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BioC 3.5: CHECK report for soGGi on veracruz2

This page was generated on 2017-10-18 14:33:11 -0400 (Wed, 18 Oct 2017).

Package 1244/1381HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
soGGi 1.8.0
Tom Carroll
Snapshot Date: 2017-10-17 17:00:52 -0400 (Tue, 17 Oct 2017)
URL: https://git.bioconductor.org/packages/soGGi
Branch: RELEASE_3_5
Last Commit: abfb66b
Last Changed Date: 2017-04-24 15:45:44 -0400 (Mon, 24 Apr 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository

Summary

Package: soGGi
Version: 1.8.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings soGGi_1.8.0.tar.gz
StartedAt: 2017-10-18 09:16:12 -0400 (Wed, 18 Oct 2017)
EndedAt: 2017-10-18 09:20:19 -0400 (Wed, 18 Oct 2017)
EllapsedTime: 247.8 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: soGGi.Rcheck
Warnings: 2

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings soGGi_1.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/soGGi.Rcheck’
* using R version 3.4.2 (2017-09-28)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘soGGi/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘soGGi’ version ‘1.8.0’
* 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 ‘soGGi’ can be installed ... WARNING
Found the following significant warnings:
  Warning: replacing previous import ‘ggplot2::Position’ by ‘BiocGenerics::Position’ when loading ‘soGGi’
See ‘/Users/biocbuild/bbs-3.5-bioc/meat/soGGi.Rcheck/00install.out’ for details.
* 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 dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... NOTE
Foreign function call to a different package:
  .Call("rle_sum_any", ..., PACKAGE = "chipseq")
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
* checking R code for possible problems ... NOTE
GetGRanges: no visible global function definition for ‘read.delim’
findconsensusRegions : <anonymous>: no visible global function
  definition for ‘weighted.mean’
getShifts: no visible global function definition for
  ‘readGAlignmentsFromBam’
getSummitScore: no visible global function definition for
  ‘readGAlignmentsFromBam’
plotRegion.ChIPprofile: no visible global function definition for
  ‘formula’
runFindSummit: no visible global function definition for
  ‘readGAlignmentsFromBam’
runRegionPlot : <anonymous>: no visible global function definition for
  ‘spline’
summitPipeline: no visible global function definition for
  ‘readGAlignmentsFromBam’
plotRegion,ChIPprofile: no visible global function definition for
  ‘formula’
Undefined global functions or variables:
  formula read.delim readGAlignmentsFromBam spline weighted.mean
Consider adding
  importFrom("stats", "formula", "spline", "weighted.mean")
  importFrom("utils", "read.delim")
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 ... WARNING
Codoc mismatches from documentation object 'c,ChIPprofile-method':
\S4method{c}{ChIPprofile}
  Code: function(x, ...)
  Docs: function(x, ..., recursive = FALSE)
  Argument names in docs not in code:
    recursive

* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... 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 ‘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: 2 WARNINGs, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.5-bioc/meat/soGGi.Rcheck/00check.log’
for details.


soGGi.Rcheck/00install.out:

* installing *source* package ‘soGGi’ ...
** R
** data
** inst
** preparing package for lazy loading
Warning: replacing previous import ‘ggplot2::Position’ by ‘BiocGenerics::Position’ when loading ‘soGGi’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: replacing previous import ‘ggplot2::Position’ by ‘BiocGenerics::Position’ when loading ‘soGGi’
* DONE (soGGi)

soGGi.Rcheck/soGGi-Ex.timings:

nameusersystemelapsed
ChIPprofile0.3300.0240.362
Ops0.7580.0320.828
groupByOverlaps0.8290.0300.905
manipulateObjects1.1920.0301.259
normalise0.9950.0751.095
normaliseQuantiles0.9840.0711.073
orientBy0.5010.0110.525
plotRegion1.6420.0731.759
pwmToCoverage0.0030.0020.006