The European Molecular Biology Open Software Suite (EMBOSS) is a
comprehensive set (about 100) of open source tools for genetic sequence
analysis. EMBOSS is produced by the European Molecular Biology Network
(EMBnet - http://www.embnet.org/).
All EMBOSS tools are all built around the same set of core libraries - AJAX
and NUCLEUS - and therefore share a unified user interface, have similar
"look and feel", and implement a uniform sequence addressing methodology.
The various components of EMBOSS are distributed under the GPL, except the
core libraries which are under the LGPL.
EMBASSY packages are third party applications which have been integrated with
the EMBOSS suite, but which are not included in the base EMBOSS distribution
for licensing or other reasons. The EMBASSY packages live in the
biology/embassy port.
===> The following configuration options are available for emboss-6.6.0_7:
DOCS=on: Build and/or install documentation
MYSQL=off: MySQL database support
X11=on: X11 (graphics) support
===> Use 'make config' to modify these settings
*/*: Refactor with IGNORE_WITH_MYSQL
- There are multiple ports which has MYSQL options and are non-DEFAULT.
Most of the time committers actually forget to check with the OPTION
enabled and in some cases they are BROKEN with newr versions of mysql.
So test with different versions of mysql and mark IGNOPRE_WITH_MYSQL
appropriately. Due to the EOL of 5.7 this has not been checked.
- Unbreak sysutils/cfengine* with MySQL 8.0 and later
- The primary purpose of running this check is having statistics of the
MySQL usability over MariaDB to explore the future possibility of
shifting to MariaDB as the default as major ports upstream have moved
their codebase to support MariaDB over MySQL.
- The following actions will also be taken after the sunset of MySQL 5.7
If a port is broken on all instances of MySQL/MariaDB:
- If a port has the option of multiple DB backends and MySQL is the
default then the DEFAULT will be changed to PGSQL/SQLITE before
2024Q1. And the OPTION will be removed before 2024Q2. If a
MAINTAINER is aware about such cases and want to prefer PGSQL over
SQLITE or vice versa please do so at your own accord. Otherwise
PGSQL will be preferred over SQLITE.
- If a port has the option of multiple DB backends and MySQL is not
the default then the the OPTION will be removed before 2024Q1.
Approved by: portmgr (blanket)
biology/emboss: fix build on powerpc*
ajfileio.c:271:7: warning: call to undeclared function 'ajSysFuncFgets'; ISO C99
and later do not support implicit function declarations
[-Wimplicit-function-declaration]
cp = ajSysFuncFgets(&buff[ipos], isize, file->fp);
^
ajfileio.c:271:5: error: incompatible integer to pointer conversion assigning to
'const char *' from 'int' [-Wint-conversion]
cp = ajSysFuncFgets(&buff[ipos], isize, file->fp);
^ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
1 warning and 1 error generated.
biology/emboss: Optionize mysql support
The port builds fine without mysql and as MySQL57 is reaching end of
life so optionize MYSQL so that other flavors can be used and still
there is an available pkg for this port.
Approved by: portmgr (blanket)
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)
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 )
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 )
*/*: Remove redundant '-[0-9]*' from CONFLICTS
The conflict checks compare the patterns first against the package
names without version (as reported by "pkg query "%n"), then - if
there was no match - agsinst the full package names including the
version (as reported by "pkg query "%n-%v").
Many CONFLICTS definitions used patterns like "bash-[0-9]*" to filter
for the bash package in any version. But that pattern is functionally
identical with just "bash".
Approved by: portmgr (blanket)
biology/emboss: Add "emboss" command in ${LOCALBASE}/bin
Standard emboss commands are installed under a special prefix because
of multiple conflicts. The emboss command turns the standard commands
into subcommands, so no special PATH is needed.
/usr/local/emboss/bin/needle [args]
can be run as
emboss needle [args]
biology/emboss: Put emboss-shell in default PATH
PREFIX is overridden by default in the port Makefile, so PREFIX/bin
is not normally in PATH. The purpose of emboss-shell is to prepend
PREFIX/bin to PATH to give access to emboss tools.
Also fix tcsh detection.
PR: 258316
Remove indefinite articles and trailing periods from COMMENT, plus
minor COMMENT typos and surrounding whitespace fixes. Categories A-C.
CR: D196
Approved by: portmgr (bapt)
Convert all :U to :tu and :L to :tl
Since FreeBSD 8.4 and FreeBSD 9.1 make(1) do support :tu and :tl as a
replacement for :U and :L (which has been marked as deprecated)
bmake which is the default on FreeBSD 10+ only support by default
:tu/:tl a hack has been added at the time to support :U and :L to ease
migration. This hack is now not necessary anymore
Note that this makes the ports tree incompatible with make(1) from
FreeBSD 8.3 or earlier
With hat: portmgr
-Repocopy devel/libtool15 -> libtool22 and libltdl15 -> libltdl22.
