arthurg has asked for the wisdom of the Perl Monks concerning the following question:

Some code stopped working 1.5 days ago, and we're unsure why. I have full, daily backups, so I could restore from them, but I'd really like to know what's happened. First, I cannot locate any changes that would account for the problem. e.g., 'find' doesn't seem to identify significant file changes in the last 5 days: 

$ find  /var/www/cgi-bin/vpweb2/VirtualPlant /usr/lib64/perl5/site_per
+l/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/site_perl/5.8.8 /usr
+/lib/perl5/site_perl /usr/lib64/perl5/vendor_perl/5.8.8/x86_64-linux-
+thread-multi /usr/lib/perl5/vendor_perl/5.8.8 /usr/lib/perl5/vendor_p
+erl /usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/5
+.8.8 -mtime -5
/var/www/cgi-bin/vpweb2/VirtualPlant/Analysis
/usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi/perllocal.pod
/usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi/auto/CPAN/.packlist
/usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi/auto/Test/Harness/.pa
+cklist
/usr/lib/perl5/5.8.8
/usr/lib/perl5/5.8.8/CPAN
/usr/lib/perl5/5.8.8/Test

[download]

(I reinstalled Test::Harness, as CPAN was reporting an old version.)

We use perl_mod and Apache; perl loaded by Apache has started reporting: 

[Mon Dec 07 11:41:51 2009] [error] [client 128.122.61.181] failed to r
+esolve handler `virtualplantCGI': Weak references are not implemented
+ in the version of perl at /usr/lib/perl5/site_perl/5.8.8/Graph/Easy/
+Group.pm line 10
BEGIN failed--compilation aborted at /usr/lib/perl5/site_perl/5.8.8/Gr
+aph/Easy/Group.pm line 10.
Compilation failed in require at /usr/lib/perl5/site_perl/5.8.8/Graph/
+Easy.pm line 12.
BEGIN failed--compilation aborted at /usr/lib/perl5/site_perl/5.8.8/Gr
+aph/Easy.pm line 12.
Compilation failed in require at /var/www/cgi-bin/vpweb2/VirtualPlant/
+Analysis/Cytoscape.pm line 348.
BEGIN failed--compilation aborted at /var/www/cgi-bin/vpweb2/VirtualPl
+ant/Analysis/Cytoscape.pm line 348.
Compilation failed in require at /var/www/cgi-bin/vpweb2/Includes.pm l
+ine 25.
BEGIN failed--compilation aborted at /var/www/cgi-bin/vpweb2/Includes.
+pm line 25.
Compilation failed in require at ...

[download]

In addition, CPAN has stopped working. Even installing it by hand fails: 


[49 root@xxx:~/Downloads/CPAN-1.9402]$ perl Makefile.PL 
Importing PAUSE public key into your GnuPG keychain... done!
(You may wish to trust it locally with 'gpg --lsign-key 450F89EC')
WARNING: SIGN is not a known parameter.
Checking if your kit is complete...
Looks good
'SIGN' is not a known MakeMaker parameter name.
Writing Makefile for CPAN

[download]


