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Port details
ncbi-entrez-direct Access to the NCBI's suite of interconnected databases
14.9.20210423_9 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 Version of this port present on the latest quarterly branch.
Maintainer: jwb@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2021-04-24 23:42:15
Last Update: 2023-01-14 11:31:17
Commit Hash: 3b383d8
Also Listed In: perl5
License: PD
Description:
Homepage    cgit ¦ Codeberg ¦ GitHub ¦ GitLab ¦ SVNWeb - no subversion history for this port
pkg-plist: as obtained via: make generate-plist
Expand this list (65 items)
Collapse this list.
  1. /usr/local/share/licenses/ncbi-entrez-direct-14.9.20210423_9/catalog.mk
  2. /usr/local/share/licenses/ncbi-entrez-direct-14.9.20210423_9/LICENSE
  3. /usr/local/share/licenses/ncbi-entrez-direct-14.9.20210423_9/PD
  4. bin/accn-at-a-time
  5. bin/align-columns
  6. bin/amino-acid-composition
  7. bin/archive-pubmed
  8. bin/between-two-genes
  9. bin/download-ncbi-data
  10. bin/download-pubmed
  11. bin/download-sequence
  12. bin/ecommon.sh
  13. bin/edirect.pl
  14. bin/efetch
  15. bin/efilter
  16. bin/einfo
  17. bin/elink
  18. bin/epost
  19. bin/esample
  20. bin/esearch
  21. bin/esummary
  22. bin/exclude-uid-lists
  23. bin/expand-current
  24. bin/fetch-pubmed
  25. bin/filter-stop-words
  26. bin/gbf2xml
  27. bin/hgvs2spdi
  28. bin/hlp-xtract.txt
  29. bin/index-extras
  30. bin/index-pubmed
  31. bin/intersect-uid-lists
  32. bin/join-into-groups-of
  33. bin/nquire
  34. bin/phrase-search
  35. bin/pm-collect
  36. bin/pm-index
  37. bin/pm-invert
  38. bin/pm-merge
  39. bin/pm-prepare
  40. bin/pm-promote
  41. bin/pm-refresh
  42. bin/pm-stash
  43. bin/print-columns
  44. bin/rchive
  45. bin/rchive.FreeBSD
  46. bin/reorder-columns
  47. bin/run-ncbi-converter
  48. bin/skip-if-file-exists
  49. bin/sort-table
  50. bin/sort-uniq-count
  51. bin/sort-uniq-count-rank
  52. bin/stream-pubmed
  53. bin/test-edirect
  54. bin/theme-aliases
  55. bin/transmute
  56. bin/transmute.FreeBSD
  57. bin/word-at-a-time
  58. bin/xml2json
  59. bin/xml2tbl
  60. bin/xtract
  61. bin/xtract.FreeBSD
  62. bin/xy-plot
  63. @owner
  64. @group
  65. @mode
Collapse this list.
Dependency lines:
  • ncbi-entrez-direct>0:biology/ncbi-entrez-direct
Conflicts:
CONFLICTS_INSTALL:
  • ebook-tools
  • p5-XML-Compile
Conflicts Matches:
There are no Conflicts Matches for this port. This is usually an error.
To install the port:
cd /usr/ports/biology/ncbi-entrez-direct/ && make install clean
To add the package, run one of these commands:
  • pkg install biology/ncbi-entrez-direct
  • pkg install ncbi-entrez-direct
NOTE: If this package has multiple flavors (see below), then use one of them instead of the name specified above.
PKGNAME: ncbi-entrez-direct
Flavors: there is no flavor information for this port.
distinfo:

Packages (timestamps in pop-ups are UTC):
ncbi-entrez-direct
ABIlatestquarterly
FreeBSD:11:aarch64pkg-falloutpkg-fallout
FreeBSD:11:amd6414.9.20210423_114.9.20210423_1
FreeBSD:11:armv6pkg-falloutpkg-fallout
FreeBSD:11:i38614.9.20210423_114.9.20210423_1
FreeBSD:11:mipspkg-falloutpkg-fallout
FreeBSD:11:mips64pkg-falloutpkg-fallout
FreeBSD:12:aarch64pkg-fallout14.9.20210423_8
FreeBSD:12:amd6414.9.20210423_914.9.20210423_8
FreeBSD:12:armv6pkg-falloutpkg-fallout
FreeBSD:12:armv7pkg-falloutpkg-fallout
FreeBSD:12:i38614.9.20210423_914.9.20210423_8
FreeBSD:12:mipspkg-falloutpkg-fallout
FreeBSD:12:mips64pkg-falloutpkg-fallout
FreeBSD:12:powerpc64pkg-falloutpkg-fallout
FreeBSD:13:aarch6414.9.20210423_914.9.20210423_8
FreeBSD:13:amd6414.9.20210423_914.9.20210423_8
FreeBSD:13:armv6pkg-falloutpkg-fallout
FreeBSD:13:armv714.9.20210423_914.9.20210423_8
FreeBSD:13:i38614.9.20210423_914.9.20210423_8
FreeBSD:13:mipspkg-falloutpkg-fallout
FreeBSD:13:mips64pkg-falloutpkg-fallout
FreeBSD:13:powerpc64pkg-falloutpkg-fallout
FreeBSD:13:riscv64pkg-falloutpkg-fallout
FreeBSD:14:aarch6414.9.20210423_8pkg-fallout
FreeBSD:14:amd6414.9.20210423_9pkg-fallout
FreeBSD:14:armv6pkg-falloutpkg-fallout
FreeBSD:14:armv714.9.20210423_8pkg-fallout
FreeBSD:14:i38614.9.20210423_9pkg-fallout
FreeBSD:14:mipspkg-falloutpkg-fallout
FreeBSD:14:mips64pkg-falloutpkg-fallout
FreeBSD:14:powerpc64pkg-falloutpkg-fallout
FreeBSD:14:riscv64pkg-falloutpkg-fallout
 
