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Package 284/294HostnameOS / ArchBUILDCHECKBUILD BIN
VanillaICE 1.4.0
Robert Scharpf
Bioconductor Changelog
Snapshot Date: 2009-04-18 11:27:48 -0700 (Sat, 18 Apr 2009)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_3/madman/Rpacks/VanillaICE
Last Changed Rev: 34811 / Revision: 38965
Last Changed Date: 2008-10-21 15:32:58 -0700 (Tue, 21 Oct 2008)
wilson2 Linux (openSUSE 11.1) / x86_64  OK  OK 
liverpool Windows Server 2003 R2 (32-bit) / x64  OK  OK  OK 
pitt Mac OS X Tiger (10.4.11) / i386  OK  OK  OK 
pelham Mac OS X Leopard (10.5.6) / i386  OK [ OK ] OK 
Package: VanillaICE
Version: 1.4.0
Command: /Library/Frameworks/R.framework/Versions/2.8/Resources/bin/R CMD check --no-vignettes VanillaICE_1.4.0.tar.gz
StartedAt: 2009-04-18 18:33:03 -0700 (Sat, 18 Apr 2009)
EndedAt: 2009-04-18 18:34:04 -0700 (Sat, 18 Apr 2009)
EllapsedTime: 60.6 seconds
RetCode: 0
Status: OK
CheckDir: VanillaICE.Rcheck
Warnings: 0

Command output

* checking for working pdflatex ... OK
* using log directory '/Users/biocbuild/bbs-2.3-bioc/meat/VanillaICE.Rcheck'
* using R version 2.8.1 Patched (2009-03-18 r48200)
* using session charset: ASCII
* checking for file 'VanillaICE/DESCRIPTION' ... OK
* this is package 'VanillaICE' version '1.4.0'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'VanillaICE' 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 name space can be loaded with stated dependencies ... 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
.genotype.emission: no visible binding for global variable 'object'
addFeatureData: no visible binding for global variable 'chromosomeArm'
genotypeEmission: no visible binding for global variable 'GT'
genotypeEmission: no visible binding for global variable 'probs'
getChromosomeArm: no visible binding for global variable
  'chromosomeAnnotation'
states<-,HmmParameter-character: no visible global function definition
  for 'hmmOptions'
states<-,HmmParameter-character: no visible global function definition
  for 'hmmOptions<-'
* checking Rd files ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... 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
* creating VanillaICE-Ex.R ... OK
* checking examples ... OK
* checking package vignettes in 'inst/doc' ... OK
* creating VanillaICE-manual.tex ... OK
* checking VanillaICE-manual.tex using pdflatex ... OK

VanillaICE.Rcheck/00install.out:

* Installing *source* package 'VanillaICE' ...
** libs
** arch - i386
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -Wall -c viterbi.c -o viterbi.o
gcc-4.2 -arch i386 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names  -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o VanillaICE.so viterbi.o -lm  -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
** arch - ppc
gcc-4.2 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/ppc  -I/usr/local/include    -fPIC  -g -O2 -Wall -c viterbi.c -o viterbi.o
gcc-4.2 -arch ppc -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names  -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o VanillaICE.so viterbi.o -lm  -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
** arch - ppc64
gcc-4.2 -arch ppc64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/ppc64  -I/usr/local/include    -fPIC  -g -O2 -Wall -c viterbi.c -o viterbi.o
gcc-4.2 -arch ppc64 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names  -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o VanillaICE.so viterbi.o -lm  -L/Library/Frameworks/R.framework/Versions/2.8/Resources/lib/ppc64 -lR -dylib_file libRblas.dylib:/Library/Frameworks/R.framework/Versions/2.8/Resources/lib/ppc64/libRblas.dylib -Wl,-framework -Wl,CoreFoundation
** arch - x86_64
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/x86_64  -I/usr/local/include    -fPIC  -g -O2 -Wall -c viterbi.c -o viterbi.o
gcc-4.2 -arch x86_64 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names  -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o VanillaICE.so viterbi.o -lm  -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
** R
** data
** inst
** preparing package for lazy loading
Loading required package: SNPchip
Loading required package: Biobase
Loading required package: tools

Welcome to Bioconductor

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

Loading required package: oligoClasses
** help
 >>> Building/Updating help pages for package 'VanillaICE'
     Formats: text html latex example 
  HmmOptions-class                  text    html    latex   example
  HmmOptions-methods                text    html    latex
  HmmParameter-class                text    html    latex   example
  HmmPredict-class                  text    html    latex   example
  addFeatureData                    text    html    latex
  calculateBreakpoints              text    html    latex
  calculateCnSE                     text    html    latex
  calculateDistance                 text    html    latex
  calls.ICE                         text    html    latex
  calls.emission                    text    html    latex
  chromosome1                       text    html    latex   example
  copyNumber.ICE                    text    html    latex
  copyNumber.emission               text    html    latex
Note: removing empty section \details in file 'copynumberEmission.Rd'
Note: removing empty section \seealso in file 'copynumberEmission.Rd'
Note: removing empty section \examples in file 'copynumberEmission.Rd'
  copynumberEmission                text    html    latex
  emission                          text    html    latex
Note: removing empty section \details in file 'findBreaks.Rd'
Note: removing empty section \examples in file 'findBreaks.Rd'
  findBreaks                        text    html    latex
  fit                               text    html    latex   example
  genomicDistance                   text    html    latex
  genotypeEmission                  text    html    latex
  getChromosomeArm                  text    html    latex
  hmm                               text    html    latex   example
  pi                                text    html    latex
Note: removing empty section \details in file 'scaleTransitionProbability.Rd'
Note: removing empty section \examples in file 'scaleTransitionProbability.Rd'
  scaleTransitionProbability        text    html    latex
  states                            text    html    latex
  transitionScale                   text    html    latex
  viterbi                           text    html    latex
** building package indices ...
* DONE (VanillaICE)