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Package 594/658HostnameOS / ArchBUILDCHECKBUILD BIN
snm 1.7.0
Brig Mecham
Snapshot Date: 2013-03-24 17:01:43 -0700 (Sun, 24 Mar 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/snm
Last Changed Rev: 70052 / Revision: 74774
Last Changed Date: 2012-10-01 15:43:56 -0700 (Mon, 01 Oct 2012)
george2 Linux (Ubuntu 12.04.1 LTS) / x86_64  OK [ OK ]
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
petty Mac OS X Leopard (10.5.8) / i386  OK  OK  OK 

Summary

Package: snm
Version: 1.7.0
Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings snm_1.7.0.tar.gz
StartedAt: 2013-03-25 04:44:42 -0700 (Mon, 25 Mar 2013)
EndedAt: 2013-03-25 04:53:11 -0700 (Mon, 25 Mar 2013)
EllapsedTime: 508.2 seconds
RetCode: 0
Status:  OK 
CheckDir: snm.Rcheck
Warnings: 0

Command output

* using log directory ‘/home/biocbuild/bbs-2.12-bioc/meat/snm.Rcheck’
* using R version 3.0.0 beta (2013-03-19 r62328)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘snm/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘snm’ version ‘1.7.0’
* 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 ... [17s/17s] 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 ... [301s/342s] OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
snm              278.041  1.432 320.065
sim.preProcessed  11.701  0.444  12.386
* 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
  ‘/home/biocbuild/bbs-2.12-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.snm0.0280.0000.027
plot.snm0.0160.0000.016
sim.doubleChannel0.0120.0000.013
sim.preProcessed11.701 0.44412.386
sim.refDesign0.0160.0000.019
sim.singleChannel0.0080.0000.008
snm278.041 1.432320.065
summary.snm0.0040.0000.006