Problems in batch mode

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Problems in batch mode

Tomas Goicoa

Dear R-users,

I am trying to run some simulations in batch mode.  In an older version
of  the program, I used

rterm --vsize=100M  --nsize=5000K --restore --save <input file> output file,

however, in the new version R 2.2.0 , the  parameters vsize and nsize are
ignored.

I can use the command memory.limit to increase memory, but I am not sure if
this corresponds to vsize and nsize.

Does anyone know how can I set these quantities now?

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Re: Problems in batch mode

Brian Ripley
Oh, please do your homework (in this case `An Introduction to R' and the
NEWS file).

R 2.2.0 is not `new' (2.2.1 is), and those flags have been obselete for
years (literally).

On Tue, 20 Dec 2005, Tomas Goicoa wrote:

>
> Dear R-users,
>
> I am trying to run some simulations in batch mode.  In an older version
> of  the program, I used
>
> rterm --vsize=100M  --nsize=5000K --restore --save <input file> output file,
>
> however, in the new version R 2.2.0 , the  parameters vsize and nsize are
> ignored.
>
> I can use the command memory.limit to increase memory, but I am not sure if
> this corresponds to vsize and nsize.
>
> Does anyone know how can I set these quantities now?

--
Brian D. Ripley,                  [hidden email]
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford,             Tel:  +44 1865 272861 (self)
1 South Parks Road,                     +44 1865 272866 (PA)
Oxford OX1 3TG, UK                Fax:  +44 1865 272595

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Extracting data from .zip file in WINDOWS version of package

Jain, Nitin
In reply to this post by Tomas Goicoa
Hello,

I am building a R-package for Genetics analysis. The accepted data is in pedigree (.ped) file format.

To load the data (say CAMP.ped) from "data" directory, I have a function "CAMP.R", which does the job.
The package builds successfully in Linux (.tar.gz) and the data loads successfully by "data(CAMP)".

However, when I build the package in WINDOWS, the data directory is zipped, and the command "data(CAMP)"
gives an error -
Error in readGenes(gfile = "CAMP.ped",....)
Genotype file CAMP.ped does not exist.

While debugging "data(CAMP)", I found that only the file "CAMP.R" is extracted temporarily, and not the file
"CAMP.ped" - which causes the error.

Linux version does not face this problem as the data directory is not zipped.

Could you please suggest a way around for this problem?

Thanks.

Best,
Nitin
______________________
Nitin Jain, PhD
<[hidden email]>
Non Clinical Statistics
Pfizer, Inc. (Groton, CT)
Bldg: 260, # 1451
Ph:  (860) 686-2526 (Office)
Fax: (860) 686-6170

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Re: Extracting data from .zip file in WINDOWS version of package

Brian Ripley
On Tue, 20 Dec 2005, Jain, Nitin wrote:

> I am building a R-package for Genetics analysis. The accepted data is in pedigree (.ped) file format.
>
> To load the data (say CAMP.ped) from "data" directory, I have a function "CAMP.R", which does the job.
> The package builds successfully in Linux (.tar.gz) and the data loads successfully by "data(CAMP)".
>
> However, when I build the package in WINDOWS, the data directory is zipped, and the command "data(CAMP)"
> gives an error -
> Error in readGenes(gfile = "CAMP.ped",....)
> Genotype file CAMP.ped does not exist.
>
> While debugging "data(CAMP)", I found that only the file "CAMP.R" is extracted temporarily, and not the file
> "CAMP.ped" - which causes the error.
>
> Linux version does not face this problem as the data directory is not zipped.

Well, not zipped by default: it can be zipped.

> Could you please suggest a way around for this problem?

You need to read the `Writing R Extensions' manual and set the appropriate
option in the DESCRIPTION file.  Search for 'ZipData'

--
Brian D. Ripley,                  [hidden email]
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford,             Tel:  +44 1865 272861 (self)
1 South Parks Road,                     +44 1865 272866 (PA)
Oxford OX1 3TG, UK                Fax:  +44 1865 272595

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Re: Extracting data from .zip file in WINDOWS version of package

Jain, Nitin
In reply to this post by Jain, Nitin
Dear Andy and Prof. Ripley,

Thank you very much for the suggestions. Tried the "ZipData" option, and it solved my problem.
I think Andy's suggestion should also work, but haven't tried it yet.

I appreciate such a speedy response.

Best regards,
Nitin

______________________
Nitin Jain, PhD
<[hidden email]>
Non Clinical Statistics
Pfizer, Inc. (Groton, CT)
Bldg: 260, # 1451
Ph:  (860) 686-2526 (Office)
Fax: (860) 686-6170



-----Original Message-----
From: Prof Brian Ripley [mailto:[hidden email]]
Sent: Tuesday, December 20, 2005 2:15 PM
To: Jain, Nitin
Cc: [hidden email]; [hidden email]
Subject: Re: [R] Extracting data from .zip file in WINDOWS version of
package


On Tue, 20 Dec 2005, Jain, Nitin wrote:

> I am building a R-package for Genetics analysis. The accepted data is in pedigree (.ped) file format.
>
> To load the data (say CAMP.ped) from "data" directory, I have a function "CAMP.R", which does the job.
> The package builds successfully in Linux (.tar.gz) and the data loads successfully by "data(CAMP)".
>
> However, when I build the package in WINDOWS, the data directory is zipped, and the command "data(CAMP)"
> gives an error -
> Error in readGenes(gfile = "CAMP.ped",....)
> Genotype file CAMP.ped does not exist.
>
> While debugging "data(CAMP)", I found that only the file "CAMP.R" is extracted temporarily, and not the file
> "CAMP.ped" - which causes the error.
>
> Linux version does not face this problem as the data directory is not zipped.

Well, not zipped by default: it can be zipped.

> Could you please suggest a way around for this problem?

You need to read the `Writing R Extensions' manual and set the appropriate
option in the DESCRIPTION file.  Search for 'ZipData'

--
Brian D. Ripley,                  [hidden email]
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford,             Tel:  +44 1865 272861 (self)
1 South Parks Road,                     +44 1865 272866 (PA)
Oxford OX1 3TG, UK                Fax:  +44 1865 272595
----------------------------------------------------------------------
LEGAL NOTICE\ Unless expressly stated otherwise, this messag...{{dropped}}

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