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This page was generated on 2022-08-12 13:20:22 -0400 (Fri, 12 Aug 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4364
palomino3Windows Server 2022 Datacenterx644.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid" 4117
merida1macOS 10.14.6 Mojavex86_644.2.1 (2022-06-23) -- "Funny-Looking Kid" 4182
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

CHECK results for IdeoViz on nebbiolo1


To the developers/maintainers of the IdeoViz package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/IdeoViz.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? 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 936/2140HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
IdeoViz 1.32.0  (landing page)
Shraddha Pai
Snapshot Date: 2022-08-11 13:55:06 -0400 (Thu, 11 Aug 2022)
git_url: https://git.bioconductor.org/packages/IdeoViz
git_branch: RELEASE_3_15
git_last_commit: 4d9ebcd
git_last_commit_date: 2022-04-26 11:21:58 -0400 (Tue, 26 Apr 2022)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: IdeoViz
Version: 1.32.0
Command: /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:IdeoViz.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings IdeoViz_1.32.0.tar.gz
StartedAt: 2022-08-11 20:33:31 -0400 (Thu, 11 Aug 2022)
EndedAt: 2022-08-11 20:37:13 -0400 (Thu, 11 Aug 2022)
EllapsedTime: 221.7 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: IdeoViz.Rcheck
Warnings: 1

