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Port details
iolib General purpose trace file (and Experiment File) reading interface
1.14.10_1 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 1.14.10Version of this port present on the latest quarterly branch.
There is no maintainer for this port.
Any concerns regarding this port should be directed to the FreeBSD Ports mailing list via ports@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2009-08-28 23:34:46
Last Update: 2024-02-22 13:23:48
Commit Hash: 3263fab
License: BSD3CLAUSE
WWW:
https://staden.sourceforge.net/
Description:
Io_lib is a library of file reading and writing code to provide a general purpose trace file (and Experiment File) reading interface. The programmer simply calls the (eg) read_reading to create a "Read" C structure with the data loaded into memory. It has been compiled and tested on a variety of Unix systems, MacOS X and MS Windows.
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 (122 items)
Collapse this list.
  1. @ldconfig
  2. /usr/local/share/licenses/io_lib-1.14.10_1/catalog.mk
  3. /usr/local/share/licenses/io_lib-1.14.10_1/LICENSE
  4. /usr/local/share/licenses/io_lib-1.14.10_1/BSD3CLAUSE
  5. bin/append_sff
  6. bin/convert_trace
  7. bin/cram_dump
  8. bin/cram_filter
  9. bin/cram_index
  10. bin/cram_size
  11. bin/extract_fastq
  12. bin/extract_qual
  13. bin/extract_seq
  14. bin/get_comment
  15. bin/hash_exp
  16. bin/hash_extract
  17. bin/hash_list
  18. bin/hash_sff
  19. bin/hash_tar
  20. bin/index_tar
  21. bin/io_lib-config
  22. bin/makeSCF
  23. bin/scf_dump
  24. bin/scf_info
  25. bin/scf_update
  26. bin/scram_flagstat
  27. bin/scram_merge
  28. bin/scram_pileup
  29. bin/scram_test
  30. bin/scramble
  31. bin/srf2fasta
  32. bin/srf2fastq
  33. bin/srf_dump_all
  34. bin/srf_extract_hash
  35. bin/srf_extract_linear
  36. bin/srf_filter
  37. bin/srf_index_hash
  38. bin/srf_info
  39. bin/srf_list
  40. bin/trace_dump
  41. bin/ztr_dump
  42. include/io_lib/Read.h
  43. include/io_lib/abi.h
  44. include/io_lib/alf.h
  45. include/io_lib/array.h
  46. include/io_lib/bam.h
  47. include/io_lib/bgzip.h
  48. include/io_lib/binning.h
  49. include/io_lib/compress.h
  50. include/io_lib/compression.h
  51. include/io_lib/cram.h
  52. include/io_lib/cram_codecs.h
  53. include/io_lib/cram_decode.h
  54. include/io_lib/cram_encode.h
  55. include/io_lib/cram_index.h
  56. include/io_lib/cram_io.h
  57. include/io_lib/cram_stats.h
  58. include/io_lib/cram_structs.h
  59. include/io_lib/deflate_interlaced.h
  60. include/io_lib/dstring.h
  61. include/io_lib/error.h
  62. include/io_lib/expFileIO.h
  63. include/io_lib/fpoint.h
  64. include/io_lib/hash_table.h
  65. include/io_lib/io_lib_config.h
  66. include/io_lib/jenkins_lookup3.h
  67. include/io_lib/mFILE.h
  68. include/io_lib/mach-io.h
  69. include/io_lib/md5.h
  70. include/io_lib/misc.h
  71. include/io_lib/open_trace_file.h
  72. include/io_lib/os.h
  73. include/io_lib/plain.h
  74. include/io_lib/pooled_alloc.h
  75. include/io_lib/sam_header.h
  76. include/io_lib/scf.h
  77. include/io_lib/scf_extras.h
  78. include/io_lib/scram.h
  79. include/io_lib/seqIOABI.h
  80. include/io_lib/sff.h
  81. include/io_lib/srf.h
  82. include/io_lib/stdio_hack.h
  83. include/io_lib/string_alloc.h
  84. include/io_lib/tar_format.h
  85. include/io_lib/thread_pool.h
  86. include/io_lib/traceType.h
  87. include/io_lib/translate.h
  88. include/io_lib/vlen.h
  89. include/io_lib/xalloc.h
  90. include/io_lib/zfio.h
  91. include/io_lib/ztr.h
  92. lib/libstaden-read.a
  93. lib/libstaden-read.so
  94. lib/libstaden-read.so.13
  95. lib/libstaden-read.so.13.0.0
  96. share/man/man1/scramble.1.gz
  97. share/man/man1/srf2fasta.1.gz
  98. share/man/man1/srf2fastq.1.gz
  99. share/man/man1/srf_index_hash.1.gz
  100. share/man/man1/srf_info.1.gz
  101. share/man/man1/srf_list.1.gz
  102. share/man/man3/ExperimentFile.3.gz
  103. share/man/man3/exp2read.3.gz
  104. share/man/man3/fread_reading.3.gz
  105. share/man/man3/fread_scf.3.gz
  106. share/man/man3/fwrite_reading.3.gz
  107. share/man/man3/fwrite_scf.3.gz
  108. share/man/man3/read2exp.3.gz
  109. share/man/man3/read2scf.3.gz
  110. share/man/man3/read_allocate.3.gz
  111. share/man/man3/read_deallocate.3.gz
  112. share/man/man3/read_reading.3.gz
  113. share/man/man3/read_scf.3.gz
  114. share/man/man3/read_scf_header.3.gz
  115. share/man/man3/scf2read.3.gz
  116. share/man/man3/write_reading.3.gz
  117. share/man/man3/write_scf.3.gz
  118. share/man/man3/write_scf_header.3.gz
  119. share/man/man4/Read.4.gz
  120. @owner
  121. @group
  122. @mode
Collapse this list.
Dependency lines:
  • io_lib>0:biology/iolib
Conflicts:
CONFLICTS_INSTALL:
  • filters
  • scramble
Conflicts Matches:
There are no Conflicts Matches for this port. This is usually an error.
To install the port:
cd /usr/ports/biology/iolib/ && make install clean
To add the package, run one of these commands:
  • pkg install biology/iolib
  • pkg install io_lib
NOTE: If this package has multiple flavors (see below), then use one of them instead of the name specified above.
PKGNAME: io_lib
Flavors: there is no flavor information for this port.
distinfo:
TIMESTAMP = 1538157628 SHA256 (jkbonfield-io_lib-io_lib-1-14-10_GH0.tar.gz) = 4bd576e52bb7e6be6c2efe42db2764b713c8b61b44a025ad0567dba052b6db1c SIZE (jkbonfield-io_lib-io_lib-1-14-10_GH0.tar.gz) = 3391479

