• using R version 2.7.0 Patched (2008-05-08 r45647)
  • using session charset: UTF-8
  • checking for file 'ADaCGH/DESCRIPTION' ... OK
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  • this is package 'ADaCGH' version '1.3-7'
  • checking package name space information ... OK
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  • checking package dependencies ... OK
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  • checking if this is a source package ... OK
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  • checking whether package 'ADaCGH' can be installed ... OK
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  • checking package directory ... OK
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  • checking for portable file names ... OK
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  • checking for sufficient/correct file permissions ... OK
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  • checking DESCRIPTION meta-information ... OK
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  • checking top-level files ... OK
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  • checking index information ... OK
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  • checking package subdirectories ... OK
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  • checking R files for non-ASCII characters ... OK
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  • checking R files for syntax errors ... OK
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  • checking whether the package can be loaded ... OK
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  • checking whether the package can be loaded with stated dependencies ... OK
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  • checking whether the name space can be loaded with stated dependencies ... OK
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  • checking for unstated dependencies in R code ... OK
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  • checking S3 generic/method consistency ... OK
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  • checking replacement functions ... OK
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  • checking foreign function calls ... OK
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  • checking R code for possible problems ... NOTE
    ACE : <anonymous>: no visible binding for global variable ‘cmm_coefs’
    ACE : <anonymous>: no visible binding for global variable ‘cmm_Sdev’
    ACE : <anonymous>: no visible binding for global variable
    ‘cmm_array.names’
    ace.analysisP_C: no visible binding for global variable ‘coefs’
    ace.analysisP_C: no visible binding for global variable ‘Sdev’
    ace.analysisP_C: no visible binding for global variable ‘array.names’
    DNAcopyDiagnosticPlots: no visible binding for global variable
    ‘smoothed.CNA.object’
    linkGene: no visible binding for global variable ‘idtype’
    linkGene2: no visible binding for global variable ‘idtype’
    mapChromOpen: no visible binding for global variable ‘main’
    mapChromOpen: no visible binding for global variable ‘chrom’
    mapChromOpen: no visible binding for global variable ‘chrom.nums’
    mapChromOpen: no visible binding for global variable ‘cnum’
    mapChromOpenA: no visible binding for global variable ‘main’
    mapChromOpenA: no visible binding for global variable ‘indexchr’
    mapChromOpenA: no visible binding for global variable ‘chrom.nums’
    mapChromOpenA: no visible binding for global variable ‘cnum’
    mapCloseAndPythonChrom: no visible binding for global variable
    ‘chrom.nums’
    mapCloseAndPythonChrom: no visible binding for global variable ‘cnum’
    mapCloseAndPythonChrom: no visible binding for global variable ‘nameIm’
    mapCloseAndPythonChrom: no visible binding for global variable
    ‘ccircle’
    mapCloseAndPythonChrom: no visible binding for global variable
    ‘indexchr’
    mapCloseAndPythonChrom: no visible binding for global variable ‘im2’
    mapCloseAndPythonChrom: no visible binding for global variable ‘idtype’
    mapCloseAndPythonChromA: no visible binding for global variable
    ‘thiscn’
    mapCloseAndPythonChromA: no visible binding for global variable
    ‘nameIm’
    mapCloseAndPythonChromA: no visible binding for global variable
    ‘ccircle’
    mapCloseAndPythonChromA: no visible binding for global variable