-Update libtool and libltdl to 2.2.6a.
-Remove devel/libtool15 and devel/libltdl15.
-Fix ports build with libtool22/libltdl22.
-Bump ports that depend on libltdl22 due to shared library version change.
-Explain what to do update in the UPDATING.
It has been tested with GNOME2, XFCE4, KDE3, KDE4 and other many wm/desktop
and applications in the runtime.
With help: marcus and kwm
Pointyhat-exp: a few times by pav
Tested by: pgollucci, "Romain Tartière" <romain@blogreen.org>, and
a few MarcusCom CVS users. Also, I might have missed a few.
Repocopy by: marcus
Approved by: portmgr
- It seems that upstream removes their distfiles from sourceforge, so add
the download site pointed by their webpage as first choice.
Noticed by: pointyhat via pav
For EMBOSS:
This patch brings EMBOSS up to date with the current version.
i. The patches included in files/ are bugfixes for files in
EMBOSS-3.0.0 that appeared after the release. They are
documented in ftp://emboss.open-bio.org/pub/EMBOSS/fixes/README
This is just 'for the record' so that we remember to remove these
patches in the next update.
ii. EMBOSS is now installed by default in LOCALBASE/emboss
This is to avoid CONFLICTS with other ports that install files
with the same names. Installing EMBOSS to another PREFIX is also
possible.
(Only the first 15 lines of the commit message are shown above )
Mass-conversion to the USE_AUTOTOOLS New World Order. The code present
in bsd.autotools.mk essentially makes this a no-op given that all the
old variables set a USE_AUTOTOOLS_COMPAT variable, which is parsed in
exactly the same way as USE_AUTOTOOLS itself.
Moreover, USE_AUTOTOOLS has already been extensively tested by the GNOME
team -- all GNOME 2.12.x ports use it.
Preliminary documentation can be found at:
http://people.FreeBSD.org/~ade/autotools.txt
which is in the process of being SGMLized before introduction into the
Porters Handbook.
Light blue touch-paper. Run.
o Main modification
graphics/gd(based on 1.8.4) -> graphics/gd1
graphics/gd2(based on 2.0.15) -> graphics/gd
graphics/p5-GD(based on 1.41) -> graphics/p5-GD1
graphics/p5-GD2(based on 2.07) -> graphics/p5-GD
japanese/gd -> japanese/gd1
japanese/gd2 -> japanese/gd
o Include some feature
WITH_XPM(w/, w/o WITHOUT_X11)
o Chase this modification
o Fix build error [1]
PR: ports/54540
Submitted by: Ports Fury
Approved by: maintainer (blanket)
Reported by: bento via kris [1]
This port is scheduled for removal on Nov 7 2003 if it is still broken at
that time and no PRs have been submitted to fix it. If you are interested
in saving this port, please send your patches to the maintainer. If the
maintainer is unresponsive or the port has no maintainer, then please
submit them via send-pr.
o Change library name from libgd to libgd1.
o Do not install everything except headers and libraries
(to avoid conflicting with graphics/gd2)
o Fix dependency on new libgd1(for many ports).
PR: ports/54100
Submitted by: Ports Fury
- Unbreak fetching of distfiles. (Needs update as soon as freeze is over.)
Submitted by: kris, bento
Approved by: Implicitly by first rule of ports freeze, I hope!
- Update to version 2.2.0 - Update included EMBASSY package EMNU - Fix a
long-standing bug in Makefile that would preclude PKGMESSAGE from being
generated properly - Consider this an interim update merely to track the
latest version - more work is required to activate the newly included
"Jemboss" Java GUI interface
- This is a fairly extensive rework of this port. - "EMBASSY" applications are
third party tools which have been adapted to function as part of EMBOSS, but
which are not included with the base EMBOSS distribution for licensing or
other reasons. This new version of the EMBOSS port now contains the three
current EMBASSY applications as well, and during installation the user is
presented with a dialog(1) menu to
- This is a fairly extensive rework of this port. - "EMBASSY" applications are
third party tools which have been adapted to function as part of EMBOSS, but
which are not included with the base EMBOSS distribution for licensing or
other reasons. This new version of the EMBOSS port now contains the three
current EMBASSY applications as well, and during installation the user is
presented with a dialog(1) menu to choose which of these should be
isntalled.
