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Things are slow!

Some of the pages ont the website are slow. I know diskio is way up. I don't know what it is but it's been going on for about three weeks. It might have been a change to the zpool recordsize on the PostgreSQL database dataset.

One way to know: copy the dataset to another dataset with the original recordsize and use that. I hope can get to that later this week.

I have not tackled the issue yet because I've been concentrating on the BSDCan and PGCon calls for papers.

Port details
py-bx-python Python module for reading, manipulating and writing genomic data sets
0.8.6 biology on this many watch lists=0 search for ports that depend on this port Find issues related to this port Report an issue related to this port 0.8.4Version of this port present on the latest quarterly branch.
Maintainer: yuri@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2017-05-06 06:28:34
Last Update: 2019-11-23 05:53:50
SVN Revision: 518184
Also Listed In: python
License: MIT
Description:
SVNWeb : Homepage

There is no configure plist information for this port.

Dependency lines:
  • py36-bx-python>0:biology/py-bx-python
To install the port: cd /usr/ports/biology/py-bx-python/ && make install clean
To add the package: pkg install py36-bx-python
PKGNAME: py36-bx-python
Package flavors (<flavor>: <package>)
  • py36: py36-bx-python
  • py27: py27-bx-python
distinfo:

Dependencies
NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.
Build dependencies:
  1. py36-numpy>0 : math/py-numpy@py36
  2. py36-python-lzo>0 : archivers/py-python-lzo@py36
  3. cython-3.6 : lang/cython@py36
  4. py36-setuptools>0 : devel/py-setuptools@py36
  5. python3.6 : lang/python36
Runtime dependencies:
  1. py36-numpy>0 : math/py-numpy@py36
  2. py36-python-lzo>0 : archivers/py-python-lzo@py36
  3. py36-setuptools>0 : devel/py-setuptools@py36
  4. python3.6 : lang/python36
There are no ports dependent upon this port

Configuration Options

USES:

Master Sites:
  1. https://codeload.github.com/bxlab/bx-python/tar.gz/v0.8.6?dummy=/
Notes from UPDATING
These upgrade notes are taken from /usr/ports/UPDATING
  • 2017-11-30
    Affects: */py*
    Author: mat@FreeBSD.org
    Reason: 
      Ports using Python via USES=python are now flavored.  All the py3-* ports
      have been removed and folded into their py-* master ports.
    
      People using Poudriere 3.2+ and binary packages do not have to do anything.
    
      For other people, to build the Python 3.6 version of, for example,
      databases/py-gdbm, you need to run:
    
        # make FLAVOR=py36 install
    
    

Number of commits found: 10

Commit History - (may be incomplete: see SVNWeb link above for full details)
DateByDescription
23 Nov 2019 05:53:50
Original commit files touched by this commit  0.8.6
Revision:518184
yuri search for other commits by this committer
biology/py-bx-python: Update 0.8.4 -> 0.8.6

Reported by:	portscout
26 Jul 2019 20:46:57
Original commit files touched by this commit  0.8.4_1
Revision:507372
gerald search for other commits by this committer
Bump PORTREVISION for ports depending on the canonical version of GCC
as defined in Mk/bsd.default-versions.mk which has moved from GCC 8.3
to GCC 9.1 under most circumstances now after revision 507371.

This includes ports
 - with USE_GCC=yes or USE_GCC=any,
 - with USES=fortran,
 - using Mk/bsd.octave.mk which in turn features USES=fortran, and
 - with USES=compiler specifying openmp, nestedfct, c11, c++0x, c++11-lang,
   c++11-lib, c++14-lang, c++17-lang, or gcc-c++11-lib
plus, everything INDEX-11 shows with a dependency on lang/gcc9 now.

