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Port details
bioparser C++ header-only parsing library for several formats in bioinformatics
3.1.0 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 View this port on Repology. pkg-fallout 3.1.0Version of this port present on the latest quarterly branch.
Maintainer: yuri@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2021-01-19 07:56:57
Last Update: 2023-08-29 07:32:45
Commit Hash: c776c74
Also Listed In: devel
License: MIT
WWW:
https://github.com/rvaser/bioparser
Description:
Bioparser is a C++ header only parsing library for several formats in bioinformatics (FASTA/Q, MHAP/PAF/SAM), with support for zlib compressed files.
Homepage    cgit ¦ Codeberg ¦ GitHub ¦ GitLab ¦ SVNWeb

Manual pages:
FreshPorts has no man page information for this port.
pkg-plist: as obtained via: make generate-plist
Expand this list (15 items)
Collapse this list.
  1. /usr/local/share/licenses/bioparser-3.1.0/catalog.mk
  2. /usr/local/share/licenses/bioparser-3.1.0/LICENSE
  3. /usr/local/share/licenses/bioparser-3.1.0/MIT
  4. include/bioparser/fasta_parser.hpp
  5. include/bioparser/fastq_parser.hpp
  6. include/bioparser/mhap_parser.hpp
  7. include/bioparser/paf_parser.hpp
  8. include/bioparser/parser.hpp
  9. include/bioparser/sam_parser.hpp
  10. lib/cmake/bioparser/bioparserConfig.cmake
  11. lib/cmake/bioparser/bioparserConfigVersion.cmake
  12. lib/cmake/bioparser/bioparserTargets.cmake
  13. @owner
  14. @group
  15. @mode
Collapse this list.
Dependency lines:
  • bioparser>0:biology/bioparser
To install the port:
cd /usr/ports/biology/bioparser/ && make install clean
To add the package, run one of these commands:
  • pkg install biology/bioparser
  • pkg install bioparser
NOTE: If this package has multiple flavors (see below), then use one of them instead of the name specified above.
PKGNAME: bioparser
Flavors: there is no flavor information for this port.
distinfo:
TIMESTAMP = 1693289836 SHA256 (rvaser-bioparser-3.1.0_GH0.tar.gz) = ddb48cb456c72cf2955adf056c9204caf65483ec0a5bbba47389bc30ed9fdd05 SIZE (rvaser-bioparser-3.1.0_GH0.tar.gz) = 1016738

Packages (timestamps in pop-ups are UTC):
bioparser
ABIaarch64amd64armv6armv7i386powerpcpowerpc64powerpc64le
FreeBSD:13:latest3.1.03.1.03.0.123.1.03.1.0---
FreeBSD:13:quarterly3.1.03.1.03.0.153.1.03.1.03.1.03.1.03.1.0
FreeBSD:14:latest3.1.03.1.03.0.153.1.03.1.03.0.15-3.0.15
FreeBSD:14:quarterly3.1.03.1.0-3.1.03.1.03.1.03.1.03.1.0
FreeBSD:15:latest3.1.03.1.0n/a3.1.0n/a3.1.03.1.03.1.0
FreeBSD:15:quarterly--n/a-n/a---
Dependencies
NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.
Build dependencies:
  1. biosoup>0 : biology/biosoup
  2. cmake : devel/cmake-core
  3. ninja : devel/ninja
Test dependencies:
  1. googletest>0 : devel/googletest
Runtime dependencies:
  1. biosoup>0 : biology/biosoup
This port is required by:
for Build
  1. biology/rampler
  2. biology/spoa

Configuration Options:
No options to configure
Options name:
biology_bioparser
USES:
cmake
FreshPorts was unable to extract/find any pkg message
Master Sites:
Expand this list (1 items)
Collapse this list.
  1. https://codeload.github.com/rvaser/bioparser/tar.gz/3.1.0?dummy=/
Collapse this list.

