Package: pcaMethods

Version: 1.48.0

Command: /Library/Frameworks/R.framework/Versions/2.15/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch pcaMethods_1.48.0.tar.gz

StartedAt: 2013-03-25 00:45:32 -0700 (Mon, 25 Mar 2013)

EndedAt: 2013-03-25 00:49:06 -0700 (Mon, 25 Mar 2013)

EllapsedTime: 213.4 seconds

RetCode: 0

Status:  OK

CheckDir: pcaMethods.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.11-bioc/meat/pcaMethods.Rcheck'
* using R version 2.15.3 (2013-03-01)
* 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 '1.48.0'
* 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 for left-over 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
plot,pcaRes: no visible binding for global variable 'y'
* 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 compiled code ... OK
* checking sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
            user system elapsed
robustSvd 57.720  1.007  59.701
kEstimate 32.390 12.821  46.866
robustPca 26.014  0.515  26.792
* checking for unstated dependencies in vignettes ... OK
* 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

NOTE: There was 1 note.
See
  '/Users/biocbuild/bbs-2.11-bioc/meat/pcaMethods.Rcheck/00check.log'
for details.

* 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 -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/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/2.15/Resources/library/Rcpp/lib/i386/libRcpp.a -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.11-bioc/meat/pcaMethods.Rcheck/pcaMethods/libs/i386
** R
** data
** inst
** preparing package for lazy loading
Creating a new generic function for 'loadings' in package 'pcaMethods'
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 'resid' from package 'stats' in package 'pcaMethods'
Creating a generic function for 'fitted' from package 'stats' in package 'pcaMethods'
Creating a generic function for 'plot' from package 'graphics' in package 'pcaMethods'
** help
*** installing help indices
** building package indices
** installing vignettes
   'missingValues.Rnw' 
   'outliers.Rnw' 
   'pcaMethods.Rnw' 
** testing if installed package can be loaded

* DONE (pcaMethods)

name	user	system	elapsed
DModX	0.058	0.010	0.067
Q2	0.252	0.011	0.263
R2VX	0.011	0.001	0.011
RnipalsPca	0.480	0.039	0.522
biplot.pcaRes	0.014	0.002	0.016
bpca	1.840	0.038	1.891
cvseg	0.012	0.001	0.012
fitted.pcaRes	0.011	0.002	0.014
kEstimate	32.390	12.821	46.866
kEstimateFast	0.399	0.164	0.575
leverage	0.016	0.003	0.020
llsImpute	0.387	0.014	0.401
nipalsPca	0.021	0.006	0.027
nlpca	2.399	0.793	3.483
nni	0.289	0.009	0.298
pca	0.096	0.005	0.105
plot.pcaRes	0.457	0.051	0.511
plotPcs	0.024	0.004	0.029
ppca	0.179	0.048	0.231
predict.pcaRes	0.014	0.001	0.016
prep	0.001	0.000	0.001
residuals.pcaRes	0.012	0.001	0.013
robustPca	26.014	0.515	26.792
robustSvd	57.720	1.007	59.701
slplot	0.024	0.005	0.029
svdImpute	0.264	0.023	0.312
svdPca	0.027	0.009	0.035
wasna	0.021	0.007	0.028