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:IdeoViz.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings IdeoViz_1.32.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.15-bioc/meat/IdeoViz.Rcheck’
* using R version 4.2.1 (2022-06-23)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘IdeoViz/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘IdeoViz’ version ‘1.32.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  'Biobase', 'IRanges', 'GenomicRanges', 'RColorBrewer', 'rtracklayer',
  'GenomeInfoDb'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 ‘IdeoViz’ 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 ... NOTE
File
  LICENSE
is not mentioned in the DESCRIPTION file.
* 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
Packages in Depends field not imported from:
  ‘Biobase’ ‘GenomeInfoDb’ ‘GenomicRanges’ ‘IRanges’ ‘RColorBrewer’
  ‘rtracklayer’
  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
.plotChromosome: no visible global function definition for ‘modifyList’
.plotChromosome: no visible global function definition for ‘axTicks’
.plotChromosome: no visible global function definition for ‘axis’
.plotChromosome: no visible global function definition for ‘polygon’
.plotChromosome: no visible global function definition for ‘rect’
.plotChromosome: no visible global function definition for ‘mtext’
.plot_values: no visible global function definition for ‘start’
.plot_values: no visible global function definition for ‘ranges’
.plot_values: no visible global function definition for ‘end’
.plot_values: no visible global function definition for ‘seqnames’
.plot_values: no visible global function definition for ‘mcols’
.plot_values: no visible global function definition for ‘modifyList’
.plot_values: no visible global function definition for ‘loess’
.plot_values: no visible binding for global variable ‘span’
.plot_values: no visible global function definition for ‘predict’
.plot_values: no visible global function definition for ‘axis’
.plot_values: no visible global function definition for ‘mtext’
.plot_values: no visible global function definition for ‘rect’
.plot_values: no visible global function definition for ‘lines’
.plot_values: no visible global function definition for ‘abline’
.printMargins: no visible global function definition for ‘par’
avgByBin: no visible global function definition for ‘GRanges’
avgByBin: no visible global function definition for ‘IRanges’
avgByBin: no visible global function definition for ‘seqnames’
avgByBin: no visible global function definition for ‘seqlevels’
avgByBin: no visible global function definition for ‘seqlevels<-’
avgByBin: no visible global function definition for ‘findOverlaps’
avgByBin: no visible global function definition for ‘ave’
avgByBin : corFunc: no visible global function definition for ‘cor’
avgByBin: no visible global function definition for ‘mcols<-’
getBins: no visible global function definition for ‘GRanges’
getBins: no visible global function definition for ‘IRanges’
getIdeo: no visible global function definition for ‘browserSession’
getIdeo: no visible global function definition for ‘genome<-’
getIdeo: no visible global function definition for ‘getTable’
getIdeo: no visible global function definition for ‘ucscTableQuery’
plotChromValuePair : <anonymous>: no visible global function definition
  for ‘seqnames’
plotChromValuePair: no visible global function definition for
  ‘seqnames’
plotChromValuePair: no visible global function definition for ‘par’
plotChromValuePair: no visible global function definition for
  ‘modifyList’
plotOnIdeo: no visible global function definition for ‘par’
plotOnIdeo: no visible global function definition for ‘layout’
plotOnIdeo: no visible global function definition for ‘mtext’
Undefined global functions or variables:
  GRanges IRanges abline ave axTicks axis browserSession cor end
  findOverlaps genome<- getTable layout lines loess mcols mcols<-
  modifyList mtext par polygon predict ranges rect seqlevels
  seqlevels<- seqnames span start ucscTableQuery
Consider adding
  importFrom("graphics", "abline", "axTicks", "axis", "layout", "lines",
             "mtext", "par", "polygon", "rect")
  importFrom("stats", "ave", "cor", "end", "loess", "predict", "start")
  importFrom("utils", "modifyList")
to your NAMESPACE file.
* checking Rd files ... NOTE
prepare_Rd: GSM733664_broadPeaks.Rd:11-12: Dropping empty section \format
prepare_Rd: GSM733664_broadPeaks.Rd:16-18: Dropping empty section \source
prepare_Rd: binned_fullGenome.Rd:12-13: Dropping empty section \format
prepare_Rd: binned_fullGenome.Rd:14-16: Dropping empty section \details
prepare_Rd: binned_fullGenome.Rd:20-22: Dropping empty section \references
prepare_Rd: binned_multiSeries.Rd:12-13: Dropping empty section \format
prepare_Rd: binned_multiSeries.Rd:14-15: Dropping empty section \details
prepare_Rd: binned_multiSeries.Rd:19-20: Dropping empty section \references
prepare_Rd: binned_singleSeries.Rd:11-12: Dropping empty section \format
prepare_Rd: binned_singleSeries.Rd:13-15: Dropping empty section \details
prepare_Rd: binned_singleSeries.Rd:19-21: Dropping empty section \references
prepare_Rd: hg18_ideo.Rd:11-12: Dropping empty section \format
prepare_Rd: hg18_ideo.Rd:13-14: Dropping empty section \details
prepare_Rd: hg18_ideo.Rd:18-19: Dropping empty section \references
prepare_Rd: wins.Rd:12-13: Dropping empty section \format
prepare_Rd: wins.Rd:14-15: Dropping empty section \details
prepare_Rd: wins.Rd:19-20: Dropping empty section \references
prepare_Rd: wins_discrete.Rd:11-12: Dropping empty section \format
prepare_Rd: wins_discrete.Rd:13-15: Dropping empty section \details
prepare_Rd: wins_discrete.Rd:19-21: Dropping empty section \references
prepare_Rd: wins_entiregenome.Rd:11-12: Dropping empty section \format
prepare_Rd: wins_entiregenome.Rd:13-15: Dropping empty section \details
prepare_Rd: wins_entiregenome.Rd:19-21: Dropping empty section \references
* 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 ... WARNING
Undocumented arguments in documentation object 'plotChromValuePair'
  ‘chrom’ ‘cytoTable’ ‘bpLim’ ‘vertical’ ‘values_GR’ ‘val_range’ ‘col’
  ‘value_cols’ ‘default_margins’ ‘addScale’ ‘ablines_y’ ‘smoothVals’
  ‘span’ ‘verbose’
Documented arguments not in \usage in documentation object 'plotChromValuePair':
  ‘chrom(character)’ ‘cytoTable(data.frame)’ ‘bpLim(numeric)’
  ‘vertical(logical)’ ‘values_GR(list’ ‘val_range(numeric)’
  ‘col(character)’ ‘value_cols(character)’ ‘default_margins(numeric)’
  ‘addScale(logical)’ ‘ablines_y(numeric)’ ‘smoothVals(logical)’
  ‘span(numeric)’ ‘verbose(logical)’

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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
avgByBin 1.283  0.201  11.563
getBins  0.590  0.027  10.431
getIdeo  0.329  0.057  49.721
* 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, 5 NOTEs
See
  ‘/home/biocbuild/bbs-3.15-bioc/meat/IdeoViz.Rcheck/00check.log’
for details.



Installation output

IdeoViz.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD INSTALL IdeoViz
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.15-bioc/R/library’
* installing *source* package ‘IdeoViz’ ...
** 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 (IdeoViz)

Tests output


Example timings

IdeoViz.Rcheck/IdeoViz-Ex.timings

nameusersystemelapsed
GSM733664_broadPeaks0.0950.0000.095
avgByBin 1.283 0.20111.563
binned_fullGenome0.0250.0000.024
binned_multiSeries0.0110.0000.011
binned_singleSeries0.0080.0000.009
getBins 0.590 0.02710.431
getIdeo 0.329 0.05749.721
hg18_ideo0.0060.0000.005
plotChromValuePair1.7590.2081.967
plotOnIdeo0.1170.0080.125
wins0.0070.0040.011
wins_discrete0.0070.0040.011
wins_entiregenome0.0180.0000.018