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Dimitri Maziuk  
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 More options Jul 16 2012, 8:09 pm
From: Dimitri Maziuk <dmitri.maz...@gmail.com>
Date: Mon, 16 Jul 2012 17:09:29 -0700 (PDT)
Local: Mon, Jul 16 2012 8:09 pm
Subject: centos 5.8 error

Hi everyone,

I've a setup that's been working for years that started failing after a
recent centos update:

fileparse(): need a valid pathname at /website/rmagic-2.21/rmagic.pl line 388

Anyone else seen this yet?

TIA
Dima


 
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Jeremy Wadsack  
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 More options Jul 26 2012, 9:01 pm
From: Jeremy Wadsack <jeremy.wads...@gmail.com>
Date: Thu, 26 Jul 2012 18:01:23 -0700
Local: Thurs, Jul 26 2012 9:01 pm
Subject: Re: centos 5.8 error

Dmitri -

fileparse is part of
File::Basename<http://perldoc.perl.org/File/Basename.html>,
so it's possible this changed with an update to that module in you perl
environment. The pathname it's complaining about the [statistics]
File_Inin your  rmagic.ini file. So first, double check that is still
valid and
hasn't changed. I don't see anything different in File::Basename
documentation than it was ten years ago. It's also possible that something
between the two (e.g. Config::IniFiles parses rmagic.ini) has changed and
is failing.

As a debug step I'd throw a print line in just above 388 in your rmagic.ini

print $statistics{File_In}

That should at least let you know if the path makes any sense to cent OS.

Jeremy Wadsack

On Mon, Jul 16, 2012 at 5:09 PM, Dimitri Maziuk <dmitri.maz...@gmail.com>wrote:


 
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Dimitri Maziuk  
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 More options Jul 27 2012, 1:09 pm
From: Dimitri Maziuk <dmaz...@bmrb.wisc.edu>
Date: Fri, 27 Jul 2012 12:09:58 -0500
Local: Fri, Jul 27 2012 1:09 pm
Subject: Re: [reportmagic-users] Re: centos 5.8 error

On 07/26/2012 08:01 PM, Jeremy Wadsack wrote:
...> Dmitri -

> As a debug step I'd throw a print line in just above 388 in your rmagic.ini

> print $statistics{File_In}

Hi Jeremy,

I actually did some poking since I posted that but I usually find my own
Perl hard to follow, with someone else's it's a non-starter.

Specifically, $statistics{File_In} is a null in line 388, and I'm not
sure I can figure out where it's initialized and to what.

> my @now = localtime;
> $now = (1900 + $now[5]) . '/' . (1 + $now[4]) . '/' . $now[3] . ' ' . $now[2] . ':' . $now[1];
> print "!!" . $statistics{File_In} . "\n";
> $statistics{File_In} =~ s/%([^%]+)%/$formatter->formatDate( $1, $now )/ge;
> my $infile;
> ($infile, undef, undef) = fileparse( $statistics{File_In}, '\..*' );

yields

> $ /website/rmagic-2.21/rmagic.pl /website/etc/analog/combined/ftp12.ini
> !!
> fileparse(): need a valid pathname at /website/rmagic-2.21/rmagic.pl line 390

The ini file has

> [statistics]
> File_In = /website/admin/logs/analog_output/ftp/ftp_2012.dat

(that hasn't been touched) and

> $ ls -l /website/admin/logs/analog_output/ftp/ftp_2012.dat
> -rw-rw-r-- 1 web stapdev 508177 Jul 22 00:01 /website/admin/logs/analog_output/ftp/ftp_2012.dat

("combined" reports are generated weekly, so 10pm last Friday timestamp
means analog part of it is still working fine.)

Where do I go from here?

Thanks,
--
Dimitri Maziuk
Programmer/sysadmin
BioMagResBank, UW-Madison -- http://www.bmrb.wisc.edu

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Jeremy Wadsack  
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 More options Jul 27 2012, 2:30 pm
From: Jeremy Wadsack <jeremy.wads...@gmail.com>
Date: Fri, 27 Jul 2012 11:30:54 -0700
Local: Fri, Jul 27 2012 2:30 pm
Subject: Re: [reportmagic-users] Re: centos 5.8 error

And it's not the best code I've every written either. ;) Honestly, I'm
having trouble following it too.

The $statistics hash is copied from a Config::IniFiles class. It should be
loading values from the ini file and mapping them. You could also try

    print $config{statistics}{File_In}

to debug the hash copy. Somehow I'm suspecting that it may be a problem in
Config::IniFiles. If this is also nul, can you check the version of the
library (perl -e 'Config::IniFiles::VERSION' should do it, I think)?

