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Package 212/234 | Hostname | OS | Arch | BUILD | CHECK | BUILD BIN |
snapCGH 1.6.0 John Marioni Last Changed Date: 2007-10-02 17:41:09 -0700 Last Changed Rev: 27709 | lamb1 | Linux (SUSE 10.1) | x86_64 | OK | OK | |
wellington | Linux (SUSE 9.2) | i686 | OK | [ OK ] | ||
liverpool | Windows Server 2003 R2 (32-bit) | x64 | OK | OK | OK | |
pitt | Mac OS X (10.4.10) | i386 | OK | OK | OK |
Package: snapCGH |
Version: 1.6.0 |
Command: /loc/biocbuild/bbs-2.1-bioc/R/bin/R CMD check snapCGH_1.6.0.tar.gz |
RetCode: 0 |
Time: 510.7 seconds |
Status: OK |
CheckDir: snapCGH.Rcheck |
Warnings: 0 |
* checking for working latex ... OK * using log directory '/extra/loc/biocbuild/bbs-2.1-bioc/meat/snapCGH.Rcheck' * using R version 2.6.0 (2007-10-03) * checking for file 'snapCGH/DESCRIPTION' ... OK * this is package 'snapCGH' version '1.6.0' * checking package dependencies ... OK * checking if this is a source package ... OK * checking whether package 'snapCGH' 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 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 generate.data: no visible binding for global variable 'zero.length.distr.non.tiled' generate.data: no visible binding for global variable 'non.zero.length.distr.non.tiled' generate.data: no visible binding for global variable 'zero.length.distr.tiled' generate.data: no visible binding for global variable 'non.zero.length.distr.tiled' processCGH: no visible binding for global variable 'RG' readPositionalInfo: no visible binding for global variable 'RGList' runPicard: possible error in segment(log2ratios, maxk = length(log2ratios), maxseg = min(length(log2ratios), maxSeg)): unused argument(s) (maxk = length(log2ratios), maxseg = min(length(log2ratios), maxSeg)) simulateData: no visible binding for global variable 'zero.length.distr.non.tiled' simulateData: no visible binding for global variable 'zero.length.distr.tiled' simulateData: no visible binding for global variable 'non.zero.length.distr.non.tiled' simulateData: no visible binding for global variable 'non.zero.length.distr.tiled' Found possibly global 'T' or 'F' in the following functions: read.clonesinfo readPositionalInfo simulateData * 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 use of $BLAS_LIBS ... OK * creating snapCGH-Ex.R ... OK * checking examples ... OK * checking package vignettes in 'inst/doc' ... OK * creating snapCGH-manual.tex ... OK * checking snapCGH-manual.tex ... OK
snapCGH.Rcheck/00install.out:
* Installing *source* package 'snapCGH' ... ** libs gcc -std=gnu99 -I/loc/biocbuild/bbs-2.1-bioc/R/include -I/loc/biocbuild/bbs-2.1-bioc/R/include -I/usr/local/include -fpic -g -O2 -Wall -c optimizer.c -o optimizer.o gcc -std=gnu99 -shared -L/usr/local/lib -o snapCGH.so optimizer.o -L/loc/biocbuild/bbs-2.1-bioc/R/lib -lR ** R ** data ** inst ** preparing package for lazy loading Loading required package: limma Loading required package: tilingArray 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: affy Loading required package: affyio Loading required package: preprocessCore Loading required package: RColorBrewer Loading required package: grid Loading required package: strucchange Loading required package: zoo Attaching package: 'zoo' The following object(s) are masked from package:base : rapply Loading required package: sandwich Loading required package: vsn Loading required package: genefilter Loading required package: survival Loading required package: splines Loading required package: geneplotter Loading required package: annotate Loading required package: AnnotationDbi Loading required package: DBI Loading required package: RSQLite Loading required package: xtable Loading required package: lattice KernSmooth 2.22 installed Copyright M. P. Wand 1997 Loading required package: pixmap Loading required package: DNAcopy Attaching package: 'DNAcopy' The following object(s) are masked from package:tilingArray : segment Loading required package: GLAD Loading required package: aws Loading required package: tcltk Loading Tcl/Tk interface ... done [1] "Have fun with GLAD" Loading required package: cluster Loading required package: aCGH Loading required package: multtest Loading required package: sma Attaching package: 'aCGH' The following object(s) are masked from package:stats : heatmap ** help Note: unmatched right brace in 'SegList' on or after line 30 Note: unmatched right brace in 'find.param.one' on or after line 18 Note: unmatched right brace in 'non.zero.length.distr.non.tiled' on or after line 9 Note: unmatched right brace in 'processCGH' on or after line 44 >>> Building/Updating help pages for package 'snapCGH' Formats: text html latex example IDProbes text html latex LargeDataObject text html latex example SegList text html latex Viterbi.five text html latex Viterbi.four text html latex Viterbi.three text html latex Viterbi.two text html latex cbind text html latex chrominfo.Mb text html latex compareSegmentations text html latex convert.output text html latex example dim text html latex example dimnames text html latex filter text html latex find.param.five text html latex find.param.four text html latex find.param.one text html latex find.param.three text html latex find.param.two text html latex findBreakPoints text html latex fit.model text html latex genomePlot text html latex example heatmapGenome text html latex example imputeMissingValues text html latex log2ratios text html latex mergeStates text html latex non.zero.length.distr.non.tiled text html latex non.zero.length.distr.tiled text html latex nudSegmentation text html latex plotSegmentedGenome text html latex example processCGH text html latex read.clonesinfo text html latex readPositionalInfo text html latex removeByWeights text html latex runBioHMM text html latex runDNAcopy text html latex runGLAD text html latex runHMM text html latex runPicard text html latex sim.structure text html latex example zero.length.distr.non.tiled text html latex zero.length.distr.tiled text html latex zoomChromosome text html latex zoomGenome text html latex ** building package indices ... * DONE (snapCGH)