Packages (timestamps in pop-ups are UTC):
io_lib
ABIaarch64amd64armv6armv7i386powerpcpowerpc64powerpc64le
FreeBSD:13:latest1.14.10_11.14.10_11.14.101.14.10_11.14.10_1-1.14.10-
FreeBSD:13:quarterly1.14.10_11.14.10_11.14.101.14.101.14.10_11.14.101.14.101.14.10
FreeBSD:14:latest1.14.10_11.14.10_11.14.101.14.10_11.14.10_11.14.10-1.14.10
FreeBSD:14:quarterly1.14.101.14.10_1-1.14.101.14.10_11.14.101.14.101.14.10
FreeBSD:15:latest1.14.10_11.14.10_1n/a1.14.10n/a1.14.101.14.101.14.10_1
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. gmake>=4.3 : devel/gmake
  2. autoconf>=2.71 : devel/autoconf
  3. automake>=1.16.5 : devel/automake
  4. libtoolize : devel/libtool
Library dependencies:
  1. libcurl.so : ftp/curl
This port is required by:
for Build
  1. biology/p5-Bio-SCF
for Run
  1. biology/p5-Bio-SCF

Configuration Options:
No options to configure
Options name:
biology_iolib
USES:
autoreconf gmake libtool
FreshPorts was unable to extract/find any pkg message
Master Sites:
Expand this list (1 items)
Collapse this list.
  1. https://codeload.github.com/jkbonfield/io_lib/tar.gz/io_lib-1-14-10?dummy=/
Collapse this list.

