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BioC 3.4: CHECK report for GenomicInteractions on malbec1

This page was generated on 2017-04-15 16:12:25 -0400 (Sat, 15 Apr 2017).

Package 511/1296HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GenomicInteractions 1.8.1
Malcolm Perry
Snapshot Date: 2017-04-14 17:17:13 -0400 (Fri, 14 Apr 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_4/madman/Rpacks/GenomicInteractions
Last Changed Rev: 125251 / Revision: 128728
Last Changed Date: 2016-12-16 12:38:56 -0500 (Fri, 16 Dec 2016)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: GenomicInteractions
Version: 1.8.1
Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings GenomicInteractions_1.8.1.tar.gz
StartedAt: 2017-04-14 22:48:18 -0400 (Fri, 14 Apr 2017)
EndedAt: 2017-04-14 22:53:16 -0400 (Fri, 14 Apr 2017)
EllapsedTime: 297.6 seconds
RetCode: 0
Status:  OK 
CheckDir: GenomicInteractions.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings GenomicInteractions_1.8.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/GenomicInteractions.Rcheck’
* using R version 3.3.3 (2017-03-06)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GenomicInteractions/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘GenomicInteractions’ version ‘1.8.1’
* 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 ‘GenomicInteractions’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is 10.9Mb
  sub-directories of 1Mb or more:
    doc       2.0Mb
    extdata   7.9Mb
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 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: 1 NOTE
See
  ‘/home/biocbuild/bbs-3.4-bioc/meat/GenomicInteractions.Rcheck/00check.log’
for details.


GenomicInteractions.Rcheck/00install.out:

* installing *source* package ‘GenomicInteractions’ ...
** R
** data
** inst
** preparing package for lazy loading
Warning: replacing previous import 'BiocGenerics::Position' by 'ggplot2::Position' when loading 'GenomicInteractions'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: replacing previous import 'BiocGenerics::Position' by 'ggplot2::Position' when loading 'GenomicInteractions'
* DONE (GenomicInteractions)

GenomicInteractions.Rcheck/GenomicInteractions-Ex.timings:

nameusersystemelapsed
GInteractions-subsetByFeatures-methods0.2760.0080.287
GenomicInteractions-class0.0760.0040.081
GenomicInteractions-package0.0000.0000.001
GenomicInteractions0.0440.0000.044
InteractionHelpers0.0680.0000.068
InteractionTrack0.4800.0000.478
annotateInteractions0.1240.0000.122
annotateRegions0.0320.0000.033
asBED-GInteractions-method0.2360.0080.244
availableDisplayPars0.0200.0000.019
calculateDistances0.0480.0000.049
categoriseInteractions0.0960.0000.098
export.bed122.1400.0042.148
export.bedpe0.1880.0040.192
export.chiasig0.1760.0000.179
export.igraph0.0760.0000.079
getters0.0640.0000.063
makeGenomicInteractionsFromFile1.8200.0161.839
plotAvgViewpoint0.2120.0000.212
plotCisTrans0.2800.0000.279
plotCounts0.3240.0080.333
plotDists0.2960.0040.299
plotInteractionAnnotations0.3840.0040.394
plotSummaryStats0.7800.0000.777
plotViewpoint0.3640.0120.376
resetAnnotations0.0320.0000.031
setters0.0480.0000.048
summariseByFeaturePairs0.8080.0000.807
summariseByFeatures0.3640.0000.366
viewPoint0.180.000.18