IdeoViz 1.10.0
Shraddha Pai
| Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/IdeoViz | | Last Changed Rev: 129126 / Revision: 131943 | | Last Changed Date: 2017-04-24 15:25:24 -0400 (Mon, 24 Apr 2017) |
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | NotNeeded | OK | WARNINGS | |  |
| tokay2 | Windows Server 2012 R2 Standard / x64 | NotNeeded | OK | WARNINGS | OK | |
| veracruz2 | OS X 10.11.6 El Capitan / x86_64 | NotNeeded | OK | [ WARNINGS ] | OK | |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings IdeoViz_1.10.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/IdeoViz.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.10.0’
* 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 ... 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 loading without being on the library search path ... 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 '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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
avgByBin 3.260 0.105 25.656
getBins 1.104 0.054 24.653
getIdeo 0.437 0.030 19.980
* 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, 4 NOTEs
See
‘/Users/biocbuild/bbs-3.5-bioc/meat/IdeoViz.Rcheck/00check.log’
for details.