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 '/Users/biocbuild/bbs-2.4-bioc/meat/aCGH.Rcheck'
* using R version 2.9.2 Patched (2009-08-24 r49420)
* using session charset: UTF-8
* 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 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
[.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’
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’
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’
* 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
** arch - i386
g++-4.0 -arch i386 -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/i386 -g3 -I/usr/local/include -fPIC -g -O2 -Wall -fasm-blocks -c hmm.cpp -o hmm.o
g++-4.2 -arch i386 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o aCGH.so hmm.o -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
** arch - ppc
g++-4.0 -arch ppc -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/ppc -g3 -I/usr/local/include -fPIC -g -O2 -Wall -fasm-blocks -c hmm.cpp -o hmm.o
g++-4.2 -arch ppc -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o aCGH.so hmm.o -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
** arch - ppc64
g++-4.0 -arch ppc64 -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/ppc64 -g3 -I/usr/local/include -fPIC -g -O2 -Wall -fasm-blocks -c hmm.cpp -o hmm.o
g++-4.2 -arch ppc64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o aCGH.so hmm.o -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
** arch - x86_64
g++-4.0 -arch x86_64 -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include -I/Library/Frameworks/R.framework/Versions/2.9/Resources/include/x86_64 -g3 -I/usr/local/include -fPIC -g -O2 -Wall -fasm-blocks -c hmm.cpp -o hmm.o
g++-4.2 -arch x86_64 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o aCGH.so hmm.o -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
** 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
aCGH text html latex example
aCGH.process text html latex example
aCGH.read.Sprocs text html latex example
aCGH.test text html latex
clusterGenome text html latex example
colorectal text html latex example
computeSD.func text html latex
fga.func text html latex example
find.genomic.events text html latex
find.hmm.states text html latex example
findAber.func text html latex
findAmplif.func text html latex
findOutliers.func text html latex
findTrans.func text html latex
gainLoss text html latex example
heatmap text html latex example
human.chrom.info.Jul03 text html latex
human.chrom.info.May04 text html latex
impute.HMM text html latex example
impute.lowess text html latex example
mergeFunc text html latex
mergeLevels text html latex example
plotFreqStat text html latex example
plotGenome text html latex example
plotHmmStates text html latex example
plotSummaryProfile text html latex example
states.hmm.func text html latex
summarize.clones text html latex example
threshold.func text html latex example
** building package indices ...
* DONE (aCGH)