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Package Details: emboss 6.6.0-3
Git Clone URL: | https://aur.archlinux.org/emboss.git (read-only, click to copy) |
---|---|
Package Base: | emboss |
Description: | A collection of molecular biology applications |
Upstream URL: | http://emboss.sourceforge.net/ |
Licenses: | |
Submitter: | Allan |
Maintainer: | mschu |
Last Packager: | mschu |
Votes: | 18 |
Popularity: | 0.000071 |
First Submitted: | 2008-12-28 12:20 |
Last Updated: | 2020-05-11 20:54 |
Dependencies (8)
- gd
- java-runtime (jdk5, tuxjdk, jre7-openjdk-infinality, java-8-openjdk-shenandoah, jre8-openjdk-infinality, java-gcj-compat, jdk9, jre9, jdk-devel, jre10, jdk8-arm64, jdk6, jdk12-openj9-bin, zulu-12-bin, jre6, jre12, jdk8-openjdk-dcevm, jdk11-graalvm-ee-bin, server-jre, jdk8-arm, jdk13-openj9-bin, jdk9-openj9-bin, jdk10, jdk11-openjdk-dcevm, jre8-openjdk-jetbrains, jre8-openjdk-shenandoah, jdk10-openj9-bin, jdk14-openj9-bin, jdk7, jre7, jre14, jdk-arm, jdk8-jetbrains, jdk7r1-j9-bin, jdk7-j9-bin, zulu-14-bin, zulu-13-bin, jdk-bcl, jre-bcl, amazon-corretto-15, jre-openj9, jdk11-openj9-bin, java-openjdk-bin, amazon-corretto-8, amazon-corretto-11, jdk11-openjdk-dcevm-conflicts-fixed, jre8, jdk8, jdk-openj9-bin, jre, jdk11-adoptopenjdk, jdk-adoptopenjdk, zulu-8-bin, zulu-11-bin, zulu-15-bin, liberica-jdk-11-bin, liberica-jdk-11-lite-bin, liberica-jre-11-full-bin, liberica-jdk-8-full-bin, liberica-jdk-full-bin, liberica-jdk-11-full-bin, liberica-jre-11-bin, liberica-jre-8-full-bin, zulu-embedded-jdk, jdk8-j9-bin, zulu-embedded-jdk11, jdk8-openj9-bin, zulu-embedded-jdk8, jre11, sapmachine-jdk-bin, jre11-jetbrains-imfix, jre-jetbrains, jdk11-graalvm-bin, jdk8-graalvm-bin, java-openjdk-loom-ea-bin, jdk-jetbrains, jre8-adoptopenjdk, java-openjdk-ea-bin, jre-openjdk, jre11-openjdk, jre7-openjdk, jre8-openjdk)
- pcre (pcre-svn)
- java-environment (jdk5, tuxjdk, jdk7-openjdk-infinality, java-8-openjdk-shenandoah, jdk8-openjdk-infinality, java-gcj-compat, jdk9, zulu-10-bin, jdk-devel, jdk8-arm64, jdk6, jdk12-openj9-bin, zulu-12-bin, jdk12, jdk8-openjdk-dcevm, jdk11-graalvm-ee-bin, jdk8-arm, jdk13-openj9-bin, jdk9-openj9-bin, jdk10, jdk11-openjdk-dcevm, jdk8-openjdk-jetbrains, jdk8-openjdk-shenandoah, jdk10-openj9-bin, jdk14-openj9-bin, jdk7, jdk-arm, jdk8-jetbrains, jdk7r1-j9-bin, jdk7-j9-bin, zulu-14-bin, zulu-13-bin, jdk-bcl, amazon-corretto-15, jdk-openj9, jdk11-openj9-bin, java-openjdk-bin, amazon-corretto-8, amazon-corretto-11, jdk11-openjdk-dcevm-conflicts-fixed, jdk8, jdk-openj9-bin, jdk, jdk11-adoptopenjdk, jdk-adoptopenjdk, zulu-8-bin, zulu-11-bin, zulu-15-bin, liberica-jdk-11-bin, liberica-jdk-11-lite-bin, liberica-jre-11-full-bin, liberica-jdk-8-full-bin, liberica-jdk-full-bin, liberica-jdk-11-full-bin, liberica-jre-11-bin, liberica-jre-8-full-bin, zulu-embedded-jdk, jdk8-j9-bin, zulu-embedded-jdk11, jdk8-openj9-bin, zulu-embedded-jdk8, jdk11, sapmachine-jdk-bin, jdk11-jetbrains-imfix, jre-jetbrains, jdk11-graalvm-bin, jdk8-graalvm-bin, java-openjdk-loom-ea-bin, jdk-jetbrains, jdk8-adoptopenjdk, java-openjdk-ea-bin, jdk-openjdk, jdk11-openjdk, jdk7-openjdk, jdk8-openjdk) (make)
- libmariadbclient (libmysqlclient55, mariadb-libs-git, mariadb103-libs, libmysqlclient56, libmysqlclient57, libmysqlclient, mariadb-libs) (make)
