Package: pcaMethods

Version: 1.49.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch pcaMethods_1.49.1.tar.gz

StartedAt: 2013-03-25 03:59:09 -0700 (Mon, 25 Mar 2013)

EndedAt: 2013-03-25 04:03:15 -0700 (Mon, 25 Mar 2013)

EllapsedTime: 245.5 seconds

RetCode: 0

Status:  OK

CheckDir: pcaMethods.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/pcaMethods.Rcheck'
* using R Under development (unstable) (2013-02-26 r62077)
* 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 '1.49.1'
* 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 for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package 'pcaMethods' can be installed ... [14s/14s] OK
* checking installed package size ... OK
* checking package directory ... 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 ... [162s/162s] OK
Examples with CPU or elapsed time > 5s
            user system elapsed
robustSvd 68.410  0.651  69.095
kEstimate 33.952 10.821  45.433
robustPca 31.285  0.364  31.678
nlpca      4.904  1.837   6.847
* 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-2.12-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/3.0/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/3.0/Resources/library/Rcpp/lib/i386/libRcpp.a -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.12-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	0.072	0.014	0.086
Q2	0.256	0.017	0.273
R2VX	0.011	0.004	0.016
RnipalsPca	0.382	0.032	0.414
biplot.pcaRes	0.023	0.008	0.032
bpca	2.022	0.032	2.055
cvseg	0.023	0.006	0.028
fitted.pcaRes	0.018	0.005	0.023
kEstimate	33.952	10.821	45.433
kEstimateFast	0.530	0.134	0.669
leverage	0.036	0.011	0.047
llsImpute	0.551	0.023	0.575
nipalsPca	0.034	0.014	0.048
nlpca	4.904	1.837	6.847
nni	0.345	0.013	0.357
pca	0.120	0.015	0.136
plot.pcaRes	0.876	0.068	0.948
plotPcs	0.045	0.013	0.058
ppca	0.171	0.062	0.234
predict.pcaRes	0.035	0.012	0.049
prep	0.012	0.009	0.020
residuals.pcaRes	0.028	0.009	0.036
robustPca	31.285	0.364	31.678
robustSvd	68.410	0.651	69.095
slplot	0.051	0.012	0.062
svdImpute	0.282	0.025	0.309
svdPca	0.056	0.018	0.074
wasna	0.041	0.016	0.057