BioC experimental data: CHECK report for RNAinteractMAPK on moscato2

Package: RNAinteractMAPK

Version: 1.0.6

Command: rm -rf RNAinteractMAPK.buildbin-libdir && mkdir RNAinteractMAPK.buildbin-libdir && E:\biocbld\bbs-2.10-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=RNAinteractMAPK.buildbin-libdir RNAinteractMAPK_1.0.6.tar.gz >RNAinteractMAPK-install.out 2>&1 && E:\biocbld\bbs-2.10-bioc\R\bin\R.exe CMD check --library=RNAinteractMAPK.buildbin-libdir --install="check:RNAinteractMAPK-install.out" --force-multiarch --no-vignettes --timings RNAinteractMAPK_1.0.6.tar.gz && mv RNAinteractMAPK.buildbin-libdir/* RNAinteractMAPK.Rcheck/ && rmdir RNAinteractMAPK.buildbin-libdir

StartedAt: 2012-09-23 13:18:06 -0700 (Sun, 23 Sep 2012)

EndedAt: 2012-09-23 13:23:18 -0700 (Sun, 23 Sep 2012)

EllapsedTime: 312.0 seconds

RetCode: 0

Status: OK

CheckDir: RNAinteractMAPK.Rcheck

Warnings: 0

* using log directory 'E:/biocbld/bbs-2.10-data-experiment/meat/RNAinteractMAPK.Rcheck'
* using R version 2.15.1 (2012-06-22)
* using platform: i386-pc-mingw32 (32-bit)
* using session charset: ISO8859-1
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 installed files from 'inst/doc' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... 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
  'E:/biocbld/bbs-2.10-data-experiment/meat/RNAinteractMAPK.Rcheck/00check.log'
for details.


install for i386

* 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

install for x64

* installing *source* package 'RNAinteractMAPK' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'RNAinteractMAPK' as RNAinteractMAPK_1.0.6.zip

* DONE (RNAinteractMAPK)

Summary

Command output