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Package 444/631HostnameOS / ArchBUILDCHECKBUILD BIN
pcaMethods 1.49.0
Henning Redestig
Snapshot Date: 2013-01-15 17:01:14 -0800 (Tue, 15 Jan 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods
Last Changed Rev: 70052 / Revision: 72575
Last Changed Date: 2012-10-01 15:43:56 -0700 (Mon, 01 Oct 2012)
george2 Linux (Ubuntu 12.04.1 LTS) / x86_64  OK  OK 
lamb2 Linux (openSUSE 11.4) / x86_64  OK [ OK ]
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
petty Mac OS X Leopard (10.5.8) / i386  OK  OK  OK 

Summary

Package: pcaMethods
Version: 1.49.0
Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings pcaMethods_1.49.0.tar.gz
StartedAt: 2013-01-16 05:06:11 -0800 (Wed, 16 Jan 2013)
EndedAt: 2013-01-16 05:09:23 -0800 (Wed, 16 Jan 2013)
EllapsedTime: 191.3 seconds
RetCode: 0
Status:  OK 
CheckDir: pcaMethods.Rcheck
Warnings: 0

Command output

* using log directory ‘/loc/home/biocbuild/bbs-2.12-bioc/meat/pcaMethods.Rcheck’
* using R Under development (unstable) (2012-12-17 r61365)
* 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 ‘1.49.0’
* 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 ... 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 installed files from ‘inst/doc’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
            user system elapsed
robustSvd 58.079  0.008  58.095
kEstimate 28.346  0.024  28.407
robustPca 26.030  0.012  26.043
nlpca      6.296  0.012   6.311
* 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
  ‘/loc/home/biocbuild/bbs-2.12-bioc/meat/pcaMethods.Rcheck/00check.log’
for details.

pcaMethods.Rcheck/00install.out:

* installing *source* package ‘pcaMethods’ ...
** libs
g++ -I/home/biocbuild/bbs-2.12-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.12-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -c nipals.cpp -o nipals.o
g++ -shared -L/usr/local/lib64 -o pcaMethods.so nipals.o -L/loc/home/biocbuild/bbs-2.12-bioc/R/library/Rcpp/lib -lRcpp -Wl,-rpath,/loc/home/biocbuild/bbs-2.12-bioc/R/library/Rcpp/lib -L/home/biocbuild/bbs-2.12-bioc/R/lib -lR
installing to /loc/home/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
   ‘missingValues.Rnw’ 
   ‘outliers.Rnw’ 
   ‘pcaMethods.Rnw’ 
** testing if installed package can be loaded

* DONE (pcaMethods)

pcaMethods.Rcheck/pcaMethods-Ex.timings:

nameusersystemelapsed
DModX0.0560.0000.082
Q20.1560.0000.155
R2VX0.0160.0000.014
RnipalsPca0.4480.0080.458
biplot.pcaRes0.0200.0040.025
bpca1.6880.0081.693
cvseg0.0200.0000.023
fitted.pcaRes0.020.000.02
kEstimate28.346 0.02428.407
kEstimateFast0.4160.0000.417
leverage0.0200.0040.025
llsImpute0.3920.0000.394
nipalsPca0.0360.0000.037
nlpca6.2960.0126.311
nni0.4160.0000.419
pca0.1120.0000.113
plot.pcaRes0.3320.0000.331
plotPcs0.0320.0000.032
ppca0.1160.0040.122
predict.pcaRes0.0320.0000.033
prep0.0160.0000.013
residuals.pcaRes0.0280.0000.025
robustPca26.030 0.01226.043
robustSvd58.079 0.00858.095
slplot0.1560.0000.155
svdImpute0.1880.0000.186
svdPca0.0480.0000.049
wasna0.0320.0000.031