Your message dated Fri, 02 Mar 2012 15:32:25 +0000
with message-id <[email protected]>
and subject line Bug#661793: fixed in bioperl 1.6.901-3
has caused the Debian Bug report #661793,
regarding bioperl: Error in berkeleydb3.pm while creating Temp file
to be marked as done.
This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.
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--
661793: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=661793
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Package: bioperl
Version: 1.6.901-2
Severity: important
Tags: upstream
When using bp_seqfeature_load.pl I have an error at build_summary_statistics
call time of berkeleydb3.pm:
Couldn't create temporary file for sorting: Inappropriate ioctl for device
It occurs in berkeleydb3.pm line 500
Looking at the code I tried to manipulate it replacing
my $s = tie %sort,'DB_File',$name,0666,O_CREAT|O_RDWR,$numeric_cmp
by
my $s = tie %sort,'DB_File',$name,O_CREAT|O_RDWR,0666,$numeric_cmp
and the error disappear.
I used below sample code to test:
require File::Temp;
use File::Temp ();
use File::Temp qw/ :seekable /;
use base 'Bio::DB::SeqFeature::Store::berkeleydb';
use DB_File;
use Fcntl qw(O_RDWR O_CREAT :flock);
my $fh = File::Temp->new() or die("Couldn't create temporary file for
sorting: $!");
my $name = $fh->filename;
my %sort;
my $numeric_cmp = DB_File::BTREEINFO->new;
$numeric_cmp->{compare} = sub { $_[0] <=> $_[1] };
$numeric_cmp->{flags} = R_DUP;
my $s = tie %sort,'DB_File',$name,0666,O_CREAT|O_RDWR,$numeric_cmp
#my $s = tie %sort,'DB_File',$name,O_CREAT|O_RDWR,0666,$numeric_cmp
or die("Couldn't create temporary file for sorting: $!");
However the same code works fine on a Red Hat on an other system (not same perl
version).
So I do not know if my fix is a correct fix, it just make the error disappear.
If I look at perldoc for DB_File I see examples like:
tie %A, "DB_File", "filename", O_CREAT|O_RDWR, 0666, $DB_HASH ;
so it seems that 0666 should be set after O_CREAT....
-- System Information:
Debian Release: wheezy/sid
APT prefers unstable
APT policy: (500, 'unstable'), (500, 'stable')
Architecture: amd64 (x86_64)
Kernel: Linux 2.6.32-5-amd64 (SMP w/1 CPU core)
Locale: LANG=en_US.UTF-8, LC_CTYPE=en_US.UTF-8 (charmap=UTF-8)
Shell: /bin/sh linked to /bin/dash
Versions of packages bioperl depends on:
ii libbio-perl-perl 1.6.901-2 BioPerl core perl modules
ii perl 5.14.2-7 Larry Wall's Practical Extraction
Versions of packages bioperl recommends:
ii bioperl-run 1.6.9-1 BioPerl wrappers: scripts
ii libace-perl 1.92-2+b2 Object-Oriented Access to ACEDB Da
ii libapache-dbi-perl 1.11-1 interface connecting apache server
ii libbio-perl-run-perl 1.6.9-1 BioPerl wrappers: modules
ii libcache-cache-perl 1.06-2 Managed caches of persistent infor
ii libdbi-perl 1.618-1 Perl Database Interface (DBI)
ii libgd-gd2-perl 1:2.46-3+b1 Perl module wrapper for libgd - gd
ii libhttp-message-perl 6.03-1 perl interface to HTTP style messa
ii liblist-moreutils-perl 0.33-1+b1 Perl module with additional list f
ii libset-scalar-perl 1.25-1 Perl interface for operations on f
ii liburi-perl 1.59-1 module to manipulate and access UR
ii libwww-perl 6.01-3 simple and consistent interface to
ii libxml-simple-perl 2.18-3 Perl module for reading and writin
ii libxml-twig-perl 1:3.39-1 Perl module for processing huge XM
ii libyaml-perl 0.80-1 YAML Ain't Markup Language
ii perl-doc 5.14.2-7 Perl documentation
Versions of packages bioperl suggests:
ii groff-base 1.21-6 GNU troff text-formatting system (
-- no debconf information
--- End Message ---
--- Begin Message ---
Source: bioperl
Source-Version: 1.6.901-3
We believe that the bug you reported is fixed in the latest version of
bioperl, which is due to be installed in the Debian FTP archive:
bioperl_1.6.901-3.debian.tar.gz
to main/b/bioperl/bioperl_1.6.901-3.debian.tar.gz
bioperl_1.6.901-3.dsc
to main/b/bioperl/bioperl_1.6.901-3.dsc
bioperl_1.6.901-3_all.deb
to main/b/bioperl/bioperl_1.6.901-3_all.deb
libbio-perl-perl_1.6.901-3_all.deb
to main/b/bioperl/libbio-perl-perl_1.6.901-3_all.deb
A summary of the changes between this version and the previous one is
attached.
Thank you for reporting the bug, which will now be closed. If you
have further comments please address them to [email protected],
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Olivier Sallou <[email protected]> (supplier of updated bioperl package)
(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing [email protected])
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA256
Format: 1.8
Date: Fri, 02 Mar 2012 11:10:36 +0100
Source: bioperl
Binary: bioperl libbio-perl-perl
Architecture: source all
Version: 1.6.901-3
Distribution: unstable
Urgency: low
Maintainer: Debian Med Packaging Team
<[email protected]>
Changed-By: Olivier Sallou <[email protected]>
Description:
bioperl - Perl tools for computational molecular biology
libbio-perl-perl - BioPerl core perl modules
Closes: 661793
Changes:
bioperl (1.6.901-3) unstable; urgency=low
.
* Team upload.
[ Olivier Sallou ]
+ add patch fix_berkeleydb3_temp_file_creation (Closes: #661793).
Fixed upstream for next release.
* debian/control: update Standards version
* debian/copyright: update Format to latest officiel URL v1.0
* debian/patches/fix_examples_perl_location: fix wrong perl location
* debian/rules: fix file access rights in dh_install
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Files:
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bioperl_1.6.901-3.debian.tar.gz
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