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This page was generated on 2023-10-20 09:38:15 -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 2205/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
wavClusteR 2.34.0  (landing page)
Federico Comoglio
Snapshot Date: 2023-10-15 14:00:07 -0400 (Sun, 15 Oct 2023)
git_url: https://git.bioconductor.org/packages/wavClusteR
git_branch: RELEASE_3_17
git_last_commit: 42acbc9
git_last_commit_date: 2023-04-25 10:32:30 -0400 (Tue, 25 Apr 2023)
kjohnson2macOS 12.6.1 Monterey / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published

CHECK results for wavClusteR on kjohnson2


To the developers/maintainers of the wavClusteR 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: wavClusteR
Version: 2.34.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:wavClusteR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings wavClusteR_2.34.0.tar.gz
StartedAt: 2023-10-19 10:00:19 -0400 (Thu, 19 Oct 2023)
EndedAt: 2023-10-19 10:09:32 -0400 (Thu, 19 Oct 2023)
EllapsedTime: 553.6 seconds
RetCode: 0
Status:   OK  
CheckDir: wavClusteR.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:wavClusteR.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings wavClusteR_2.34.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/wavClusteR.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 ‘wavClusteR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘wavClusteR’ version ‘2.34.0’
* 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 ‘wavClusteR’ 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
'library' or 'require' call to ‘doMC’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
annotateClusters: no visible binding for global variable ‘Percentage’
annotateClusters: no visible binding for global variable ‘Compartment’
estimateFDR: no visible global function definition for ‘DNAString’
estimateFDR: no visible global function definition for ‘lines’
estimateFDR: no visible global function definition for ‘legend’
estimateFDR: no visible global function definition for ‘axis’
exportGR: no visible global function definition for ‘write.table’
filterClustersCWT: no visible global function definition for
  ‘DNAString’
filterClustersMRN: no visible global function definition for
  ‘txtProgressBar’
filterClustersMRN: no visible global function definition for
  ‘setTxtProgressBar’
getClustersMRN: no visible global function definition for
  ‘registerDoMC’
getComplSubst: no visible global function definition for ‘DNAStringSet’
getExpInterval: no visible global function definition for ‘par’
getExpInterval: no visible global function definition for ‘lines’
getExpInterval: no visible global function definition for ‘legend’
getExpInterval: no visible global function definition for ‘polygon’
getExpInterval: no visible global function definition for ‘rect’
getExpInterval: no visible global function definition for ‘text’
getLogOdd: no visible global function definition for ‘dbinom’
getMetaCoverage: no visible global function definition for ‘axis’
getMetaGene: no visible global function definition for ‘grid’
getMetaGene: no visible global function definition for ‘axis’
getMetaGene: no visible global function definition for ‘abline’
getMetaTSS: no visible global function definition for ‘grid’
getMetaTSS: no visible global function definition for ‘axis’
plotSizeDistribution: no visible global function definition for ‘hist’
plotStatistics: no visible binding for global variable ‘panel.smooth’
plotStatistics : panelCor: no visible global function definition for
  ‘par’
plotStatistics : panelCor: no visible global function definition for
  ‘strwidth’
plotStatistics : panelCor: no visible global function definition for
  ‘text’
plotStatistics: no visible global function definition for ‘pairs’
plotSubstitutions: no visible global function definition for ‘par’
plotSubstitutions: no visible global function definition for ‘barplot’
processChunk: no visible global function definition for ‘extractAt’
processMD: no visible global function definition for ‘registerDoMC’
readSortedBam: no visible global function definition for ‘scanBamFlag’
readSortedBam : <anonymous>: no visible binding for global variable
  ‘rname’
readSortedBam : <anonymous>: no visible binding for global variable
  ‘qwidth’
Undefined global functions or variables:
  Compartment DNAString DNAStringSet Percentage abline axis barplot
  dbinom extractAt grid hist legend lines pairs panel.smooth par
  polygon qwidth rect registerDoMC rname scanBamFlag setTxtProgressBar
  strwidth text txtProgressBar write.table
Consider adding
  importFrom("graphics", "abline", "axis", "barplot", "grid", "hist",
             "legend", "lines", "pairs", "panel.smooth", "par",
             "polygon", "rect", "strwidth", "text")
  importFrom("stats", "dbinom")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar",
             "write.table")
to your NAMESPACE file.
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                      user system elapsed
annotateClusters     6.957  0.194  12.663
filterClusters       4.135  0.063   7.310
plotStatistics       4.123  0.062   7.470
plotSizeDistribution 4.037  0.060   7.104
getMetaGene          4.030  0.066   6.452
getMetaCoverage      3.927  0.062   6.294
getClusters          3.629  0.041   6.435
getHighConfSub       3.007  0.036   5.294
getAllSub            2.982  0.036   5.010
plotSubstitutions    2.978  0.035   5.365
* 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/wavClusteR.Rcheck/00check.log’
for details.



Installation output

wavClusteR.Rcheck/00install.out

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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL wavClusteR
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library’
* installing *source* package ‘wavClusteR’ ...
** 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 (wavClusteR)

Tests output


Example timings

wavClusteR.Rcheck/wavClusteR-Ex.timings

nameusersystemelapsed
FitMixtureModel0.0480.0050.095
annotateClusters 6.957 0.19412.663
filterClusters4.1350.0637.310
getAllSub2.9820.0365.010
getClusters3.6290.0416.435
getExpInterval0.0380.0050.077
getHighConfSub3.0070.0365.294
getMetaCoverage3.9270.0626.294
getMetaGene4.0300.0666.452
getMetaTSS0.1730.0100.335
plotSizeDistribution4.0370.0607.104
plotStatistics4.1230.0627.470
plotSubstitutions2.9780.0355.365
readSortedBam0.0920.0050.173