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BioC 3.4: CHECK report for chipenrich on malbec1

This page was generated on 2017-04-15 16:11:39 -0400 (Sat, 15 Apr 2017).

Package 192/1296HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
chipenrich 1.12.1
Raymond G. Cavalcante
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/chipenrich
Last Changed Rev: 127283 / Revision: 128728
Last Changed Date: 2017-03-09 18:15:22 -0500 (Thu, 09 Mar 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
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: chipenrich
Version: 1.12.1
Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings chipenrich_1.12.1.tar.gz
StartedAt: 2017-04-14 21:29:59 -0400 (Fri, 14 Apr 2017)
EndedAt: 2017-04-14 21:32:46 -0400 (Fri, 14 Apr 2017)
EllapsedTime: 166.5 seconds
RetCode: 0
Status:  OK 
CheckDir: chipenrich.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings chipenrich_1.12.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/chipenrich.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 ‘chipenrich/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘chipenrich’ version ‘1.12.1’
* 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
plot_spline_length 19.112  0.024  19.162
chipenrich         11.676  0.040  11.748
plot_gene_coverage  7.552  0.004   7.572
* 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_segments0.4360.0040.451
assign_peaks0.9000.0000.902
calc_peak_gene_overlap0.6880.0120.700
chipenrich11.676 0.04011.748
load_peaks0.0440.0000.059
num_peaks_per_gene0.7560.0000.758
plot_dist_to_tss0.2920.0000.295
plot_gene_coverage7.5520.0047.572
plot_spline_length19.112 0.02419.162
read_bed0.0520.0000.052
read_bedgff0.0320.0000.033
supported_genesets0.0040.0000.005
supported_genomes0.0000.0000.001
supported_locusdefs0.0040.0000.003
supported_methods0.0000.0000.001
supported_read_lengths0.0080.0000.006