Back to the "Multiple platform build/check report" A  B  C  D  E  F  G  H  I  J  K  L  M  N  O [P] Q  R  S  T  U  V  W  X  Y  Z 

Package 392/553HostnameOS / ArchBUILDCHECKBUILD BIN
pcaMethods 1.42.0
Wolfram Stacklies
Snapshot Date: 2012-09-23 17:01:39 -0700 (Sun, 23 Sep 2012)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_10/madman/Rpacks/pcaMethods
Last Changed Rev: 64678 / Revision: 69725
Last Changed Date: 2012-03-30 15:05:02 -0700 (Fri, 30 Mar 2012)
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: 1.42.0
Command: /home/biocbuild/bbs-2.10-bioc/R/bin/R CMD check --no-vignettes --timings pcaMethods_1.42.0.tar.gz
StartedAt: 2012-09-24 02:45:37 -0700 (Mon, 24 Sep 2012)
EndedAt: 2012-09-24 02:48:38 -0700 (Mon, 24 Sep 2012)
EllapsedTime: 180.3 seconds
RetCode: 0
Status:  OK 
CheckDir: pcaMethods.Rcheck
Warnings: 0

Command output

* using log directory ‘/loc/home/biocbuild/bbs-2.10-bioc/meat/pcaMethods.Rcheck’
* using R version 2.15.1 (2012-06-22)
* 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 ‘1.42.0’
* 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 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 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 installed files from ‘inst/doc’ ... 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

NOTE: There were 3 notes.
See
  ‘/loc/home/biocbuild/bbs-2.10-bioc/meat/pcaMethods.Rcheck/00check.log’
for details.

pcaMethods.Rcheck/00install.out:

* installing *source* package ‘pcaMethods’ ...
** libs
g++ -I/home/biocbuild/bbs-2.10-bioc/R/include -DNDEBUG  -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.10-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -Wall -c nipals.cpp -o nipals.o
g++ -shared -L/usr/local/lib64 -o pcaMethods.so nipals.o -L/loc/home/biocbuild/bbs-2.10-bioc/R/library/Rcpp/lib -lRcpp -Wl,-rpath,/loc/home/biocbuild/bbs-2.10-bioc/R/library/Rcpp/lib -L/home/biocbuild/bbs-2.10-bioc/R/lib -lR
installing to /loc/home/biocbuild/bbs-2.10-bioc/meat/pcaMethods.Rcheck/pcaMethods/libs
** 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 ‘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
** installing vignettes
   ‘missingValues.Rnw’ 
   ‘outliers.Rnw’ 
   ‘pcaMethods.Rnw’ 
** testing if installed package can be loaded

* DONE (pcaMethods)

pcaMethods.Rcheck/pcaMethods-Ex.timings:

nameusersystemelapsed
DModX0.2200.0080.248
Q20.1800.0120.197
RnipalsPca0.4560.0040.457
biplot-dot-pcaRes0.0200.0040.019
bpca2.0360.0042.044
cvseg0.0160.0000.016
fitted-dot-pcaRes0.0160.0000.016
kEstimate33.614 0.02433.731
kEstimateFast0.3960.0000.395
leverage0.0160.0040.019
llsImpute0.3560.0000.358
nipalsPca0.0200.0000.018
nlpca2.6960.0042.699
nni0.2640.0000.262
pca0.0880.0040.091
plot-dot-pcaRes0.3040.0040.309
plotPcs0.0240.0000.023
ppca0.2040.0040.208
predict-dot-pcaRes0.0160.0000.016
prep0.0000.0000.001
residuals-dot-pcaRes0.0120.0040.014
robustPca21.630 0.01221.655
robustSvd48.507 0.02048.936
slplot0.0280.0000.030
svdImpute0.1760.0000.178
svdPca0.0240.0000.026
wasna0.0240.0000.022