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CHECK report for SPIA on veracruz1

This page was generated on 2018-04-12 13:33:06 -0400 (Thu, 12 Apr 2018).

Package 1329/1472HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SPIA 2.30.0
Adi Laurentiu Tarca
Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018)
URL: https://git.bioconductor.org/packages/SPIA
Branch: RELEASE_3_6
Last Commit: 458818f
Last Changed Date: 2017-10-30 12:39:25 -0400 (Mon, 30 Oct 2017)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: SPIA
Version: 2.30.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings SPIA_2.30.0.tar.gz
StartedAt: 2018-04-12 09:51:34 -0400 (Thu, 12 Apr 2018)
EndedAt: 2018-04-12 09:58:18 -0400 (Thu, 12 Apr 2018)
EllapsedTime: 404.0 seconds
RetCode: 0
Status:  OK 
CheckDir: SPIA.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings SPIA_2.30.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/SPIA.Rcheck’
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘SPIA/DESCRIPTION’ ... OK
* this is package ‘SPIA’ version ‘2.30.0’
* 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 ‘SPIA’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘graphics’
A package should be listed in only one of these fields.
* 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
Package in Depends field not imported from: ‘KEGGgraph’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
combfunc: no visible global function definition for ‘na.omit’
combfunc: no visible global function definition for ‘pnorm’
combfunc: no visible global function definition for ‘qnorm’
getP2: no visible global function definition for ‘qchisq’
getP2: no visible global function definition for ‘pnorm’
getP2: no visible global function definition for ‘qnorm’
makeSPIAdata: no visible global function definition for ‘parseKGML’
makeSPIAdata: no visible global function definition for ‘nodes’
makeSPIAdata: no visible global function definition for ‘na.omit’
makeSPIAdata: no visible global function definition for ‘edges’
plotP: no visible global function definition for ‘na.omit’
plotP: no visible global function definition for ‘pnorm’
plotP: no visible global function definition for ‘qnorm’
plotP: no visible global function definition for ‘text’
spia: no visible global function definition for ‘pdf’
spia: no visible global function definition for ‘par’
spia: no visible global function definition for ‘phyper’
spia: no visible global function definition for ‘median’
spia: no visible global function definition for ‘sd’
spia: no visible global function definition for ‘density’
spia: no visible global function definition for ‘dev.off’
spia: no visible global function definition for ‘p.adjust’
Undefined global functions or variables:
  density dev.off edges median na.omit nodes p.adjust par parseKGML pdf
  phyper pnorm qchisq qnorm sd text
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("graphics", "par", "text")
  importFrom("stats", "density", "median", "na.omit", "p.adjust",
             "phyper", "pnorm", "qchisq", "qnorm", "sd")
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 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
Examples with CPU or elapsed time > 5s
                user system elapsed
spia         274.975 18.634 298.924
plotP         56.706  4.467  62.168
makeSPIAdata   5.782  0.255   6.141
* 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: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.6-bioc/meat/SPIA.Rcheck/00check.log’
for details.



Installation output

SPIA.Rcheck/00install.out

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

Tests output


Example timings

SPIA.Rcheck/SPIA-Ex.timings

nameusersystemelapsed
combfunc0.0280.0000.028
makeSPIAdata5.7820.2556.141
plotP56.706 4.46762.168
spia274.975 18.634298.924