Jeremy Wadsack

On Fri, Jul 27, 2012 at 10:09 AM, Dimitri Maziuk <dmaz...@bmrb.wisc.edu>wrote:


 
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Dimitri Maziuk  
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 More options Jul 27 2012, 3:37 pm
From: Dimitri Maziuk <dmaz...@bmrb.wisc.edu>
Date: Fri, 27 Jul 2012 14:37:36 -0500
Local: Fri, Jul 27 2012 3:37 pm
Subject: Re: [reportmagic-users] Re: centos 5.8 error

On 07/27/2012 01:30 PM, Jeremy Wadsack wrote:
...

> The $statistics hash is copied from a Config::IniFiles class. It should be
> loading values from the ini file and mapping them. You could also try

>     print $config{statistics}{File_In}

> to debug the hash copy. Somehow I'm suspecting that it may be a problem in
> Config::IniFiles. If this is also nul, can you check the version of the
> library (perl -e 'Config::IniFiles::VERSION' should do it, I think)?

$ rpm -q perl-Config-IniFiles
perl-Config-IniFiles-2.72-1.el5

Here's the hash:

> use Data::Dumper;
> $Data::Dumper::Indent = 3;
> print Dumper(\%config);
> print "\n";
> print "!!" . $statistics{File_In} . "\n";
> $statistics{File_In} =~ s/%([^%]+)%/$formatter->formatDate( $1, $now )/ge;
> my $infile;
> ($infile, undef, undef) = fileparse( $statistics{File_In}, '\..*' );

output:

--
Dimitri Maziuk
Programmer/sysadmin
BioMagResBank, UW-Madison -- http://www.bmrb.wisc.edu

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Jeremy Wadsack  
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 More options Jul 27 2012, 4:30 pm
From: Jeremy Wadsack <jeremy.wads...@gmail.com>
Date: Fri, 27 Jul 2012 13:30:53 -0700
Local: Fri, Jul 27 2012 4:30 pm
Subject: Re: [reportmagic-users] Re: centos 5.8 error

Yeah. For whatever reason, %config doesn't have any of the loaded data from
the language files or your settings. So I'm pretty certain that it's an
issue with Config::IniFiles.

Shlomi Fish was been maintaining that module for years now, and it's currently
at 2.77 <http://sourceforge.net/projects/config-inifiles/>. The last
version I installed that I know is working is 2.39. That's a lot of
variance.

Can you determine if that was recently updated? That would help decide if
we should look there.

Jeremy Wadsack

On Fri, Jul 27, 2012 at 12:37 PM, Dimitri Maziuk <dmaz...@bmrb.wisc.edu>wrote:


 
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Dimitri Maziuk  
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 More options Jul 27 2012, 4:38 pm
From: Dimitri Maziuk <dmaz...@bmrb.wisc.edu>
Date: Fri, 27 Jul 2012 15:38:53 -0500
Local: Fri, Jul 27 2012 4:38 pm
Subject: Re: [reportmagic-users] Re: centos 5.8 error

On 07/27/2012 03:30 PM, Jeremy Wadsack wrote:

[ Config::IniFiles. ]

> Can you determine if that was recently updated? That would help decide if
> we should look there.

Yep. According to yum.log
  Jun 10 16:34:15 Updated: perl-Config-IniFiles-2.72-1.el5.noarch
which is about when it broke.

--
Dimitri Maziuk
Programmer/sysadmin
BioMagResBank, UW-Madison -- http://www.bmrb.wisc.edu

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Jeremy Wadsack  
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 More options Jul 27 2012, 4:49 pm
From: Jeremy Wadsack <jeremy.wads...@gmail.com>
Date: Fri, 27 Jul 2012 13:49:10 -0700
Local: Fri, Jul 27 2012 4:49 pm
Subject: Re: [reportmagic-users] Re: centos 5.8 error

Which fixes "insecure temporary file usage":
https://lists.fedoraproject.org/pipermail/epel-package-announce/2012-...

I'm not having much luck digging through the fedora build logs to see what
the diff was for that patch. Maybe you know it better? I'm guessing that
patching the temporary file usage broke something that reportmagic uses
that doesn't have a corresponding test case in Config::IniFiles.

