aCGH 1.18.1
Jane Fridlyand
| Bioconductor Changelog | | Snapshot Date: 2009-10-20 11:27:33 -0700 (Tue, 20 Oct 2009) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_4/madman/Rpacks/aCGH | | Last Changed Rev: 42112 / Revision: 42512 | | Last Changed Date: 2009-10-01 16:44:04 -0700 (Thu, 01 Oct 2009) |
| wilson1 | 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 (10.5.8) / i386 | OK | OK | OK |
* checking for working pdflatex ... OK
* using log directory 'E:/biocbld/bbs-2.4-bioc/meat/aCGH.Rcheck'
* using R version 2.9.2 (2009-08-24)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'aCGH/DESCRIPTION' ... OK
* this is package 'aCGH' version '1.18.1'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'aCGH' 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
[.aCGH: no visible binding for global variable 'joan'
changeProp.func: no visible binding for global variable
'data.screen.norm.thres'
computeSD.func: no visible binding for global variable 'states.bic'
findAber.func: no visible binding for global variable 'states.bic'
findAmplif.func: no visible binding for global variable 'res3'
findAmplif.func: no visible binding for global variable 'res2'
findAmplif.func: no visible binding for global variable 'res1'
findAmplif.func: no visible binding for global variable 'states.bic'
findOutliers.func: no visible binding for global variable 'madGenome'
findOutliers.func: no visible binding for global variable 'states.bic'
findTrans.func: no visible binding for global variable 'res1'
findTrans.func: no visible binding for global variable 'res2'
findTrans.func: no visible binding for global variable 'states.bic'
mergeFunc: no visible binding for global variable 'states.bic'
plotCGH.func: no visible binding for global variable 'data.cgh'
plotCGH.func: no visible binding for global variable 'map.cgh'
plotCGH.hmm.func: no visible binding for global variable 'dat'
plotCGH.hmm.func: no visible binding for global variable 'states.bic'
plotCGH.hmm.func: no visible binding for global variable 'res4'
plotCGH.hmm.func: no visible binding for global variable 'res2'
plotCGH.hmm.func: no visible binding for global variable 'res1'
plotCGH.hmm.func: no visible binding for global variable 'res3'
plotChrom.grey.samples.func: no visible binding for global variable
'states.bic'
plotChrom.grey.samples.func: no visible binding for global variable
'res4'
plotChrom.grey.samples.func: no visible binding for global variable
'res2'
plotChrom.grey.samples.func: no visible binding for global variable
'res1'
plotChrom.grey.samples.func: no visible binding for global variable
'res3'
plotChrom.hmm.func: no visible binding for global variable 'states.bic'
plotChrom.hmm.func: no visible binding for global variable 'res4'
plotChrom.hmm.func: no visible binding for global variable 'res2'
plotChrom.hmm.func: no visible binding for global variable 'res1'
plotChrom.hmm.func: no visible binding for global variable 'res3'
plotChrom.samples.func: no visible binding for global variable
'states.bic'
plotChrom.samples.func: no visible binding for global variable 'res4'
plotChrom.samples.func: no visible binding for global variable 'res2'
plotChrom.samples.func: no visible binding for global variable 'res1'
plotChrom.samples.func: no visible binding for global variable 'res3'
plotfreq.givenstat.final.colors.func: no visible binding for global
variable 'stats'
plotfreq.givenstat.final.colors.func: no visible binding for global
variable 'statsPerm'
plotfreq.givenstat.final.colors.func: possible error in gainLoss(dat =
data, cols = cols, thres = thres, quant = quant.col): unused
argument(s) (quant = quant.col)
plotfreq.stat.chrom.final.func: no visible binding for global variable
'.mt.naNUM'
plotfreq.stat.chrom.final.func: no visible global function definition
for 'exit'
plotfreq.stat.final.func: no visible binding for global variable
'.mt.naNUM'
plotFreqStatColors: no visible global function definition for
'plotfreq.stat'
plotFreqStatGrey: no visible global function definition for
'plotfreq.stat'
plotGeneSign: no visible binding for global variable '.mt.naNUM'
plotSummaryProfile: no visible binding for global variable
'numchromgain'
plotSummaryProfile: no visible binding for global variable
'numchromloss'
plotSummaryProfile: no visible binding for global variable 'numtrans'
plotSummaryProfile: no visible binding for global variable
'numtrans.binary'
plotSummaryProfile: no visible binding for global variable 'numaber'
plotSummaryProfile: no visible binding for global variable 'numamplif'
plotSummaryProfile: no visible binding for global variable
'numamplif.binary'
plotSummaryProfile: no visible binding for global variable
'numamplicon'
plotSummaryProfile: no visible binding for global variable
'sizeamplicon'
* checking Rd files ... OK
* checking Rd files against version 2 parser ... 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
* checking examples ... OK
* checking package vignettes in 'inst/doc' ... SKIPPED
* checking PDF version of manual ... OK
* Installing *source* package 'aCGH' ...
** libs
making DLL ...
g++ -I"e:/biocbld/bbs-2.4-bioc/R/include" -g3 -O2 -Wall -c hmm.cpp -o hmm.o
g++ -shared -s -o aCGH.dll tmp.def hmm.o -lm -Le:/biocbld/bbs-2.4-bioc/R/bin -lR
... done
** R
** data
** demo
** inst
** preparing package for lazy loading
Loading required package: splines
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material. To view, type
'openVignette()'. To cite Bioconductor, see
'citation("Biobase")' and for packages 'citation(pkgname)'.
** help
*** installing help indices
>>> Building/Updating help pages for package 'aCGH'
Formats: text html latex example chm
aCGH text html latex example chm
aCGH.process text html latex example chm
aCGH.read.Sprocs text html latex example chm
aCGH.test text html latex chm
clusterGenome text html latex example chm
colorectal text html latex example chm
computeSD.func text html latex chm
fga.func text html latex example chm
find.genomic.events text html latex chm
find.hmm.states text html latex example chm
findAber.func text html latex chm
findAmplif.func text html latex chm
findOutliers.func text html latex chm
findTrans.func text html latex chm
gainLoss text html latex example chm
heatmap text html latex example chm
human.chrom.info.Jul03 text html latex chm
human.chrom.info.May04 text html latex chm
impute.HMM text html latex example chm
impute.lowess text html latex example chm
mergeFunc text html latex chm
mergeLevels text html latex example chm
plotFreqStat text html latex example chm
plotGenome text html latex example chm
plotHmmStates text html latex example chm
plotSummaryProfile text html latex example chm
states.hmm.func text html latex chm
summarize.clones text html latex example chm
threshold.func text html latex example chm
Microsoft HTML Help Compiler 4.74.8702
Compiling e:\biocbld\BBS-2~1.4-B\meat\ACGH~1.RCH\00_PKG~1\aCGH\chm\aCGH.chm
Compile time: 0 minutes, 0 seconds
30 Topics
262 Local links
0 Internet links
1 Graphic
Created e:\biocbld\BBS-2~1.4-B\meat\ACGH~1.RCH\00_PKG~1\aCGH\chm\aCGH.chm, 73,723 bytes
Compression decreased file by 88,888 bytes.
** building package indices ...
** MD5 sums
* DONE (aCGH)