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This page was generated on 2023-10-20 09:38:12 -0400 (Fri, 20 Oct 2023).

HostnameOSArch (*)R versionInstalled pkgs
kjohnson2macOS 12.6.1 Montereyarm644.3.1 (2023-06-16) -- "Beagle Scouts" 4347
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Package 1892/2230HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
seqPattern 1.32.0  (landing page)
Vanja Haberle
Snapshot Date: 2023-10-15 14:00:07 -0400 (Sun, 15 Oct 2023)
git_url: https://git.bioconductor.org/packages/seqPattern
git_branch: RELEASE_3_17
git_last_commit: db815f4
git_last_commit_date: 2023-04-25 10:37:15 -0400 (Tue, 25 Apr 2023)
kjohnson2macOS 12.6.1 Monterey / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published

CHECK results for seqPattern on kjohnson2


To the developers/maintainers of the seqPattern 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: seqPattern
Version: 1.32.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:seqPattern.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings seqPattern_1.32.0.tar.gz
StartedAt: 2023-10-19 00:24:00 -0400 (Thu, 19 Oct 2023)
EndedAt: 2023-10-19 00:28:15 -0400 (Thu, 19 Oct 2023)
EllapsedTime: 255.0 seconds
RetCode: 0
Status:   OK  
CheckDir: seqPattern.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:seqPattern.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings seqPattern_1.32.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/seqPattern.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 ‘seqPattern/DESCRIPTION’ ... OK
* this is package ‘seqPattern’ version ‘1.32.0’
* 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 ‘seqPattern’ 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 ... NOTE
Problems with news in ‘NEWS’:
  Cannot process chunk/lines:
    Version 0.99.1 released in the development branch (07/01/2015)
* 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 ‘parallel’ 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
.pattern.smoothscatter: no visible global function definition for
  ‘mclapply’
.pattern.smoothscatter : <anonymous>: no visible global function
  definition for ‘png’
.pattern.smoothscatter : <anonymous>: no visible global function
  definition for ‘par’
.pattern.smoothscatter : <anonymous>: no visible global function
  definition for ‘colorRampPalette’
.pattern.smoothscatter : <anonymous>: no visible global function
  definition for ‘axis’
.pattern.smoothscatter : <anonymous>: no visible global function
  definition for ‘box’
.pattern.smoothscatter : <anonymous>: no visible global function
  definition for ‘lines’
.pattern.smoothscatter : <anonymous>: no visible global function
  definition for ‘text’
.pattern.smoothscatter : <anonymous>: no visible global function
  definition for ‘abline’
.pattern.smoothscatter : <anonymous>: no visible global function
  definition for ‘dev.off’
.pattern.smoothscatter: no visible global function definition for ‘png’
.pattern.smoothscatter: no visible global function definition for ‘par’
.pattern.smoothscatter: no visible global function definition for
  ‘colorRampPalette’
.pattern.smoothscatter: no visible global function definition for
  ‘axis’
.pattern.smoothscatter: no visible global function definition for ‘box’
.pattern.smoothscatter: no visible global function definition for
  ‘lines’
.pattern.smoothscatter: no visible global function definition for
  ‘text’
.pattern.smoothscatter: no visible global function definition for
  ‘abline’
.pattern.smoothscatter: no visible global function definition for
  ‘dev.off’
.plot.motif.heatmap: no visible global function definition for ‘par’
.plot.motif.heatmap: no visible global function definition for ‘image’
.plot.motif.heatmap: no visible global function definition for ‘axis’
.plot.motif.heatmap: no visible global function definition for ‘box’
.plot.motif.heatmap: no visible global function definition for ‘lines’
.plot.motif.heatmap: no visible global function definition for ‘text’
.plot.motif.heatmap: no visible global function definition for ‘abline’
.plot.windowed.average: no visible global function definition for
  ‘rainbow’
.plot.windowed.average : <anonymous>: no visible global function
  definition for ‘lines’
.plot.windowed.average: no visible global function definition for
  ‘legend’
