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BioC 3.4: CHECK report for GGBase on morelia

This page was generated on 2017-04-15 16:22:43 -0400 (Sat, 15 Apr 2017).

Package 526/1296HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GGBase 3.36.0
VJ Carey
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/GGBase
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  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository

Summary

Package: GGBase
Version: 3.36.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings GGBase_3.36.0.tar.gz
StartedAt: 2017-04-15 02:54:21 -0700 (Sat, 15 Apr 2017)
EndedAt: 2017-04-15 02:57:40 -0700 (Sat, 15 Apr 2017)
EllapsedTime: 199.1 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: GGBase.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings GGBase_3.36.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/GGBase.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 ‘GGBase/DESCRIPTION’ ... OK
* this is package ‘GGBase’ version ‘3.36.0’
* 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 ‘GGBase’ can be installed ... WARNING
Found the following significant warnings:
  Warning: replacing previous import ‘IRanges::which’ by ‘Matrix::which’ when loading ‘GGBase’
See ‘/Users/biocbuild/bbs-3.4-bioc/meat/GGBase.Rcheck/00install.out’ for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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 ... NOTE
'library' or 'require' call to ‘snpStats’ which was already attached by Depends.
  Please remove these calls from your code.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
getSS: no visible global function definition for ‘installed.packages’
Undefined global functions or variables:
  installed.packages
Consider adding
  importFrom("utils", "installed.packages")
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 ‘tests’ ... OK
* checking tests ...
  Running ‘MAFfilter.R’
  Running ‘make.R’
  Running ‘plot_EvG.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: 1 WARNING, 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.4-bioc/meat/GGBase.Rcheck/00check.log’
for details.


GGBase.Rcheck/00install.out:

* installing *source* package ‘GGBase’ ...
** R
** inst
** preparing package for lazy loading
Warning: replacing previous import ‘IRanges::which’ by ‘Matrix::which’ when loading ‘GGBase’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: replacing previous import ‘IRanges::which’ by ‘Matrix::which’ when loading ‘GGBase’
* DONE (GGBase)

GGBase.Rcheck/GGBase-Ex.timings:

nameusersystemelapsed
MAFfilter3.8040.1834.066
clipPCs0.0010.0000.001
externalize0.0010.0010.001
make_smlSet3.4400.0763.525
plot_EvG3.8720.1494.197
rsid-class0.0020.0000.003
smlSet-class0.0020.0000.002