Dependencies
NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.
Build dependencies:
  1. bash : shells/bash
  2. go119 : lang/go119
  3. perl5>=5.32.r0<5.33 : lang/perl5.32
Runtime dependencies:
  1. p5-libwww>=0 : www/p5-libwww
  2. p5-LWP-Protocol-https>=0 : www/p5-LWP-Protocol-https
  3. p5-XML-Simple>=0 : textproc/p5-XML-Simple
  4. curl : ftp/curl
  5. perl5>=5.32.r0<5.33 : lang/perl5.32
This port is required by:
for Run
  1. biology/biostar-tools

Configuration Options:
Options name:
USES:
FreshPorts was unable to extract/find any pkg message
Master Sites:
Expand this list (1 items)
Collapse this list.
  1. ftp://ftp.ncbi.nlm.nih.gov/entrez/entrezdirect/versions/14.9.20210423/
Collapse this list.

Number of commits found: 16

Commit History - (may be incomplete: for full details, see links to repositories near top of page)
CommitCreditsLog message
14.9.20210423_9
14 Jan 2023 11:31:17
commit hash:3b383d833aadb5e3e89d8ee3db1fef37ac239af6commit hash:3b383d833aadb5e3e89d8ee3db1fef37ac239af6commit hash:3b383d833aadb5e3e89d8ee3db1fef37ac239af6commit hash:3b383d833aadb5e3e89d8ee3db1fef37ac239af6 files touched by this commit
Dmitri Goutnik (dmgk) search for other commits by this committer
all: Bump PORTVERSION after lang/go{118,119} update
14.9.20210423_8
11 Dec 2022 11:17:27
commit hash:d9ad1002d517a618a299e45ae70075f2cfc66d2acommit hash:d9ad1002d517a618a299e45ae70075f2cfc66d2acommit hash:d9ad1002d517a618a299e45ae70075f2cfc66d2acommit hash:d9ad1002d517a618a299e45ae70075f2cfc66d2a files touched by this commit
Dmitri Goutnik (dmgk) search for other commits by this committer
all: Bump PORTREVISION after lang/go{118,119} update
14.9.20210423_7
06 Oct 2022 19:24:26
commit hash:bde51869ee0206eeaa2849d8ef28b14da59727a3commit hash:bde51869ee0206eeaa2849d8ef28b14da59727a3commit hash:bde51869ee0206eeaa2849d8ef28b14da59727a3commit hash:bde51869ee0206eeaa2849d8ef28b14da59727a3 files touched by this commit
Dmitri Goutnik (dmgk) search for other commits by this committer
all: Bump PORTREVISION after lang/go{118,119} update
14.9.20210423_6
08 Sep 2022 16:33:18
commit hash:f05c98fffb232735c05ba30d43fb279085b813d7commit hash:f05c98fffb232735c05ba30d43fb279085b813d7commit hash:f05c98fffb232735c05ba30d43fb279085b813d7commit hash:f05c98fffb232735c05ba30d43fb279085b813d7 files touched by this commit
Dmitri Goutnik (dmgk) search for other commits by this committer
all: Bump PORTREVISION after lang/go{118,119} update
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)
14.9.20210423_5
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)
14.9.20210423_5
07 Sep 2022 10:26:41
commit hash:b86221feeafaacbff38b27dd5999866460e3a67bcommit hash:b86221feeafaacbff38b27dd5999866460e3a67bcommit hash:b86221feeafaacbff38b27dd5999866460e3a67bcommit hash:b86221feeafaacbff38b27dd5999866460e3a67b files touched by this commit
Tobias C. Berner (tcberner) search for other commits by this committer
cleanup: remove trailing whitepaces
14.9.20210423_5
03 Aug 2022 21:35:13
commit hash:4476f89764d3ee73d216c2d56df149e8d4c62c24commit hash:4476f89764d3ee73d216c2d56df149e8d4c62c24commit hash:4476f89764d3ee73d216c2d56df149e8d4c62c24commit hash:4476f89764d3ee73d216c2d56df149e8d4c62c24 files touched by this commit
Dmitri Goutnik (dmgk) search for other commits by this committer
all: Bump PORTREVISION after Go update

