[Bug 537138] New: Bioperl doesn't bootstrap on other platforms, circular dependencies
by Red Hat Bugzilla
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Summary: Bioperl doesn't bootstrap on other platforms, circular dependencies
https://bugzilla.redhat.com/show_bug.cgi?id=537138
Summary: Bioperl doesn't bootstrap on other platforms, circular
dependencies
Product: Fedora
Version: 11
Platform: All
OS/Version: Linux
Status: NEW
Severity: medium
Priority: low
Component: perl-bioperl-run
AssignedTo: alexl(a)users.sourceforge.net
ReportedBy: loupgaroublond(a)gmail.com
QAContact: extras-qa(a)fedoraproject.org
CC: alexl(a)users.sourceforge.net,
fedora-perl-devel-list(a)redhat.com
Classification: Fedora
Description of problem: perl-bioperl and perl-bioperl-run have circular build
dependencies effectively
While this situation is not explicit it's based on runtime only requirements
enforced by the packages. It makes it hard to bootstrap this on a system that
doesn't already have an earlier version of bioperl.
perl-bioperl has a runtime requirement on a dependency that is fulfilled by
perl-bioperl-run. perl-bioperl-run has a build time dependency on something
provided by perl-bioperl. Without a perl-bioperl-run package, it's impossible
to install bioperl to build a newer bioperl-run. This presents a problem when
trying to bootstrap this is centos.
Version-Release number of selected component (if applicable):
perl-bioperl 1.6.1 (based of the 1.6.0 spec file with only a version change)
perl-bioperl-run 1.6.1-1
How reproducible:
I'm guessing it is based on theory, i haven't tried to reproduce it on a second
machine.
Steps to Reproduce:
1. Build a perl-bioperl package on enterprise linux 5
2. Add it to a repo your system can access.
3. Try building a perl-bioperl-run package starting with rpmbuild -bs on the
.spec file.
4. Try installing perl-bioperl to fill the BR
Actual results:
[root@bofh016 SPECS]# rpmbuild -bs perl-bioperl-run.spec
error: Failed build dependencies:
perl(Bio::Root::Version) >= 1.5.9 is needed by
perl-bioperl-run-1.6.1-1.noarch
[root@bofh016 SPECS]# yum install perl-bioperl-1.6.1-2.el5.noarch
Loaded plugins: fastestmirror
Loading mirror speeds from cached hostfile
* addons: archive.cs.uu.nl
* base: archive.cs.uu.nl
* extras: archive.cs.uu.nl
* updates: archive.cs.uu.nl
Setting up Install Process
Resolving Dependencies
--> Running transaction check
---> Package perl-bioperl.noarch 0:1.6.1-2.el5 set to be updated
--> Processing Dependency: perl(Bio::Tools::Run::Phylo::Phylip::ProtPars) for
package: perl-bioperl
--> Processing Dependency: perl(List::MoreUtils) for package: perl-bioperl
--> Processing Dependency: perl(Test::Warn) for package: perl-bioperl
--> Processing Dependency: perl(Test::Exception) for package: perl-bioperl
--> Processing Dependency: perl(Bio::Tools::Run::Alignment::Clustalw) for
package: perl-bioperl
--> Processing Dependency: perl(Bio::Tools::Run::Phylo::Molphy::ProtML) for
package: perl-bioperl
--> Processing Dependency: perl(Bio::Tools::Run::Phylo::Phylip::ProtDist) for
package: perl-bioperl
--> Processing Dependency: perl(Bio::ASN1::EntrezGene) for package:
perl-bioperl
--> Processing Dependency: perl(XML::Simple) for package: perl-bioperl
--> Processing Dependency: perl(Bio::Tools::Run::Phylo::Phylip::Neighbor) for
package: perl-bioperl
--> Running transaction check
---> Package perl-List-MoreUtils.x86_64 0:0.22-2.el5 set to be updated
---> Package perl-Test-Exception.noarch 0:0.26-2.el5 set to be updated
--> Processing Dependency: perl(Sub::Uplevel) for package: perl-Test-Exception
---> Package perl-Test-Warn.noarch 0:0.11-2.el5 set to be updated
---> Package perl-XML-Simple.noarch 0:2.14-4.fc6 set to be updated
---> Package perl-bioperl.noarch 0:1.6.1-2.el5 set to be updated
--> Processing Dependency: perl(Bio::Tools::Run::Phylo::Phylip::ProtPars) for
package: perl-bioperl
