[Gmod-ajax] UCSC to JSON script problematic...

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[Gmod-ajax] UCSC to JSON script problematic...

crislawrence
I was preparing to attempt to use the ucsc-to-json script.  But I am stuck at --help:

newhelios mbc-exp>bin/ucsc-to-json.pl --help
"distinct" is not exported by the List::MoreUtils module
Can't continue after import errors at bin/ucsc-to-json.pl line 112
BEGIN failed--compilation aborted at bin/ucsc-to-json.pl line 112.

I am using 1.11.1.  I ran ./setup.sh again to be sure any new dependencies were handled.  The result was the same.  The perl is 5.10.1 running on CentOS 6.5.

This is my first attempt to use this script.  Any suggestions?

Thx.

- Cris
------------------------------------------------------------------------------
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security intelligence. It gives you real-time visual feedback on key
security issues and trends.  Skip the complicated setup - simply import
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Re: UCSC to JSON script problematic...

crislawrence
As a follow-up…I tried the same script on 1.11.0 on a CentOS system running perl 5.18.0 and the script runs fine.  So the script is not compatible with 5.10.1, I guess.

- Cris

On Jan 31, 2014, at 10:22 AM, Cris Lawrence - UPenn <[hidden email]> wrote:

> I was preparing to attempt to use the ucsc-to-json script.  But I am stuck at --help:
>
> newhelios mbc-exp>bin/ucsc-to-json.pl --help
> "distinct" is not exported by the List::MoreUtils module
> Can't continue after import errors at bin/ucsc-to-json.pl line 112
> BEGIN failed--compilation aborted at bin/ucsc-to-json.pl line 112.
>
> I am using 1.11.1.  I ran ./setup.sh again to be sure any new dependencies were handled.  The result was the same.  The perl is 5.10.1 running on CentOS 6.5.
>
> This is my first attempt to use this script.  Any suggestions?
>
> Thx.
>
> - Cris
> ------------------------------------------------------------------------------
> WatchGuard Dimension instantly turns raw network data into actionable
> security intelligence. It gives you real-time visual feedback on key
> security issues and trends.  Skip the complicated setup - simply import
> a virtual appliance and go from zero to informed in seconds.
> http://pubads.g.doubleclick.net/gampad/clk?id=123612991&iu=/4140/ostg.clktrk
> _______________________________________________
> Gmod-ajax mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax


------------------------------------------------------------------------------
WatchGuard Dimension instantly turns raw network data into actionable
security intelligence. It gives you real-time visual feedback on key
security issues and trends.  Skip the complicated setup - simply import
a virtual appliance and go from zero to informed in seconds.
http://pubads.g.doubleclick.net/gampad/clk?id=123612991&iu=/4140/ostg.clktrk
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Re: UCSC to JSON script problematic...

Keiran Raine
I expect it is that you need a later version of List::MoreUtils:

perl -le 'eval "require $ARGV[0]" and print $ARGV[0]->VERSION' List::MoreUtils

Will give you the version.  You should be able to just update the single module to a later version

Keiran Raine
Principal Bioinformatician
Cancer Genome Project
Wellcome Trust Sanger Institute

Tel:+44 (0)1223 834244 Ext: 7703
Office: H104

On 31 Jan 2014, at 15:29, Cris Lawrence - UPenn <[hidden email]> wrote:

As a follow-up…I tried the same script on 1.11.0 on a CentOS system running perl 5.18.0 and the script runs fine.  So the script is not compatible with 5.10.1, I guess.

- Cris

On Jan 31, 2014, at 10:22 AM, Cris Lawrence - UPenn <[hidden email]> wrote:

I was preparing to attempt to use the ucsc-to-json script.  But I am stuck at --help:

newhelios mbc-exp>bin/ucsc-to-json.pl --help
"distinct" is not exported by the List::MoreUtils module
Can't continue after import errors at bin/ucsc-to-json.pl line 112
BEGIN failed--compilation aborted at bin/ucsc-to-json.pl line 112.

