BioC 2.12: CHECK report for snm on pelham

Package: snm

Version: 1.8.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch snm_1.8.0.tar.gz

StartedAt: 2013-05-01 11:04:01 -0700 (Wed, 01 May 2013)

EndedAt: 2013-05-01 11:11:29 -0700 (Wed, 01 May 2013)

EllapsedTime: 447.6 seconds

RetCode: 0

Status: OK

CheckDir: snm.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/snm.Rcheck'
* using R version 3.0.0 Patched (2013-04-08 r62531)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'snm/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'snm' version '1.8.0'
* 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 for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package 'snm' can be installed ... [13s/13s] OK
* checking installed package size ... OK
* checking package directory ... 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 for unstated dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
calcArrayEffects: warning in matrix(rff@ranef[offset:(-1 + offset +
  nrow(lf$FL$trms[[i]]$Zt))], nr = length(unique(snm.obj$int.var[,
  i]))): partial argument match of 'nr' to 'nrow'
fit.model: warning in matrix(0, nr = 1, nc = 1): partial argument match
  of 'nr' to 'nrow'
fit.model: warning in matrix(0, nr = 1, nc = 1): partial argument match
  of 'nc' to 'ncol'
fit.model: warning in matrix(rff@resid, nr = dim(Y.pooled)[1]): partial
  argument match of 'nr' to 'nrow'
sim.doubleChannel: warning in matrix(gmeans, nr = np, nc = na): partial
  argument match of 'nr' to 'nrow'
sim.doubleChannel: warning in matrix(gmeans, nr = np, nc = na): partial
  argument match of 'nc' to 'ncol'
sim.doubleChannel: warning in matrix(rnorm(length(data), 0, 0.25), nr =
  nrow(data), nc = ncol(data)): partial argument match of 'nr' to
  'nrow'
sim.doubleChannel: warning in matrix(rnorm(length(data), 0, 0.25), nr =
  nrow(data), nc = ncol(data)): partial argument match of 'nc' to
  'ncol'
sim.function.var: warning in matrix(0, nr = length(lab), nc = ncol(x)):
  partial argument match of 'nr' to 'nrow'
sim.function.var: warning in matrix(0, nr = length(lab), nc = ncol(x)):
  partial argument match of 'nc' to 'ncol'
sim.intensity.dep: warning in matrix(0, nr = ncol(x), nc = spline.dim):
  partial argument match of 'nr' to 'nrow'
sim.intensity.dep: warning in matrix(0, nr = ncol(x), nc = spline.dim):
  partial argument match of 'nc' to 'ncol'
sim.preProcessed: warning in matrix(gmeans, nr = np, nc = na): partial
  argument match of 'nr' to 'nrow'
sim.preProcessed: warning in matrix(gmeans, nr = np, nc = na): partial
  argument match of 'nc' to 'ncol'
sim.preProcessed: warning in matrix(rnorm(length(data), 0, 0.25), nr =
  nrow(data), nc = ncol(data)): partial argument match of 'nr' to
  'nrow'
sim.preProcessed: warning in matrix(rnorm(length(data), 0, 0.25), nr =
  nrow(data), nc = ncol(data)): partial argument match of 'nc' to
  'ncol'
sim.probe.specific: warning in matrix(0, nr = length(lab), nc =
  ncol(x)): partial argument match of 'nr' to 'nrow'
sim.probe.specific: warning in matrix(0, nr = length(lab), nc =
  ncol(x)): partial argument match of 'nc' to 'ncol'
sim.refDesign: warning in matrix(gmeans, nr = np, nc = na): partial
  argument match of 'nr' to 'nrow'
sim.refDesign: warning in matrix(gmeans, nr = np, nc = na): partial
  argument match of 'nc' to 'ncol'
sim.refDesign: warning in matrix(rnorm(length(M), 0, 0.25), nr =
  nrow(M), nc = ncol(M)): partial argument match of 'nr' to 'nrow'
sim.refDesign: warning in matrix(rnorm(length(M), 0, 0.25), nr =
  nrow(M), nc = ncol(M)): partial argument match of 'nc' to 'ncol'
sim.singleChannel: warning in matrix(gmeans, nr = np, nc = na): partial
  argument match of 'nr' to 'nrow'
sim.singleChannel: warning in matrix(gmeans, nr = np, nc = na): partial
  argument match of 'nc' to 'ncol'
sim.singleChannel: warning in matrix(rnorm(length(data), 0, 0.25), nr =
  nrow(data), nc = ncol(data)): partial argument match of 'nr' to
  'nrow'
sim.singleChannel: warning in matrix(rnorm(length(data), 0, 0.25), nr =
  nrow(data), nc = ncol(data)): partial argument match of 'nc' to
  'ncol'
snm.diagnostic.plot: warning in axis(side = 2, at = 500, label = "
  500+"): partial argument match of 'label' to 'labels'
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... [311s/318s] OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
snm              267.674 24.428 299.044
sim.preProcessed  10.785  0.786  11.648
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignettes ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There was 1 note.
See
  '/Users/biocbuild/bbs-2.12-bioc/meat/snm.Rcheck/00check.log'
for details.

* installing *source* package 'snm' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (snm)

name	user	system	elapsed
fitted.snm	0.010	0.006	0.018
plot.snm	0.009	0.004	0.013
sim.doubleChannel	0.009	0.002	0.011
sim.preProcessed	10.785	0.786	11.648
sim.refDesign	0.241	0.064	0.307
sim.singleChannel	0.003	0.006	0.010
snm	267.674	24.428	299.044
summary.snm	0.003	0.006	0.009

Summary

Command output