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IMPORTANT NOTE: R was configured with --enable-strict-barrier on lamb1 |
Package 2/247 | Hostname | OS | Arch | BUILD | CHECK | BUILD BIN |
aCGH1.11.0Jane FridlyandLast Changed Date: 2007-05-11 21:56:41 -0700 Last Changed Rev: 24616 | lamb1 | Linux (SUSE 10.1) | x86_64 | OK | WARNINGS | |
wellington | Linux (SUSE 9.2) | i686 | OK | WARNINGS | ||
liverpool | Windows Server 2003 R2 (32-bit) | x64 | OK | WARNINGS | OK | |
pitt | Mac OS X (10.4.10) | i386 | OK | [ WARNINGS ] | OK |
Package: aCGH |
Version: 1.11.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check aCGH_1.11.0.tar.gz |
RetCode: 0 |
Time: 190.6 seconds |
Status: WARNINGS |
CheckDir: aCGH.Rcheck |
Warnings: 1 |
* checking for working latex ... OK * using log directory '/Users/biocbuild/bbs-2.1-bioc/meat/aCGH.Rcheck' * using R version 2.6.0 Under development (unstable) (2007-08-10 r42465) * checking for file 'aCGH/DESCRIPTION' ... OK * this is package 'aCGH' version '1.11.0' * 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 for unstated dependencies in R code ... OK * checking S3 generic/method consistency ... WARNING floor: function(x) floor.func: function(x, floor, x.na) See section 'Generic functions and methods' of the 'Writing R Extensions' manual. * 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' Found possibly global 'T' or 'F' in the following functions: combine.func plotfreq.givenstat.final.colors.func plotfreq.stat.chrom.final.func plotfreq.stat.final.func * 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 aCGH-Ex.R ... OK * checking examples ... OK * checking package vignettes in 'inst/doc' ... OK * creating aCGH-manual.tex ... OK * checking aCGH-manual.tex ... OK WARNING: There was 1 warning, see /Users/biocbuild/bbs-2.1-bioc/meat/aCGH.Rcheck/00check.log for details
aCGH.Rcheck/00install.out:
* Installing *source* package 'aCGH' ... ** libs ** arch - i386 g++-4.0 -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -g3 -msse3 -fPIC -g -O2 -Wall -march=nocona -c hmm.cpp -o hmm.o g++-4.0 -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -dynamiclib -Wl,-macosx_version_min -Wl,10.3 -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 ** arch - ppc g++-4.0 -arch ppc -isysroot /Developer/SDKs/MacOSX10.4u.sdk -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc -g3 -I/usr/local/include -fPIC -g -O2 -Wall -c hmm.cpp -o hmm.o g++-4.0 -arch ppc -isysroot /Developer/SDKs/MacOSX10.4u.sdk -dynamiclib -Wl,-macosx_version_min -Wl,10.3 -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 ** R ** data ** demo ** inst ** preparing package for lazy loading Loading required package: cluster Loading required package: survival Loading required package: splines Loading required package: multtest 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: sma ** help Note: unmatched right brace in 'aCGH.process' on or after line 28 >>> 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 example 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)