Package: igvR

Version: 1.6.1

Command: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:igvR.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings igvR_1.6.1.tar.gz

StartedAt: 2020-04-15 05:42:54 -0400 (Wed, 15 Apr 2020)

EndedAt: 2020-04-15 05:49:09 -0400 (Wed, 15 Apr 2020)

EllapsedTime: 374.2 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: igvR.Rcheck

Warnings: 1

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:igvR.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings igvR_1.6.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.10-bioc/meat/igvR.Rcheck’
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-pc-linux-gnu (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 ‘1.6.1’
* 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 ... 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 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 ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* 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’ ... WARNING
  Found ‘inst/doc/makefile’: should be ‘Makefile’ and will be ignored
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING
See
  ‘/home/biocbuild/bbs-3.10-bioc/meat/igvR.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL igvR
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.10-bioc/R/library’
* installing *source* package ‘igvR’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
See system.file("LICENSE", package="MotifDb") for use restrictions.
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
See system.file("LICENSE", package="MotifDb") for use restrictions.
** testing if installed package can be loaded from final location
See system.file("LICENSE", package="MotifDb") for use restrictions.
** testing if installed package keeps a record of temporary installation path
* DONE (igvR)

name	user	system	elapsed
DataFrameAnnotationTrack-class	0.012	0.000	0.012
DataFrameQuantitativeTrack-class	0.012	0.000	0.011
GRangesAnnotationTrack-class	0.092	0.000	0.094
GRangesQuantitativeTrack-class	0.036	0.000	0.039
GenomicAlignmentTrack-class	0.228	0.000	0.251
UCSCBedAnnotationTrack-class	0.544	0.024	0.574
UCSCBedGraphQuantitativeTrack-class	0.104	0.020	0.125
VariantTrack-class	0.768	0.044	0.858
displayTrack	0.000	0.000	0.002
enableMotifLogoPopups	0.000	0.000	0.002
getGenomicRegion	0.004	0.000	0.001
getSupportedGenomes	0	0	0
getTrackNames	0	0	0
igvR-class	0.000	0.004	0.002
ping	0	0	0
removeTracksByName	0.004	0.000	0.003
setGenome	0	0	0
showGenomicRegion	0.000	0.000	0.001
trackInfo	0.004	0.000	0.001
trackSize-DataFrameAnnotationTrack-method	0.012	0.000	0.013
trackSize-UCSCBedAnnotationTrack-method	0.152	0.016	0.169