Package: igvR

Version: 1.4.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:igvR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings igvR_1.4.0.tar.gz

StartedAt: 2019-10-16 03:47:19 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 03:52:52 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 333.5 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: igvR.Rcheck

Warnings: 2

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:igvR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings igvR_1.4.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/igvR.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘igvR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘igvR’ version ‘1.4.0’
* package encoding: UTF-8
* 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 ‘igvR’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  8.5Mb
  sub-directories of 1Mb or more:
    browserCode   5.2Mb
    extdata       1.6Mb
    lib           1.3Mb
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented S4 classes:
  ‘GenomicAlignmentTrack’
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... WARNING
Undocumented arguments in documentation object 'getSupportedGenomes,igvR-method'
  ‘genomeName’

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 include directives in Makefiles ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... 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: 2 WARNINGs, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.9-bioc/meat/igvR.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL igvR
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘igvR’ ...
** using staged installation
** R
** 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 (igvR)

name	user	system	elapsed
DataFrameAnnotationTrack-class	0.014	0.003	0.017
DataFrameQuantitativeTrack-class	0.011	0.002	0.014
GRangesAnnotationTrack-class	0.104	0.018	0.121
GRangesQuantitativeTrack-class	0.032	0.006	0.038
GenomicAlignmentsTrack-class	0.271	0.051	0.326
UCSCBedAnnotationTrack-class	0.834	0.092	0.928
UCSCBedGraphQuantitativeTrack-class	0.203	0.003	0.208
VariantTrack-class	0.920	0.014	0.935
displayTrack	0.003	0.000	0.004
getGenomicRegion	0.001	0.000	0.002
getSupportedGenomes	0.000	0.000	0.001
getTrackNames	0.001	0.000	0.001
igvR-class	0.003	0.000	0.003
ping	0.000	0.000	0.001
removeTracksByName	0.007	0.001	0.007
setGenome	0.001	0.000	0.001
showGenomicRegion	0.001	0.000	0.002
trackInfo	0.003	0.001	0.003
trackSize-DataFrameAnnotationTrack-method	0.014	0.001	0.015
trackSize-UCSCBedAnnotationTrack-method	0.207	0.026	0.234