--> Processing Dependency: perl(Bio::Tools::Run::Alignment::Clustalw) for
package: perl-bioperl
--> Processing Dependency: perl(Bio::Tools::Run::Phylo::Molphy::ProtML) for
package: perl-bioperl
--> Processing Dependency: perl(Bio::Tools::Run::Phylo::Phylip::ProtDist) for
package: perl-bioperl
--> Processing Dependency: perl(Bio::ASN1::EntrezGene) for package:
perl-bioperl
--> Processing Dependency: perl(Bio::Tools::Run::Phylo::Phylip::Neighbor) for
package: perl-bioperl
--> Running transaction check
---> Package perl-Sub-Uplevel.noarch 0:0.18-2.el5 set to be updated
---> Package perl-bioperl.noarch 0:1.6.1-2.el5 set to be updated
--> Processing Dependency: perl(Bio::Tools::Run::Phylo::Phylip::ProtPars) for
package: perl-bioperl
--> Processing Dependency: perl(Bio::Tools::Run::Alignment::Clustalw) for
package: perl-bioperl
--> Processing Dependency: perl(Bio::Tools::Run::Phylo::Molphy::ProtML) for
package: perl-bioperl
--> Processing Dependency: perl(Bio::Tools::Run::Phylo::Phylip::ProtDist) for
package: perl-bioperl
--> Processing Dependency: perl(Bio::ASN1::EntrezGene) for package:
perl-bioperl
--> Processing Dependency: perl(Bio::Tools::Run::Phylo::Phylip::Neighbor) for
package: perl-bioperl
--> Finished Dependency Resolution
perl-bioperl-1.6.1-2.el5.noarch from centos-5-genomics has depsolving problems
--> Missing Dependency: perl(Bio::Tools::Run::Phylo::Phylip::Neighbor) is
needed by package perl-bioperl-1.6.1-2.el5.noarch (centos-5-genomics)
perl-bioperl-1.6.1-2.el5.noarch from centos-5-genomics has depsolving problems
--> Missing Dependency: perl(Bio::Tools::Run::Phylo::Phylip::ProtPars) is
needed by package perl-bioperl-1.6.1-2.el5.noarch (centos-5-genomics)
perl-bioperl-1.6.1-2.el5.noarch from centos-5-genomics has depsolving problems
--> Missing Dependency: perl(Bio::Tools::Run::Phylo::Phylip::ProtDist) is
needed by package perl-bioperl-1.6.1-2.el5.noarch (centos-5-genomics)
perl-bioperl-1.6.1-2.el5.noarch from centos-5-genomics has depsolving problems
--> Missing Dependency: perl(Bio::Tools::Run::Alignment::Clustalw) is needed
by package perl-bioperl-1.6.1-2.el5.noarch (centos-5-genomics)
perl-bioperl-1.6.1-2.el5.noarch from centos-5-genomics has depsolving problems
--> Missing Dependency: perl(Bio::ASN1::EntrezGene) is needed by package
perl-bioperl-1.6.1-2.el5.noarch (centos-5-genomics)
perl-bioperl-1.6.1-2.el5.noarch from centos-5-genomics has depsolving problems
--> Missing Dependency: perl(Bio::Tools::Run::Phylo::Molphy::ProtML) is
needed by package perl-bioperl-1.6.1-2.el5.noarch (centos-5-genomics)
Error: Missing Dependency: perl(Bio::ASN1::EntrezGene) is needed by package
perl-bioperl-1.6.1-2.el5.noarch (centos-5-genomics)
Error: Missing Dependency: perl(Bio::Tools::Run::Alignment::Clustalw) is needed
by package perl-bioperl-1.6.1-2.el5.noarch (centos-5-genomics)
Error: Missing Dependency: perl(Bio::Tools::Run::Phylo::Phylip::Neighbor) is
needed by package perl-bioperl-1.6.1-2.el5.noarch (centos-5-genomics)
Error: Missing Dependency: perl(Bio::Tools::Run::Phylo::Molphy::ProtML) is
needed by package perl-bioperl-1.6.1-2.el5.noarch (centos-5-genomics)
Error: Missing Dependency: perl(Bio::Tools::Run::Phylo::Phylip::ProtDist) is
needed by package perl-bioperl-1.6.1-2.el5.noarch (centos-5-genomics)
Error: Missing Dependency: perl(Bio::Tools::Run::Phylo::Phylip::ProtPars) is
needed by package perl-bioperl-1.6.1-2.el5.noarch (centos-5-genomics)
You could try using --skip-broken to work around the problem
You could try running: package-cleanup --problems
package-cleanup --dupes
rpm -Va --nofiles --nodigest
Expected results:
A source package
Additional info:
I'm going to push a fedora package to our private repo to make this work, but
i'm wondering how this could be solved for EPEL in the future. Ideally we would
like to run bioperl out of EPEL directly rather than running our own private
builds.
