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This page was generated on 2024-04-18 11:32:16 -0400 (Thu, 18 Apr 2024).

HostnameOSArch (*)R versionInstalled pkgs
kjohnson1macOS 13.6.1 Venturaarm644.3.3 (2024-02-29) -- "Angel Food Cake" 4388
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 1637/2266HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
quantsmooth 1.68.0  (landing page)
Jan Oosting
Snapshot Date: 2024-04-16 09:00:03 -0400 (Tue, 16 Apr 2024)
git_url: https://git.bioconductor.org/packages/quantsmooth
git_branch: RELEASE_3_18
git_last_commit: ac99e3f
git_last_commit_date: 2023-10-24 09:37:03 -0400 (Tue, 24 Oct 2023)
kjohnson1macOS 13.6.1 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published

CHECK results for quantsmooth on kjohnson1


To the developers/maintainers of the quantsmooth 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: quantsmooth
Version: 1.68.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:quantsmooth.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings quantsmooth_1.68.0.tar.gz
StartedAt: 2024-04-18 00:10:27 -0400 (Thu, 18 Apr 2024)
EndedAt: 2024-04-18 00:12:43 -0400 (Thu, 18 Apr 2024)
EllapsedTime: 135.9 seconds
RetCode: 0
Status:   OK  
CheckDir: quantsmooth.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:quantsmooth.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings quantsmooth_1.68.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.18-bioc-mac-arm64/meat/quantsmooth.Rcheck’
* using R version 4.3.3 (2024-02-29)
* 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 Ventura 13.6.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘quantsmooth/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘quantsmooth’ version ‘1.68.0’
* 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 ‘quantsmooth’ can be installed ... OK
* checking installed package size ... OK
* 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
Package in Depends field not imported from: ‘grid’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.getChrombands: no visible global function definition for ‘data’
drawSimpleChrom: no visible global function definition for ‘rect’
drawSimpleChrom: no visible global function definition for ‘lines’
drawSimpleChrom: no visible global function definition for ‘yinch’
drawSimpleChrom: no visible global function definition for ‘symbols’
drawSimpleChrom: no visible global function definition for ‘xinch’
grid.chromosome: no visible global function definition for ‘gray’
grid.chromosome: no visible global function definition for
  ‘pushViewport’
grid.chromosome: no visible global function definition for ‘viewport’
grid.chromosome: no visible global function definition for ‘grid.rect’
grid.chromosome: no visible global function definition for ‘gpar’
grid.chromosome: no visible global function definition for
  ‘grid.circle’
grid.chromosome: no visible global function definition for ‘unit’
grid.chromosome: no visible global function definition for ‘grid.text’
grid.chromosome: no visible global function definition for
  ‘popViewport’
lengthChromosome: no visible global function definition for ‘aggregate’
paintCytobands: no visible global function definition for ‘gray’
paintCytobands: no visible global function definition for ‘rect’
paintCytobands: no visible global function definition for ‘yinch’
paintCytobands: no visible global function definition for ‘symbols’
paintCytobands: no visible global function definition for ‘text’
paintCytobands: no visible global function definition for ‘xinch’
plotSmoothed: no visible global function definition for ‘abline’
plotSmoothed: no visible global function definition for ‘points’
plotSmoothed: no visible global function definition for ‘lines’
prepareGenomePlot: no visible global function definition for ‘par’
prepareGenomePlot: no visible global function definition for ‘axis’
prepareGenomePlot: no visible global function definition for ‘lines’
qs.grid.semicircle: no visible global function definition for
  ‘grid.polygon’
qs.semicircle: no visible global function definition for ‘polygon’
qs.semicircle: no visible global function definition for ‘lines’
Undefined global functions or variables:
  abline aggregate axis data gpar gray grid.circle grid.polygon
  grid.rect grid.text lines par points polygon popViewport pushViewport
  rect symbols text unit viewport xinch yinch
Consider adding
  importFrom("grDevices", "gray")
  importFrom("graphics", "abline", "axis", "lines", "par", "points",
             "polygon", "rect", "symbols", "text", "xinch", "yinch")
  importFrom("stats", "aggregate")
  importFrom("utils", "data")
to your NAMESPACE file.
* checking Rd files ... NOTE
checkRd: (-1) chrom.bands.Rd:36: Escaped LaTeX specials: \_
* 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 sizes of PDF files under ‘inst/doc’ ... 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: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.18-bioc-mac-arm64/meat/quantsmooth.Rcheck/00check.log’
for details.



Installation output

quantsmooth.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library’
* installing *source* package ‘quantsmooth’ ...
** using staged installation
** R
** data
** 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 (quantsmooth)

Tests output


Example timings

quantsmooth.Rcheck/quantsmooth-Ex.timings

nameusersystemelapsed
drawSimpleChrom0.0090.0010.010
getChangedRegions0.5000.0170.517
getLambdaMin1.7990.0361.838
grid.chromosome0.0340.0020.037
lengthChromosome0.0680.0100.602
numericCHR0.0010.0010.001
paintCytobands0.0720.0060.077
plotSmoothed0.3200.0090.332
position2Cytoband0.0450.0030.048
quantsmooth0.0490.0030.053
quantsmooth.cv0.1180.0040.123
quantsmooth.seg0.0100.0030.013