BioC experimental data: CHECK report for RNAinteractMAPK on pitt

Package: RNAinteractMAPK

Version: 1.0.6

Command: /Library/Frameworks/R.framework/Versions/2.15/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch RNAinteractMAPK_1.0.6.tar.gz

StartedAt: 2012-06-21 15:12:37 -0700 (Thu, 21 Jun 2012)

EndedAt: 2012-06-21 15:17:48 -0700 (Thu, 21 Jun 2012)

EllapsedTime: 311.4 seconds

RetCode: 0

Status: OK

CheckDir: RNAinteractMAPK.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.11-data-experiment/meat/RNAinteractMAPK.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 'RNAinteractMAPK/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'RNAinteractMAPK' version '1.0.6'
* 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 'RNAinteractMAPK' can be installed ... OK
* checking installed package size ... NOTE
  installed size is 11.3Mb
  sub-directories of 1Mb or more:
    data      6.7Mb
    extdata   3.6Mb
* 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
MAPK.cv.TPS: warning in matrix(0, nr = 6, nc = 6): partial argument
  match of 'nr' to 'nrow'
MAPK.cv.TPS: warning in matrix(0, nr = 6, nc = 6): partial argument
  match of 'nc' to 'ncol'
MAPK.cv.TPS: warning in matrix(0, nr = 64, nc = 56): partial argument
  match of 'nr' to 'nrow'
MAPK.cv.TPS: warning in matrix(0, nr = 64, nc = 56): partial argument
  match of 'nc' to 'ncol'
MAPK.cv.TPS: warning in matrix(0, nr = 8, nc = 56): partial argument
  match of 'nr' to 'nrow'
MAPK.cv.TPS: warning in matrix(0, nr = 8, nc = 56): partial argument
  match of 'nc' to 'ncol'
MAPK.estimate.TPS: warning in matrix(z, nr = n.in, nc = n.in): partial
  argument match of 'nr' to 'nrow'
MAPK.estimate.TPS: warning in matrix(z, nr = n.in, nc = n.in): partial
  argument match of 'nc' to 'ncol'
MAPK.estimate.TPS: warning in matrix(znew, nr = n.out, nc = n.out):
  partial argument match of 'nr' to 'nrow'
MAPK.estimate.TPS: warning in matrix(znew, nr = n.out, nc = n.out):
  partial argument match of 'nc' to 'ncol'
MAPK.estimate.TPS: warning in matrix(zpred, nr = n.in, nc = n.in):
  partial argument match of 'nr' to 'nrow'
MAPK.estimate.TPS: warning in matrix(zpred, nr = n.in, nc = n.in):
  partial argument match of 'nc' to 'ncol'
MAPK.getCV: warning in matrix(NA, nr = length(y), nc = nlevels(y)):
  partial argument match of 'nr' to 'nrow'
MAPK.getCV: warning in matrix(NA, nr = length(y), nc = nlevels(y)):
  partial argument match of 'nc' to 'ncol'
MAPK.getXY: warning in matrix(0, nr = length(I), nc = 2): partial
  argument match of 'nr' to 'nrow'
MAPK.getXY: warning in matrix(0, nr = length(I), nc = 2): partial
  argument match of 'nc' to 'ncol'
MAPK.plot.TPS.single: warning in matrix(col[257], nr = n.out, nc =
  n.out): partial argument match of 'nr' to 'nrow'
MAPK.plot.TPS.single: warning in matrix(col[257], nr = n.out, nc =
  n.out): partial argument match of 'nc' to 'ncol'
MAPK.plot.heatmap.raster: warning in matrix(colid, nr = nrow(X), nc =
  ncol(X)): partial argument match of 'nr' to 'nrow'
MAPK.plot.heatmap.raster: warning in matrix(colid, nr = nrow(X), nc =
  ncol(X)): partial argument match of 'nc' to 'ncol'
MAPK.report.gene.lists.paper: warning in matrix(row.names(p.value), nr
  = dim(p.value)[1], nc = dim(p.value)[2]): partial argument match of
  'nr' to 'nrow'
MAPK.report.gene.lists.paper: warning in matrix(row.names(p.value), nr
  = dim(p.value)[1], nc = dim(p.value)[2]): partial argument match of
  'nc' to 'ncol'
MAPK.report.gene.lists.paper: warning in matrix(colnames(p.value), nr =
  dim(p.value)[2], nc = dim(p.value)[1]): partial argument match of
  'nr' to 'nrow'
MAPK.report.gene.lists.paper: warning in matrix(colnames(p.value), nr =
  dim(p.value)[2], nc = dim(p.value)[1]): partial argument match of
  'nc' to 'ncol'
MAPK.report.gene.lists.paper: warning in matrix(main, nr =
  dim(p.value)[1], nc = dim(p.value)[2]): partial argument match of
  'nr' to 'nrow'
MAPK.report.gene.lists.paper: warning in matrix(main, nr =
  dim(p.value)[1], nc = dim(p.value)[2]): partial argument match of
  'nc' to 'ncol'
MAPK.report.gene.lists.paper: warning in matrix(main, nr =
  dim(p.value)[2], nc = dim(p.value)[1]): partial argument match of
  'nr' to 'nrow'
MAPK.report.gene.lists.paper: warning in matrix(main, nr =
  dim(p.value)[2], nc = dim(p.value)[1]): partial argument match of
  'nc' to 'ncol'
MAPK.report.gene.lists.paper: warning in matrix(names(maint) %in%
  controls, nr = dim(p.value)[1], nc = dim(p.value)[2]): partial
  argument match of 'nr' to 'nrow'
MAPK.report.gene.lists.paper: warning in matrix(names(maint) %in%
  controls, nr = dim(p.value)[1], nc = dim(p.value)[2]): partial
  argument match of 'nc' to 'ncol'
MAPK.report.gene.lists.paper: warning in matrix(names(maint) %in%
  controls, nr = dim(p.value)[2], nc = dim(p.value)[1]): partial
  argument match of 'nr' to 'nrow'
MAPK.report.gene.lists.paper: warning in matrix(names(maint) %in%
  controls, nr = dim(p.value)[2], nc = dim(p.value)[1]): partial
  argument match of 'nc' to 'ncol'
MAPK.smooth.scatter: warning in matrix(colid, nr = nrow(D$z), nc =
  ncol(D$z)): partial argument match of 'nr' to 'nrow'
MAPK.smooth.scatter: warning in matrix(colid, nr = nrow(D$z), nc =
  ncol(D$z)): partial argument match of 'nc' to 'ncol'
* 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... 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 were 2 notes.
See
  '/Users/biocbuild/bbs-2.11-data-experiment/meat/RNAinteractMAPK.Rcheck/00check.log'
for details.

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

* DONE (RNAinteractMAPK)

name	user	system	elapsed
Dmel2PPMAPK	3.785	0.142	3.963
ElpB1phenotype	0.009	0.002	0.011
Networks	0.007	0.002	0.010
PhysicalInteractions	0.009	0.002	0.012
RNAinteractMAPK-package	2.221	0.129	2.367
cellTiterGlo	0.007	0.001	0.008
dsRNAiDilutionSeriesData	0.062	0.072	0.140
mRNAdoubleKDefficiency	0.007	0.002	0.009
mRNAsingleKDefficiency	0.007	0.001	0.008
pathwayMembership	0.004	0.001	0.006
singleKDphenotype	0.014	0.003	0.017

Summary

Command output