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BioC 2.14: CHECK report for chipenrich on petty

This page was generated on 2014-10-08 09:01:14 -0700 (Wed, 08 Oct 2014).

Package 140/824HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
chipenrich 1.2.0
Ryan P. Welch
Snapshot Date: 2014-10-07 17:20:37 -0700 (Tue, 07 Oct 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_14/madman/Rpacks/chipenrich
Last Changed Rev: 88838 / Revision: 95116
Last Changed Date: 2014-04-11 14:07:21 -0700 (Fri, 11 Apr 2014)
zin2 Linux (Ubuntu 12.04.4 LTS) / x86_64  NotNeeded  OK  OK 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  OK  OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK [ OK ] OK 
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK 

Summary

Package: chipenrich
Version: 1.2.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch chipenrich_1.2.0.tar.gz
StartedAt: 2014-10-07 21:12:44 -0700 (Tue, 07 Oct 2014)
EndedAt: 2014-10-07 21:22:24 -0700 (Tue, 07 Oct 2014)
EllapsedTime: 579.9 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 --no-multiarch chipenrich_1.2.0.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-2.14-bioc/meat/chipenrich.Rcheck’
* using R version 3.1.1 (2014-07-10)
* using platform: x86_64-apple-darwin10.8.0 (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 ‘1.2.0’
* 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 ... [27s/29s] 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 ... NOTE
chipenrich: no visible binding for global variable ‘P.value’
load_peaks: no visible binding for global variable ‘chrom’
read_bed: no visible binding for global variable ‘chrom’
read_peaks: no visible binding for global variable ‘chrom’
setup_ldef: no visible binding for global variable ‘chrom’
test_binomial: no visible binding for global variable ‘geneid’
test_fisher_exact: no visible binding for global variable ‘geneid’
test_gam: no visible binding for global variable ‘geneid’
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [298s/300s] OK
Examples with CPU or elapsed time > 5s
                       user system elapsed
chipenrich          121.907  1.338 123.834
plot_spline_length   77.043  1.911  79.383
plot_expected_peaks  76.656  1.386  78.297
* 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

NOTE: There was 1 note.
See
  ‘/Users/biocbuild/bbs-2.14-bioc/meat/chipenrich.Rcheck/00check.log’
for details.

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
chipenrich121.907 1.338123.834
plot_dist_to_tss4.6110.0654.682
plot_expected_peaks76.656 1.38678.297
plot_spline_length77.043 1.91179.383
supported_genesets0.0160.0010.017
supported_genomes0.0100.0010.012
supported_locusdefs0.0070.0020.008
supported_methods0.0010.0000.001
supported_read_lengths0.0080.0010.009