Number of commits found: 9

Commit History - (may be incomplete: for full details, see links to repositories near top of page)
CommitCreditsLog message
3.1.0
29 Aug 2023 07:32:45
commit hash: c776c74fb18aed04025448ac7a033381c28306f1commit hash: c776c74fb18aed04025448ac7a033381c28306f1commit hash: c776c74fb18aed04025448ac7a033381c28306f1commit hash: c776c74fb18aed04025448ac7a033381c28306f1 files touched by this commit
Yuri Victorovich (yuri) search for other commits by this committer
biology/bioparser: update 3.0.15 → 3.1.0

Reported by:	portscout
07 Sep 2022 21:58:51
commit hash: fb16dfecae4a6efac9f3a78e0b759fb7a3c53de4commit hash: fb16dfecae4a6efac9f3a78e0b759fb7a3c53de4commit hash: fb16dfecae4a6efac9f3a78e0b759fb7a3c53de4commit hash: fb16dfecae4a6efac9f3a78e0b759fb7a3c53de4 files touched by this commit
Stefan Eßer (se) search for other commits by this committer
Remove WWW entries moved into port Makefiles

Commit b7f05445c00f has added WWW entries to port Makefiles based on
WWW: lines in pkg-descr files.

This commit removes the WWW: lines of moved-over URLs from these
pkg-descr files.

Approved by:		portmgr (tcberner)
3.0.15
07 Sep 2022 21:10:59
commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52 files touched by this commit
Stefan Eßer (se) search for other commits by this committer
Add WWW entries to port Makefiles

It has been common practice to have one or more URLs at the end of the
ports' pkg-descr files, one per line and prefixed with "WWW:". These
URLs should point at a project website or other relevant resources.

Access to these URLs required processing of the pkg-descr files, and
they have often become stale over time. If more than one such URL was
present in a pkg-descr file, only the first one was tarnsfered into
the port INDEX, but for many ports only the last line did contain the
port specific URL to further information.

There have been several proposals to make a project URL available as
a macro in the ports' Makefiles, over time.
(Only the first 15 lines of the commit message are shown above View all of this commit message)
3.0.15
21 Sep 2021 16:41:49
commit hash: e681b893285177cfcf3daa754a7f00b4baf9d898commit hash: e681b893285177cfcf3daa754a7f00b4baf9d898commit hash: e681b893285177cfcf3daa754a7f00b4baf9d898commit hash: e681b893285177cfcf3daa754a7f00b4baf9d898 files touched by this commit
Yuri Victorovich (yuri) search for other commits by this committer
biology/bioparser: Update 3.0.12-2 -> 3.0.15

Reported by:	portscout
3.0.12.2
07 Apr 2021 08:09:01
commit hash: cf118ccf875508b9a1c570044c93cfcc82bd455ccommit hash: cf118ccf875508b9a1c570044c93cfcc82bd455ccommit hash: cf118ccf875508b9a1c570044c93cfcc82bd455ccommit hash: cf118ccf875508b9a1c570044c93cfcc82bd455c files touched by this commit
Mathieu Arnold (mat) search for other commits by this committer
One more small cleanup, forgotten yesterday.
Reported by:	lwhsu
3.0.12.2
06 Apr 2021 14:31:07
commit hash: 305f148f482daf30dcf728039d03d019f88344ebcommit hash: 305f148f482daf30dcf728039d03d019f88344ebcommit hash: 305f148f482daf30dcf728039d03d019f88344ebcommit hash: 305f148f482daf30dcf728039d03d019f88344eb files touched by this commit
Mathieu Arnold (mat) search for other commits by this committer
Remove # $FreeBSD$ from Makefiles.
3.0.12.2
03 Feb 2021 19:08:28
Revision:563906Original commit files touched by this commit
yuri search for other commits by this committer
biology/bioparser: Update 3.0.12 -> 3.0.12-2

Install target is added.
3.0.12
19 Jan 2021 09:56:15
Revision:562040Original commit files touched by this commit
yuri search for other commits by this committer
biology/bioparser: Cosmetic changes
3.0.12
19 Jan 2021 07:56:50
Revision:562033Original commit files touched by this commit
yuri search for other commits by this committer
New port: biology/bioparser: C++ header only parsing library for several formats
in bioinformatics

Number of commits found: 9