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RNAinteractMAPK 1.0.6
Bernd Fischer
Snapshot Date: 2012-09-23 10:15:26 -0700 (Sun, 23 Sep 2012)
URL: https://hedgehog.fhcrc.org/bioc-data/trunk/experiment/pkgs/RNAinteractMAPK
Last Changed Rev: 2037 / Revision: 2159
Last Changed Date: 2012-03-30 15:20:09 -0700 (Fri, 30 Mar 2012)
lamb2 Linux (openSUSE 11.4) / 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: 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: 2012-09-23 12:58:59 -0700 (Sun, 23 Sep 2012)
EndedAt: 2012-09-23 13:03:29 -0700 (Sun, 23 Sep 2012)
EllapsedTime: 270.7 seconds
RetCode: 0
Status:  OK 
CheckDir: RNAinteractMAPK.Rcheck
Warnings: 0

Command output

* using log directory '/Users/biocbuild/bbs-2.10-data-experiment/meat/RNAinteractMAPK.Rcheck'
* using R version 2.15.1 (2012-06-22)
* 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-2.10-data-experiment/meat/RNAinteractMAPK.Rcheck/00check.log'
for details.

RNAinteractMAPK.Rcheck/00install.out:

* 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)

RNAinteractMAPK.Rcheck/RNAinteractMAPK-Ex.timings:

nameusersystemelapsed
Dmel2PPMAPK2.8320.0862.919
ElpB1phenotype0.0070.0020.008
Networks0.0060.0020.007
PhysicalInteractions0.0030.0010.004
RNAinteractMAPK-package1.8530.0951.952
cellTiterGlo0.0060.0010.007
dsRNAiDilutionSeriesData0.0540.0570.112
mRNAdoubleKDefficiency0.0060.0010.007
mRNAsingleKDefficiency0.0060.0010.007
pathwayMembership0.0030.0010.004
singleKDphenotype0.0110.0020.013