Number of commits found: 49

Commit History - (may be incomplete: for full details, see links to repositories near top of page)
CommitCreditsLog message
1.14.10_1
22 Feb 2024 13:23:48
commit hash: 3263fab7c963afd4a3c558e479ca67f2a1c9e3e9commit hash: 3263fab7c963afd4a3c558e479ca67f2a1c9e3e9commit hash: 3263fab7c963afd4a3c558e479ca67f2a1c9e3e9commit hash: 3263fab7c963afd4a3c558e479ca67f2a1c9e3e9 files touched by this commit
Muhammad Moinur Rahman (bofh) search for other commits by this committer
biology/iolib: Moved man to share/man

Approved by:    portmgr (blanket)
1.14.10
01 Nov 2023 22:11:47
commit hash: 05f0f44a557a53913001d6debf17965dfb799288commit hash: 05f0f44a557a53913001d6debf17965dfb799288commit hash: 05f0f44a557a53913001d6debf17965dfb799288commit hash: 05f0f44a557a53913001d6debf17965dfb799288 files touched by this commit
Rodrigo Osorio (rodrigo) search for other commits by this committer
*/*: Update WWW to use HTTPS for sourceforge.net projects

Homepage link is permanent redirected to its HTTPS counterpart
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)
1.14.10
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)
1.14.10
20 Jul 2022 14:20:57
commit hash: 37526bbd4e50616d87f70e1c788ae4895d88d671commit hash: 37526bbd4e50616d87f70e1c788ae4895d88d671commit hash: 37526bbd4e50616d87f70e1c788ae4895d88d671commit hash: 37526bbd4e50616d87f70e1c788ae4895d88d671 files touched by this commit
Tobias C. Berner (tcberner) search for other commits by this committer
biology: remove 'Created by' lines

A big Thank You to the original contributors of these ports:

  *  Aaron Dalton <aaron@FreeBSD.org>
  *  Akinori MUSHA aka knu <knu@idaemons.org>
  *  Andrey Zakhvatov
  *  Bob Zimmermann <rpz@cse.wustl.edu>
  *  Camson Huynh <chuynh@biolateral.com.au>
  *  Dan Siercks <dsiercks@uwm.edu>
  *  Fernan Aguero <fernan@iib.unsam.edu.ar>
  *  Hannes Hauswedell <h2+fbsdports@fsfe.org>
  *  J. Bacon <jwb@FreeBSD.org>
  *  Jason Bacon <jwb@FreeBSD.org>
  *  Jeremy <karlj000@unbc.ca>
(Only the first 15 lines of the commit message are shown above View all of this commit message)
1.14.10
06 Feb 2022 18:36:07
commit hash: bdd2d4af9630fdc1157d49bd193e8195c3240e9ecommit hash: bdd2d4af9630fdc1157d49bd193e8195c3240e9ecommit hash: bdd2d4af9630fdc1157d49bd193e8195c3240e9ecommit hash: bdd2d4af9630fdc1157d49bd193e8195c3240e9e files touched by this commit
Stefan Eßer (se) search for other commits by this committer
Update CONFLICTS definitions in categories a* to c*

Update the CONFLICTS definitions of ports in the following categories:

- accessibility
- archivers
- audio
- benchmarks
- biology
- cad
- chinese
- comms
- converters

An attempt has been made to use generic conflicts patterns that do not
have to be updated whenever a new version of a conflicting port is
added to the ports system.

There is a misunderstanding that the port being built/installed has to
be omitted from the conflicts pattern. This is not true - the port
being built is implicitly non-conflicting due to logic in bsd.port.mk.

Approved by:	portmgr (implicit)
1.14.10
19 May 2021 19:56:24
commit hash: 809338d451b2d3e438c1fa44fb30184aa18ff3a6commit hash: 809338d451b2d3e438c1fa44fb30184aa18ff3a6commit hash: 809338d451b2d3e438c1fa44fb30184aa18ff3a6commit hash: 809338d451b2d3e438c1fa44fb30184aa18ff3a6 files touched by this commit
Danilo Egea Gondolfo (danilo) search for other commits by this committer
biology/iolib: Drop maintainership
1.14.10
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.
1.14.10
01 Apr 2019 19:33:15
Revision:497508Original commit files touched by this commit
danilo search for other commits by this committer
- Fix build in head i386
1.14.10
05 Nov 2018 19:45:23
Revision:484210Original commit files touched by this commit
linimon search for other commits by this committer
Remove the incorrect typedefs to fix build on tier-2.

PR:		232390
Submitted by:	Piotr Kubaj
Approved by:	portmgr (tier-2 blanket)
1.14.10
05 Nov 2018 19:42:38
Revision:484209Original commit files touched by this commit
linimon search for other commits by this committer
Remove the inccorrect typedefs to fix build on tier-2.

