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 |
* 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
* 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)