Package: pcaMethods

Version: 1.37.0

Command: /Library/Frameworks/R.framework/Versions/2.14/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch pcaMethods_1.37.0.tar.gz

StartedAt: 2011-05-09 16:11:35 -0700 (Mon, 09 May 2011)

EndedAt: 2011-05-09 16:15:55 -0700 (Mon, 09 May 2011)

EllapsedTime: 259.4 seconds

RetCode: 0

Status:  OK

CheckDir: pcaMethods.Rcheck

Warnings: 0

* using log directory ‘/Users/biocbuild/bbs-2.9-bioc/meat/pcaMethods.Rcheck’
* using R version 2.14.0 Under development (unstable) (2011-04-24 r55634)
* 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 ‘1.37.0’
* 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 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 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 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 sizes of PDF files under ‘inst/doc’ ... NOTE
  ‘qpdf’ made some significant size reductions:
     compacted ‘pcaMethods.pdf’ from 345Kb to 184Kb
  consider running tools::compactPDF() on these files
* 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

* installing *source* package ‘pcaMethods’ ...
** libs
*** arch - i386
g++-4.2 -arch i386 -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include -I/Library/Frameworks/R.framework/Versions/2.14/Resources/include/i386  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.14/Resources/library/Rcpp/include"   -fPIC  -g -O2 -c nipals.cpp -o nipals.o
g++-4.2 -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

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 ...
*** tangling vignette sources ...
   ‘missingValues.Rnw’ 
   ‘outliers.Rnw’ 
   ‘pcaMethods.Rnw’ 
** testing if installed package can be loaded

* DONE (pcaMethods)

name	user	system	elapsed
DModX	0.075	0.009	0.098
Q2	0.287	0.008	0.305
RnipalsPca	0.631	0.046	0.681
biplot.pcaRes	0.021	0.001	0.022
bpca	2.679	0.041	2.735
fitted.pcaRes	0.015	0.001	0.016
kEstimate	43.555	13.408	57.627
kEstimateFast	0.541	0.139	0.695
leverage	0.026	0.002	0.027
llsImpute	0.520	0.010	0.542
nipalsPca	0.036	0.007	0.044
nlpca	3.416	0.900	4.542
nni	0.423	0.010	0.542
pca	0.153	0.003	0.181
plot.pcaRes	0.763	0.063	0.983
plotPcs	0.035	0.002	0.038
ppca	0.182	0.048	0.246
predict.pcaRes	0.026	0.001	0.028
prep	0.003	0.001	0.004
residuals.pcaRes	0.024	0.002	0.026
robustPca	30.506	0.591	31.851
robustSvd	69.575	1.349	72.907
slplot	0.036	0.002	0.037
svdImpute	0.448	0.026	0.476
svdPca	0.042	0.009	0.052
wasna	0.034	0.007	0.040