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BioC 3.6: CHECK report for chipenrich on veracruz1

This page was generated on 2017-08-16 13:44:23 -0400 (Wed, 16 Aug 2017).

Package 208/1410HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
chipenrich 2.1.1
Raymond G. Cavalcante
Snapshot Date: 2017-08-15 17:18:21 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/chipenrich
Last Changed Rev: 129611 / Revision: 131943
Last Changed Date: 2017-05-15 09:43:03 -0400 (Mon, 15 May 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: chipenrich
Version: 2.1.1
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings chipenrich_2.1.1.tar.gz
StartedAt: 2017-08-16 00:59:33 -0400 (Wed, 16 Aug 2017)
EndedAt: 2017-08-16 01:06:09 -0400 (Wed, 16 Aug 2017)
EllapsedTime: 396.3 seconds
RetCode: 0
Status:  OK 
CheckDir: chipenrich.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings chipenrich_2.1.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/chipenrich.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 ‘chipenrich/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘chipenrich’ version ‘2.1.1’
* 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 ‘chipenrich’ 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 ... 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
             user system elapsed
broadenrich 7.545  0.274   8.072
polyenrich  5.957  0.284   6.388
* 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: OK

chipenrich.Rcheck/00install.out:

* installing *source* package ‘chipenrich’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (chipenrich)

chipenrich.Rcheck/chipenrich-Ex.timings:

nameusersystemelapsed
assign_peak_segments0.5650.0050.594
assign_peaks1.3700.0321.443
broadenrich7.5450.2748.072
calc_peak_gene_overlap0.4530.0130.475
chipenrich2.3290.0702.470
load_peaks0.040.000.04
num_peaks_per_gene0.9010.0160.939
plot_chipenrich_spline2.5350.1322.722
plot_dist_to_tss0.2550.0100.276
plot_gene_coverage0.9370.0541.009
plot_polyenrich_spline2.9730.2513.331
polyenrich5.9570.2846.388
read_bed0.2000.0020.208
supported_genesets0.0090.0010.009
supported_genomes0.0020.0000.003
supported_locusdefs0.0100.0010.011
supported_methods0.0010.0000.001
supported_read_lengths0.0080.0010.009