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This page was generated on 2023-10-20 09:37:59 -0400 (Fri, 20 Oct 2023).

HostnameOSArch (*)R versionInstalled pkgs
kjohnson2macOS 12.6.1 Montereyarm644.3.1 (2023-06-16) -- "Beagle Scouts" 4347
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 311/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
CGHbase 1.60.0  (landing page)
Mark van de Wiel
Snapshot Date: 2023-10-15 14:00:07 -0400 (Sun, 15 Oct 2023)
git_url: https://git.bioconductor.org/packages/CGHbase
git_branch: RELEASE_3_17
git_last_commit: d4b32f0
git_last_commit_date: 2023-04-25 09:46:52 -0400 (Tue, 25 Apr 2023)
kjohnson2macOS 12.6.1 Monterey / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published

CHECK results for CGHbase on kjohnson2


To the developers/maintainers of the CGHbase package:
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: CGHbase
Version: 1.60.0
Command: /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
StartedAt: 2023-10-17 08:34:27 -0400 (Tue, 17 Oct 2023)
EndedAt: 2023-10-17 08:35:47 -0400 (Tue, 17 Oct 2023)
EllapsedTime: 80.5 seconds
RetCode: 0
Status:   OK  
CheckDir: CGHbase.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   /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
###
##############################################################################
##############################################################################


* 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.



Installation output

CGHbase.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL CGHbase
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library’
* installing *source* package ‘CGHbase’ ...
** using staged installation
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (CGHbase)

Tests output


Example timings

CGHbase.Rcheck/CGHbase-Ex.timings

nameusersystemelapsed
class.cghCall0.0790.0020.123
class.cghRaw0.3270.0360.610
class.cghRegions0.2210.0070.355
class.cghSeg0.0360.0010.059
copynumber0.0390.0040.066
frequencyPlot000
frequencyPlotCalls000
make_cghRaw0.0660.0020.102
summaryPlot0.0000.0000.001