Check results for 'ADaCGH'

using R version 2.11.0 Under development (unstable) (2010-02-01 r51089)
using session charset: UTF-8
checking for file 'ADaCGH/DESCRIPTION' ... OK
this is package 'ADaCGH' version '1.3-13'
checking package name space information ... OK
checking package dependencies ... OK
checking if this is a source package ... OK
checking for executable files ... OK
checking whether package 'ADaCGH' 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 package can be unloaded cleanly ... OK
checking whether the name space can be loaded with stated dependencies ... OK
checking whether the name space can be unloaded cleanly ... 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
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’
DNAcopyDiagnosticPlots: no visible binding for global variable
‘smoothed.CNA.object’
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’
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’
caughtError: no visible global function definition for
‘caughtOtherPackageError.Web’
caughtOtherError: no visible global function definition for
‘caughtOtherError.Web’
caughtOurError: no visible global function definition for
‘caughtOurError.Web’
linkGene: no visible binding for global variable ‘idtype’
linkGene: no visible binding for global variable ‘organism’
linkGene2: no visible binding for global variable ‘idtype’
linkGene2: no visible binding for global variable ‘organism’
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’
mapChromOpen: no visible binding for global variable ‘imgheight’
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’
mapChromOpenA: no visible binding for global variable ‘imgheight’
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
‘html_js’
mapCloseAndPythonChrom: no visible binding for global variable ‘idtype’
mapCloseAndPythonChrom: no visible binding for global variable
‘organism’
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
‘html_js’
mapCloseAndPythonChromA: no visible binding for global variable
‘idtype’
mapCloseAndPythonChromA: no visible binding for global variable
‘organism’
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.ansari.test.default : pansari: no visible binding for global
variable ‘R_pansari’
my.ansari.test.default : qansari: no visible binding for global
variable ‘R_qansari’
my.sw3b: no visible binding for global variable ‘PSW.p.crit’
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: no visible global function definition for ‘getbdry’
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: no visible global function definition for
‘getbdry’
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’
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’
plot.cw.superimpA: no visible binding for global variable
‘positions.merge1’
plot.cw.superimpA : funp: no visible binding for global variable
‘nameImage’
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’
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’
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’
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’
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
checking Rd metadata ... OK
checking Rd cross-references ... WARNING
Missing link(s) in documentation object './man/mpiInit.Rd':
‘[varSelRF]{basicClusterInit.Rd}’

See the information in section 'Cross-references' of the 'Writing R
Extensions' manual.
checking for missing documentation entries ... OK
checking for code/documentation mismatches ... OK
checking Rd \usage sections ... OK
checking Rd contents ... 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
checking examples ... OK
checking PDF version of manual ... OK