Bump Go ports PORTREVISION after GO_DEFAULT and lang/go118 update.
14.9.20210423_4
14 Jul 2022 12:46:05
commit hash:153cb65ac8a05356245dd09d1ff48c2a6afafc5acommit hash:153cb65ac8a05356245dd09d1ff48c2a6afafc5acommit hash:153cb65ac8a05356245dd09d1ff48c2a6afafc5acommit hash:153cb65ac8a05356245dd09d1ff48c2a6afafc5a files touched by this commit
Dmitri Goutnik (dmgk) search for other commits by this committer
all: Bump PORTREVISION after lang/go{117,118} update
14.9.20210423_3
07 Jun 2022 21:56:10
commit hash:309cdeccd802bb370a42e80cc4468da17c8dab35commit hash:309cdeccd802bb370a42e80cc4468da17c8dab35commit hash:309cdeccd802bb370a42e80cc4468da17c8dab35commit hash:309cdeccd802bb370a42e80cc4468da17c8dab35 files touched by this commit
Dmitri Goutnik (dmgk) search for other commits by this committer
*/*: Bump port revisons after lang/go{117,118} update
14.9.20210423_2
06 Jun 2022 18:19:10
commit hash:b16eb860cc492d498eea6df7f481c93bbc851167commit hash:b16eb860cc492d498eea6df7f481c93bbc851167commit hash:b16eb860cc492d498eea6df7f481c93bbc851167commit hash:b16eb860cc492d498eea6df7f481c93bbc851167 files touched by this commit
Dmitri Goutnik (dmgk) search for other commits by this committer
*/*: Repair after switching to versioned Go ports

- Add 1.17 to USES=go for ports that still need go117, remove GO_PORT;
- Add missing ${SETENV} ${MAKE_ENV} to repair BINARY_ALIAS;
- Remove explicit dependencies on lang/go.

PR:		264336
Reviewed by:	ygy jwb yuri mikael drtr0jan@yandex.ru decke mat
Differential Revision:	https://reviews.freebsd.org/D35346
14.9.20210423_2
30 Mar 2022 07:01:44
commit hash:d690b5102f75bf70e3cfb280a84c9f3eaf4ec653commit hash:d690b5102f75bf70e3cfb280a84c9f3eaf4ec653commit hash:d690b5102f75bf70e3cfb280a84c9f3eaf4ec653commit hash:d690b5102f75bf70e3cfb280a84c9f3eaf4ec653 files touched by this commit
Guangyuan Yang (ygy) search for other commits by this committer
*/*: Bump PORTREVISION after lang/go 1.18 update
14.9.20210423_1
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)
14.9.20210423_1
10 Jan 2022 15:15:39
commit hash:bcaf25a8c8046b094f6b5ab5bc258333bc326ee1commit hash:bcaf25a8c8046b094f6b5ab5bc258333bc326ee1commit hash:bcaf25a8c8046b094f6b5ab5bc258333bc326ee1commit hash:bcaf25a8c8046b094f6b5ab5bc258333bc326ee1 files touched by this commit
Stefan Eßer (se) search for other commits by this committer
Fix CONFLICTS entries of multiple ports

There have been lots of missing CONFLICTS_INSTALL entries, either
because conflicting ports were added without updating existing ports,
due to name changes of generated packages, due to mis-understanding
the format and semantics of the conflicts entries, or just due to
typoes in package names.

This patch is the result of a comparison of all files contained in
the official packages with each other. This comparison was based on
packages built with default options and may therefore have missed
further conflicts with optionally installed files.

Where possible, version numbers in conflicts entries have been
generalized, some times taking advantage of the fact that a port
(Only the first 15 lines of the commit message are shown above View all of this commit message)
14.9.20210423_1
26 Apr 2021 16:53:11
commit hash:dd7bec77114786adf79d35c325337a59c9684848commit hash:dd7bec77114786adf79d35c325337a59c9684848commit hash:dd7bec77114786adf79d35c325337a59c9684848commit hash:dd7bec77114786adf79d35c325337a59c9684848 files touched by this commit
Jason W. Bacon (jwb) search for other commits by this committer
biology/ncbi-entrez-direct: Update to 14.9.20210423_1

A few fixes to pass upstream test script
14.9.20210423
24 Apr 2021 23:40:16
commit hash:ab50f8435a78a574ac5ce683004b078c5baf209dcommit hash:ab50f8435a78a574ac5ce683004b078c5baf209dcommit hash:ab50f8435a78a574ac5ce683004b078c5baf209dcommit hash:ab50f8435a78a574ac5ce683004b078c5baf209d files touched by this commit
Jason W. Bacon (jwb) search for other commits by this committer
biology/ncbi-entrez-direct: Access to the NCBI's interconnected databases

Entrez Direct (EDirect) provides access to the NCBI's suite of interconnected
databases (publication, sequence, structure, gene, variation, expression, etc.)
from a UNIX terminal window.

Number of commits found: 16