I am using 1.11.1.  I ran ./setup.sh again to be sure any new dependencies were handled.  The result was the same.  The perl is 5.10.1 running on CentOS 6.5.

This is my first attempt to use this script.  Any suggestions?

Thx.

- Cris
------------------------------------------------------------------------------
WatchGuard Dimension instantly turns raw network data into actionable
security intelligence. It gives you real-time visual feedback on key
security issues and trends.  Skip the complicated setup - simply import
a virtual appliance and go from zero to informed in seconds.
http://pubads.g.doubleclick.net/gampad/clk?id=123612991&iu=/4140/ostg.clktrk
_______________________________________________
Gmod-ajax mailing list
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------------------------------------------------------------------------------
WatchGuard Dimension instantly turns raw network data into actionable
security intelligence. It gives you real-time visual feedback on key
security issues and trends.  Skip the complicated setup - simply import
a virtual appliance and go from zero to informed in seconds.
http://pubads.g.doubleclick.net/gampad/clk?id=123612991&iu=/4140/ostg.clktrk
_______________________________________________
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-- The Wellcome Trust Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE.

------------------------------------------------------------------------------
WatchGuard Dimension instantly turns raw network data into actionable
security intelligence. It gives you real-time visual feedback on key
security issues and trends.  Skip the complicated setup - simply import
a virtual appliance and go from zero to informed in seconds.
http://pubads.g.doubleclick.net/gampad/clk?id=123612991&iu=/4140/ostg.clktrk
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Re: UCSC to JSON script problematic...

Robert Buels-2
What version of List::MoreUtils is the minimum?  I can add it to setup.sh.


Robert Buels
Lead Developer
JBrowse - http://jbrowse.org

On 01/31/2014 08:13 AM, Keiran Raine wrote:

> I expect it is that you need a later version of List::MoreUtils:
>
> perl -le 'eval "require $ARGV[0]" and print
> $ARGV[0]->VERSION' List::MoreUtils
>
> Will give you the version.  You should be able to just update the single
> module to a later version
>
> Keiran Raine
> Principal Bioinformatician
> Cancer Genome Project
> Wellcome Trust Sanger Institute
>
> [hidden email] <mailto:[hidden email]>
> Tel:+44 (0)1223 834244 Ext: 7703
> Office: H104
>
> On 31 Jan 2014, at 15:29, Cris Lawrence - UPenn <[hidden email]
> <mailto:[hidden email]>> wrote:
>
>> As a follow-up…I tried the same script on 1.11.0 on a CentOS system
>> running perl 5.18.0 and the script runs fine.  So the script is not