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13 years, 10 months
[Bug 530137] New: Fedora::Bugzilla - $bug->blocks_bug() fail
by Red Hat Bugzilla
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comments should be made in the comments box of this bug.
Summary: Fedora::Bugzilla - $bug->blocks_bug() fail
https://bugzilla.redhat.com/show_bug.cgi?id=530137
Summary: Fedora::Bugzilla - $bug->blocks_bug() fail
Product: Fedora
Version: 11
Platform: All
OS/Version: Linux
Status: NEW
Severity: medium
Priority: low
Component: perl-Fedora-Bugzilla
AssignedTo: cweyl(a)alumni.drew.edu
ReportedBy: jpirko(a)redhat.com
QAContact: extras-qa(a)fedoraproject.org
CC: cweyl(a)alumni.drew.edu,
fedora-perl-devel-list(a)redhat.com, mmaslano(a)redhat.com
Classification: Fedora
Target Release: ---
Created an attachment (id=365567)
--> (https://bugzilla.redhat.com/attachment.cgi?id=365567)
test script
Description of problem:
When I try to get bugs that bz depends on, it fails in a way below and returns
only one bz "0".
Version-Release number of selected component (if applicable):
0.10-1 - I tried 0.13 from CPAN and problem is still there.
How reproducible:
Always
Steps to Reproduce:
run attached script
Actual results:
blocks_bug
Use of uninitialized value $_[1] in exists at
/usr/lib/perl5/vendor_perl/5.10.0/MooseX/AttributeHelpers/MethodProvider/ImmutableHash.pm
line 10.
0
all_blocked_bugs
Expected results:
blocks_bug
499884
all_blocked_bugs
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13 years, 10 months
[Bug 519710] New: flags argument of $pool->refresh() undocumented
by Red Hat Bugzilla
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comments should be made in the comments box of this bug.
Summary: flags argument of $pool->refresh() undocumented
https://bugzilla.redhat.com/show_bug.cgi?id=519710
Summary: flags argument of $pool->refresh() undocumented
Product: Fedora
Version: 11
Platform: All
OS/Version: Linux
Status: NEW
Severity: medium
Priority: low
Component: perl-Sys-Virt
AssignedTo: steve(a)silug.org
ReportedBy: mbooth(a)redhat.com
QAContact: extras-qa(a)fedoraproject.org
CC: steve(a)silug.org, berrange(a)redhat.com,
fedora-perl-devel-list(a)redhat.com
Classification: Fedora
Target Release: ---
Description of problem:
man Sys::Virt::StoragePool says:
$pool->refresh();
Refresh the storage pool state. Typically this will rescan the list
of storage volumes.
However this code:
$pool->refresh();
dies with:
Usage: Sys::Virt::StoragePool::refresh(pool, flags) at
/home/mbooth/src/virt-v2v/snapshot/virt-snapshot.pl line 328.
