R Installation Problems at Ideom with latest Java and R 3.1.2

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Li

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Dec 12, 2014, 10:11:51 PM12/12/14
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Hi,

I am a new user on the ideom.  Java JRE 8, update 25 and R.3.1.2 (32 and 64 bits) are installed in PCs with Win7 or 8.1.  In ideom, try to install the R packages in the R script menu, but has difficulties to complete.  Here are latest errors.  Hope you could guide me to overcome these.  Thanks.

The downloaded binary packages are in
        C:\Users\Norman1\AppData\Local\Temp\RtmpcVEJG1\downloaded_packages
> a
Error: object 'a' not found
> source ("http://puma.ibls.gla.ac.uk/mzmatch.R/install_mzmatch.R")
trying URL 'http://puma.ibls.gla.ac.uk/mzmatch.R/mzmatch.R.tar.gz'
Content type 'application/x-gzip' length 117291 bytes (114 Kb)
opened URL
downloaded 114 Kb

ERROR: dependency 'R.utils' is not available for package 'mzmatch.R'
* removing 'C:/software/R-3.1.2/library/mzmatch.R'
Warning messages:
1: In download.file("http://puma.ibls.gla.ac.uk/mzmatch.R/mzmatch.R.tar.gz",  :
  downloaded length 117291 != reported length 117291
2: running command '"C:/software/R-3.1.2/bin/x64/
R" CMD INSTALL -l "C:\software\R-3.1.2\library" "mzmatch.R.tar.gz"' had status 1
3: In install.packages(pkgs = "mzmatch.R.tar.gz", repos = NULL, type = "source") :
  installation of package ‘mzmatch.R.tar.gz’ had non-zero exit status
> library (rJava)
> if (.Platform$OS.type == 'windows' & .Platform$r_arch == 'i386') {print('Loading XP 32bit startup')
+ .jinit ()}
> library (mzmatch.R)
Error in library(mzmatch.R) : there is no package called ‘mzmatch.R’
> mzmatch.init (16000)

Li

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Dec 12, 2014, 10:53:19 PM12/12/14
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Use old R 2.0.1 and do the same installation of R Script Menu, similar errors occur:


The downloaded binary packages are in
        C:\Users\Norman1\AppData\Local\Temp\RtmpeG3dyE\downloaded_packages
Warning: unable to access index for repository http://brainarray.mbni.med.umich.edu/bioc/bin/windows/contrib/2.15

> a
Error: object 'a' not found
> source ("http://puma.ibls.gla.ac.uk/mzmatch.R/install_mzmatch.R")
trying URL 'http://puma.ibls.gla.ac.uk/mzmatch.R/mzmatch.R.tar.gz'
Content type 'application/x-gzip' length 117291 bytes (114 Kb)
opened URL
downloaded 114 Kb

ERROR: dependency 'R.utils' is not available for package 'mzmatch.R'
* removing 'C:/software/R-2.15.1/library/mzmatch.R'
Warning messages:
1: running command 'C:/software/R-2.15.1/bin/x64/R CMD INSTALL -l "C:/software/R-2.15.1/library"   "mzmatch.R.tar.gz"' had status 1
2: In install.packages(pkgs = "mzmatch.R.tar.gz", repos = NULL, type = "source") :

  installation of package ‘mzmatch.R.tar.gz’ had non-zero exit status
> library (rJava)
Warning message:
package ‘rJava’ was built under R version 2.15.3
> if (.Platform$OS.type == 'windows' & .Platform$r_arch == 'i386') {print('Loading XP 32bit startup')
+ .jinit ()}
> library (mzmatch.R)
Error in library(mzmatch.R) : there is no package called ‘mzmatch.R’
> mzmatch.init (16000)
Error: could not find function "mzmatch.init"

Li

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Dec 15, 2014, 8:56:14 PM12/15/14
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Installed R.Utlis and mzMatch.  Use Rgui 32 bit, process the demo data in ideom combined box.  The process moved ahead in R.  But it stop with a major error

...
Error: A fatal exception has occurred. Program will exit.
Invalid initial heap size: -Xms16000m
The specified size exceeds the maximum representable size.
Error: Could not create the Java Virtual Machine.
...



On Friday, December 12, 2014 10:11:51 PM UTC-5, Li wrote:

Darren Creek

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Dec 15, 2014, 11:43:32 PM12/15/14
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For 32bit R it can only access 4Gb of RAM, so you'll need to set the available RAM to something like 3500 (in column E on IDEOM settings sheet towards the bottom). 
Note that with this memory it will only work for smaller studes (e.g. <30 samples on average). For larger studies you'd need the 64 bit version. 
Nevertheless, good idea to try the 32bit version to troubleshoot the issues you've been having with R packages.

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--
Dr Darren Creek
 
NHMRC CJ Martin Fellow / Lecturer
Drug Delivery, Disposition and Dynamics
Monash Institute of Pharmaceutical Sciences
Monash University, Parkville campus
381 Royal Parade, Parkville, Vic, 3052
 

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