>> compatible with 5.10.1, I guess.
>>
>> - Cris
>>
>> On Jan 31, 2014, at 10:22 AM, Cris Lawrence - UPenn <[hidden email]
>> <mailto:[hidden email]>> wrote:
>>
>>> I was preparing to attempt to use the ucsc-to-json script.  But I am
>>> stuck at --help:
>>>
>>> newhelios mbc-exp>bin/ucsc-to-json.pl --help
>>> "distinct" is not exported by the List::MoreUtils module
>>> Can't continue after import errors at bin/ucsc-to-json.pl line 112
>>> BEGIN failed--compilation aborted at bin/ucsc-to-json.pl line 112.
>>>
>>> I am using 1.11.1.  I ran ./setup.sh again to be sure any new
>>> dependencies were handled.  The result was the same.  The perl is
>>> 5.10.1 running on CentOS 6.5.
>>>
>>> This is my first attempt to use this script.  Any suggestions?
>>>
>>> Thx.
>>>
>>> - Cris
>>> ------------------------------------------------------------------------------
>>> WatchGuard Dimension instantly turns raw network data into actionable
>>> security intelligence. It gives you real-time visual feedback on key
>>> security issues and trends.  Skip the complicated setup - simply import
>>> a virtual appliance and go from zero to informed in seconds.
>>> http://pubads.g.doubleclick.net/gampad/clk?id=123612991&iu=/4140/ostg.clktrk
>>> _______________________________________________
>>> Gmod-ajax mailing list
>>> [hidden email]
>>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>>
>>
>> ------------------------------------------------------------------------------
>> WatchGuard Dimension instantly turns raw network data into actionable
>> security intelligence. It gives you real-time visual feedback on key
>> security issues and trends.  Skip the complicated setup - simply import
>> a virtual appliance and go from zero to informed in seconds.
>> http://pubads.g.doubleclick.net/gampad/clk?id=123612991&iu=/4140/ostg.clktrk
>> _______________________________________________
>> Gmod-ajax mailing list
>> [hidden email]
>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>
>
> -- The Wellcome Trust Sanger Institute is operated by Genome Research
> Limited, a charity registered in England with number 1021457 and a
> company registered in England with number 2742969, whose registered
> office is 215 Euston Road, London, NW1 2BE.
>
>
> ------------------------------------------------------------------------------
> WatchGuard Dimension instantly turns raw network data into actionable
> security intelligence. It gives you real-time visual feedback on key
> security issues and trends.  Skip the complicated setup - simply import
> a virtual appliance and go from zero to informed in seconds.
> http://pubads.g.doubleclick.net/gampad/clk?id=123612991&iu=/4140/ostg.clktrk
>
>
>
> _______________________________________________
> Gmod-ajax mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>