    ‘indexchr’
    mapCloseAndPythonChromA: no visible binding for global variable ‘im2’
    mapCloseAndPythonChromA: no visible binding for global variable
    ‘idtype’
    mapLinkChrom: no visible binding for global variable ‘simplepos’
    mapLinkChrom: no visible binding for global variable ‘chrom’
    mapLinkChrom: no visible binding for global variable ‘logr’
    mapLinkChrom : f1: no visible binding for global variable ‘nameIm’
    my.sw3b: no visible binding for global variable ‘PSW.p.crit’
    plateauPlot.DNAcopy: no visible global function definition for
    ‘plot.DNAcopy2’
    plateauPlot.DNAcopy: no visible global function definition for
    ‘plot.DNAcopy3’
    plateauPlot.DNAcopy: no visible global function definition for
    ‘plot.DNAcopy4’
    plot.adacgh.chromosomewide: no visible binding for global variable
    ‘positions.merge1’
    plot.adacgh.genomewide: no visible binding for global variable
    ‘positions.merge1’
    plotChromWide: no visible binding for global variable ‘indexchr’
    plotChromWide: no visible binding for global variable ‘chrom.nums’
    plotChromWide: no visible binding for global variable ‘cnum’
    plotChromWide: no visible binding for global variable ‘nameIm’
    plotChromWide: no visible binding for global variable ‘pch’
    plotChromWide: no visible binding for global variable ‘ylim’
    plotChromWide: no visible binding for global variable ‘simplepos’
    plotChromWideA: no visible binding for global variable ‘thiscn’
    plotChromWideA: no visible binding for global variable ‘nameIm’
    plotChromWideA: no visible binding for global variable ‘pch’
    plotChromWideA: no visible binding for global variable ‘ylim’
    plotChromWideA: no visible binding for global variable ‘simplepos’
    plot.cw.superimp: no visible binding for global variable
    ‘positions.merge1’
    plot.cw.superimpA: no visible binding for global variable
    ‘positions.merge1’
    plot.cw.superimpA : funp: no visible binding for global variable
    ‘nameImage’
    plotGenomeWide: no visible binding for global variable ‘main’
    plotGenomeWide: no visible binding for global variable ‘pch’
    plotGenomeWide: no visible binding for global variable ‘ylim’
    plotGenomeWide: no visible binding for global variable ‘simplepos’
    plot.gw.superimp: no visible binding for global variable ‘ymin’
    plot.gw.superimp: no visible binding for global variable ‘ymax’
    plot.gw.superimp: no visible binding for global variable
    ‘positions.merge1’
    pngCircleRegion : usr2pngCircle: no visible binding for global variable
    ‘im2’
    pngCircleRegion: no visible binding for global variable ‘simplepos’
    pngCircleRegion: no visible binding for global variable ‘indexchr’
    pngCircleRegion: no visible binding for global variable ‘logr’
    pngCircleRegionA : usr2pngCircle: no visible binding for global
    variable ‘im2’
    pngCircleRegionA: no visible binding for global variable ‘simplepos’
    pngCircleRegionA: no visible binding for global variable ‘logr’
    pSegmentBioHMM_A : <anonymous>: no visible binding for global variable
    ‘slave_chrom’
    pSegmentBioHMM_A : <anonymous>: no visible binding for global variable
    ‘slave_kb’
    pSegmentCGHseg : <anonymous>: no visible binding for global variable
    ‘slave_cnum’
    pSegmentCGHseg : <anonymous>: no visible binding for global variable
    ‘cghseg.s.slave’
    pSegmentDNAcopy_A : papfunc: no visible binding for global variable
    ‘slave_smooth’
    pSegmentDNAcopy_A : papfunc: no visible binding for global variable
    ‘slave_cnum’
    pSegmentDNAcopy_A : papfunc: no visible binding for global variable
    ‘slave_alpha’
    pSegmentDNAcopy_A : papfunc: no visible binding for global variable
    ‘slave_nperm’
    pSegmentDNAcopy_A : papfunc: no visible binding for global variable
    ‘slave_kmax’
    pSegmentDNAcopy_A : papfunc: no visible binding for global variable
    ‘slave_nmin’
    pSegmentDNAcopy_A : papfunc: no visible binding for global variable
    ‘slave_overlap’
    pSegmentDNAcopy_A : papfunc: no visible binding for global variable
    ‘slave_trim’
    pSegmentDNAcopy_A : papfunc: no visible binding for global variable
    ‘slave_undo.prune’
    pSegmentDNAcopy_A : papfunc: no visible binding for global variable
    ‘slave_undo.SD’
    pSegmentDNAcopy_A : papfunc: no visible binding for global variable
    ‘slave_sbdry’