Jeremy Wadsack

On Fri, Jul 27, 2012 at 1:38 PM, Dimitri Maziuk <dmaz...@bmrb.wisc.edu>wrote:


 
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Dimitri Maziuk  
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 More options Jul 27 2012, 4:57 pm
From: Dimitri Maziuk <dmaz...@bmrb.wisc.edu>
Date: Fri, 27 Jul 2012 15:57:52 -0500
Local: Fri, Jul 27 2012 4:57 pm
Subject: Re: [reportmagic-users] Re: centos 5.8 error

On 07/27/2012 03:49 PM, Jeremy Wadsack wrote:

> Which fixes "insecure temporary file usage":
> https://lists.fedoraproject.org/pipermail/epel-package-announce/2012-...

> I'm not having much luck digging through the fedora build logs to see what
> the diff was for that patch. Maybe you know it better? I'm guessing that
> patching the temporary file usage broke something that reportmagic uses
> that doesn't have a corresponding test case in Config::IniFiles.

I can't even see where rmagic.pl reads its argv[1] into ini hash... :(

Perhaps something in the upstream changelog since 2.72? I can file a bug
report against centos rpm, but having more details than just "broke
report magic" would be useful.

--
Dimitri Maziuk
Programmer/sysadmin
BioMagResBank, UW-Madison -- http://www.bmrb.wisc.edu

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Jeremy Wadsack  
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 More options Jul 27 2012, 5:18 pm
From: Jeremy Wadsack <jeremy.wads...@gmail.com>
Date: Fri, 27 Jul 2012 14:18:55 -0700
Local: Fri, Jul 27 2012 5:18 pm
Subject: Re: [reportmagic-users] Re: centos 5.8 error

Oh, I agree that "breaks something in reportmagic" is a terrible bug
report. That's why I was looking for the changelog/diff for that update to
see if that could pin it down.

As to where rmagic read ars[1], that's complicated. In
wadg::rm::Settings<https://github.com/jeremywadsack/reportmagic/blob/master/wadg/rm/Sett...>it
read the whole command line around line 79 and assigns anything that
doesn't start with '-' to a list of filenames. Around line 118 it iterates
through the list until it finds one that Config::IniFiles can parse.

Note that if no arguments are given it looks for 'rmagic.ini' in the curent
folder and then in the script's folder (lines 89-108).

BTW, all that traces from line 230 in rmagic.pl.

Does that help any?

Jeremy Wadsack

On Fri, Jul 27, 2012 at 1:57 PM, Dimitri Maziuk <dmaz...@bmrb.wisc.edu>wrote:


 
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Dimitri Maziuk  
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 More options Jul 27 2012, 5:38 pm
From: Dimitri Maziuk <dmaz...@bmrb.wisc.edu>
Date: Fri, 27 Jul 2012 16:38:01 -0500
Local: Fri, Jul 27 2012 5:38 pm
Subject: Re: [reportmagic-users] Re: centos 5.8 error

On 07/27/2012 04:18 PM, Jeremy Wadsack wrote:
..

> As to where rmagic read ars[1], that's complicated. In
> wadg::rm::Settings<https://github.com/jeremywadsack/reportmagic/blob/master/wadg/rm/Sett...>it
> read the whole command line around line 79 and assigns anything that
> doesn't start with '-' to a list of filenames. Around line 118 it iterates
> through the list until it finds one that Config::IniFiles can parse.
...
> Does that help any?

Not really: I can add more dumps (Settings.pm):

> use Data::Dumper;
> $Data::Dumper::Indent = 3;
>         while( @filenames ) {
>                 $parms{-file} = shift @filenames;
> print "\n1\n";
> print Dumper( \%parms );
>                 my %hash;
>                 tie %hash, 'Config::IniFiles', ( %parms ) ;
> print "\n2\n";
> print Dumper( \%hash );

and get this:

but I don't understand what it means. I thought "tie" was supposed to
intialize %hash to contents of /website/etc/analog/combined/ftp12.ini,
but clearly I thought wrong... like I said, my Perl sucks.

--
Dimitri Maziuk
Programmer/sysadmin
BioMagResBank, UW-Madison -- http://www.bmrb.wisc.edu

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Jeremy Wadsack  
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 More options Jul 27 2012, 6:05 pm
From: Jeremy Wadsack <jeremy.wads...@gmail.com>
Date: Fri, 27 Jul 2012 15:05:30 -0700
Local: Fri, Jul 27 2012 6:05 pm
Subject: Re: [reportmagic-users] Re: centos 5.8 error

Your Perl is right. (And I'm trying very hard not to write ruby in my
examples back.) It should bind the contents of the file to the hash.

The output is interesting though, because it clearly means that it *is* getting
some of the contents of the file. Each section in the ini file (e.g.
[statistics], [reports], etc.) is being loaded as a key in the hash. What
it's not getting is the settings below that.