------------------------------------------------------------------------------
WatchGuard Dimension instantly turns raw network data into actionable
security intelligence. It gives you real-time visual feedback on key
security issues and trends.  Skip the complicated setup - simply import
a virtual appliance and go from zero to informed in seconds.
http://pubads.g.doubleclick.net/gampad/clk?id=123612991&iu=/4140/ostg.clktrk
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Re: UCSC to JSON script problematic...

Keiran Raine
Looks to be 0.28

Keiran

> On 31 Jan 2014, at 21:30, "Robert Buels" <[hidden email]> wrote:
>
> What version of List::MoreUtils is the minimum?  I can add it to setup.sh.
>
>
> Robert Buels
> Lead Developer
> JBrowse - http://jbrowse.org
>
>> On 01/31/2014 08:13 AM, Keiran Raine wrote:
>> I expect it is that you need a later version of List::MoreUtils:
>>
>> perl -le 'eval "require $ARGV[0]" and print
>> $ARGV[0]->VERSION' List::MoreUtils
>>
>> Will give you the version.  You should be able to just update the single
>> module to a later version
>>
>> Keiran Raine
>> Principal Bioinformatician
>> Cancer Genome Project
>> Wellcome Trust Sanger Institute
>>
>> [hidden email] <mailto:[hidden email]>
>> Tel:+44 (0)1223 834244 Ext: 7703
>> Office: H104
>>
>> On 31 Jan 2014, at 15:29, Cris Lawrence - UPenn <[hidden email]
>> <mailto:[hidden email]>> wrote:
>>
>>> As a follow-up…I tried the same script on 1.11.0 on a CentOS system
>>> running perl 5.18.0 and the script runs fine.  So the script is not
>>> compatible with 5.10.1, I guess.
>>>
>>> - Cris
>>>
>>> On Jan 31, 2014, at 10:22 AM, Cris Lawrence - UPenn <[hidden email]
>>> <mailto:[hidden email]>> wrote:
>>>
>>>> I was preparing to attempt to use the ucsc-to-json script.  But I am
>>>> stuck at --help:
>>>>
>>>> newhelios mbc-exp>bin/ucsc-to-json.pl --help
>>>> "distinct" is not exported by the List::MoreUtils module
>>>> Can't continue after import errors at bin/ucsc-to-json.pl line 112
>>>> BEGIN failed--compilation aborted at bin/ucsc-to-json.pl line 112.
>>>>
>>>> I am using 1.11.1.  I ran ./setup.sh again to be sure any new
>>>> dependencies were handled.  The result was the same.  The perl is
>>>> 5.10.1 running on CentOS 6.5.
>>>>
>>>> This is my first attempt to use this script.  Any suggestions?
>>>>
>>>> Thx.
>>>>
>>>> - Cris
>>>> ------------------------------------------------------------------------------
>>>> WatchGuard Dimension instantly turns raw network data into actionable
>>>> security intelligence. It gives you real-time visual feedback on key
>>>> security issues and trends.  Skip the complicated setup - simply import
>>>> a virtual appliance and go from zero to informed in seconds.
>>>> http://pubads.g.doubleclick.net/gampad/clk?id=123612991&iu=/4140/ostg.clktrk
>>>> _______________________________________________
>>>> Gmod-ajax mailing list
>>>> [hidden email]
>>>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>>>
>>>
>>> ------------------------------------------------------------------------------
>>> WatchGuard Dimension instantly turns raw network data into actionable
>>> security intelligence. It gives you real-time visual feedback on key
>>> security issues and trends.  Skip the complicated setup - simply import
>>> a virtual appliance and go from zero to informed in seconds.
>>> http://pubads.g.doubleclick.net/gampad/clk?id=123612991&iu=/4140/ostg.clktrk
>>> _______________________________________________
>>> Gmod-ajax mailing list
>>> [hidden email]
>>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>>
>>
>> -- The Wellcome Trust Sanger Institute is operated by Genome Research
>> Limited, a charity registered in England with number 1021457 and a
>> company registered in England with number 2742969, whose registered
>> office is 215 Euston Road, London, NW1 2BE.
>>
>>
>> ------------------------------------------------------------------------------
>> WatchGuard Dimension instantly turns raw network data into actionable
>> security intelligence. It gives you real-time visual feedback on key
>> security issues and trends.  Skip the complicated setup - simply import
>> a virtual appliance and go from zero to informed in seconds.
>> http://pubads.g.doubleclick.net/gampad/clk?id=123612991&iu=/4140/ostg.clktrk
>>
>>
>>
>> _______________________________________________
>> Gmod-ajax mailing list
>> [hidden email]
>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>>
------------------------------------------------------------------------------
WatchGuard Dimension instantly turns raw network data into actionable
security intelligence. It gives you real-time visual feedback on key
security issues and trends.  Skip the complicated setup - simply import
a virtual appliance and go from zero to informed in seconds.
http://pubads.g.doubleclick.net/gampad/clk?id=123612991&iu=/4140/ostg.clktrk
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Re: UCSC to JSON script problematic...

Robert Buels-2
OK added, coming out in 1.11.2.


Robert Buels
Lead Developer
JBrowse - http://jbrowse.org

On 02/01/2014 12:15 AM, Keiran Raine wrote:

> Looks to be 0.28
>
> Keiran
>
>> On 31 Jan 2014, at 21:30, "Robert Buels" <[hidden email]> wrote:
>>
>> What version of List::MoreUtils is the minimum?  I can add it to setup.sh.
>>
>>
>> Robert Buels
>> Lead Developer
>> JBrowse - http://jbrowse.org
>>
>>> On 01/31/2014 08:13 AM, Keiran Raine wrote:
>>> I expect it is that you need a later version of List::MoreUtils:
>>>
>>> perl -le 'eval "require $ARGV[0]" and print
>>> $ARGV[0]->VERSION' List::MoreUtils
>>>
>>> Will give you the version.  You should be able to just update the single
>>> module to a later version
>>>
>>> Keiran Raine
>>> Principal Bioinformatician
>>> Cancer Genome Project
>>> Wellcome Trust Sanger Institute
>>>
>>> [hidden email] <mailto:[hidden email]>
>>> Tel:+44 (0)1223 834244 Ext: 7703
>>> Office: H104
>>>
>>> On 31 Jan 2014, at 15:29, Cris Lawrence - UPenn <[hidden email]
>>> <mailto:[hidden email]>> wrote:
>>>
>>>> As a follow-up…I tried the same script on 1.11.0 on a CentOS system
>>>> running perl 5.18.0 and the script runs fine.  So the script is not
>>>> compatible with 5.10.1, I guess.
>>>>
>>>> - Cris
>>>>
>>>> On Jan 31, 2014, at 10:22 AM, Cris Lawrence - UPenn <[hidden email]
>>>> <mailto:[hidden email]>> wrote:
>>>>
>>>>> I was preparing to attempt to use the ucsc-to-json script.  But I am
>>>>> stuck at --help:
>>>>>
>>>>> newhelios mbc-exp>bin/ucsc-to-json.pl --help
>>>>> "distinct" is not exported by the List::MoreUtils module
>>>>> Can't continue after import errors at bin/ucsc-to-json.pl line 112
>>>>> BEGIN failed--compilation aborted at bin/ucsc-to-json.pl line 112.
>>>>>
>>>>> I am using 1.11.1.  I ran ./setup.sh again to be sure any new
>>>>> dependencies were handled.  The result was the same.  The perl is
>>>>> 5.10.1 running on CentOS 6.5.
>>>>>
>>>>> This is my first attempt to use this script.  Any suggestions?
>>>>>
>>>>> Thx.
>>>>>
>>>>> - Cris
>>>>> ------------------------------------------------------------------------------
>>>>> WatchGuard Dimension instantly turns raw network data into actionable
>>>>> security intelligence. It gives you real-time visual feedback on key
>>>>> security issues and trends.  Skip the complicated setup - simply import
>>>>> a virtual appliance and go from zero to informed in seconds.
>>>>> http://pubads.g.doubleclick.net/gampad/clk?id=123612991&iu=/4140/ostg.clktrk
>>>>> _______________________________________________
>>>>> Gmod-ajax mailing list
>>>>> [hidden email]
>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>>>>
>>>>
>>>> ------------------------------------------------------------------------------
>>>> WatchGuard Dimension instantly turns raw network data into actionable
>>>> security intelligence. It gives you real-time visual feedback on key
>>>> security issues and trends.  Skip the complicated setup - simply import
>>>> a virtual appliance and go from zero to informed in seconds.
>>>> http://pubads.g.doubleclick.net/gampad/clk?id=123612991&iu=/4140/ostg.clktrk
>>>> _______________________________________________
>>>> Gmod-ajax mailing list
>>>> [hidden email]
>>>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>>>
>>>
>>> -- The Wellcome Trust Sanger Institute is operated by Genome Research
>>> Limited, a charity registered in England with number 1021457 and a
>>> company registered in England with number 2742969, whose registered
>>> office is 215 Euston Road, London, NW1 2BE.
>>>
>>>
>>> ------------------------------------------------------------------------------
>>> WatchGuard Dimension instantly turns raw network data into actionable
>>> security intelligence. It gives you real-time visual feedback on key
>>> security issues and trends.  Skip the complicated setup - simply import
>>> a virtual appliance and go from zero to informed in seconds.
>>> http://pubads.g.doubleclick.net/gampad/clk?id=123612991&iu=/4140/ostg.clktrk
>>>
>>>
>>>
>>> _______________________________________________
>>> Gmod-ajax mailing list
>>> [hidden email]
>>> https://lists.sourceforge.net/lists/listinfo/gmod-ajax
>>>

------------------------------------------------------------------------------
WatchGuard Dimension instantly turns raw network data into actionable
security intelligence. It gives you real-time visual feedback on key
security issues and trends.  Skip the complicated setup - simply import
a virtual appliance and go from zero to informed in seconds.
http://pubads.g.doubleclick.net/gampad/clk?id=123612991&iu=/4140/ostg.clktrk
_______________________________________________
Gmod-ajax mailing list
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