[50 root@xxx:~/Downloads/CPAN-1.9402]$ make test
cp lib/CPAN.pm blib/lib/CPAN.pm
cp lib/CPAN/CacheMgr.pm blib/lib/CPAN/CacheMgr.pm
cp lib/CPAN/FTP/netrc.pm blib/lib/CPAN/FTP/netrc.pm
cp lib/CPAN/LWP/UserAgent.pm blib/lib/CPAN/LWP/UserAgent.pm
cp lib/CPAN/FTP.pm blib/lib/CPAN/FTP.pm
cp lib/CPAN/Queue.pm blib/lib/CPAN/Queue.pm
cp lib/CPAN/Distroprefs.pm blib/lib/CPAN/Distroprefs.pm
cp lib/CPAN/Kwalify/distroprefs.yml blib/lib/CPAN/Kwalify/distroprefs.
+yml
cp lib/CPAN/Kwalify.pm blib/lib/CPAN/Kwalify.pm
cp lib/CPAN/Module.pm blib/lib/CPAN/Module.pm
cp lib/CPAN/Author.pm blib/lib/CPAN/Author.pm
cp lib/CPAN/Debug.pm blib/lib/CPAN/Debug.pm
cp lib/CPAN/API/HOWTO.pod blib/lib/CPAN/API/HOWTO.pod
cp lib/CPAN/Complete.pm blib/lib/CPAN/Complete.pm
cp lib/CPAN/FirstTime.pm blib/lib/CPAN/FirstTime.pm
cp lib/CPAN/Exception/blocked_urllist.pm blib/lib/CPAN/Exception/block
+ed_urllist.pm
cp lib/CPAN/Distrostatus.pm blib/lib/CPAN/Distrostatus.pm
cp lib/CPAN/Prompt.pm blib/lib/CPAN/Prompt.pm
cp lib/CPAN/Tarzip.pm blib/lib/CPAN/Tarzip.pm
cp lib/CPAN/Admin.pm blib/lib/CPAN/Admin.pm
cp lib/CPAN/URL.pm blib/lib/CPAN/URL.pm
cp lib/CPAN/Version.pm blib/lib/CPAN/Version.pm
cp lib/CPAN/DeferredCode.pm blib/lib/CPAN/DeferredCode.pm
cp lib/CPAN/Distribution.pm blib/lib/CPAN/Distribution.pm
cp lib/CPAN/Nox.pm blib/lib/CPAN/Nox.pm
cp lib/CPAN/Exception/RecursiveDependency.pm blib/lib/CPAN/Exception/R
+ecursiveDependency.pm
cp lib/CPAN/Bundle.pm blib/lib/CPAN/Bundle.pm
cp lib/CPAN/Shell.pm blib/lib/CPAN/Shell.pm
cp lib/CPAN/InfoObj.pm blib/lib/CPAN/InfoObj.pm
cp lib/CPAN/HandleConfig.pm blib/lib/CPAN/HandleConfig.pm
cp lib/CPAN/Exception/yaml_not_installed.pm blib/lib/CPAN/Exception/ya
+ml_not_installed.pm
cp lib/CPAN/Index.pm blib/lib/CPAN/Index.pm
cp lib/CPAN/Kwalify/distroprefs.dd blib/lib/CPAN/Kwalify/distroprefs.d
+d
cp scripts/cpan blib/script/cpan
/usr/bin/perl "-MExtUtils::MY" -e "MY->fixin(shift)" blib/script/cpan
PERL_DL_NONLAZY=1 /usr/bin/perl "-MExtUtils::Command::MM" "-e" "test_h
+arness(0, 'blib/lib', 'blib/arch')" t/*.t
t/00signature.t ........ skipped: No Module::Signature found [INC = /r
+oot/Downloads/CPAN-1.9402/blib/lib /root/Downloads/CPAN-1.9402/blib/a
+rch /usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi /usr/l
+ib/perl5/site_perl/5.8.8 /usr/lib/perl5/site_perl /usr/lib64/perl5/ve
+ndor_perl/5.8.8/x86_64-linux-thread-multi /usr/lib/perl5/vendor_perl/
+5.8.8 /usr/lib/perl5/vendor_perl /usr/lib64/perl5/5.8.8/x86_64-linux-
+thread-multi /usr/lib/perl5/5.8.8 .]
t/01loadme.t ........... ok   
t/02nox.t .............. ok   
t/03pkgs.t ............. ok     
t/04clean_load.t ....... ok     
t/10version.t .......... ok     
t/11mirroredby.t ....... ok   
t/12cpan.t ............. 1/28 Use of uninitialized value in concatenat
+ion (.) or string at /usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi
+/Scalar/Util.pm line 30.

gzip: /root/Downloads/CPAN-1.9402/t/CPAN/authors/01mailrc.txt: not in 
+gzip format
Use of uninitialized value in concatenation (.) or string at /usr/lib6
+4/perl5/5.8.8/x86_64-linux-thread-multi/Scalar/Util.pm line 30.

gzip: /root/Downloads/CPAN-1.9402/t/CPAN/modules/02packages.details.tx
+t: not in gzip format
Use of uninitialized value in concatenation (.) or string at /usr/lib6
+4/perl5/5.8.8/x86_64-linux-thread-multi/Scalar/Util.pm line 30.

gzip: /root/Downloads/CPAN-1.9402/t/CPAN/modules/03modlist.data: not i
+n gzip format
t/12cpan.t ............. ok     
t/13tarzip.t ........... Use of uninitialized value in concatenation (
+.) or string at /usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi/Scal
+ar/Util.pm line 30.
Undefined subroutine &Compress::Zlib::gzopen called at /root/Downloads
+/CPAN-1.9402/blib/lib/CPAN/Tarzip.pm line 122.
# Looks like your test died before it could output anything.
t/13tarzip.t ........... Dubious, test returned 255 (wstat 65280, 0xff
+00)
Failed 1/1 subtests 
t/14forkbomb.t ......... skipped: test only run when called with --doi
+t
t/30shell.t ............ skipped: no Expect, maybe try env CPAN_RUN_SH
+ELL_TEST_WITHOUT_EXPECT=1
t/31sessions.t ......... Use of uninitialized value in concatenation (
+.) or string at /usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi/Scal
+ar/Util.pm line 30, <DATA> line 579.

