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BioC 3.4: CHECK report for COHCAP on morelia

This page was generated on 2017-04-15 16:25:09 -0400 (Sat, 15 Apr 2017).

Package 246/1296HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
COHCAP 1.16.0
Charles Warden
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/COHCAP
Last Changed Rev: 122710 / Revision: 128728
Last Changed Date: 2016-10-17 14:45:06 -0400 (Mon, 17 Oct 2016)
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: COHCAP
Version: 1.16.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings COHCAP_1.16.0.tar.gz
StartedAt: 2017-04-15 00:15:50 -0700 (Sat, 15 Apr 2017)
EndedAt: 2017-04-15 00:16:59 -0700 (Sat, 15 Apr 2017)
EllapsedTime: 69.1 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 COHCAP_1.16.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/COHCAP.Rcheck’
* using R version 3.3.3 (2017-03-06)
* using platform: x86_64-apple-darwin13.4.0 (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 ‘1.16.0’
* 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 ... 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.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’
Undefined global functions or variables:
  COHCAP.27k COHCAP.450k.HMM COHCAP.450k.UCSC 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 ... OK
Examples with CPU or elapsed time > 5s
                                user system elapsed
COHCAP.integrate.avg.by.island 4.786  0.406   6.148
COHCAP.avg.by.island           4.502  0.305   6.490
COHCAP.integrate.avg.by.site   4.407  0.336   6.466
COHCAP.site                    2.953  0.150   5.459
* 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
  ‘/Users/biocbuild/bbs-3.4-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.preprocess0.0240.0080.195
COHCAP.annotate2.2100.1344.248
COHCAP.avg.by.island4.5020.3056.490
COHCAP.avg.by.site3.4580.2204.718
COHCAP.denovo3.4630.1994.235
COHCAP.integrate.avg.by.island4.7860.4066.148
COHCAP.integrate.avg.by.site4.4070.3366.466
COHCAP.qc1.5650.0652.079
COHCAP.site2.9530.1505.459