Package: IdeoViz

Version: 1.20.0

Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:IdeoViz.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings IdeoViz_1.20.0.tar.gz

StartedAt: 2019-10-16 02:27:55 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 02:31:15 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 199.9 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: IdeoViz.Rcheck

Warnings: 1

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:IdeoViz.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings IdeoViz_1.20.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/IdeoViz.Rcheck’
* using R version 3.6.1 (2019-07-05)
* 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 ‘1.20.0’
* 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 : : 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 'avgByBin'
  ‘xpr’
Documented arguments not in \usage in documentation object 'avgByBin':
  ‘xpr(data.frame’

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 or elapsed time > 5s
          user system elapsed
avgByBin 1.128  0.080  16.956
getBins  0.389  0.000  12.492
getIdeo  0.352  0.016  11.539
* 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-3.9-bioc/meat/IdeoViz.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL IdeoViz
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* installing to library ‘/home/biocbuild/bbs-3.9-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)

name	user	system	elapsed
GSM733664_broadPeaks	0.59	0.00	0.59
avgByBin	1.128	0.080	16.956
binned_fullGenome	0.030	0.000	0.029
binned_multiSeries	0.008	0.004	0.012
binned_singleSeries	0.009	0.000	0.010
getBins	0.389	0.000	12.492
getIdeo	0.352	0.016	11.539
hg18_ideo	0.003	0.004	0.007
plotChromValuePair	0.802	0.020	0.822
plotOnIdeo	0.183	0.004	0.187
wins	0.011	0.000	0.011
wins_discrete	0.008	0.000	0.009
wins_entiregenome	0.005	0.004	0.010