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### Running command:
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### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:CGHbase.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings CGHbase_1.60.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/CGHbase.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-apple-darwin20 (64-bit)
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CGHbase/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CGHbase’ version ‘1.60.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘CGHbase’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
* checking top-level files ... OK
* checking for left-over 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 namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... NOTE
Package in Depends field not imported from: ‘methods’
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
':::' call which should be '::': ‘Biobase:::assayDataElement’
See the note in ?`:::` about the use of this operator.
Unexported object imported by a ':::' call: ‘Biobase:::assayDataDims’
See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.makeEmptyFeatureData: no visible global function definition for ‘is’
.makeEmptyFeatureData: no visible global function definition for ‘new’
.makeEmptyFeatureDataForRegions: no visible global function definition
for ‘is’
.makeEmptyFeatureDataForRegions: no visible global function definition
for ‘new’
frequencyPlotCalls: no visible global function definition for ‘rect’
frequencyPlotCalls: no visible global function definition for ‘box’
frequencyPlotCalls: no visible global function definition for ‘abline’
frequencyPlotCalls: no visible global function definition for ‘axis’
frequencyPlotCalls: no visible global function definition for ‘mtext’
frequencyPlotCalls: no visible global function definition for ‘median’
make_cghRaw: no visible global function definition for ‘read.table’
make_cghRaw: no visible global function definition for ‘new’
summaryPlot: no visible global function definition for ‘rect’
summaryPlot: no visible global function definition for ‘box’
summaryPlot: no visible global function definition for ‘abline’
summaryPlot: no visible global function definition for ‘axis’
summaryPlot: no visible global function definition for ‘mtext’
summaryPlot: no visible global function definition for ‘median’
frequencyPlot,cghRegions-missing: no visible global function definition
for ‘par’
frequencyPlot,cghRegions-missing: no visible global function definition
for ‘barplot’
frequencyPlot,cghRegions-missing: no visible global function definition
for ‘segments’
frequencyPlot,cghRegions-missing: no visible global function definition
for ‘gray’
frequencyPlot,cghRegions-missing: no visible global function definition
for ‘box’
frequencyPlot,cghRegions-missing: no visible global function definition
for ‘axis’
initialize,cghCall: no visible global function definition for ‘new’
initialize,cghCall: no visible global function definition for
‘callNextMethod’
initialize,cghRaw: no visible global function definition for ‘new’
initialize,cghRaw: no visible global function definition for
‘callNextMethod’
initialize,cghRegions: no visible global function definition for ‘new’
initialize,cghRegions: no visible global function definition for
‘callNextMethod’
initialize,cghSeg: no visible global function definition for ‘new’
initialize,cghSeg: no visible global function definition for
‘callNextMethod’
plot.cghRegions,cghRegions-missing: no visible global function
definition for ‘layout’
plot.cghRegions,cghRegions-missing: no visible global function
definition for ‘par’
plot.cghRegions,cghRegions-missing: no visible global function
definition for ‘segments’
plot.cghRegions,cghRegions-missing: no visible global function
definition for ‘axis’
plot,cghCall-missing: no visible global function definition for ‘par’
plot,cghCall-missing: no visible global function definition for ‘rect’
plot,cghCall-missing: no visible global function definition for ‘axis’
plot,cghCall-missing: no visible global function definition for ‘box’
plot,cghCall-missing: no visible global function definition for
‘abline’
plot,cghCall-missing: no visible global function definition for ‘mtext’
plot,cghCall-missing: no visible global function definition for ‘title’
plot,cghCall-missing: no visible global function definition for
‘segments’
plot,cghCall-missing: no visible global function definition for
‘median’
plot,cghCall-missing : <anonymous>: no visible global function
definition for ‘mad’
plot,cghRaw-missing: no visible global function definition for ‘mtext’
plot,cghRaw-missing: no visible global function definition for ‘abline’
plot,cghRaw-missing: no visible global function definition for ‘axis’
plot,cghRaw-missing: no visible global function definition for ‘median’
plot,cghRaw-missing : <anonymous>: no visible global function
definition for ‘mad’
plot,cghSeg-missing: no visible global function definition for ‘mtext’
plot,cghSeg-missing: no visible global function definition for ‘abline’
plot,cghSeg-missing: no visible global function definition for ‘axis’
plot,cghSeg-missing: no visible global function definition for
‘segments’
plot,cghSeg-missing: no visible global function definition for ‘median’
plot,cghSeg-missing : <anonymous>: no visible global function
definition for ‘mad’
Undefined global functions or variables:
abline axis barplot box callNextMethod gray is layout mad median
mtext new par read.table rect segments title
Consider adding
importFrom("grDevices", "gray")
importFrom("graphics", "abline", "axis", "barplot", "box", "layout",
"mtext", "par", "rect", "segments", "title")
importFrom("methods", "callNextMethod", "is", "new")
importFrom("stats", "mad", "median")
importFrom("utils", "read.table")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking examples ... OK
* checking PDF version of manual ... OK
* DONE
Status: 3 NOTEs
See
‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/CGHbase.Rcheck/00check.log’
for details.
