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ParallLogicReg log file (check_x86_64_linux)

Fri Feb 15 10:58:53 2013: Checking package ParallLogicReg (SVN revision 5) ...
* using log directory ‘/mnt/building/build_2013-02-15-08-50/RF_PKG_CHECK/PKGS/ParallLogicReg.Rcheck’
* using R version 2.15.2 Patched (2013-02-13 r61942)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* checking for file ‘ParallLogicReg/DESCRIPTION’ ... OK
* this is package ‘ParallLogicReg’ version ‘1.0-0’
* checking CRAN incoming feasibility ... NOTE
Maintainer: ‘Unitsa Sangket ’
New submission
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for executable files ... OK
* checking for hidden files and directories ... OK
* checking whether package ‘ParallLogicReg’ can be installed ... [1s/2s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking for unstated dependencies in R code ... WARNING
‘library’ or ‘require’ calls not declared from:
  ‘LogicReg’ ‘Rmpi’
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of the ‘Writing R Extensions’ manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... WARNING
Foreign function call without ‘PACKAGE’ argument:
  .Call("mpi_finalize", ...)
See the chapter ‘System and foreign language interfaces’ of the
‘Writing R Extensions’ manual.
* checking R code for possible problems ... NOTE
Job_management: no visible global function definition for
  ‘mpi.spawn.Rslaves’
Job_management: no visible global function definition for
  ‘mpi.comm.size’
Job_management: no visible global function definition for ‘mpi.quit’
Job_management : .Last: no visible global function definition for
  ‘mpi.comm.size’
Job_management : .Last: no visible global function definition for
  ‘mpi.close.Rslaves’
Job_management : foldslave: no visible global function definition for
  ‘mpi.send.Robj’
Job_management : foldslave: no visible global function definition for
  ‘mpi.recv.Robj’
Job_management : foldslave: no visible global function definition for
  ‘mpi.any.source’
Job_management : foldslave: no visible global function definition for
  ‘mpi.any.tag’
Job_management : foldslave: no visible global function definition for
  ‘mpi.get.sourcetag’
Job_management : foldslave: no visible global function definition for
  ‘genes_nperm’
Job_management: no visible global function definition for
  ‘mpi.universe.size’
Job_management: no visible binding for global variable ‘len_gid’
Job_management: no visible binding for global variable ‘begin’
Job_management: no visible global function definition for
  ‘mpi.bcast.Robj2slave’
Job_management: no visible global function definition for
  ‘mpi.bcast.cmd’
Job_management: no visible global function definition for
  ‘mpi.recv.Robj’
Job_management: no visible global function definition for
  ‘mpi.any.source’
Job_management: no visible global function definition for ‘mpi.any.tag’
Job_management: no visible global function definition for
  ‘mpi.get.sourcetag’
Job_management: no visible global function definition for
  ‘mpi.send.Robj’
Job_management: no visible global function definition for
  ‘mpi.close.Rslaves’
ParallLogicReg : genes_nperm: no visible global function definition for
  ‘logreg’
SeqLogicReg: no visible binding for global variable ‘begin’
SeqLogicReg: no visible binding for global variable ‘ngenes_skip’
SeqLogicReg: no visible binding for global variable ‘gidlist_here’
SeqLogicReg: no visible binding for global variable ‘gene01’
SeqLogicReg: no visible binding for global variable ‘nperm’
SeqLogicReg: no visible binding for global variable ‘niter’
SeqLogicReg: no visible global function definition for ‘logreg’
SeqLogicReg: no visible binding for global variable ‘resp’
SeqLogicReg: no visible binding for global variable ‘perYY’
SeqLogicReg: no visible binding for global variable ‘Chr’
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  ‘Job_management’ ‘ParallLogicReg’ ‘SeqLogicReg’
All user-level objects in a package should have documentation entries.
See the chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... WARNING
Assignments in \usage in documentation object 'ParallLogicReg':
  output = ParallLogicReg(infile, resp, begin, end, nperm, niter)

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See the chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... WARNING
Warning: parse error in file ‘ParallLogicReg-Ex.R’:
1: unexpected ‘in’
60: end=10                          # the last gene id that will be run
61: in
   ^
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking examples ... ERROR
Running examples in ‘ParallLogicReg-Ex.R’ failed
The error most likely occurred in:

> ### Name: ParallLogicReg
> ### Title: Logic regression analyses using parallel computing
> ### Aliases: ParallLogiReg
> 
> ### ** Examples
> 
> #--------------------------------------------------------------------------
> #An example run on Sun Grid Engine.
> #You have to create two files, which are a ".sh" file, and a ".R" file.
> #for more information please visit http://math.acadiau.ca/ACMMaC/Rmpi/submitting.html
> #--------------------------------------------------------------------------
> 
> #File 1 (R_script.sh):
> ###########################################################################
> #!/bin/bash
> 
> # Run in the current directory
> #$ -cwd
> 
> #$ -j y
> 
> #$ -V
> 
> # Run using bash
> #$ -S /bin/bash
> 
> # Set the number of processors
> # For example, 2 means one processor is master and slave1, 
> # and the rest of processors are slaves.
> #$ -pe lam 2
> 
> # Run the job. 
> # lamrun -np 1 R  --slave CMD BATCH R_script.R R_script_sh.Rout
> 
> ###########################################################################
> #!!! remove "#" out from "lamrun" command when run the file
> 
> 
> #File 2 (R_script.R):
> ###########################################################################
> library(ParallLogicReg)
> 
> resp=c(rep(0,2935),rep(1,1745))	# number of controls = 2,935; number of cases = 1,745
>  
> nperm=20			# number of permutations
> niter=20				# number of iterations
> begin=1				# the first gene id that will be run
> end=10				# the last gene id that will be run
> in=("input.txt")   	# data will be run
Error: unexpected 'in' in "in"
Execution halted
Run time: 26.44 seconds.