Back to Multiple platform build/check report for BioC 3.9
ABCDEFGH[I]JKLMNOPQRSTUVWXYZ

CHECK report for igvR on malbec2

This page was generated on 2019-10-16 12:14:21 -0400 (Wed, 16 Oct 2019).

Package 799/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
igvR 1.4.0
Paul Shannon
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/igvR
Branch: RELEASE_3_9
Last Commit: 862aad9
Last Changed Date: 2019-05-02 11:54:11 -0400 (Thu, 02 May 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK [ WARNINGS ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: igvR
Version: 1.4.0
Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:igvR.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings igvR_1.4.0.tar.gz
StartedAt: 2019-10-16 02:28:35 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 02:32:33 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 238.3 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: igvR.Rcheck
Warnings: 2

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:igvR.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings igvR_1.4.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/igvR.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 ‘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   5.3Mb
    extdata       1.6Mb
    lib           1.4Mb
* 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
  ‘/home/biocbuild/bbs-3.9-bioc/meat/igvR.Rcheck/00check.log’
for details.



Installation output

igvR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL igvR
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/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)

Tests output


Example timings

igvR.Rcheck/igvR-Ex.timings

nameusersystemelapsed
DataFrameAnnotationTrack-class0.0140.0000.014
DataFrameQuantitativeTrack-class0.0070.0040.011
GRangesAnnotationTrack-class0.0920.0080.100
GRangesQuantitativeTrack-class0.0260.0040.029
GenomicAlignmentsTrack-class0.2470.0160.294
UCSCBedAnnotationTrack-class0.5200.0360.556
UCSCBedGraphQuantitativeTrack-class0.1400.0000.156
VariantTrack-class0.7190.0000.718
displayTrack0.0010.0000.002
getGenomicRegion0.0010.0000.000
getSupportedGenomes000
getTrackNames0.0000.0000.001
igvR-class0.0010.0010.002
ping000
removeTracksByName0.0030.0000.003
setGenome0.0000.0000.001
showGenomicRegion0.0010.0000.001
trackInfo0.0020.0000.001
trackSize-DataFrameAnnotationTrack-method0.0060.0040.011
trackSize-UCSCBedAnnotationTrack-method0.1260.0040.130