I wonder if you can just test Config::IniFiles directly against that file
in a separate perl script.

use Config::IniFiles;
my $cfg = Config::IniFiles->new( -file => "/website/etc/analog/combined/
ftp12.ini" );
print "The source is " . $cfg->val( 'settings', 'File_In' );

tie %hash, 'Config::IniFiles', ( -file => "/website/etc/analog/combined/
ftp12.ini" ) ;
print "The source is " . $hash{settings}{File_In};

Jeremy Wadsack

On Fri, Jul 27, 2012 at 2:38 PM, Dimitri Maziuk <dmaz...@bmrb.wisc.edu>wrote:


 
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Dimitri Maziuk  
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 More options Jul 27 2012, 6:40 pm
From: Dimitri Maziuk <dmaz...@bmrb.wisc.edu>
Date: Fri, 27 Jul 2012 17:40:09 -0500
Local: Fri, Jul 27 2012 6:40 pm
Subject: Re: [reportmagic-users] Re: centos 5.8 error

On 07/27/2012 05:05 PM, Jeremy Wadsack wrote:

> I wonder if you can just test Config::IniFiles directly against that file
> in a separate perl script.

Should've thought of that... it works except it's
$hash{statistics}{File_In}. Well, it sort of works because

my $cfg = Config::IniFiles->new( -file =>
"/website/etc/analog/combined/ftp12.ini" );
print Dumper($cfg);

prints the whole thing whereas

tie %hash, 'Config::IniFiles', ( -file =>
"/website/etc/analog/combined/ftp12.ini" ) ;
print Dumper(\%hash);

only prints section names which I really don't get but whatever -- it
does get the filename, QED.

FWIW, if I add around line 259

print "+ " . $config{statistics}{File_In} . "\n";
%statistics = %{$config{statistics}};
print "++ " . $statistics{File_In} . "\n";

I get

+ sample.dat
++

So how exactly is '%' supposed to work in this excuse for a programming
language?

--
Dimitri Maziuk
Programmer/sysadmin
BioMagResBank, UW-Madison -- http://www.bmrb.wisc.edu

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Dimitri Maziuk  
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 More options Jul 27 2012, 6:57 pm
From: Dimitri Maziuk <dmaz...@bmrb.wisc.edu>
Date: Fri, 27 Jul 2012 17:57:39 -0500
Local: Fri, Jul 27 2012 6:57 pm
Subject: Re: [reportmagic-users] Re: centos 5.8 error

Well duh. Proper output from rmagic.pl, with the right parameter, is

1
$VAR1 = {
          '-file' => './rmagic.pl',
          '-default' => 'reports'
        };

2
$VAR1 = {};

1
$VAR1 = {
          '-file' => './rmagic.sample',
          '-default' => 'reports'
        };

2
$VAR1 = {
          'statistics' => {},
          'reports' => {},
          'QUICK' => {},
          'graphs' => {},
          'navigation' => {},
          'website' => {}
        };
+ /website/admin/logs/analog_output/ftp/ftp_2012.dat
++

The 1 and 2 dumps are coming from Settings.pm (line 118) and for some
reason they're dumped twice.

So it is getting the filename all right, it's just not maling it past
%statistics = %{$config{statistics}};

--
Dimitri Maziuk
Programmer/sysadmin
BioMagResBank, UW-Madison -- http://www.bmrb.wisc.edu

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Jeremy Wadsack  
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 More options Jul 27 2012, 7:08 pm
From: Jeremy Wadsack <jeremy.wads...@gmail.com>
Date: Fri, 27 Jul 2012 16:08:54 -0700
Local: Fri, Jul 27 2012 7:08 pm
Subject: Re: [reportmagic-users] Re: centos 5.8 error

Ah, so it's failing in the hash copy.

The reason Settings gets called twice is that it's looking for a default
file because (I think) none was given on the command-line. So it's trying
several options. It bails immediately on 'rmagic.pl' because it knows
that's the program itself and then goes to the next matching file.

I actually don't recall how %{} works in terms of coercing something into a
hash. It also may have changed since I last was really good at Perl. The
thing is, %config isn't *really* a hash, it's a module that's tied to a
hash to make it act like one. So the reason Dump only shows the first
elements (and not the contained hash elements) I think is related to that.

Still I think that `%statistics = %{$config{statistics}};` should work.
Especially since it has worked for at least 10 years or more. Perl 5.x
hasn't changed that much.

If you dump $config{statistics} from rmagic.pl does that iterate the hash
members? It seems that something between the tie and the hash copy is
failing.

