BioC 2.13: CHECK report for pcaMethods on zin1

* using log directory ‘/home/biocbuild/bbs-2.13-bioc/meat/pcaMethods.Rcheck’
* using R version 3.0.3 (2014-03-06)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘pcaMethods/DESCRIPTION’ ... OK
* this is package ‘pcaMethods’ version ‘1.52.1’
* 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 ... [9s/9s] 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
Namespace in Imports field not imported from: ‘BiocGenerics’
  All declared Imports should be used.
Packages in Depends field not imported from:
  ‘Biobase’ ‘Rcpp’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of 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 line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [87s/87s] OK
Examples with CPU or elapsed time > 5s
            user system elapsed
robustSvd 42.151  0.004  42.252
kEstimate 18.641  0.004  18.732
robustPca 18.381  0.008  18.418
* 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

NOTE: There were 2 notes.
See
  ‘/home/biocbuild/bbs-2.13-bioc/meat/pcaMethods.Rcheck/00check.log’
for details.

* installing *source* package ‘pcaMethods’ ...
** libs
g++ -I/home/biocbuild/bbs-2.13-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/home/biocbuild/bbs-2.13-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -Wall -c nipals.cpp -o nipals.o
g++ -shared -L/usr/local/lib -o pcaMethods.so nipals.o -L/home/biocbuild/bbs-2.13-bioc/R/lib -lR
installing to /home/biocbuild/bbs-2.13-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	0.040	0.004	0.043
Q2	0.144	0.008	0.165
R2VX	0.008	0.000	0.007
RnipalsPca	0.280	0.004	0.282
biplot.pcaRes	0.012	0.000	0.013
bpca	1.168	0.000	1.172
cvseg	0.072	0.000	0.111
fitted.pcaRes	0.008	0.000	0.011
kEstimate	18.641	0.004	18.732
kEstimateFast	0.244	0.000	0.244
leverage	0.016	0.000	0.015
llsImpute	0.280	0.000	0.279
nipalsPca	0.016	0.000	0.018
nlpca	3.092	0.000	3.095
nni	0.208	0.000	0.208
pca	0.072	0.004	0.075
plot.pcaRes	0.248	0.000	0.247
plotPcs	0.024	0.000	0.023
ppca	0.088	0.000	0.087
predict.pcaRes	0.016	0.000	0.016
prep	0.004	0.000	0.005
residuals.pcaRes	0.016	0.000	0.014
robustPca	18.381	0.008	18.418
robustSvd	42.151	0.004	42.252
slplot	0.020	0.000	0.022
svdImpute	0.124	0.004	0.130
svdPca	0.024	0.000	0.023
wasna	0.008	0.004	0.016

BioC 2.13: CHECK report for pcaMethods on zin1

Summary

Command output