.plot.windowed.average: no visible global function definition for
  ‘abline’
.smoothScatter: no visible global function definition for
  ‘colorRampPalette’
.smoothScatter: no visible binding for global variable ‘blues9’
.smoothScatter: no visible binding for global variable ‘box’
.smoothScatter: no visible global function definition for ‘par’
.smoothScatter: no visible global function definition for ‘xy.coords’
.smoothScatter: no visible global function definition for ‘image’
.smoothScatter: no visible global function definition for ‘points’
plotPatternOccurrenceAverage: no visible global function definition for
  ‘rainbow’
getPatternOccurrenceList,DNAStringSet: no visible global function
  definition for ‘installed.packages’
getPatternOccurrenceList,DNAStringSet: no visible global function
  definition for ‘detectCores’
getPatternOccurrenceList,DNAStringSet: no visible global function
  definition for ‘mclapply’
plotMotifScanScores,DNAStringSet-matrix: no visible global function
  definition for ‘png’
plotMotifScanScores,DNAStringSet-matrix: no visible global function
  definition for ‘colorRampPalette’
plotMotifScanScores,DNAStringSet-matrix: no visible global function
  definition for ‘layout’
plotMotifScanScores,DNAStringSet-matrix: no visible global function
  definition for ‘par’
plotMotifScanScores,DNAStringSet-matrix: no visible global function
  definition for ‘box’
plotMotifScanScores,DNAStringSet-matrix: no visible global function
  definition for ‘dev.off’
plotPatternDensityMap,DNAStringSet: no visible global function
  definition for ‘installed.packages’
plotPatternDensityMap,DNAStringSet: no visible global function
  definition for ‘detectCores’
plotPatternOccurrenceAverage,DNAStringSet: no visible global function
  definition for ‘rainbow’
Undefined global functions or variables:
  abline axis blues9 box colorRampPalette detectCores dev.off image
  installed.packages layout legend lines mclapply par png points
  rainbow text xy.coords
Consider adding
  importFrom("grDevices", "blues9", "colorRampPalette", "dev.off", "png",
             "rainbow", "xy.coords")
  importFrom("graphics", "abline", "axis", "box", "image", "layout",
             "legend", "lines", "par", "points", "text")
  importFrom("utils", "installed.packages")
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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                             user system elapsed
plotPatternDensityMap      13.112  0.227  23.824
plotMotifDensityMap         8.730  0.170  15.838
motifScanHits               4.046  0.056   7.245
plotMotifOccurrenceAverage  3.652  0.041   6.654
plotMotifScanScores         3.390  0.058   6.086
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 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-3.17-bioc-mac-arm64/meat/seqPattern.Rcheck/00check.log’
for details.



Installation output

seqPattern.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library’
* installing *source* package ‘seqPattern’ ...
** 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 (seqPattern)

Tests output

seqPattern.Rcheck/tests/runTests.Rout


R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> BiocGenerics:::testPackage("seqPattern")
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following object is masked from 'package:utils':

    findMatches

The following objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: IRanges
Loading required package: XVector
Loading required package: GenomeInfoDb

Attaching package: 'Biostrings'

The following object is masked from 'package:base':

    strsplit



RUNIT TEST PROTOCOL -- Thu Oct 19 00:27:57 2023 
*********************************************** 
Number of test functions: 6 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
seqPattern RUnit Tests - 6 test functions, 0 errors, 0 failures
Number of test functions: 6 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
  4.710   0.294   8.904 

Example timings

seqPattern.Rcheck/seqPattern-Ex.timings

nameusersystemelapsed
getPatternOccurrenceList1.3760.0632.586
motifScanHits4.0460.0567.245
motifScanScores1.8990.0383.514
plotMotifDensityMap 8.730 0.17015.838
plotMotifOccurrenceAverage3.6520.0416.654
plotMotifScanScores3.3900.0586.086
plotPatternDensityMap13.112 0.22723.824
plotPatternOccurrenceAverage2.0050.0403.634