Package: pcaMethods

Version: 1.32.0

Command: /Library/Frameworks/R.framework/Versions/2.12/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch pcaMethods_1.32.0.tar.gz

StartedAt: 2010-12-20 08:12:05 -0800 (Mon, 20 Dec 2010)

EndedAt: 2010-12-20 08:16:07 -0800 (Mon, 20 Dec 2010)

EllapsedTime: 241.7 seconds

RetCode: 0

Status:  OK

CheckDir: pcaMethods.Rcheck

Warnings: 0

* using log directory ‘/Users/biocbuild/bbs-2.7-bioc/meat/pcaMethods.Rcheck’
* using R version 2.12.1 Patched (2010-12-17 r53867)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘pcaMethods/DESCRIPTION’ ... OK
* this is package ‘pcaMethods’ version ‘1.32.0’
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package ‘pcaMethods’ can be installed ... 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 name space can be loaded with stated dependencies ... OK
* checking whether the name space 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 ... OK
* 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 data for non-ASCII characters ... 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 ... OK
* checking examples ... OK
* checking package vignettes in ‘inst/doc’ ... SKIPPED
* checking PDF version of manual ... OK

* installing *source* package ‘pcaMethods’ ...
** libs
*** arch - i386
g++ -arch i386 -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include -I/Library/Frameworks/R.framework/Versions/2.12/Resources/include/i386 -I/Library/Frameworks/R.framework/Versions/2.12/Resources/library/Rcpp/include -I/usr/local/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/2.12/Resources/library/Rcpp/lib/i386/libRcpp.a -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.7-bioc/meat/pcaMethods.Rcheck/pcaMethods/libs/i386
** R
** data
** inst
** preparing package for lazy loading

Welcome to Bioconductor

  Vignettes contain introductory material. To view, type
  'openVignette()'. To cite Bioconductor, see
  'citation("Biobase")' and for packages 'citation(pkgname)'.


Attaching package: 'pls'

The following object(s) are masked from 'package:stats':

    loadings

Creating a new generic function for "print" in "pcaMethods"
Creating a new generic function for "biplot" in "pcaMethods"
Creating a new generic function for "summary" in "pcaMethods"
Creating a new generic function for "predict" in "pcaMethods"
Creating a new generic function for "residuals" in "pcaMethods"
Creating a new generic function for "resid" in "pcaMethods"
Creating a new generic function for "fitted" in "pcaMethods"
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded

* DONE (pcaMethods)

name	user	system	elapsed
DModX	0.069	0.008	0.076
Q2	0.262	0.007	0.270
RnipalsPca	0.605	0.040	0.649
biplot.pcaRes	0.020	0.002	0.022
bpca	2.720	0.037	2.767
fitted.pcaRes	0.019	0.002	0.020
kEstimate	44.650	14.488	60.880
kEstimateFast	0.575	0.159	0.750
leverage	0.026	0.002	0.028
llsImpute	0.555	0.013	0.580
nipalsPca	0.045	0.008	0.052
nlpca	3.762	1.111	5.023
nni	0.477	0.015	0.505
pca	0.167	0.004	0.174
plot.pcaRes	1.161	0.082	1.267
plotPcs	0.034	0.002	0.036
ppca	0.182	0.056	0.240
predict.pcaRes	0.026	0.002	0.028
prep	0.003	0.000	0.003
residuals.pcaRes	0.027	0.002	0.029
robustPca	30.293	0.740	31.741
robustSvd	66.971	1.343	69.970
slplot	0.043	0.003	0.046
svdImpute	0.432	0.024	0.465
svdPca	0.044	0.010	0.053
wasna	0.041	0.007	0.047