BioC 3.2: CHECK report for pcaMethods on linux1.bioconductor.org

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### Running command:
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###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings pcaMethods_1.60.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/pcaMethods.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-pc-linux-gnu (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 ... [10s/10s] 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [50s/50s] OK
Examples with CPU or elapsed time > 5s
            user system elapsed
robustSvd 20.705  0.000  20.716
kEstimate 14.080  0.019  14.129
robustPca  8.914  0.000   8.915
* 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
  ‘/home/biocbuild/bbs-3.2-bioc/meat/pcaMethods.Rcheck/00check.log’
for details.

* installing *source* package ‘pcaMethods’ ...
** libs
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -Wall -c RcppExports.cpp -o RcppExports.o
g++ -I/home/biocbuild/bbs-3.2-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-3.2-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -Wall -c nipals.cpp -o nipals.o
g++ -shared -L/home/biocbuild/bbs-3.2-bioc/R/lib -L/usr/local/lib -o pcaMethods.so RcppExports.o nipals.o -L/home/biocbuild/bbs-3.2-bioc/R/lib -lR
installing to /home/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	0.004	0.050
Q2	0.163	0.009	0.170
R2VX-pcaRes-method	0.011	0.000	0.011
RnipalsPca	0.255	0.000	0.255
biplot-methods	0.009	0.003	0.012
bpca	1.184	0.000	1.184
cvseg	0.013	0.000	0.013
fitted-methods	0.008	0.000	0.008
kEstimate	14.080	0.019	14.129
kEstimateFast	0.122	0.000	0.123
leverage-pcaRes-method	0.008	0.000	0.008
llsImpute	0.209	0.000	0.209
nipalsPca	0.011	0.004	0.016
nlpca	2.097	0.004	2.100
nni	0.154	0.000	0.154
pca	0.050	0.000	0.051
plot.pcaRes	0.267	0.004	0.270
plotPcs	0.012	0.000	0.014
ppca	0.048	0.000	0.047
predict-methods	0.061	0.000	0.061
prep	0.001	0.000	0.001
rediduals-methods	0.007	0.000	0.007
robustPca	8.914	0.000	8.915
robustSvd	20.705	0.000	20.716
slplot-pcaRes-method	0.015	0.000	0.016
svdImpute	0.093	0.000	0.093
svdPca	0.021	0.000	0.022
wasna-pcaRes-method	0.019	0.000	0.019

BioC 3.2: CHECK report for pcaMethods on linux1.bioconductor.org

Summary

Command output