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Package 510/565HostnameOS / ArchBUILDCHECKBUILD BIN
snm 1.5.0
Brig Mecham
Snapshot Date: 2012-06-20 15:22:40 -0700 (Wed, 20 Jun 2012)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/snm
Last Changed Rev: 64680 / Revision: 66885
Last Changed Date: 2012-03-30 15:15:56 -0700 (Fri, 30 Mar 2012)
lamb1 Linux (openSUSE 12.1) / x86_64  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
pitt Mac OS X Leopard (10.5.8) / i386  OK [ OK ] OK 
perceval Mac OS X Leopard (10.5.8) / i386  OK  OK  OK 

Summary

Package: snm
Version: 1.5.0
Command: /Library/Frameworks/R.framework/Versions/2.15/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch snm_1.5.0.tar.gz
StartedAt: 2012-06-21 03:44:12 -0700 (Thu, 21 Jun 2012)
EndedAt: 2012-06-21 03:51:14 -0700 (Thu, 21 Jun 2012)
EllapsedTime: 422.3 seconds
RetCode: 0
Status:  OK 
CheckDir: snm.Rcheck
Warnings: 0

Command output

* using log directory '/Users/biocbuild/bbs-2.11-bioc/meat/snm.Rcheck'
* using R version 2.15.0 Patched (2012-04-26 r59216)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'snm/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'snm' version '1.5.0'
* 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 whether package 'snm' can be installed ... 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 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 sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... OK
* 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-2.11-bioc/meat/snm.Rcheck/00check.log'
for details.

snm.Rcheck/00install.out:

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

* DONE (snm)

snm.Rcheck/snm-Ex.timings:

nameusersystemelapsed
fitted.snm0.0010.0000.001
plot.snm0.0000.0010.000
sim.doubleChannel000
sim.preProcessed8.0481.0329.239
sim.refDesign0.0010.0010.000
sim.singleChannel0.0010.0000.001
snm243.747 38.274296.463
summary.snm0.0010.0010.001