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Package 328/462HostnameOS / ArchBUILDCHECKBUILD BIN
pcaMethods 1.37.0
Wolfram Stacklies
Snapshot Date: 2011-05-09 07:20:56 -0700 (Mon, 09 May 2011)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/pcaMethods
Last Changed Rev: 54802 / Revision: 55359
Last Changed Date: 2011-04-13 15:36:43 -0700 (Wed, 13 Apr 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 (64-bit) / x64  OK  OK  OK 
pelham Mac OS X Leopard (10.5.8) / i386  OK  OK  OK 

Summary

Package: pcaMethods
Version: 1.37.0
Command: E:\biocbld\bbs-2.9-bioc\R\bin\R.exe CMD check --no-vignettes --timings pcaMethods_1.37.0.tar.gz
StartedAt: 2011-05-09 14:55:17 -0700 (Mon, 09 May 2011)
EndedAt: 2011-05-09 14:58:10 -0700 (Mon, 09 May 2011)
EllapsedTime: 172.4 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 2.14.0 Under development (unstable) (2011-04-17 r55484)
* 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 '1.37.0'
* 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 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 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 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 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  -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

Welcome to Bioconductor

  Vignettes contain introductory material. To view, type
  'browseVignettes()'. 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 ...
*** tangling vignette sources ...
   'missingValues.Rnw' 
   'outliers.Rnw' 
   'pcaMethods.Rnw' 
** testing if installed package can be loaded

* DONE (pcaMethods)

pcaMethods.Rcheck/pcaMethods-Ex.timings:

nameusersystemelapsed
DModX0.050.000.04
Q20.180.010.22
RnipalsPca0.500.000.52
biplot.pcaRes0.020.000.01
bpca1.730.021.77
fitted.pcaRes0.020.000.02
kEstimate29.67 0.0029.90
kEstimateFast0.360.000.36
leverage0.020.010.03
llsImpute0.370.000.39
nipalsPca0.020.020.03
nlpca2.760.002.80
nni0.350.000.38
pca0.120.000.15
plot.pcaRes0.420.000.42
plotPcs0.040.000.04
ppca0.090.000.11
predict.pcaRes0.030.000.03
prep0.020.000.02
residuals.pcaRes0.010.000.09
robustPca20.31 0.0520.71
robustSvd46.67 0.0146.91
slplot0.030.020.05
svdImpute0.190.000.18
svdPca0.030.000.04
wasna0.030.000.03