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Package 2/609HostnameOS / ArchBUILDCHECKBUILD BIN
a4Base 1.6.0
Tobias Verbeke
Snapshot Date: 2013-03-24 16:21:20 -0700 (Sun, 24 Mar 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_11/madman/Rpacks/a4Base
Last Changed Rev: 70050 / Revision: 74773
Last Changed Date: 2012-10-01 15:16:24 -0700 (Mon, 01 Oct 2012)
lamb1 Linux (openSUSE 12.1) / x86_64  OK  WARNINGS 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  WARNINGS  OK 
perceval Mac OS X Leopard (10.5.8) / i386  OK [ WARNINGS ] OK 

Summary

Package: a4Base
Version: 1.6.0
Command: /Library/Frameworks/R.framework/Versions/2.15/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch a4Base_1.6.0.tar.gz
StartedAt: 2013-03-24 22:20:15 -0700 (Sun, 24 Mar 2013)
EndedAt: 2013-03-24 22:26:04 -0700 (Sun, 24 Mar 2013)
EllapsedTime: 348.1 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: a4Base.Rcheck
Warnings: 1

Command output

* using log directory '/Users/biocbuild/bbs-2.11-bioc/meat/a4Base.Rcheck'
* using R version 2.15.3 (2013-03-01)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'a4Base/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'a4Base' version '1.6.0'
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Packages which this enhances but not available for checking:
  'gridSVG' 'JavaGD'
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking whether package 'a4Base' 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 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 ... WARNING
Foreign function call with 'PACKAGE' argument in a base package:
  .C("bincode", ..., PACKAGE = "base")
Packages should not make .C/.Call/.Fortran calls to base packages. They
are not part of the API, for use only by R itself and subject to change
without notice.
* checking R code for possible problems ... NOTE
a4palette: warning in rgb(9, 53, 122, alpha = alpha, max = 255):
  partial argument match of 'max' to 'maxColorValue'
a4palette: warning in rgb(42, 142, 191, alpha = alpha, max = 255):
  partial argument match of 'max' to 'maxColorValue'
a4palette: warning in rgb(148, 198, 223, alpha = alpha, max = 255):
  partial argument match of 'max' to 'maxColorValue'
a4palette: warning in rgb(35, 125, 38, alpha = alpha, max = 255):
  partial argument match of 'max' to 'maxColorValue'
a4palette: warning in rgb(127, 195, 28, alpha = alpha, max = 255):
  partial argument match of 'max' to 'maxColorValue'
a4palette: warning in rgb(191, 225, 141, alpha = alpha, max = 255):
  partial argument match of 'max' to 'maxColorValue'
heatmap.expressionSet: warning in grid.layout(nrow = heatmap.grid.nrow,
  ncol = heatmap.grid.ncol, width = grid.layout.col.widths, heights =
  grid.layout.row.heights): partial argument match of 'width' to
  'widths'
heatmap.expressionSet: warning in grid.layout(nrow = 1, ncol = 5, width
  = unit(c(1, 1, 30, legend.width[1], 1), c("null", "grobwidth",
  "points", attr(legend.width, "unit"), "null"), c(vector(mode =
  "list", length = 1), list(title.toplot.grob), vector(mode = "list",
  length = 3)))): partial argument match of 'width' to 'widths'
plotLogRatio: warning in viewport(x = 0, y = 0, w = 1, h = 1, just =
  c("left", "bottom"), layout = grid.layout(nrow = nr + 14, ncol = 1)):
  partial argument match of 'w' to 'width'
plotLogRatio: warning in viewport(x = 0, y = 0, w = 1, h = 1, just =
  c("left", "bottom"), layout = grid.layout(nrow = nr + 14, ncol = 1)):
  partial argument match of 'h' to 'height'
replicates: warning in vector("numeric", len = length(x)): partial
  argument match of 'len' to 'length'
plotLogRatio: no visible global function definition for 'JavaGD'
plotLogRatio: no visible global function definition for 'grid.garnish'
plotLogRatio: no visible global function definition for
  'grid.hyperlink'
plotLogRatio: no visible global function definition for 'grid.script'
plotLogRatio: no visible global function definition for 'gridToSVG'
* 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 examples ... OK
Examples with CPU or elapsed time > 5s
                  user system elapsed
spectralMap     26.859  4.465  35.032
computeLogRatio 13.310  0.628  14.348
plotLogRatio    12.048  0.519  13.137
* checking PDF version of manual ... OK

WARNING: There was 1 warning.
NOTE: There were 2 notes.
See
  '/Users/biocbuild/bbs-2.11-bioc/meat/a4Base.Rcheck/00check.log'
for details.

a4Base.Rcheck/00install.out:

* installing *source* package 'a4Base' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded

* DONE (a4Base)

a4Base.Rcheck/a4Base-Ex.timings:

nameusersystemelapsed
a4palette0.0200.0050.025
addQuantilesColors3.6260.2773.932
boxPlot3.5920.3153.970
combineTwoExpressionSet000
computeLogRatio13.310 0.62814.348
createExpressionSet0.0660.0000.066
filterVarInt2.9640.2223.254
heatmap.expressionSet0.0010.0010.001
histPvalue3.4410.3103.823
histpvalueplotter3.1260.2763.429
lassoReg2.9890.2373.267
logReg0.0000.0000.001
nlcvTT000
plot1gene3.2530.2914.298
plotComb2Samples2.7990.2753.605
plotCombMultSamples3.3890.3844.226
plotCombination2genes3.0940.2253.331
plotLogRatio12.048 0.51913.137
probabilitiesPlot0.0010.0000.000
probe2gene3.1490.1623.380
profilesPlot2.7040.2152.944
propdegenescalculation3.1570.3093.748
replicates0.0030.0000.003
spectralMap26.859 4.46535.032
tTest3.2330.3654.117
volcanoPlot3.2670.3673.798