PR:		232390
Submitted by:	Piotr Kubaj
Approved by:	portmgr (tier-2 blanket)
1.14.10
28 Sep 2018 18:47:50
Revision:480878Original commit files touched by this commit
danilo search for other commits by this committer
- Update to 1-14-10
- Move USES to make portlint happy
1.14.9
02 Jul 2018 00:47:14
Revision:473692Original commit files touched by this commit
linimon search for other commits by this committer
Mark various ports broken on mips64 and, where appropriate, mips.

While here, pet portlint.

Approved by:	portmgr (tier-2 blanket)
1.14.9
13 May 2017 03:35:51
Revision:440746Original commit files touched by this commit
linimon search for other commits by this committer
Mark some ports failing on power64.  In cases where the error message
was a stub, provide a real one.

While here, pet portlint.

Approved by:	portmgr (tier-2 blanket)
1.14.9
28 Feb 2017 08:33:44
Revision:435006Original commit files touched by this commit
mat search for other commits by this committer
Fix USE_GITHUB's GH_TAGNAME usage.

Sponsored by:	Absolight
1.14.9
24 Feb 2017 18:57:57
Revision:434741Original commit files touched by this commit
danilo search for other commits by this committer
- Update to 1.14.9
- Use github
1.14.8
01 May 2016 01:03:48
Revision:414372Original commit files touched by this commit
danilo search for other commits by this committer
- Update to 1.14.8
1.14.7
01 Apr 2016 13:29:17
Revision:412344Original commit files touched by this commit
mat search for other commits by this committer
Remove ${PORTSDIR}/ from dependencies, Mk and categories a, b, and c.

With hat:	portmgr
Sponsored by:	Absolight
1.14.7
20 Feb 2016 16:05:59
Revision:409251Original commit files touched by this commit
danilo search for other commits by this committer
- Update to 1.14.7
1.14.6
09 Nov 2015 16:02:13
Revision:401113Original commit files touched by this commit
danilo search for other commits by this committer
- Update to 1.14.6
1.14.5
06 Nov 2015 12:03:25
Revision:400926Original commit files touched by this commit
danilo search for other commits by this committer
- Update to 1.14.5
1.14.4
07 Oct 2015 00:26:34
Revision:398730Original commit files touched by this commit
danilo search for other commits by this committer
- Update to 1.14.4
1.14.3
01 Oct 2015 23:28:23
Revision:398397Original commit files touched by this commit
danilo search for other commits by this committer
- Update to 1.14.3
1.14.2
20 Sep 2015 19:59:04
Revision:397395Original commit files touched by this commit
olgeni search for other commits by this committer
Typos, whitespace and capitalization fixes (A-F).
1.14.2
17 Sep 2015 12:54:48
Revision:397111Original commit files touched by this commit
danilo search for other commits by this committer
- Update to 1.14.2
1.14.1
13 Sep 2015 18:05:55
Revision:396842Original commit files touched by this commit
danilo search for other commits by this committer
- Update to 1.14.1
1.14.0
12 Jul 2015 18:25:07
Revision:391830Original commit files touched by this commit
danilo search for other commits by this committer
- Update to 1.14.0
- Use install-strip
1.13.10
04 Mar 2015 13:17:47
Revision:380435Original commit files touched by this commit
danilo search for other commits by this committer
- Update to 1.13.10
1.13.9
30 Jan 2015 21:49:29
Revision:378185Original commit files touched by this commit
danilo search for other commits by this committer
- Update to 1.13.9
1.13.8
14 Jan 2015 13:15:50
Revision:377013Original commit files touched by this commit
danilo search for other commits by this committer
- Update to 1.13.8
1.13.7
20 Oct 2014 07:10:48
Revision:371237Original commit files touched by this commit
bapt search for other commits by this committer
Cleanup plist
1.13.7
31 May 2014 18:03:08
Revision:355999Original commit files touched by this commit
danilo search for other commits by this committer
- I forgot to svn add a new patch
1.13.7
31 May 2014 17:57:07
Revision:355998Original commit files touched by this commit
danilo search for other commits by this committer
- Update from 1.13.5 to 1.13.7
- Add libtool to USES
- Take maintainership
1.13.5
26 Apr 2014 02:35:37
Revision:352216Original commit files touched by this commit
miwi search for other commits by this committer
- Update to version 1.13.5

