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 'E:/biocbld/bbs-2.3-bioc/meat/VanillaICE.Rcheck'
* using R version 2.8.1 (2008-12-22)
* using session charset: ISO8859-1
* 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 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 R.css in E:/biocbld/bbs-2.3-bioc/meat/VanillaICE.Rcheck
---------- Making package VanillaICE ------------
adding build stamp to DESCRIPTION
installing NAMESPACE file and metadata
making DLL ...
making viterbi.d from viterbi.c
gcc -std=gnu99 -Ie:/biocbld/bbs-2.3-bioc/R/include -O3 -Wall -c viterbi.c -o viterbi.o
windres --preprocessor="gcc -E -xc -DRC_INVOKED" -I e:/biocbld/bbs-2.3-bioc/R/include -i VanillaICE_res.rc -o VanillaICE_res.o
gcc -std=gnu99 -shared -s -o VanillaICE.dll VanillaICE.def viterbi.o VanillaICE_res.o -Le:/biocbld/bbs-2.3-bioc/R/bin -lm -lR
... DLL made
installing DLL
installing R files
installing inst files
installing data files
preparing package VanillaICE 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
installing man source files
installing indices
not zipping data
installing help
>>> Building/Updating help pages for package 'VanillaICE'
Formats: text html latex example chm
HmmOptions-class text html latex example chm
HmmOptions-methods text html latex chm
HmmParameter-class text html latex example chm
HmmPredict-class text html latex example chm
addFeatureData text html latex chm
calculateBreakpoints text html latex chm
calculateCnSE text html latex chm
calculateDistance text html latex chm
calls.ICE text html latex chm
calls.emission text html latex chm
chromosome1 text html latex example chm
copyNumber.ICE text html latex chm
copyNumber.emission text html latex chm
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'
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 chm
emission text html latex chm
Note: removing empty section \details in file 'findBreaks.Rd'
Note: removing empty section \examples in file 'findBreaks.Rd'
Note: removing empty section \details in file 'findBreaks.Rd'
Note: removing empty section \examples in file 'findBreaks.Rd'
findBreaks text html latex chm
fit text html latex example chm
genomicDistance text html latex chm
genotypeEmission text html latex chm
getChromosomeArm text html latex chm
hmm text html latex example chm
pi text html latex chm
Note: removing empty section \details in file 'scaleTransitionProbability.Rd'
Note: removing empty section \examples in file 'scaleTransitionProbability.Rd'
Note: removing empty section \details in file 'scaleTransitionProbability.Rd'
Note: removing empty section \examples in file 'scaleTransitionProbability.Rd'
scaleTransitionProbability text html latex chm
states text html latex chm
transitionScale text html latex chm
viterbi text html latex chm
Microsoft HTML Help Compiler 4.74.8702
Compiling e:\biocbld\bbs-2.3-bioc\meat\VanillaICE.Rcheck\00_pkg_src\VanillaICE\chm\VanillaICE.chm
Compile time: 0 minutes, 2 seconds
27 Topics
141 Local links
0 Internet links
1 Graphic
Created e:\biocbld\bbs-2.3-bioc\meat\VanillaICE.Rcheck\00_pkg_src\VanillaICE\chm\VanillaICE.chm, 39,615 bytes
Compression decreased file by 58,949 bytes.
adding MD5 sums
* DONE (VanillaICE)