Re: Issue with Safe::World module recommended for Gbrowse 2.0

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Re: Issue with Safe::World module recommended for Gbrowse 2.0

Dave Clements, GMOD Help Desk-3
Hi Zhi-Wei,

Safe::World is not needed in GBrowse 2.  See

Dave C.

On Mon, May 3, 2010 at 8:30 PM, Zhi-Wei Lu <[hidden email]> wrote:
Hi all,

I am attempting to install gbrowse 2.0.x on Ubuntu 9.10 with perl 5.10.0, I have installed all dependencies except
Safe::World.  I am getting this

Unknown operator name "threadsv" at blib/lib/Safe/World/Compartment.pm line 95.
make: *** [test_dynamic] Error 2
 GMPASSOS/Safe-World-0.14.tar.gz
 /usr/bin/make test -- NOT OK
//hint// to see the cpan-testers results for installing this module, try:
 reports GMPASSOS/Safe-World-0.14.tar.gz
Running make install
 make test had returned bad status, won't install without force
Failed during this command:
 GMPASSOS/Safe-World-0.14.tar.gz              : make_test NO

I also saw Lincoln's bug report about Safe::World and perl 5.10

https://rt.cpan.org/Public/Bug/Display.html?id=42172


I would appreciate if someone can shed some lights on how this module (or without this module) will affect the operation of Gbrowse 2.0.
Thank you very much for your help.

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Re: Issue with Safe::World module recommended for Gbrowse 2.0

Lincoln Stein
Hi Zhi-Wei,

Unfortunately Safe::World does not work on versions of perl after 5.8. It is optional for GBrowse -- basically it allows users to upload annotation files that contain perl callbacks. Without Safe::World, the callbacks are not used.

I have recently added a notification to the Build script that tells people not to worry if Safe::World is not installed, and not to bother with perl 5.10.

I would very much like to restore the functionality provided by Safe::World. It may be possible to use the vanilla Safe module instead, but I ran into all sorts of complications with namespaces when I initially tried it. If there is anyone on the mailing list who would like to give it a try, I would welcome it.

Lincoln

On Mon, May 3, 2010 at 11:30 PM, Zhi-Wei Lu <[hidden email]> wrote:
Hi all,

I am attempting to install gbrowse 2.0.x on Ubuntu 9.10 with perl 5.10.0, I have installed all dependencies except
Safe::World.  I am getting this

Unknown operator name "threadsv" at blib/lib/Safe/World/Compartment.pm line 95.
make: *** [test_dynamic] Error 2
 GMPASSOS/Safe-World-0.14.tar.gz
 /usr/bin/make test -- NOT OK
//hint// to see the cpan-testers results for installing this module, try:
 reports GMPASSOS/Safe-World-0.14.tar.gz
Running make install
 make test had returned bad status, won't install without force
Failed during this command:
 GMPASSOS/Safe-World-0.14.tar.gz              : make_test NO

I also saw Lincoln's bug report about Safe::World and perl 5.10

https://rt.cpan.org/Public/Bug/Display.html?id=42172


I would appreciate if someone can shed some lights on how this module (or without this module) will affect the operation of Gbrowse 2.0.

Thank you very much for your help.

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Gmod-gbrowse mailing list
[hidden email]
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Lincoln D. Stein
Director, Informatics and Biocomputing Platform
Ontario Institute for Cancer Research
101 College St., Suite 800
Toronto, ON, Canada M5G0A3
416 673-8514
Assistant: Renata Musa <[hidden email]>

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