Package: pcaMethods

Version: 1.34.0

Command: /home/biocbuild/bbs-2.8-bioc/R/bin/R CMD check --no-vignettes --timings pcaMethods_1.34.0.tar.gz

StartedAt: 2011-02-24 21:45:32 -0800 (Thu, 24 Feb 2011)

EndedAt: 2011-02-24 21:48:07 -0800 (Thu, 24 Feb 2011)

EllapsedTime: 154.7 seconds

RetCode: 0

Status:  OK

CheckDir: pcaMethods.Rcheck

Warnings: 0

* using log directory ‘/loc/home/biocbuild/bbs-2.8-bioc/meat/pcaMethods.Rcheck’
* using R version 2.13.0 Under development (unstable) (2011-01-10 r53950)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘pcaMethods/DESCRIPTION’ ... OK
* this is package ‘pcaMethods’ version ‘1.34.0’
* 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
g++ -I/home/biocbuild/bbs-2.8-bioc/R/include  -I/usr/local/include -I"/home/biocbuild/bbs-2.8-bioc/R/library/Rcpp/include"   -fpic  -g -O2 -c nipals.cpp -o nipals.o
g++ -shared -L/usr/local/lib64 -o pcaMethods.so nipals.o -L/loc/home/biocbuild/bbs-2.8-bioc/R/library/Rcpp/lib -lRcpp -Wl,-rpath,/loc/home/biocbuild/bbs-2.8-bioc/R/library/Rcpp/lib -L/home/biocbuild/bbs-2.8-bioc/R/lib -lR
installing to /loc/home/biocbuild/bbs-2.8-bioc/meat/pcaMethods.Rcheck/pcaMethods/libs
** R
** data
** inst
** preparing package for lazy loading

Welcome to Bioconductor

  Vignettes contain introductory material. To view, type
  'browseVignettes()'. 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	0.040	0.004	0.050
Q2	0.224	0.000	0.224
RnipalsPca	0.460	0.004	0.465
biplot.pcaRes	0.012	0.004	0.014
bpca	1.748	0.004	1.752
fitted.pcaRes	0.012	0.000	0.012
kEstimate	32.650	0.004	32.722
kEstimateFast	0.480	0.004	0.487
leverage	0.016	0.000	0.019
llsImpute	0.376	0.000	0.378
nipalsPca	0.024	0.000	0.021
nlpca	3.168	0.004	3.178
nni	0.296	0.000	0.298
pca	0.104	0.004	0.105
plot.pcaRes	0.444	0.004	0.447
plotPcs	0.020	0.000	0.022
ppca	0.120	0.000	0.117
predict.pcaRes	0.012	0.004	0.017
prep	0.004	0.000	0.001
residuals.pcaRes	0.016	0.000	0.018
robustPca	20.909	0.008	21.038
robustSvd	46.775	0.020	46.868
slplot	0.024	0.000	0.023
svdImpute	0.180	0.000	0.182
svdPca	0.036	0.000	0.033
wasna	0.020	0.000	0.021