology  Deprecated files touched by this commit Pacific Biosciences patched and stripped down SeqAn
biology/pbseqan: Pacific Biosciences patched and stripped down SeqAn

Approved by:    jrm (mentor)
Differential Revision:  https://reviews.freebsd.org/D15152
Number of commits: 147 (showing only 100 on this page) 1 | 2  »  
Login
User Login
Create account

Servers and bandwidth provided by
New York Internet, iXsystems, and RootBSD

This site
What is FreshPorts?
About the authors
Issues
FAQ
How big is it?
The latest upgrade!
Privacy
Forums
Blog
Contact

Search
Enter Keywords:
 
more...

Latest Vulnerabilities
h2oAug 25
h2o-develAug 25
giteaAug 22
clamavAug 21
clamav-milterAug 21
nodeAug 21
node10Aug 21
node8Aug 21
vlcAug 20
nsdAug 19
libgit2Aug 18
xdmAug 18
apache24Aug 17
userminAug 17
webminAug 17

18 vulnerabilities affecting 94 ports have been reported in the past 14 days

* - modified, not new

All vulnerabilities

Last updated:
2019-08-25 19:37:17


Ports
Home
Categories
Deleted ports
Sanity Test Failures
Newsfeeds

Statistics
Graphs
NEW Graphs (Javascript)
Traffic

Calculated hourly:
Port count 37382
Broken 453
Deprecated 165
Ignore 711
Forbidden 3
Restricted 162
No CDROM 74
Vulnerable 32
Expired 8
Set to expire 135
Interactive 0
new 24 hours 39
new 48 hours47
new 7 days86
new fortnight118
new month190

Servers and bandwidth provided by
New York Internet, iXsystems, and RootBSD
Valid HTML, CSS, and RSS.
Copyright © 2000-2019 Dan Langille. All rights reserved.