Package: pcaMethods

Version: 1.36.0

Command: /Library/Frameworks/R.framework/Versions/2.13/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch pcaMethods_1.36.0.tar.gz

StartedAt: 2011-10-20 16:29:16 -0700 (Thu, 20 Oct 2011)

EndedAt: 2011-10-20 16:33:40 -0700 (Thu, 20 Oct 2011)

EllapsedTime: 264.2 seconds

RetCode: 0

Status:  OK

CheckDir: pcaMethods.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.8-bioc/meat/pcaMethods.Rcheck'
* using R version 2.13.2 (2011-09-30)
* 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 '1.36.0'
* checking package namespace 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 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 ... 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 422Kb to 291Kb
  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/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.13/Resources/library/Rcpp/include"   -fPIC  -g -O2 -Wall -fasm-blocks -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/2.13/Resources/library/Rcpp/lib/i386/libRcpp.a -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.8-bioc/meat/pcaMethods.Rcheck/pcaMethods/libs/i386
** R
** data
** inst
** preparing package for lazy loading
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	0.120	0.007	0.137
Q2	0.269	0.008	0.300
RnipalsPca	0.603	0.050	0.661
biplot.pcaRes	0.021	0.001	0.027
bpca	2.636	0.037	2.709
fitted.pcaRes	0.015	0.001	0.016
kEstimate	42.961	13.684	57.381
kEstimateFast	0.547	0.130	0.682
leverage	0.025	0.002	0.027
llsImpute	0.523	0.011	0.565
nipalsPca	0.034	0.007	0.047
nlpca	3.247	0.877	4.287
nni	0.411	0.010	0.421
pca	0.152	0.003	0.156
plot.pcaRes	0.768	0.064	0.856
plotPcs	0.035	0.003	0.039
ppca	0.171	0.046	0.222
predict.pcaRes	0.027	0.001	0.028
prep	0.003	0.001	0.002
residuals.pcaRes	0.023	0.001	0.024
robustPca	31.254	0.728	33.380
robustSvd	69.784	1.338	72.710
slplot	0.036	0.002	0.038
svdImpute	0.262	0.017	0.279
svdPca	0.230	0.017	0.251
wasna	0.033	0.006	0.040