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BioC 3.6: CHECK report for plethy on malbec1

This page was generated on 2017-08-16 13:20:58 -0400 (Wed, 16 Aug 2017).

Package 1005/1410HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
plethy 1.15.0
Daniel Bottomly
Snapshot Date: 2017-08-15 17:18:21 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/plethy
Last Changed Rev: 129129 / Revision: 131943
Last Changed Date: 2017-04-24 15:50:57 -0400 (Mon, 24 Apr 2017)
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
veracruz1 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: plethy
Version: 1.15.0
Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings plethy_1.15.0.tar.gz
StartedAt: 2017-08-16 01:25:42 -0400 (Wed, 16 Aug 2017)
EndedAt: 2017-08-16 01:27:37 -0400 (Wed, 16 Aug 2017)
EllapsedTime: 114.2 seconds
RetCode: 0
Status:  OK 
CheckDir: plethy.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings plethy_1.15.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/plethy.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘plethy/DESCRIPTION’ ... OK
* this is package ‘plethy’ version ‘1.15.0’
* 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 ‘plethy’ 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 ... NOTE
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘csv.to.table’ ‘find.break.ranges.integer’ ‘fix.time’ ‘multi.grep’
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
generate.sample.buxco : <anonymous> : <anonymous> : <anonymous> :
  <anonymous>: no visible global function definition for ‘rnorm’
make.db.package: no visible global function definition for
  ‘packageDescription’
mvtsplot.data.frame: no visible global function definition for ‘colors’
mvtsplot.data.frame: no visible global function definition for ‘par’
mvtsplot.data.frame: no visible global function definition for ‘layout’
mvtsplot.data.frame: no visible global function definition for
  ‘strwidth’
mvtsplot.data.frame: no visible global function definition for ‘abline’
mvtsplot.data.frame: no visible global function definition for ‘mtext’
mvtsplot.data.frame: no visible global function definition for ‘plot’
mvtsplot.data.frame: no visible global function definition for ‘bxp’
mvtsplot.data.frame : <anonymous>: no visible binding for global
  variable ‘median’
mvtsplot.data.frame: no visible global function definition for ‘lines’
mvtsplot.data.frame: no visible global function definition for ‘Axis’
mvtsplot.data.frame: no visible global function definition for ‘legend’
retrieveMatrix,BuxcoDB: no visible global function definition for
  ‘terms’
tsplot,BuxcoDB: no visible binding for global variable ‘Days’
tsplot,BuxcoDB: no visible binding for global variable ‘Value’
tsplot,BuxcoDB: no visible binding for global variable ‘Sample_Name’
Undefined global functions or variables:
  Axis Days Sample_Name Value abline bxp colors layout legend lines
  median mtext packageDescription par plot rnorm strwidth terms
Consider adding
  importFrom("grDevices", "colors")
  importFrom("graphics", "Axis", "abline", "bxp", "layout", "legend",
             "lines", "mtext", "par", "plot", "strwidth")
  importFrom("stats", "median", "rnorm", "terms")
  importFrom("utils", "packageDescription")
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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.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 NOTEs
See
  ‘/home/biocbuild/bbs-3.6-bioc/meat/plethy.Rcheck/00check.log’
for details.


plethy.Rcheck/00install.out:

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

plethy.Rcheck/plethy-Ex.timings:

nameusersystemelapsed
BuxcoDB0.8680.0120.881
add_query_funcs0.2360.0040.241
dbImport0.6440.0080.656
parsing1.2920.1801.475
plethy1.1040.1801.285
utilities2.6200.2122.835