Jeremy Wadsack

On Fri, Jul 27, 2012 at 3:57 PM, Dimitri Maziuk <dmaz...@bmrb.wisc.edu>wrote:


 
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Dimitri Maziuk  
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 More options Jul 30 2012, 1:14 pm
From: Dimitri Maziuk <dmaz...@bmrb.wisc.edu>
Date: Mon, 30 Jul 2012 12:14:44 -0500
Local: Mon, Jul 30 2012 1:14 pm
Subject: Re: [reportmagic-users] Re: centos 5.8 error

On 07/27/2012 06:08 PM, Jeremy Wadsack wrote:

> Ah, so it's failing in the hash copy.

> The reason Settings gets called twice is that it's looking for a default
> file because (I think) none was given on the command-line.

Right. It was Friday afternoon, that's my excuse.

> I actually don't recall how %{} works in terms of coercing something into a
> hash. It also may have changed since I last was really good at Perl. The
> thing is, %config isn't *really* a hash, it's a module that's tied to a
> hash to make it act like one.

So I wonder if something inside IniFiles object changed in or around
2.72 to make it not quite work as a hash.

> Still I think that `%statistics = %{$config{statistics}};` should work.

Here's the test case:

> use Config::IniFiles;
> use Data::Dumper;
> $Data::Dumper::Indent = 3;
> tie %hash, 'Config::IniFiles', ( -file => "/website/etc/analog/combined/ftp12.ini" ) ;
> print Dumper(\%hash);
> print "The source is " . $hash{statistics}{File_In};
> print "\n========================================\n";
> %copy = %{ $hash{ statistics } };
> print "The copy is " . $copy{File_In};
> print "\n========================================\n";

and the output:

> $ ./simple.pl
> $VAR1 = {
>           'statistics' => {},
>           'navigation' => {},
>           'reports' => {},
>           'DIRECTORY' => {},
>           'QUICK' => {},
>           'graphs' => {},
>           'website' => {}
>         };
> The source is /website/admin/logs/analog_output/ftp/ftp_2012.dat
> ========================================
> Use of uninitialized value in concatenation (.) or string at ./simple.pl line 28.
> The copy is
> ========================================

Looks like a heisenbug to me: worked until I looked at it.

--
Dimitri Maziuk
Programmer/sysadmin
BioMagResBank, UW-Madison -- http://www.bmrb.wisc.edu

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Dimitri Maziuk  
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 More options Aug 2 2012, 1:09 pm
From: Dimitri Maziuk <dmaz...@bmrb.wisc.edu>
Date: Thu, 02 Aug 2012 12:09:09 -0500
Local: Thurs, Aug 2 2012 1:09 pm
Subject: Re: [reportmagic-users] Re: centos 5.8 error

FYI: the fix is slated for the next epel update.

According to RedHat that version of Config::IniFiles requires (but did
not explicitly Require at RPM level) a newer List::MoreUtils (0.33+) to
function properly.

(https://bugzilla.redhat.com/show_bug.cgi?id=844460)

Thanks Jeremy,
--
Dimitri Maziuk
Programmer/sysadmin
BioMagResBank, UW-Madison -- http://www.bmrb.wisc.edu

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Jeremy Wadsack  
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 More options Aug 2 2012, 3:07 pm
From: Jeremy Wadsack <jeremy.wads...@gmail.com>
Date: Thu, 2 Aug 2012 12:07:31 -0700
Local: Thurs, Aug 2 2012 3:07 pm
Subject: Re: [reportmagic-users] Re: centos 5.8 error

Thanks for following up on that, Dmitri!

Jeremy Wadsack

On Thu, Aug 2, 2012 at 10:09 AM, Dimitri Maziuk <dmaz...@bmrb.wisc.edu>wrote:


 
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 More options Aug 5 2012, 5:49 pm
From: Dimitri Maziuk <dmaz...@bmrb.wisc.edu>
Date: Sun, 05 Aug 2012 16:49:25 -0500
Local: Sun, Aug 5 2012 5:49 pm
Subject: Re: [reportmagic-users] Re: centos 5.8 error

On 08/02/2012 02:07 PM, Jeremy Wadsack wrote:

> Thanks for following up on that, Dmitri!

I got the updates from epel-testing and re-run our reports & it's
confirmed fixed (perl-List-MoreUtils-0.33-5 and
perl-Config-IniFiles-2.72-2).

--
Dimitri Maziuk
Programmer/sysadmin
BioMagResBank, UW-Madison -- http://www.bmrb.wisc.edu

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