BioC 2.14: CHECK report for pcaMethods on petty

Package: pcaMethods

Version: 1.54.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch pcaMethods_1.54.0.tar.gz

StartedAt: 2014-10-07 23:23:30 -0700 (Tue, 07 Oct 2014)

EndedAt: 2014-10-07 23:27:59 -0700 (Tue, 07 Oct 2014)

EllapsedTime: 269.0 seconds

RetCode: 0

Status:  OK

CheckDir: pcaMethods.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch pcaMethods_1.54.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-2.14-bioc/meat/pcaMethods.Rcheck’
* using R version 3.1.1 (2014-07-10)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘pcaMethods/DESCRIPTION’ ... OK
* this is package ‘pcaMethods’ version ‘1.54.0’
* 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 ... [17s/20s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... NOTE
File
  LICENSE
is not mentioned in the DESCRIPTION file.
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [154s/156s] OK
Examples with CPU or elapsed time > 5s
            user system elapsed
robustSvd 71.837  2.166  74.623
kEstimate 33.790  0.083  34.238
robustPca 32.739  0.994  34.410
* 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 3 notes.
See
  ‘/Users/biocbuild/bbs-2.14-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/3.1/Resources/library/Rcpp/include"   -fPIC  -mtune=core2 -g -O2 -Wall  -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 -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.14-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	0.197	0.004	0.202
Q2	0.193	0.009	0.221
R2VX	0.011	0.001	0.011
RnipalsPca	0.466	0.010	0.478
biplot.pcaRes	0.022	0.002	0.023
bpca	2.382	0.009	2.424
cvseg	0.022	0.001	0.023
fitted.pcaRes	0.018	0.000	0.017
kEstimate	33.790	0.083	34.238
kEstimateFast	0.379	0.004	0.384
leverage	0.025	0.002	0.027
llsImpute	0.646	0.005	0.652
nipalsPca	0.028	0.001	0.028
nlpca	3.124	0.018	3.341
nni	0.434	0.002	0.466
pca	0.144	0.004	0.162
plot.pcaRes	0.722	0.005	0.773
plotPcs	0.034	0.002	0.042
ppca	0.142	0.003	0.158
predict.pcaRes	0.023	0.001	0.024
prep	0.004	0.000	0.005
residuals.pcaRes	0.020	0.001	0.023
robustPca	32.739	0.994	34.410
robustSvd	71.837	2.166	74.623
slplot	0.037	0.003	0.053
svdImpute	0.265	0.004	0.279
svdPca	0.041	0.001	0.041
wasna	0.029	0.002	0.031