Version-Release number of selected component (if applicable):
perl-Sys-Virt-0.2.0-2.fc11.x86_64
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13 years, 10 months
[Bug 519648] New: virStorageVolLookupBy* not implemented
by Red Hat Bugzilla
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comments should be made in the comments box of this bug.
Summary: virStorageVolLookupBy* not implemented
https://bugzilla.redhat.com/show_bug.cgi?id=519648
Summary: virStorageVolLookupBy* not implemented
Product: Fedora
Version: 11
Platform: All
OS/Version: Linux
Status: NEW
Severity: medium
Priority: low
Component: perl-Sys-Virt
AssignedTo: steve(a)silug.org
ReportedBy: mbooth(a)redhat.com
QAContact: extras-qa(a)fedoraproject.org
CC: steve(a)silug.org, berrange(a)redhat.com,
fedora-perl-devel-list(a)redhat.com
Depends on: 519647
Classification: Fedora
Target Release: ---
Clone Of: 519647
+++ This bug was initially created as a clone of Bug #519647 +++
Description of problem:
The following calls available in the C api have no perl bindings:
virStorageVolLookupByKey
virStorageVolLookupByName
virStorageVolLookupByPath
Version-Release number of selected component (if applicable):
perl-Sys-Virt-0.2.0-2.fc11.x86_64
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13 years, 10 months
[Bug 513987] New: man Sys::Virt: get_node_info onwards is confusing
by Red Hat Bugzilla
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comments should be made in the comments box of this bug.
Summary: man Sys::Virt: get_node_info onwards is confusing
https://bugzilla.redhat.com/show_bug.cgi?id=513987
Summary: man Sys::Virt: get_node_info onwards is confusing
Product: Fedora
Version: 11
Platform: All
OS/Version: Linux
Status: NEW
Severity: medium
Priority: low
Component: perl-Sys-Virt
AssignedTo: steve(a)silug.org
ReportedBy: mbooth(a)redhat.com
QAContact: extras-qa(a)fedoraproject.org
CC: steve(a)silug.org, berrange(a)redhat.com,
fedora-perl-devel-list(a)redhat.com
Classification: Fedora
Target Release: ---
Description of problem:
man Sys::Virt says:
my $info = $con->get_node_info()
Returns a hash reference summarising the capabilities of the host
node. The elements of the hash are as follows:
However, what follows does not appear to be a description of the hash. At that
same point, the convention for describing a method changes. $vmm is variously
referred to as $con or $conn. Unless, of course, these methods are genuinely
different in some way that isn't clear.
Version-Release number of selected component (if applicable):
perl-Sys-Virt-0.2.0-2.fc11.i586
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13 years, 10 months
[Bug 499243] New: Net::DBus::Object does not correctly validate requested method name to invoke
by Red Hat Bugzilla
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comments should be made in the comments box of this bug.
Summary: Net::DBus::Object does not correctly validate requested method name to invoke
https://bugzilla.redhat.com/show_bug.cgi?id=499243
Summary: Net::DBus::Object does not correctly validate
requested method name to invoke
Product: Fedora
Version: rawhide
Platform: All
OS/Version: Linux
Status: NEW
Keywords: Security
Severity: medium
Priority: low
Component: perl-Net-DBus
AssignedTo: cweyl(a)alumni.drew.edu
ReportedBy: berrange(a)redhat.com
QAContact: extras-qa(a)fedoraproject.org
CC: berrange(a)redhat.com, cweyl(a)alumni.drew.edu,
fedora-perl-devel-list(a)redhat.com
Classification: Fedora
Target Release: ---
Description of problem:
There is a security issue in the implementation of Net::DBus::Object.
In the place where it dispatches RPC calls, it simply does
$self->can($method_name)
so, it allows the dbus client to invoke any method that the service side object
implements. Many service implementors would like ability to restrict this to
just allow methods they explicitly export in the introspection XML data.
Furthermore, the current check also allows direct invocation of several
internal impl methods of Net::DBus::Object itself.
This allows a remote client to do a denial of service by calling 'disconnect'
which unregisters the object from the bus. It also allows the remote client to
emit signals on the object which others clients may then act on.