    pSegmentDNAcopy_A : papfunc: no visible binding for global variable
    ‘slave_sbn’
    pSegmentDNAcopy_A : papfunc: no visible binding for global variable
    ‘slave_merge’
    pSegmentDNAcopy_A : papfunc: no visible binding for global variable
    ‘slave_pv_th_merge’
    pSegmentDNAcopy_A : papfunc: no visible binding for global variable
    ‘slave_ansari_sign’
    pSegmentDNAcopy_A : papfunc: no visible binding for global variable
    ‘slave_merge_tmin’
    pSegmentDNAcopy_A : papfunc: no visible binding for global variable
    ‘slave_merge_tmax’
    pSegmentDNAcopy_axc : <anonymous>: no visible binding for global
    variable ‘slave_alpha’
    pSegmentDNAcopy_axc : <anonymous>: no visible binding for global
    variable ‘slave_nperm’
    pSegmentDNAcopy_axc : <anonymous>: no visible binding for global
    variable ‘slave_kmax’
    pSegmentDNAcopy_axc : <anonymous>: no visible binding for global
    variable ‘slave_nmin’
    pSegmentDNAcopy_axc : <anonymous>: no visible binding for global
    variable ‘slave_overlap’
    pSegmentDNAcopy_axc : <anonymous>: no visible binding for global
    variable ‘slave_trim’
    pSegmentDNAcopy_axc : <anonymous>: no visible binding for global
    variable ‘slave_undo.prune’
    pSegmentDNAcopy_axc : <anonymous>: no visible binding for global
    variable ‘slave_undo.SD’
    pSegmentDNAcopy_axc : <anonymous>: no visible binding for global
    variable ‘slave_sbdry’
    pSegmentDNAcopy_axc : <anonymous>: no visible binding for global
    variable ‘slave_sbn’
    pSegmentGLAD : <anonymous>: no visible binding for global variable
    ‘slave_chrom’
    pSegmentHMM_A : <anonymous>: no visible binding for global variable
    ‘slave_chrom’
    pSegmentPSW: no visible binding for global variable
    ‘.__ADaCGH_WEB_APPL’
    pSegmentPSW : <anonymous>: no visible binding for global variable
    ‘sl.chrom.numeric’
    pSegmentPSW : <anonymous>: no visible binding for global variable
    ‘sl.sign’
    pSegmentPSW : <anonymous>: no visible binding for global variable
    ‘sl.p.crit’
    pSegmentPSW : <anonymous>: no visible binding for global variable
    ‘sl.nIter’
    pSegmentPSW : <anonymous>: no visible binding for global variable
    ‘sl.prec’
    pSegmentPSW : <anonymous>: no visible binding for global variable
    ‘sl.name’
    pSegmentPSW : <anonymous>: no visible binding for global variable
    ‘colnamesdata’
    pSegmentWavelets : funwv: no visible binding for global variable
    ‘miDiff’
    PSWtoPaLS: no visible binding for global variable
    ‘.__PSW_PALS.Lost_for_PaLS.txt’
    PSWtoPaLS: no visible binding for global variable
    ‘.__PSW_PALS.Gained_for_PaLS.txt’
    segmentPlot : <anonymous>: no visible binding for global variable
    ‘cnum_slave’
    segmentPlot : <anonymous>: no visible binding for global variable
    ‘pos_slave’
    segmentPlot : <anonymous>: no visible binding for global variable
    ‘main_slave’
    sw.plot3: multiple local function definitions for ‘f1’ with different
    formal arguments
    writeResults.DNAcopy: no visible global function definition for
    ‘print.olshen.results’
    writeResults.DNAcopy: no visible binding for global variable ‘merged’
  • checking Rd files ... OK
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  • checking Rd cross-references ... OK
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  • checking for missing documentation entries ... OK
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  • checking for code/documentation mismatches ... OK
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  • checking Rd \usage sections ... OK
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  • checking data for non-ASCII characters ... OK
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  • checking line endings in C/C++/Fortran sources/headers ... OK
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  • checking line endings in Makefiles ... OK
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  • checking for portable use of $BLAS_LIBS ... OK
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  • creating ADaCGH-Ex.R ... OK
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  • checking examples ... OK
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  • creating ADaCGH-manual.tex ... OK
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  • checking ADaCGH-manual.tex using pdflatex ... OK
    •