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}
}
Search Criteria
Package Details: emboss 6.6.0-1
| Git Clone URL: | https://aur.archlinux.org/emboss.git (read-only) |
|---|---|
| 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: | 17 |
| Popularity: | 0.000017 |
| First Submitted: | 2008-12-28 12:20 |
| Last Updated: | 2016-04-25 09:10 |
Dependencies (5)
- gd (gd-headless)
- java-runtime (intellij-jdk, java-gcj-compat, jdk, jdk-arm, jdk-dcevm, jdk-devel, jdk5, jdk6, jdk7, jdk8, jdk8-j9-bin, jdk9-openj9-bin, jre, jre-devel, jre6, jre7, jre7-openjdk-infinality, jre8, jre8-openjdk-infinality, jre8-openjdk-jetbrains, jre8-openjdk-jetbrains-git, server-jre, tuxjdk, zulu-jdk, jre7-openjdk, jre8-openjdk, jre9-openjdk)
- pcre (pcre-svn)
- libmysqlclient (libmysqlclient55, mroonga, mysql51) (optional)
- postgresql-libs (agensgraph-git, postgresql-9.3, postgresql-9.4, postgresql-9.5, postgresql-beta-libs, postgresql-git, postgresql-lts-libs, postgresql-src-libs) (optional)
Required by (0)
Sources (1)
Latest Comments
Rhinoceros commented on 2016-09-05 06:35
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
anadon commented on 2013-10-17 17:17
The 6.5.7 package has moved to the old directory. The new one is located at this link:
ftp://emboss.open-bio.org/pub/EMBOSS/EMBOSS-6.6.0.tar.gz
mschu commented on 2013-09-03 09:26
I don't see why this should be out of date. Download fails, but the EMBOSS webpage still links the same version, so this is an upstream fault and not one of the package.
mschu commented on 2012-09-05 11:54
Updated.
Please do mark the package out-of-date if it is, so I can spot them right away in the package list.
Anonymous comment on 2012-09-05 08:14
There is a new version available:
pkgver=6.5.7
md5sums=('6a2cb3f93d5e9415c74ab0f6b1ede5f0')
But makepkg still fails with this error message:
configure: error: Java OS include directory /usr/lib/jvm/java-7-openjdk/include/linux does not exist
==> ERROR: A failure occurred in build().
Aborting...
mschu commented on 2012-06-29 16:48
Thank you for the message, install seems to have changed its location. Updated.