For the dbus 'system' bus, the service can be running as root, and client as an
unprivileged user, so this flaw may allow a client to run things they
shouldn't. While impact of being able to emit signals / invoke improper methods
*may* be limited by the need to have ACLs registered with dbus system bus
instance, the degree of protection depends on how well the app author wrote
their ACLs. So one can't rely on this.
For the dbus 'session' bus, everything is running as unprivileged user, so
impact is reasonably low, denial of service.
This issue is already public via upstream bug report
https://rt.cpan.org/Ticket/Display.html?id=45034
And I have a patch available which should resolve it
http://hg.berrange.com/libraries/net-dbus--devel?cs=be26112c5fdd
Version-Release number of selected component (if applicable):
How reproducible:
Always
Steps to Reproduce:
1. Run the 'examples/example-service.pl' file from source tar.gz
2. In another terminal run
$ dbus-send --session --print-reply --dest=org.designfu.SampleService
/SomeObject org.designfu.SampleInterface.HelloWorld "string:hello"
$ dbus-send --session --print-reply --dest=org.designfu.SampleService
/SomeObject org.designfu.SampleInterface.disconnect
$ dbus-send --session --print-reply --dest=org.designfu.SampleService
/SomeObject org.designfu.SampleInterface.HelloWorld "string:hello"
Actual results:
The 'disconnect' method was allowed
$ dbus-send --session --print-reply --dest=org.designfu.SampleService
/SomeObject org.designfu.SampleInterface.HelloWorld "string:hello"
method return sender=:1.61 -> dest=:1.62 reply_serial=2
array [
string "Hello"
string " from example-service.pl"
]
$ dbus-send --session --print-reply --dest=org.designfu.SampleService
/SomeObject org.designfu.SampleInterface.disconnect
method return sender=:1.61 -> dest=:1.63 reply_serial=2
$ dbus-send --session --print-reply --dest=org.designfu.SampleService
/SomeObject org.designfu.SampleInterface.HelloWorld "string:hello"
Error org.freedesktop.DBus.Error.UnknownMethod: Method "HelloWorld" with
signature "s" on interface "org.designfu.SampleInterface" doesn't exist
Expected results:
The 'disconnect' method should be denied
$ dbus-send --session --print-reply --dest=org.designfu.SampleService
/SomeObject org.designfu.SampleInterface.HelloWorld "string:hello"
method return sender=:1.65 -> dest=:1.66 reply_serial=2
array [
string "Hello"
string " from example-service.pl"
]
$ dbus-send --session --print-reply --dest=org.designfu.SampleService
/SomeObject org.designfu.SampleInterface.disconnect
Error org.freedesktop.DBus.Error.Failed: No such method SomeObject->disconnect
$ dbus-send --session --print-reply --dest=org.designfu.SampleService
/SomeObject org.designfu.SampleInterface.HelloWorld "string:hello"
method return sender=:1.65 -> dest=:1.68 reply_serial=2
array [
string "Hello"
string " from example-service.pl"
]
Additional info:
Bug affects all Fedora releases.
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13 years, 10 months
[Bug 496369] New: make check fails
by Red Hat Bugzilla
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comments should be made in the comments box of this bug.
Summary: make check fails
https://bugzilla.redhat.com/show_bug.cgi?id=496369
Summary: make check fails
Product: Fedora
Version: rawhide
Platform: s390x
OS/Version: Linux
Status: NEW
Severity: medium
Priority: medium
Component: perl-IPC-Shareable
AssignedTo: tcallawa(a)redhat.com
ReportedBy: karsten(a)redhat.com
QAContact: extras-qa(a)fedoraproject.org
CC: tcallawa(a)redhat.com, fedora-perl-devel-list(a)redhat.com
Classification: Fedora
Target Release: ---
Description of problem:
As I'm no perl expert I need your help with a build failure on s390x.
Full logs are available at
http://s390.koji.fedoraproject.org/koji/taskinfo?taskID=49521
Could you take a look at it, please ? It is blocking the builds of several
other
perl packages atm.