PR:		238330
19 Jun 2019 08:08:31
Original commit files touched by this commit  0.8.4
Revision:504521
yuri search for other commits by this committer
biology/py-bx-python: Update 0.8.2 -> 0.8.4

Reported by:	pirtscout
12 Dec 2018 01:35:36
Original commit files touched by this commit  0.8.2_1
Revision:487272
gerald search for other commits by this committer
Bump PORTREVISION for ports depending on the canonical version of GCC
defined via Mk/bsd.default-versions.mk which has moved from GCC 7.4 t
GCC 8.2 under most circumstances.

This includes ports
 - with USE_GCC=yes or USE_GCC=any,
 - with USES=fortran,
 - using Mk/bsd.octave.mk which in turn features USES=fortran, and
 - with USES=compiler specifying openmp, nestedfct, c11, c++0x, c++11-lang,
   c++11-lib, c++14-lang, c++17-lang, or gcc-c++11-lib
plus, as a double check, everything INDEX-11 showed depending on lang/gcc7.

PR:		231590
26 Aug 2018 09:50:41
Original commit files touched by this commit  0.8.2
Revision:478115
yuri search for other commits by this committer
biology/py-bx-python: Update 0.8.1 -> 0.8.2

Reported by:	portscout
20 Jun 2018 17:05:44
Original commit files touched by this commit  0.8.1_1
Revision:472884
mat search for other commits by this committer
Use PY_FLAVOR for dependencies.

FLAVOR is the current port's flavor, it should not be used outside of
this scope.

Sponsored by:	Absolight
10 Mar 2018 17:46:06
Original commit files touched by this commit  0.8.1_1
Revision:464084
gerald search for other commits by this committer
Bump PORTREVISIONs of all users of math/mpc that we just updated to
version 1.1.0 (via revision 464079).
10 Feb 2018 00:09:57
Original commit files touched by this commit  0.8.1
Revision:461348
yuri search for other commits by this committer
biology/py-bx-python: Update to 0.8.1

Additional port changes:
* Changed to DISTVERSION.
* Added USE_PYTHON=cython.
* Added stripping.
* Updated maintainer e-mail.

Reported compiler warnings to the upstream.

Reported by:	portscout
Approved by:	tcberner (mentor)
Differential Revision:	https://reviews.freebsd.org/D14283
30 Nov 2017 15:50:34
Original commit files touched by this commit  0.7.4
Revision:455210  Sanity Test Failure
mat search for other commits by this committer
Convert Python ports to FLAVORS.

  Ports using USE_PYTHON=distutils are now flavored.  They will
  automatically get flavors (py27, py34, py35, py36) depending on what
  versions they support.

  There is also a USE_PYTHON=flavors for ports that do not use distutils
  but need FLAVORS to be set.  A USE_PYTHON=noflavors can be set if
  using distutils but flavors are not wanted.

  A new USE_PYTHON=optsuffix that will add PYTHON_PKGNAMESUFFIX has been
  added to cope with Python ports that did not have the Python
  PKGNAMEPREFIX but are flavored.

  USES=python now also exports a PY_FLAVOR variable that contains the
(Only the first 15 lines of the commit message are shown above View all of this commit message)
06 May 2017 06:07:04
Original commit files touched by this commit  0.7.4
Revision:440232
miwi search for other commits by this committer
bx-python is a python library and associated set of scripts to allow for rapid
implementation of genome scale analyses. The library contains a variety of
useful modules, but the particular strengths are:

Classes for reading and working with genome-scale multiple local alignments
(in MAF, AXT, and LAV formats). Generic data structure for indexing on disk
files that contain blocks of data associated with intervals on various
sequences (used, for example, to provide random access to individual
alignments in huge files; optomized for use over network filesystems).
Data structures for working with intervals on sequences:
 * "Binned bitsets" which act just like chromosome sized bit arrays,
   but lazily allocate regions and allow large blocks of all set or
   all unset bits to be stored compactly
 * "Intersecter" for performing fast intersection tests that preserve
   both query and target intervals and associated annotation

WWW: https://github.com/bxlab/bx-python

PR:		218757
Submitted by:	Yuri Victorovich <yuri@rawbw.com>

Number of commits found: 10

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