[Debian-med-packaging] Bug#661793: bioperl: Error in berkeleydb3.pm while creating Temp file
Olivier Sallou
olivier.sallou at irisa.fr
Fri Mar 2 08:28:06 UTC 2012
Le 3/3/12 12:04 AM, Florent Angly a écrit :
> Hi Olivier,
>
> Do you have an simple example that reproduces this error?
I have put a sample script extracted from berkeleydb3.pm to reproduce
the error in the bug
>
> The syntax for tying to a DB_File is, according to `perldoc DB_File`:
>> [$X =] tie %hash, 'DB_File', [$filename, $flags, $mode, $DB_HASH] ;
>> [$X =] tie %hash, 'DB_File', $filename, $flags, $mode, $DB_BTREE ;
> So, the order of the parameters is important and you cannot simply
> interchange them.
I don't, it is upstream.... ;-)
In the perldoc
(http://perldoc.perl.org/DB_File.html#Using-DB_File-with-Berkeley-DB-version-2-or-greater)
examples there is:
tie
<http://perldoc.perl.org/functions/tie.html>%h,"DB_File","tree",O_RDWR|O_CREAT,0666,$DB_BTREE
while in the berkeleydb3.pm there is
tie %sort,'DB_File',$name,0666,O_CREAT|O_RDWR,$numeric_cmp
In the patch I propose, I set "O_RDWR|O_CREAT, 0666" instead of "0666,O_CREAT|O_RDWR".
Si it is upstream that put parameters in the wrong order.
Though it works in a previous perl on a Reat Hat system I tested.
>
> The Perl module in question is at
> https://github.com/bioperl/bioperl-live/blob/master/Bio/DB/SeqFeature/Store/berkeleydb3.pm.
> The calling script has created and opened a temporary file and it is
> trying to put a Berkeley database in this temporary file. This
> Berkeley DB creation step fails. I suspect that it may be a permission
> problem... Does the mode 0644 solve the problem? Is there enough space
> on the disk?
>
> Running the script as follows will help diagnostic what went wrong:
>> perl -d `which bp_seqfeature_load.pl` [options]
> Then press 'c' and send the entire backtrace of the crash when it
> happens.
There is no crash, the error is raised and script ends.
>
> Best,
>
> Florent
>
>
>
>
> On 01/03/12 20:23, Olivier Sallou wrote:
>> 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
>>
>>
>>
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>
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--
Olivier Sallou
IRISA / University of Rennes 1
Campus de Beaulieu, 35000 RENNES - FRANCE
Tel: 02.99.84.71.95
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