Version-Release number of selected component (if applicable):
perl-IPC-Shareable-0.60-9.fc11
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13 years, 10 months
[Bug 473874] New: rpmbuild generates perl provides/depends differently in F-10 than any prior level
by Red Hat Bugzilla
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comments should be made in the comments box of this bug.
Summary: rpmbuild generates perl provides/depends differently in F-10 than any prior level
https://bugzilla.redhat.com/show_bug.cgi?id=473874
Summary: rpmbuild generates perl provides/depends differently
in F-10 than any prior level
Product: Fedora
Version: rawhide
Platform: All
OS/Version: Linux
Status: NEW
Severity: urgent
Priority: medium
Component: rpm
AssignedTo: pmatilai(a)redhat.com
ReportedBy: cweyl(a)alumni.drew.edu
QAContact: extras-qa(a)fedoraproject.org
CC: pmatilai(a)redhat.com, jnovy(a)redhat.com,
fedora-perl-devel-list(a)redhat.com, ffesti(a)redhat.com
Classification: Fedora
Description of problem:
rpm in F10+ processes Perl depends/requires differently than in any prior level
of Fedora.
e.g., see koji scratch builds of perl-Data-TreeDumper:
dist-f9: https://koji.fedoraproject.org/koji/taskinfo?taskID=965620
dist-f10: https://koji.fedoraproject.org/koji/taskinfo?taskID=965622
dist-f11: https://koji.fedoraproject.org/koji/taskinfo?taskID=965644
Note dist-f9's list of provides/requires from the build.log:
Provides:
perl(Data::TreeDumper) = 0.35
Requires:
perl >= 0:5.006
perl(:MODULE_COMPAT_5.10.0)
perl(Carp)
perl(Check::ISA)
perl(Class::ISA)
perl(Exporter)
perl(Sort::Naturally)
perl(Text::Wrap)
perl(strict)
perl(warnings)
...and dist-f10, f11:
Provides:
perl(Data::TreeDumper) = 0.35
perl(Potatoe)
perl(SuperObject)
perl(SuperObjectWithAutoload)
perl(TiedArray)
perl(TiedHandle)
perl(TiedHash)
perl(TiedScalar)
perl(Vegetable)
Requires:
perl >= 0:5.006
perl(AutoLoader)
perl(Carp)
perl(Check::ISA)
perl(Class::ISA)
perl(Data::TreeDumper)
perl(Devel::Peek)
perl(Exporter)
perl(Sort::Naturally)
perl(Text::Wrap)
perl(Tie::Array)
perl(Tie::Handle)
perl(Tie::Hash)
perl(Tie::Scalar)
perl(strict)
perl(warnings)
Note the additional "provides" found under f10+ (e.g. perl(Potatoe)) are from
scripts stored in %_docdir, without their executable bit set; also note the
additional requires (e.g. perl(Tie::Array)) not present in the package built
under dist-f9. This is a major change of behaviour from all versions prior to
F-10, and may result in many of the nearly 1000 Perl packages in Fedora to
start generating unexpected requires/provides when they're rebuilt.
Version-Release number of selected component (if applicable):
rpm-4.6.0-0.rc1.7
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13 years, 10 months
[Bug 456144] New: Package build failed
by Red Hat Bugzilla
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comments should be made in the comments box of this bug report.
https://bugzilla.redhat.com/show_bug.cgi?id=456144
Summary: Package build failed
Product: Fedora
Version: rawhide
Platform: All
OS/Version: Linux
Status: NEW
Severity: medium
Priority: low
Component: amavisd-new
AssignedTo: steve(a)silug.org
ReportedBy: miguel.filho(a)gmail.com
QAContact: extras-qa(a)fedoraproject.org
CC: fedora-perl-devel-list(a)redhat.com
I've tried to build the 2.6.1 using the devel branch on CentOS 5, but two
patches fail to apply.
amavisd-conf.patch
amavisd-db.patch
I'm submitting updated patches that work.
------- Additional Comments From miguel.filho(a)gmail.com 2008-07-21 14:10 EST -------
Created an attachment (id=312286)
--> (https://bugzilla.redhat.com/attachment.cgi?id=312286&action=view)
Updated fix for amavisd-nanny
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13 years, 10 months