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BioC 3.4: CHECK report for COHCAP on zin1

This page was generated on 2016-09-21 03:38:44 -0700 (Wed, 21 Sep 2016).

Package 239/1257HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
COHCAP 1.14.5
Charles Warden
Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/COHCAP
Last Changed Rev: 120840 / Revision: 121152
Last Changed Date: 2016-09-11 14:48:21 -0700 (Sun, 11 Sep 2016)
zin1 Linux (Ubuntu 16.04 LTS) / x86_64  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / 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: 1.14.5
Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings COHCAP_1.14.5.tar.gz
StartedAt: 2016-09-20 04:52:56 -0700 (Tue, 20 Sep 2016)
EndedAt: 2016-09-20 04:53:29 -0700 (Tue, 20 Sep 2016)
EllapsedTime: 33.5 seconds
RetCode: 0
Status:  OK 
CheckDir: COHCAP.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings COHCAP_1.14.5.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/COHCAP.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-pc-linux-gnu (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 ‘1.14.5’
* 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 global function definition for ‘read.table’
COHCAP.annotate: no visible global function definition for ‘data’
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.annotate: no visible global function definition for
  ‘write.table’
COHCAP.avg.by.island: no visible global function definition for
  ‘read.table’
COHCAP.avg.by.island: no visible global function definition for
  ‘p.adjust’
COHCAP.avg.by.island: no visible global function definition for
  ‘write.table’
COHCAP.avg.by.island: no visible global function definition for ‘pdf’
COHCAP.avg.by.island: no visible global function definition for ‘plot’
COHCAP.avg.by.island: no visible global function definition for
  ‘abline’
COHCAP.avg.by.island: no visible global function definition for ‘lm’
COHCAP.avg.by.island: no visible global function definition for
  ‘dev.off’
COHCAP.avg.by.site: no visible global function definition for
  ‘fisher.test’
COHCAP.avg.by.site: no visible global function definition for
  ‘p.adjust’
COHCAP.avg.by.site: no visible global function definition for ‘aov’
COHCAP.avg.by.site: no visible global function definition for
  ‘write.table’
COHCAP.denovo: no visible global function definition for ‘write.table’
COHCAP.integrate.avg.by.island: no visible global function definition
  for ‘write.table’
COHCAP.integrate.avg.by.island: no visible global function definition
  for ‘read.table’
COHCAP.integrate.avg.by.island: no visible global function definition
  for ‘p.adjust’
COHCAP.integrate.avg.by.island: no visible global function definition
  for ‘pdf’
COHCAP.integrate.avg.by.island: no visible global function definition
  for ‘plot’
COHCAP.integrate.avg.by.island: no visible global function definition
  for ‘cor.test’
COHCAP.integrate.avg.by.island: no visible binding for global variable
  ‘na.rm’
COHCAP.integrate.avg.by.island: no visible global function definition
  for ‘legend’
COHCAP.integrate.avg.by.island: no visible global function definition
  for ‘dev.off’
COHCAP.integrate.avg.by.site: no visible global function definition for
  ‘write.table’
COHCAP.integrate.avg.by.site: no visible global function definition for
  ‘read.table’
COHCAP.qc: no visible global function definition for ‘colors’
COHCAP.qc: no visible global function definition for ‘read.table’
COHCAP.qc: no visible global function definition for ‘pdf’
COHCAP.qc: no visible global function definition for ‘quantile’
COHCAP.qc: no visible global function definition for ‘density’
COHCAP.qc: no visible global function definition for ‘plot’
COHCAP.qc: no visible global function definition for ‘legend’
COHCAP.qc: no visible global function definition for ‘lines’
COHCAP.qc: no visible global function definition for ‘dev.off’
COHCAP.qc: no visible global function definition for ‘write.table’
COHCAP.qc: no visible global function definition for ‘dist’
COHCAP.qc: no visible global function definition for ‘hclust’
COHCAP.qc: no visible global function definition for ‘as.dendrogram’
COHCAP.qc: no visible global function definition for ‘dendrapply’
COHCAP.qc: no visible global function definition for ‘par’
COHCAP.qc: no visible global function definition for ‘prcomp’
COHCAP.qc: no visible global function definition for ‘na.omit’
COHCAP.site: no visible global function definition for ‘read.table’
COHCAP.site: no visible global function definition for ‘write.table’
COHCAP.site: no visible global function definition for ‘p.adjust’
annova.2way.pvalue: no visible global function definition for ‘aov’
annova.pvalue: no visible global function definition for ‘aov’
colLab: no visible global function definition for ‘is.leaf’
cor.test.est: no visible global function definition for ‘cor.test’
cor.test.est: no visible binding for global variable ‘na.rm’
cor.test.pvalue: no visible global function definition for ‘cor.test’
cor.test.pvalue: no visible binding for global variable ‘na.rm’
custom.cor: no visible global function definition for ‘cor’
lm.pvalue: no visible global function definition for ‘lm’
lm.pvalue2: no visible global function definition for ‘lm’
ttest2: no visible global function definition for ‘t.test’
Undefined global functions or variables:
  COHCAP.27k COHCAP.450k.HMM COHCAP.450k.UCSC abline aov as.dendrogram
  colors cor cor.test data dendrapply density dev.off dist fisher.test
  hclust is.leaf legend lines lm na.omit na.rm p.adjust par pdf plot
  prcomp quantile read.table t.test write.table
Consider adding
  importFrom("grDevices", "colors", "dev.off", "pdf")
  importFrom("graphics", "abline", "legend", "lines", "par", "plot")
  importFrom("stats", "aov", "as.dendrogram", "cor", "cor.test",
             "dendrapply", "density", "dist", "fisher.test", "hclust",
             "is.leaf", "lm", "na.omit", "p.adjust", "prcomp",
             "quantile", "t.test")
  importFrom("utils", "data", "read.table", "write.table")
to your NAMESPACE file.
* 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
* 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
  ‘/home/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.preprocess0.0160.0000.023
COHCAP.annotate1.8600.0441.953
COHCAP.avg.by.island2.8960.1603.082
COHCAP.avg.by.site2.5000.1362.667
COHCAP.denovo2.3280.1282.486
COHCAP.integrate.avg.by.island3.2000.1523.410
COHCAP.integrate.avg.by.site2.8960.1683.113
COHCAP.qc1.2880.0441.338
COHCAP.site2.1600.0802.258