PR:		188863
Submitted by:	ports fury
1.13.0_1
12 Apr 2014 07:42:33
Revision:351071Original commit files touched by this commit
culot search for other commits by this committer
- Back to the heap, I don't use this port anymore
1.13.0_1
20 Jan 2014 17:02:11
Revision:340411Original commit files touched by this commit
bapt search for other commits by this committer
Support stage
Conver USE_GMAKE
1.13.0_1
11 Dec 2013 14:43:51
Revision:336171Original commit files touched by this commit
bapt search for other commits by this committer
In preparation for making libtool generate libraries with a sane name, fix all
LIB_DEPENDS in biology
1.13.0_1
20 Sep 2013 15:55:44
Revision:327709Original commit files touched by this commit
bapt search for other commits by this committer
Add NO_STAGE all over the place in preparation for the staging support (cat:
biology)
1.13.0_1
11 Jul 2013 16:26:27
Revision:322783Original commit files touched by this commit
sunpoet search for other commits by this committer
- Update to 7.31.0
- Bump PORTREVISION for ftp/curl shlib change
- Add TEST_DEPENDS
- Convert to new options framework
- Adjust options:
  - Add COOKIES
  - Add CYASSL, NSS, POLARSSL, THREADED_RESOLVER, TLS_SRP [1]
  - Add GSSAPI and SPNEGO [2]
  - Remove KERBEROS4
  - Rename LIBIDN to IDN
  - Remove TRACKMEMORY [1]
- Sort option handler
- Add SLAVEDIRS: ftp/curl-hiphop
- Cosmetic change
- Cleanup Makefile header
- While I'm here, fix typo (PORTREVSION) in x11-wm/ede/Makefile

Changes:	http://curl.haxx.se/changes.html
PR:		ports/172325 (-exp run), ports/177369 (based on) [1]
Submitted by:	Hirohisa Yamaguchi <umq@ueo.co.jp> [1], hrs (via email) [2]
Exp run by:	miwi
1.13.0
30 Apr 2013 15:41:49
Revision:316940Original commit files touched by this commit
culot search for other commits by this committer
- Update to 1.13.0
- Improve COMMENT (remove leading article, add missing space)
- Remove unneeded BSD license file
- Trim Makefile's header
- Pet portlint (move LICENSE section earlier, change tab to space in WWW link)

Changes:	http://sourceforge.net/p/staden/news/2013/03/iolib-1130-released/
1.12.5
09 Nov 2011 15:26:04
Original commit files touched by this commit
miwi search for other commits by this committer
- Remove WITH_FBSD10_FIX, is no longer needed
1.12.5
29 Oct 2011 11:10:22
Original commit files touched by this commit
miwi search for other commits by this committer
- Fix build on FreeBSD 10
1.12.5
11 Feb 2011 13:11:45
Original commit files touched by this commit
culot search for other commits by this committer
- Update to 1.12.5

Changes:        http://sourceforge.net/news/?group_id=100316&id=297223
1.12.4
04 Dec 2010 07:34:27
Original commit files touched by this commit
ade search for other commits by this committer
Sync to new bsd.autotools.mk
1.12.4
20 Oct 2010 05:53:20
Original commit files touched by this commit
culot search for other commits by this committer
Update my MAINTAINER address to culot@FreeBSD.org.

Approved by:    sahil@ (mentor)
1.12.4
02 Aug 2010 16:06:38
Original commit files touched by this commit
bapt search for other commits by this committer
Fix typo in maintainer mail address

Submitted by:   Frederic Culot <frederic _at_ culot.org> (maintainer)
Approved by:    jadawin@ (co-mentor)
1.12.4
02 Aug 2010 15:09:22
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- Update to 1.12.4
- Add libcurl as dependency
- Submitter is now maintainer

PR:             ports/149079
Submitted by:   Frederic Coulot <frederic _at_ coulot.org> (maintainer)
Approved by:    jadawin@ (co-mentor)
1.12.2
21 May 2010 06:19:18
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- Update to 1.12.2
- Reset maintainer
1.12.1
28 Aug 2009 23:34:20
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Io_lib is a library of file reading and writing code to provide a
general purpose trace file (and Experiment File) reading interface.
The programmer simply calls the (eg) read_reading to create a "Read"
C structure with the data loaded into memory. It has been compiled
and tested on a variety of unix systems, MacOS X and MS Windows.

WWW:    http://staden.sourceforge.net/

PR:             ports/138254
Submitted by:   Wen Heping <wenheping at gmail.com>

Number of commits found: 49