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Package 272/389HostnameOS / ArchBUILDCHECKBUILD BIN
pcaMethods 1.30.0
Wolfram Stacklies
Snapshot Date: 2010-10-04 11:22:20 -0700 (Mon, 04 Oct 2010)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_6/madman/Rpacks/pcaMethods
Last Changed Rev: 46401 / Revision: 49923
Last Changed Date: 2010-04-22 11:21:23 -0700 (Thu, 22 Apr 2010)
wilson1 Linux (openSUSE 11.1) / x86_64  OK  OK 
liverpool Windows Server 2003 R2 (32-bit) / x64  OK  OK  OK 
gewurz Windows Server 2008 R2 Enterprise (64-bit) / x64  OK  OK  OK 
pelham Mac OS X Leopard (10.5.8) / i386  OK [ OK ] OK 

Summary

Package: pcaMethods
Version: 1.30.0
Command: /Library/Frameworks/R.framework/Versions/2.11/Resources/bin/R CMD check --no-vignettes --timings pcaMethods_1.30.0.tar.gz
StartedAt: 2010-10-04 18:06:09 -0700 (Mon, 04 Oct 2010)
EndedAt: 2010-10-04 18:10:39 -0700 (Mon, 04 Oct 2010)
EllapsedTime: 270.3 seconds
RetCode: 0
Status:  OK 
CheckDir: pcaMethods.Rcheck
Warnings: 0

Command output

* checking for working pdflatex ... OK
* using log directory '/Users/biocbuild/bbs-2.6-bioc/meat/pcaMethods.Rcheck'
* using R version 2.11.1 Patched (2010-05-31 r52167)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'pcaMethods/DESCRIPTION' ... OK
* this is package 'pcaMethods' version '1.30.0'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'pcaMethods' can be installed ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level 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 name space can be loaded with stated dependencies ... OK
* checking whether the name space 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 ... OK
* 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 data for non-ASCII characters ... 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 ... OK
* checking examples ... OK
* checking package vignettes in 'inst/doc' ... SKIPPED
* checking PDF version of manual ... OK

pcaMethods.Rcheck/00install.out:

* install options are ' --no-html'

* installing *source* package ‘pcaMethods’ ...
** libs
*** arch - i386
g++ -arch i386 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/i386 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/library/Rcpp/include -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks -c nipals.cpp -o nipals.o
g++ -arch i386 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o pcaMethods.so nipals.o /Library/Frameworks/R.framework/Versions/2.11/Resources/library/Rcpp/lib/i386/libRcpp.a -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.6-bioc/meat/pcaMethods.Rcheck/pcaMethods/libs/i386
*** arch - ppc
g++ -arch ppc -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/ppc -I/Library/Frameworks/R.framework/Versions/2.11/Resources/library/Rcpp/include -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks -c nipals.cpp -o nipals.o
g++ -arch ppc -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o pcaMethods.so nipals.o /Library/Frameworks/R.framework/Versions/2.11/Resources/library/Rcpp/lib/ppc/libRcpp.a -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.6-bioc/meat/pcaMethods.Rcheck/pcaMethods/libs/ppc
*** arch - x86_64
g++ -arch x86_64 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include -I/Library/Frameworks/R.framework/Versions/2.11/Resources/include/x86_64 -I/Library/Frameworks/R.framework/Versions/2.11/Resources/library/Rcpp/include -I/usr/local/include    -fPIC  -g -O2 -Wall -fasm-blocks -c nipals.cpp -o nipals.o
g++ -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o pcaMethods.so nipals.o /Library/Frameworks/R.framework/Versions/2.11/Resources/library/Rcpp/lib/x86_64/libRcpp.a -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.6-bioc/meat/pcaMethods.Rcheck/pcaMethods/libs/x86_64
** R
** data
** inst
** preparing package for lazy loading

Welcome to Bioconductor

  Vignettes contain introductory material. To view, type
  'openVignette()'. To cite Bioconductor, see
  'citation("Biobase")' and for packages 'citation(pkgname)'.


Attaching package: 'pls'

The following object(s) are masked from 'package:stats':

    loadings

Creating a new generic function for "print" in "pcaMethods"
Creating a new generic function for "biplot" in "pcaMethods"
Creating a new generic function for "summary" in "pcaMethods"
Creating a new generic function for "predict" in "pcaMethods"
Creating a new generic function for "residuals" in "pcaMethods"
Creating a new generic function for "resid" in "pcaMethods"
Creating a new generic function for "fitted" in "pcaMethods"
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded

* DONE (pcaMethods)

pcaMethods.Rcheck/pcaMethods-Ex.timings:

nameusersystemelapsed
DModX0.0740.0050.080
Q20.2980.0070.308
RnipalsPca0.6320.0450.693
biplot.pcaRes0.0200.0010.022
bpca2.8910.0462.975
fitted.pcaRes0.0180.0010.020
kEstimate48.85513.60264.687
kEstimateFast0.6060.1460.764
leverage0.0280.0030.031
llsImpute0.5840.0100.595
nipalsPca0.0900.0080.098
nlpca3.7010.9524.676
nni0.5160.0110.529
pca0.1680.0030.172
plot.pcaRes1.1050.0641.183
plotPcs0.0330.0020.035
ppca0.2060.0540.261
predict.pcaRes0.0290.0020.030
prep0.0030.0010.003
residuals.pcaRes0.0240.0010.026
robustPca30.810 0.63631.673
robustSvd69.510 1.57472.536
slplot0.0370.0020.039
svdImpute0.3410.0460.391
svdPca0.0580.0170.077
wasna0.0410.0050.050