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Package 362/516HostnameOS / ArchBUILDCHECKBUILD BIN
pcaMethods 1.40.0
Wolfram Stacklies
Snapshot Date: 2012-01-08 18:22:44 -0800 (Sun, 08 Jan 2012)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_9/madman/Rpacks/pcaMethods
Last Changed Rev: 59920 / Revision: 61898
Last Changed Date: 2011-10-31 15:59:03 -0700 (Mon, 31 Oct 2011)
wilson2 Linux (openSUSE 11.4) / x86_64  OK  OK 
liverpool Windows Server 2003 R2 (32-bit) / x64  OK [ OK ] OK 
gewurz Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
pitt Mac OS X Leopard (10.5.8) / i386  OK  OK  OK 

Summary

Package: pcaMethods
Version: 1.40.0
Command: E:\biocbld\bbs-2.9-bioc\R\bin\R.exe CMD check --no-vignettes --timings --no-multiarch pcaMethods_1.40.0.tar.gz
StartedAt: 2012-01-09 04:40:05 -0800 (Mon, 09 Jan 2012)
EndedAt: 2012-01-09 04:42:37 -0800 (Mon, 09 Jan 2012)
EllapsedTime: 152.1 seconds
RetCode: 0
Status:  OK  
CheckDir: pcaMethods.Rcheck
Warnings: 0

Command output

* using log directory 'E:/biocbld/bbs-2.9-bioc/meat/pcaMethods.Rcheck'
* using R version 2.14.1 (2011-12-22)
* using platform: i386-pc-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'pcaMethods/DESCRIPTION' ... OK
* this is package 'pcaMethods' version '1.40.0'
* 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 whether package 'pcaMethods' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for portable file names ... 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 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
File 'pcaMethods/R/pca.R':
  .onLoad calls:
    require("methods")

Package startup functions should not change the search path.
See section 'Good practice' in ?.onAttach.

* 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 ... NOTE
S3 methods shown with full name in documentation object 'biplot.pcaRes':
  'biplot.pcaRes'

S3 methods shown with full name in documentation object 'dim.pcaRes':
  'dim.pcaRes'

S3 methods shown with full name in documentation object 'fitted.pcaRes':
  'fitted.pcaRes'

S3 methods shown with full name in documentation object 'loadings.pcaRes':
  'loadings.pcaRes'

S3 methods shown with full name in documentation object 'plot.pcaRes':
  'plot.pcaRes'

S3 methods shown with full name in documentation object 'predict.pcaRes':
  'predict.pcaRes'

S3 methods shown with full name in documentation object 'residuals.pcaRes':
  'residuals.pcaRes'

S3 methods shown with full name in documentation object 'scores.pcaRes':
  'scores.pcaRes'

The \usage entries for S3 methods should use the \method markup and not
their full name.
See the chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* 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 examples ... OK
* checking for unstated dependencies in vignettes ... NOTE
'library' or 'require' call not declared from: 'lattice'
* 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

pcaMethods.Rcheck/00install.out:

* installing *source* package 'pcaMethods' ...
** libs
g++  -I"E:/biocbld/BBS-2˜1.9-B/R/include"    -I"E:/biocbld/bbs-2.9-bioc/R/library/Rcpp/include"      -O2 -Wall  -mtune=core2 -c nipals.cpp -o nipals.o
g++ -shared -s -static-libgcc -o pcaMethods.dll tmp.def nipals.o E:/biocbld/bbs-2.9-bioc/R/library/Rcpp/lib/i386/libRcpp.a -LE:/biocbld/BBS-2˜1.9-B/R/bin/i386 -lR
installing to E:/biocbld/bbs-2.9-bioc/meat/pcaMethods.Rcheck/pcaMethods/libs/i386
** R
** data
** inst
** preparing package for lazy loading
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 'residuals' 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'
** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
   'missingValues.Rnw' 
   'outliers.Rnw' 
   'pcaMethods.Rnw' 
** testing if installed package can be loaded

* DONE (pcaMethods)

pcaMethods.Rcheck/pcaMethods-Ex.timings:

nameusersystemelapsed
DModX0.120.000.12
Q20.190.000.20
RnipalsPca0.330.000.33
biplot-dot-pcaRes0.010.010.03
bpca1.520.001.53
cvseg0.020.000.02
fitted-dot-pcaRes000
kEstimate25.51 0.0025.61
kEstimateFast0.330.000.33
leverage0.020.000.01
llsImpute0.320.000.33
nipalsPca0.030.000.03
nlpca2.680.022.72
nni0.280.000.28
pca0.070.000.06
plot-dot-pcaRes0.360.000.36
plotPcs0.010.000.02
ppca0.110.000.10
predict-dot-pcaRes0.000.000.04
prep000
residuals-dot-pcaRes0.000.000.03
robustPca18.06 0.0418.13
robustSvd40.75 0.0441.01
slplot0.030.000.05
svdImpute0.190.000.19
svdPca0.030.000.03
wasna0.010.000.01