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I wonder if it is a regression introduced by EMBOSS 6.0.0, where the BaseDirectory is used instead of the RootDirectory. When I build EMBOSS with AJAX_FIXED_ROOT=/usr/share/EMBOSS after configuring with --prefix=/usr, the Base and Root directories are set as follows:
anx178 ↱emboss↲$ embossversion --full
Reports the current EMBOSS version number
PackageName: EMBOSS
LibraryVersion: 6.1.0...
2009-11-06 05:58:27 UTC in EMBOSS Suite
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Hello,
from its version 1.12, the Staden io-lib is installed under the name ‘staden-read’ instead of ‘read’. The following patch allows SRF to be built against these versions.
Best regards,
--
Charles Plessy
Debian Med packaging team
http://www.debian.org/devel/debian-med
Tsurumi, Kanagawa, Japan.
2009-08-16 00:44:24 UTC in Sequence Read Format
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Dear EMBOSS developers,
The latest release contains the following file: ‘EMBOSS-6.1.0/doc/programs/text/frestdist.txt’. However, it is also contained in PHYLIPNEW-3.68 (although not in an identical version). This complicates slightly the packaging of PHYLIPNEW in Debian (I had to release a new version of the Debian emboss-doc package, in which frestdist.txt is deleted). Can you remove...
2009-08-04 12:17:42 UTC in EMBOSS Suite
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Dear EMBOSS developers,
install-jemboss-server.sh contains ‘read’ instructions that will fail if /bin/sh is an alternative POSIX-compliant shell such as ‘dash’. Bash will by default read into REPLY, so replacing ‘read’ by ‘read REPLY’ solves that issue.
In addition, the echo command does not always produce the same output on all shells. For this reason, the POSIX standard...
2009-06-13 02:52:09 UTC in EMBOSS Suite
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Here is an updated version of the patch. It also renames libread to libstaden-read, as discussed with James and the Fedora maintainer: http://lists.debian.org/debian-med/2008/09/msg00003.html
Have a nice day,
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Charles Plessy
Debian Med packaging team.
2009-05-27 02:06:03 UTC in Staden Package
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Hi Flávio
The following patch does two things:
a) it removes the encoding key, that is now obsolete.
b) it adds the categories MedicalSoftware (more relevant but less supported) and the Education (less relevant but at least one “Main” category must be supported).
You can find the specification there:
http://standards.freedesktop.org/menu-spec/latest/index.html
---...
2009-05-03 04:40:28 UTC in Epigrass
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Dear all,
I just read on a mailing list that the command `getconf LFS_CFLAGS' can be useful to solve the problem elegantly.
Have a nice day,
--
Charles Plessy.
2009-02-10 04:10:24 UTC in Mapping and Assembly with Qualities
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Dear Maq developers,
Ma1 0.7.1 has been packaged for Debian and our automatic build log parsers detected the following warnings:
Function `gzopen64' implicitly converted to pointer at fastq2bfq.c:30
Function `gzopen64' implicitly converted to pointer at maqmap_conv.c:57
Function `gzopen64' implicitly converted to pointer at simulate.c:83
Function `gzopen64' implicitly converted to...
2008-11-18 00:33:38 UTC in Mapping and Assembly with Qualities
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Dear maq developers,
The Debian Med project prepared an installation package for maq on the Debian operating system, which summary is at the following URL: http://packages.debian.org/sid/maq
We disabled the -m64 option with the below patch:
--- a/configure.ac
+++ b/configure.ac
@@ -23,10 +23,7 @@ case "${host_cpu}-${host_os}" in
AC_COMPILE_IFELSE([AC_LANG_PROGRAM]...
2008-11-16 13:39:09 UTC in Mapping and Assembly with Qualities
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Dear developpers,
recent versions of eprimer3 have new parameters such as divalent ion concentration (PRIMER_DIVALENT_CONC). Can you update eprimer3 to use them? Many thanks !
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Charles Plessy,
designing primers with eprimer3 this night.
2008-09-12 15:15:03 UTC in EMBOSS Suite
