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Why was the website so slow for so long?

The cause of the slowdown was a change to the ZFS dataset. In conjunction with the database server, very little caching was being done. This combination resulted in increased disk I/O as the system churned through the database. Details in the blog post which outlines the various things which changed. Many graphs.

non port: biology/tophat/Makefile
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Number of commits found XX: 3

Sun, 8 Mar 2020
[ 17:01 antoine ] Original commit   Revision:528058
528058 audio/abraca/Makefile
528058 audio/ardour5/Makefile
528058 audio/cplay/Makefile
528058 audio/cpp-xmms2/Makefile
528058 audio/exaile/Makefile
528058 audio/p5-xmms2/Makefile
528058 benchmarks/glmark2/Makefile
528058 biology/haplohseq/Makefile
528058 biology/tophat/Makefile
528058 cad/lepton-eda/Makefile

(Only the first 10 of 187 ports in this commit are shown above. View all ports for this commit)
Deprecate some ports using deprecated version of python

With hat:	portmgr
Wed, 11 Dec 2019
[ 17:53 jbeich ] Original commit   Revision:519824
519824 archivers/innoextract/Makefile
519824 archivers/tardy/Makefile
519824 astro/libkgeomap/Makefile
519824 astro/libosmium/Makefile
519824 audio/ardour/Makefile
519824 audio/ardour5/Makefile
519824 audio/clementine-player/Makefile
519824 audio/cpp-xmms2/Makefile
519824 audio/csound/Makefile
519824 audio/faust-lv2/Makefile

(Only the first 10 of 417 ports in this commit are shown above. View all ports for this commit)
devel/boost-*: update to 1.72.0

Changes:	http://www.boost.org/users/history/version_1_72_0.html
PR:		241449
Exp-run by:	antoine
Differential Revision:	https://reviews.freebsd.org/D22136
Fri, 27 Sep 2019
[ 00:49 jwb ] Original commit   Revision:512997
512997 biology/Makefile
512997 biology/tophat
512997 biology/tophat/Makefile
512997 biology/tophat/distinfo
512997 biology/tophat/files
512997 biology/tophat/files/patch-configure
512997 biology/tophat/files/patch-src-samtools-0.1.18-Makefile
512997 biology/tophat/files/patch-src_Makefile.in
512997 biology/tophat/files/tophat-test
512997 biology/tophat/pkg-descr

(Only the first 10 of 11 ports in this commit are shown above. View all ports for this commit)
biology/tophat: Fast splice junction mapper for RNA-Seq reads

TopHat is a fast splice junction mapper for RNA-Seq reads. It aligns RNA-Seq
reads to mammalian-sized genomes using the ultra high-throughput short read
aligner Bowtie, and then analyzes the mapping results to identify splice
junctions between exons.

Note:

TopHat has been Superseded by HISAT2 and is no longer maintained upstream.
This port is provided mainly for revisiting old studies where TopHat was used.

Number of commits found XX: 3

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