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BioC 3.0: CHECK report for COHCAP on perceval

This page was generated on 2015-04-10 09:59:08 -0700 (Fri, 10 Apr 2015).

Package 188/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
COHCAP 1.4.0
Charles Warden
Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/COHCAP
Last Changed Rev: 98405 / Revision: 102249
Last Changed Date: 2015-01-16 11:24:50 -0800 (Fri, 16 Jan 2015)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  NotNeeded  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  OK  OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK [ OK ] OK 
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK 

Summary

Package: COHCAP
Version: 1.4.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch COHCAP_1.4.0.tar.gz
StartedAt: 2015-04-10 00:12:03 -0700 (Fri, 10 Apr 2015)
EndedAt: 2015-04-10 00:13:44 -0700 (Fri, 10 Apr 2015)
EllapsedTime: 100.5 seconds
RetCode: 0
Status:  OK 
CheckDir: COHCAP.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch COHCAP_1.4.0.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/COHCAP.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘COHCAP/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘COHCAP’ version ‘1.4.0’
* 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 ‘COHCAP’ can be installed ... [1s/5s] 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
COHCAP.annotate: no visible binding for global variable
  ‘COHCAP.450k.UCSC’
COHCAP.annotate: no visible binding for global variable
  ‘COHCAP.450k.HMM’
COHCAP.annotate: no visible binding for global variable ‘COHCAP.27k’
COHCAP.avg.by.site: no visible binding for global variable
  ‘integrate.folder’
COHCAP.integrate.avg.by.island: no visible binding for global variable
  ‘na.rm’
cor.test.est: no visible binding for global variable ‘na.rm’
cor.test.pvalue: no visible binding for global variable ‘na.rm’
* 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 ... [36s/63s] OK
Examples with CPU or elapsed time > 5s
                                user system elapsed
COHCAP.integrate.avg.by.island 5.944  0.596  11.779
COHCAP.avg.by.island           5.579  0.460  10.461
COHCAP.integrate.avg.by.site   5.433  0.507   9.541
COHCAP.avg.by.site             4.743  0.396   7.074
COHCAP.site                    4.640  0.297   6.341
COHCAP.annotate                4.089  0.233  11.201
* 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

NOTE: There was 1 note.
See
  ‘/Users/biocbuild/bbs-3.0-bioc/meat/COHCAP.Rcheck/00check.log’
for details.

COHCAP.Rcheck/00install.out:

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

COHCAP.Rcheck/COHCAP-Ex.timings:

nameusersystemelapsed
COHCAP.BSSeq.preprocess0.0360.0501.441
COHCAP.annotate 4.089 0.23311.201
COHCAP.avg.by.island 5.579 0.46010.461
COHCAP.avg.by.site4.7430.3967.074
COHCAP.integrate.avg.by.island 5.944 0.59611.779
COHCAP.integrate.avg.by.site5.4330.5079.541
COHCAP.qc2.1540.1434.166
COHCAP.site4.6400.2976.341