- postgresql-libs (agensgraph-git, postgresql-libs-1c, postgresql-libs-10, postgresql-src-beta-libs, postgresql-libs-9.5, postgresql-libs-9.4, postgresql-src-libs, postgresql-libs-11, postgresql-lts-libs, postgresql-libs-12, postgresql-libs-9.6) (make)
- libmariadbclient (libmysqlclient55, mariadb-libs-git, mariadb103-libs, libmysqlclient56, libmysqlclient57, libmysqlclient, mariadb-libs) (optional)
- postgresql-libs (agensgraph-git, postgresql-libs-1c, postgresql-libs-10, postgresql-src-beta-libs, postgresql-libs-9.5, postgresql-libs-9.4, postgresql-src-libs, postgresql-libs-11, postgresql-lts-libs, postgresql-libs-12, postgresql-libs-9.6) (optional)
Latest Comments
1 2 3 Next › Last »
Rhinoceros commented on 2020-05-11 07:57
I feel like history is repeating itself, but…
Like the two previous commentators (from over two years ago now!), install failed because installation of
/usr/bin/wordcount
conflicts withtexlive-latexextra
. IMO there really shouldn't be conflicts with official packages, especially when it's something as common as this.I fixed it by just installing
/usr/bin/wordcount
under a different name:ironcyborg commented on 2020-02-10 14:35
The file conflict between this and 'texlive-latexextra' on '/usr/bin/wordcount' is unfortunately still present. Any suggestion?
anadon commented on 2018-04-30 22:24
There is a file conflict between this and 'texlive-latexextra' on '/usr/bin/wordcount' which needs to be addressed.
mschu commented on 2018-03-02 10:21
emboss now puts its .h files in /usr/include/emboss/*. This should solve all conflicting headers, and libs work on my machine.
anadon commented on 2018-02-28 18:29
@mschu Please merge in previous commenter's fixes for this package. But this doesn't fully fix the problem.
Rhinoceros commented on 2016-09-05 06:35
Like two previous commentators, install failed because installation of /usr/bin/showdb conflicts with sqlite. IMO there really shouldn't be conflicts with official packages, especially when it's something as common as sqlite.
I fixed it by just installing /usr/bin/showdb under a different name. IMO it shouldn't be in `/opt`, because there will still be problems with conflicting binaries in $PATH, although @antony's suggestion is not bad.
--- emboss.orig/PKGBUILD 2016-04-25 19:10:09.000000000 +1000
+++ emboss/PKGBUILD 2016-09-05 16:09:49.756095544 +1000
@@ -30,4 +30,5 @@
make DESTDIR="$pkgdir" install
rm -f "$pkgdir/usr/include/{pcre,pcreposix}.h"
+ mv "$pkgdir"/usr/bin/showdb{,-emboss}
}
slackalaxy commented on 2016-06-17 10:29
hobbypunk,
I maintain EMBOSS and EMBASSY for Slackware at SlackBuilds.org and I uploaded their sources to SF here:
https://sourceforge.net/projects/sboppetrov/files/EMBOSS/
The link you provided may not be active in the near future.
-Petar
anntzer commented on 2016-05-05 17:38
This currently conflicts with the widely used sqlite because of the presence of /usr/bin/showdb.
Because this package provides so many executables in /usr/bin, perhaps it would make sense to rename them as /usr/bin/emboss-*?
hobbypunk commented on 2015-12-09 22:53
please update the link to:
http://www.student.oulu.fi/~ppetrov/source/EMBOSS-6.6.0/EMBOSS-6.6.0.tar.gz
the md5sum is the same ;)
hobbypunk commented on 2015-10-21 19:57
Hey, there are 2 little problems with your PKGBUILD, the source is offline, here is one that works "http://science-annex.org/pub/emboss/" and you should switch from "/usr" to "/opt/emboss", without the showdb file conflicts with showdb from sqlite