BioC 2.12: CHECK report for pcaMethods on pelham

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/pcaMethods.Rcheck'
* using R version 3.0.0 beta (2013-03-21 r62346)
* using platform: x86_64-apple-darwin10.8.0 (64-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/17s] 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 ... NOTE
File '/Users/biocbuild/bbs-2.12-bioc/meat/pcaMethods.Rcheck/pcaMethods/libs/pcaMethods.so':
  Found non-API calls to R: 'Rf_EncodeComplex', 'Rf_EncodeReal',
    'Rf_formatComplex', 'Rf_formatReal'

Compiled code should not call non-API entry points in R.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking installed files from 'inst/doc' ... OK
* checking examples ... [164s/166s] OK
Examples with CPU or elapsed time > 5s
            user system elapsed
robustSvd 76.162  2.150  78.975
kEstimate 34.957  0.198  35.696
robustPca 33.860  0.968  35.011
nlpca      6.451  0.144   6.633
* 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 were 2 notes.
See
  '/Users/biocbuild/bbs-2.12-bioc/meat/pcaMethods.Rcheck/00check.log'
for details.

* installing *source* package 'pcaMethods' ...
** libs
llvm-g++-4.2 -arch x86_64 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2  -c nipals.cpp -o nipals.o
llvm-g++-4.2 -arch x86_64 -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/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
** 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	0.082	0.007	0.110
Q2	0.291	0.015	0.316
R2VX	0.016	0.001	0.017
RnipalsPca	0.558	0.022	0.589
biplot.pcaRes	0.027	0.003	0.031
bpca	2.276	0.034	2.350
cvseg	0.030	0.002	0.031
fitted.pcaRes	0.021	0.001	0.022
kEstimate	34.957	0.198	35.696
kEstimateFast	0.389	0.006	0.397
leverage	0.124	0.004	0.128
llsImpute	0.500	0.007	0.510
nipalsPca	0.037	0.002	0.039
nlpca	6.451	0.144	6.633
nni	0.375	0.003	0.381
pca	0.131	0.005	0.138
plot.pcaRes	0.524	0.006	0.532
plotPcs	0.038	0.003	0.042
ppca	0.151	0.010	0.164
predict.pcaRes	0.031	0.003	0.037
prep	0.010	0.002	0.012
residuals.pcaRes	0.029	0.002	0.031
robustPca	33.860	0.968	35.011
robustSvd	76.162	2.150	78.975
slplot	0.045	0.005	0.051
svdImpute	0.281	0.004	0.292
svdPca	0.146	0.003	0.153
wasna	0.038	0.004	0.047

Summary

Command output