BioC 3.2: CHECK report for pcaMethods on oaxaca

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings pcaMethods_1.60.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/pcaMethods.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘pcaMethods/DESCRIPTION’ ... OK
* this is package ‘pcaMethods’ version ‘1.60.0’
* 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 ... [11s/11s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ 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 dependencies in R code ... NOTE
'library' or 'require' call to ‘matrixStats’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
* 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 compiled code ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [57s/58s] OK
Examples with CPU or elapsed time > 5s
            user system elapsed
robustSvd 23.718  0.657  24.399
kEstimate 15.047  0.055  15.116
robustPca 10.936  0.286  11.264
* 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 vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.2-bioc/meat/pcaMethods.Rcheck/00check.log’
for details.

* installing *source* package ‘pcaMethods’ ...
** libs
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c RcppExports.cpp -o RcppExports.o
clang++ -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -I"/Library/Frameworks/R.framework/Versions/3.2/Resources/library/Rcpp/include"   -fPIC  -Wall -mtune=core2 -g -O2  -c nipals.cpp -o nipals.o
clang++ -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o pcaMethods.so RcppExports.o nipals.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-3.2-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-pcaRes-method	0.045	0.006	0.051
Q2	0.170	0.005	0.190
R2VX-pcaRes-method	0.01	0.00	0.01
RnipalsPca	0.254	0.005	0.261
biplot-methods	0.012	0.001	0.013
bpca	1.053	0.016	1.070
cvseg	0.013	0.001	0.013
fitted-methods	0.008	0.000	0.008
kEstimate	15.047	0.055	15.116
kEstimateFast	0.161	0.001	0.163
leverage-pcaRes-method	0.011	0.000	0.012
llsImpute	0.256	0.002	0.258
nipalsPca	0.015	0.001	0.015
nlpca	2.513	0.008	2.522
nni	0.211	0.001	0.212
pca	0.068	0.002	0.070
plot.pcaRes	0.303	0.003	0.305
plotPcs	0.015	0.001	0.016
ppca	0.066	0.004	0.070
predict-methods	0.009	0.000	0.009
prep	0.002	0.000	0.002
rediduals-methods	0.011	0.000	0.012
robustPca	10.936	0.286	11.264
robustSvd	23.718	0.657	24.399
slplot-pcaRes-method	0.023	0.002	0.025
svdImpute	0.127	0.001	0.128
svdPca	0.023	0.000	0.024
wasna-pcaRes-method	0.018	0.002	0.020

BioC 3.2: CHECK report for pcaMethods on oaxaca

Summary

Command output