...

[download]

<code>

Replies are listed 'Best First'.
Re: CPAN and "Weak references"
by almut (Canon) on Dec 07, 2009 at 20:10 UTC
    Weak references are not implemented in the version of perl

    Usually, this has to do with the XS component of Scalar::Util not being found (in which case weaken() is not available): 

    $ perl -MScalar::Util=weaken -e'weaken(\my $var)'

$ sudo mv /usr/lib/perl5/5.8.8/x86_64-linux-thread-multi/auto/List/Uti
+l/Util.so /usr/lib/perl5/5.8.8/x86_64-linux-thread-multi/auto/List/Ut
+il/Util.so_hide

$ perl -MScalar::Util=weaken -e'weaken(\my $var)'
Weak references are not implemented in the version of perl at -e line 
+0
BEGIN failed--compilation aborted.

    [download]
[reply]
[d/l]
[select]
      Thanks Almut, but that doesn't seem to be the case; auto/List/Util/Util.so is in an element of @INC: 
      $ perl -MScalar::Util=weaken -e'weaken(\my $var)'
Weak references are not implemented in the version of perl at -e line 
+0
BEGIN failed--compilation aborted.

      [download]
      $ locate Util.so
/usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi/auto/List/Util/Util.s
+o
/usr/lib64/perl5/vendor_perl/5.8.8/x86_64-linux-thread-multi/auto/APR/
+Util/Util.so
/usr/lib64/perl5/vendor_perl/5.8.8/x86_64-linux-thread-multi/auto/Apac
+he2/ConnectionUtil/ConnectionUtil.so
/usr/lib64/perl5/vendor_perl/5.8.8/x86_64-linux-thread-multi/auto/Apac
+he2/RequestUtil/RequestUtil.so
/usr/lib64/perl5/vendor_perl/5.8.8/x86_64-linux-thread-multi/auto/Apac
+he2/ServerUtil/ServerUtil.so
/usr/lib64/perl5/vendor_perl/5.8.8/x86_64-linux-thread-multi/auto/Apac
+he2/Util/Util.so
/usr/lib64/perl5/vendor_perl/5.8.8/x86_64-linux-thread-multi/auto/ModP
+erl/Util/Util.so

      [download]
      
$ perl -e 'print join( "\n", @INC), "\n";'
/usr/lib64/perl5/site_perl/5.8.8/x86_64-linux-thread-multi
/usr/lib/perl5/site_perl/5.8.8
/usr/lib/perl5/site_perl
/usr/lib64/perl5/vendor_perl/5.8.8/x86_64-linux-thread-multi
/usr/lib/perl5/vendor_perl/5.8.8
/usr/lib/perl5/vendor_perl
/usr/lib64/perl5/5.8.8/x86_64-linux-thread-multi
/usr/lib/perl5/5.8.8
.

      [download]
[reply]
[d/l]
[select]

        You might additionally want to check whether Util.so is in fact being loaded: 

        $ strace -efile perl -MScalar::Util=weaken -e'weaken(\my $var)' 2>&1 |
+ grep Util\.so

        [download]

        With a working installation, the results should look something like 

        stat("/usr/lib/perl5/5.8.8/auto/List/Util/Util.so", 0x63b140) = -1 ENO
+ENT (No such file or directory)
stat("/usr/lib/perl5/5.8.8/x86_64-linux-thread-multi/auto/List/Util/Ut
+il.so", {st_mode=S_IFREG|0555, st_size=40616, ...}) = 0
open("/usr/lib/perl5/5.8.8/x86_64-linux-thread-multi/auto/List/Util/Ut
+il.so", O_RDONLY) = 6

        [download]

        Otherwise, you'd get stat()s with ENOENT only (several dozens, typically), or maybe an attempted open() with EACCES (Permission denied), but no successful open()

[reply]
[d/l]
[select]

        But List::Util (to which List/Util/Util.so belongs) is a different module than Scalar::Util. Most likely, in your upgrade, your Perl did not compile the XS component of Scalar::Util, and your search seems to confirm that for me. So, reinstall Scalar::Util and make sure you have a matching C compiler for the Perl you're using available, so the XS component gets compiled.

[reply]
[d/l]
Re: CPAN and "Weak references"
by Khen1950fx (Canon) on Dec 08, 2009 at 04:18 UTC
    Adam Kennedy wrote a module that fixes this problem. Try Task::Weaken. I've used it with excellent results.
[reply]
Re: CPAN and "Weak references"
by ikegami (Patriarch) on Dec 07, 2009 at 21:44 UTC
    Have you tried reinstalling it?
[reply]

Back to Seekers of Perl Wisdom