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This page was generated on 2024-12-23 12:05 -0500 (Mon, 23 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4744
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4487
merida1macOS 12.7.5 Montereyx86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4515
kjohnson1macOS 13.6.6 Venturaarm644.4.2 (2024-10-31) -- "Pile of Leaves" 4467
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 1640/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
quantsmooth 1.72.0  (landing page)
Jan Oosting
Snapshot Date: 2024-12-19 13:00 -0500 (Thu, 19 Dec 2024)
git_url: https://git.bioconductor.org/packages/quantsmooth
git_branch: RELEASE_3_20
git_last_commit: 7f84d09
git_last_commit_date: 2024-10-29 09:26:37 -0500 (Tue, 29 Oct 2024)
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


CHECK results for quantsmooth on palomino8

To the developers/maintainers of the quantsmooth package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/quantsmooth.git to reflect on this report. See Troubleshooting Build Report for more information.
- 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: 1.72.0
Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:quantsmooth.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings quantsmooth_1.72.0.tar.gz
StartedAt: 2024-12-20 04:56:14 -0500 (Fri, 20 Dec 2024)
EndedAt: 2024-12-20 04:57:17 -0500 (Fri, 20 Dec 2024)
EllapsedTime: 63.2 seconds
RetCode: 0
Status:   OK  
CheckDir: quantsmooth.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:quantsmooth.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings quantsmooth_1.72.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/quantsmooth.Rcheck'
* using R version 4.4.2 (2024-10-31 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.3.0
    GNU Fortran (GCC) 13.3.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'quantsmooth/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'quantsmooth' version '1.72.0'
* 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 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 code 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 ... 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
  'F:/biocbuild/bbs-3.20-bioc/meat/quantsmooth.Rcheck/00check.log'
for details.


Installation output

quantsmooth.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL quantsmooth
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.20-bioc/R/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
drawSimpleChrom000
getChangedRegions0.170.030.20
getLambdaMin0.770.020.78
grid.chromosome0.030.000.03
lengthChromosome0.060.000.45
numericCHR0.020.000.02
paintCytobands0.070.000.08
plotSmoothed0.240.010.25
position2Cytoband0.040.000.05
quantsmooth0.050.000.04
quantsmooth.cv0.080.000.08
quantsmooth.seg000