BioC 2.12: CHECK report for pcaMethods on petty

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/pcaMethods.Rcheck'
* using R version 3.0.1 (2013-05-16)
* 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 '1.50.0'
* 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 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 ... [16s/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 ... OK
* checking sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... [185s/188s] OK
Examples with CPU or elapsed time > 5s
            user system elapsed
robustSvd 86.867  1.802  89.689
robustPca 39.289  0.881  40.717
kEstimate 38.418  0.143  39.038
nlpca      7.093  0.054   7.216
* 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
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 -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
** testing if installed package can be loaded
* DONE (pcaMethods)

name	user	system	elapsed
DModX	0.088	0.009	0.100
Q2	0.225	0.012	0.250
R2VX	0.015	0.001	0.016
RnipalsPca	0.610	0.030	0.693
biplot.pcaRes	0.029	0.002	0.032
bpca	2.505	0.034	2.697
cvseg	0.031	0.002	0.034
fitted.pcaRes	0.024	0.001	0.027
kEstimate	38.418	0.143	39.038
kEstimateFast	0.523	0.005	0.540
leverage	0.038	0.002	0.040
llsImpute	0.603	0.006	0.618
nipalsPca	0.040	0.001	0.041
nlpca	7.093	0.054	7.216
nni	0.570	0.003	0.581
pca	0.150	0.004	0.156
plot.pcaRes	0.508	0.005	0.521
plotPcs	0.041	0.002	0.044
ppca	0.183	0.004	0.188
predict.pcaRes	0.049	0.001	0.050
prep	0.018	0.001	0.022
residuals.pcaRes	0.149	0.002	0.155
robustPca	39.289	0.881	40.717
robustSvd	86.867	1.802	89.689
slplot	0.050	0.003	0.054
svdImpute	0.288	0.002	0.293
svdPca	0.058	0.002	0.059
wasna	0.035	0.004	0.040

BioC 2.12: CHECK report for pcaMethods on petty

Summary

Command output