Back to Multiple platform build/check report for BioC 3.13
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This page was generated on 2021-10-15 15:05:37 -0400 (Fri, 15 Oct 2021).

CHECK results for cghMCR on nebbiolo1

To the developers/maintainers of the cghMCR package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/cghMCR.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 280/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
cghMCR 1.50.0  (landing page)
J. Zhang
Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021)
git_url: https://git.bioconductor.org/packages/cghMCR
git_branch: RELEASE_3_13
git_last_commit: ee62229
git_last_commit_date: 2021-05-19 11:37:24 -0400 (Wed, 19 May 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: cghMCR
Version: 1.50.0
Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:cghMCR.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings cghMCR_1.50.0.tar.gz
StartedAt: 2021-10-14 09:12:43 -0400 (Thu, 14 Oct 2021)
EndedAt: 2021-10-14 09:14:43 -0400 (Thu, 14 Oct 2021)
EllapsedTime: 119.4 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: cghMCR.Rcheck
Warnings: 1

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:cghMCR.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings cghMCR_1.50.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/cghMCR.Rcheck’
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘cghMCR/DESCRIPTION’ ... OK
* this is package ‘cghMCR’ version ‘1.50.0’
* 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 ‘cghMCR’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is 64.9Mb
  sub-directories of 1Mb or more:
    sampleData  63.8Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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
'library' or 'require' call to ‘DNAcopy’ which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘CNTools’ ‘DNAcopy’ ‘limma’ ‘methods’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘adjustSegments’ ‘alignGenes’ ‘drawSegs’ ‘getAdjustments’
  ‘highlightChrom’ ‘markChrom’
* checking S3 generic/method consistency ... NOTE
Found the following apparent S3 methods exported but not registered:
  plot.DNAcopy
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
SGOL: no visible global function definition for ‘segBy’
SGOL: no visible global function definition for ‘rs’
drawSegs : drawSegLine: no visible global function definition for
  ‘lines’
dropGenes: no visible global function definition for ‘approx’
getAlteredSegs: no visible global function definition for ‘quantile’
getLineData: no visible global function definition for ‘median’
getSegData: no visible global function definition for ‘read.maimages’
getSegData: no visible global function definition for
  ‘normalizeWithinArrays’
getSegData: no visible global function definition for
  ‘backgroundCorrect’
getSegData: no visible global function definition for ‘CNA’
getSegData: no visible global function definition for ‘segment’
getSegData: no visible global function definition for ‘smooth.CNA’
highlightChrom: no visible global function definition for ‘polygon’
markChrom: no visible global function definition for ‘polygon’
plot.DNAcopy: no visible global function definition for ‘png’
plot.DNAcopy: no visible global function definition for ‘par’
plot.DNAcopy: no visible global function definition for ‘axis’
plot.DNAcopy: no visible global function definition for ‘box’
plot.DNAcopy: no visible global function definition for ‘points’
plot.DNAcopy: no visible global function definition for ‘lines’
plot.DNAcopy: no visible global function definition for ‘dev.off’
plot.MCR: no visible global function definition for ‘png’
plot.MCR: no visible global function definition for ‘par’
plot.MCR: no visible global function definition for ‘dev.off’
plotSGOL: no visible global function definition for ‘lines’
plotSGOL: no visible global function definition for ‘axis’
plotSGOL: no visible global function definition for ‘box’
showMCR : <anonymous>: no visible global function definition for
  ‘median’
showMCR: no visible global function definition for ‘lines’
showMCR: no visible global function definition for ‘median’
showSegment : getMean: no visible global function definition for
  ‘median’
topGenes: no visible global function definition for ‘quantile’
Undefined global functions or variables:
  CNA approx axis backgroundCorrect box dev.off lines median
  normalizeWithinArrays par png points polygon quantile read.maimages
  rs segBy segment smooth.CNA
Consider adding
  importFrom("grDevices", "dev.off", "png")
  importFrom("graphics", "axis", "box", "lines", "par", "points",
             "polygon")
  importFrom("stats", "approx", "median", "quantile")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented S4 methods:
  generic '[' and siglist 'SGOL,ANY,ANY,ANY'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.13-bioc/meat/cghMCR.Rcheck/00check.log’
for details.



Installation output

cghMCR.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL cghMCR
###
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* installing to library ‘/home/biocbuild/bbs-3.13-bioc/R/library’
* installing *source* package ‘cghMCR’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** 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 (cghMCR)

Tests output


Example timings

cghMCR.Rcheck/cghMCR-Ex.timings

nameusersystemelapsed
SGOL-class0.0010.0000.002
cghMCR-class0.0810.0040.087
cghMCR0.0150.0000.015
mergeMCRProbes3.4950.0153.512
plot.DNAcopy000