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ParallLogicReg log file (check_x86_64_windows)
* using log directory 'R:/run/building/build_2013-02-15-08-50/RF_PKG_CHECK/PKGS/ParallLogicReg.Rcheck'
* using R version 2.15.2 Patched (2013-01-31 r61797)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 hidden files and directories ... OK
* checking whether package 'ParallLogicReg' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for portable file names ... 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'
61: end=10 # the last gene id that will be run
62: 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: 18.89 seconds.