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Package 362/514HostnameOS / ArchBUILDCHECKBUILD BIN
pcaMethods 1.40.0
Wolfram Stacklies
Snapshot Date: 2012-03-23 18:21:46 -0700 (Fri, 23 Mar 2012)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_9/madman/Rpacks/pcaMethods
Last Changed Rev: 59920 / Revision: 64395
Last Changed Date: 2011-10-31 15:59:03 -0700 (Mon, 31 Oct 2011)
wilson2 Linux (openSUSE 11.4) / x86_64  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
pitt Mac OS X Leopard (10.5.8) / i386  OK [ OK ] OK 

Summary

Package: pcaMethods
Version: 1.40.0
Command: /Library/Frameworks/R.framework/Versions/2.14/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch pcaMethods_1.40.0.tar.gz
StartedAt: 2012-03-24 03:05:21 -0700 (Sat, 24 Mar 2012)
EndedAt: 2012-03-24 03:09:33 -0700 (Sat, 24 Mar 2012)
EllapsedTime: 252.4 seconds
RetCode: 0
Status:  OK 
CheckDir: pcaMethods.Rcheck
Warnings: 0

Command output

* using log directory '/Users/biocbuild/bbs-2.9-bioc/meat/pcaMethods.Rcheck'
* using R version 2.14.2 (2012-02-29)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'pcaMethods/DESCRIPTION' ... OK
* this is package 'pcaMethods' version '1.40.0'
* 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 whether package 'pcaMethods' 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 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
File 'pcaMethods/R/pca.R':
  .onLoad calls:
    require("methods")

Package startup functions should not change the search path.
See section 'Good practice' in ?.onAttach.

* 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 ... NOTE
S3 methods shown with full name in documentation object 'biplot.pcaRes':
  'biplot.pcaRes'

S3 methods shown with full name in documentation object 'dim.pcaRes':
  'dim.pcaRes'

S3 methods shown with full name in documentation object 'fitted.pcaRes':
  'fitted.pcaRes'

S3 methods shown with full name in documentation object 'loadings.pcaRes':
  'loadings.pcaRes'

S3 methods shown with full name in documentation object 'plot.pcaRes':
  'plot.pcaRes'

S3 methods shown with full name in documentation object 'predict.pcaRes':
  'predict.pcaRes'

S3 methods shown with full name in documentation object 'residuals.pcaRes':
  'residuals.pcaRes'

S3 methods shown with full name in documentation object 'scores.pcaRes':
  'scores.pcaRes'

The \usage entries for S3 methods should use the \method markup and not
their full name.
See the chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* 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 line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for portable compilation flags in Makevars ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking sizes of PDF files under 'inst/doc' ... OK
* checking examples ... OK
* checking for unstated dependencies in vignettes ... NOTE
'library' or 'require' call not declared from: 'lattice'
* 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

pcaMethods.Rcheck/00install.out:

* installing *source* package 'pcaMethods' ...
** libs
*** arch - i386
g++ -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/Rcpp/include"   -fPIC  -g -O2 -Wall -fasm-blocks -c nipals.cpp -o nipals.o
g++ -arch i386 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o pcaMethods.so nipals.o /Library/Frameworks/R.framework/Versions/2.14/Resources/library/Rcpp/lib/i386/libRcpp.a -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.9-bioc/meat/pcaMethods.Rcheck/pcaMethods/libs/i386
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for 'print' from package 'base' in package 'pcaMethods'
Creating a generic function for 'biplot' from package 'stats' in package 'pcaMethods'
Creating a generic function for 'summary' from package 'base' in package 'pcaMethods'
Creating a generic function for 'predict' from package 'stats' in package 'pcaMethods'
Creating a generic function for 'residuals' from package 'stats' in package 'pcaMethods'
Creating a generic function for 'resid' from package 'stats' in package 'pcaMethods'
Creating a generic function for 'fitted' from package 'stats' in package 'pcaMethods'
** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
   'missingValues.Rnw' 
   'outliers.Rnw' 
   'pcaMethods.Rnw' 
** testing if installed package can be loaded

* DONE (pcaMethods)

pcaMethods.Rcheck/pcaMethods-Ex.timings:

nameusersystemelapsed
DModX0.1500.0120.174
Q20.2900.0140.306
RnipalsPca0.5170.0400.563
biplot-dot-pcaRes0.0200.0020.023
bpca2.4010.0302.476
cvseg0.0100.0010.010
fitted-dot-pcaRes0.0150.0010.016
kEstimate39.95912.59053.812
kEstimateFast0.5470.1650.724
leverage0.0230.0030.027
llsImpute0.5580.0120.579
nipalsPca0.1020.0100.116
nlpca3.6071.0774.816
nni0.3910.0120.404
pca0.1280.0060.135
plot-dot-pcaRes0.7200.0790.809
plotPcs0.0290.0030.031
ppca0.1620.0630.226
predict-dot-pcaRes0.0240.0030.028
prep0.0020.0000.002
residuals-dot-pcaRes0.0190.0020.022
robustPca31.310 0.76332.459
robustSvd69.413 1.54172.173
slplot0.0330.0040.036
svdImpute0.2650.0220.293
svdPca0.2700.0190.290
wasna0.0350.0090.044