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BioC 3.5: CHECK report for mdgsa on veracruz2

This page was generated on 2017-10-18 14:32:46 -0400 (Wed, 18 Oct 2017).

Package 771/1381HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
mdgsa 1.8.0
David Montaner
Snapshot Date: 2017-10-17 17:00:52 -0400 (Tue, 17 Oct 2017)
URL: https://git.bioconductor.org/packages/mdgsa
Branch: RELEASE_3_5
Last Commit: b73ba7d
Last Changed Date: 2017-04-24 15:45:44 -0400 (Mon, 24 Apr 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: mdgsa
Version: 1.8.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings mdgsa_1.8.0.tar.gz
StartedAt: 2017-10-18 05:43:13 -0400 (Wed, 18 Oct 2017)
EndedAt: 2017-10-18 05:45:33 -0400 (Wed, 18 Oct 2017)
EllapsedTime: 140.7 seconds
RetCode: 0
Status:  OK 
CheckDir: mdgsa.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings mdgsa_1.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/mdgsa.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 ‘mdgsa/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘mdgsa’ 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 ‘mdgsa’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
* 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
getGOnames: no visible global function definition for
  ‘packageDescription’
getKEGGnames: no visible global function definition for
  ‘packageDescription’
getOntology: no visible global function definition for
  ‘packageDescription’
goLeaves: no visible global function definition for
  ‘packageDescription’
index.normalize: no visible global function definition for ‘qqnorm’
index.standardize: no visible global function definition for ‘sd’
mdGsa: no visible global function definition for ‘quasibinomial’
mdGsa: no visible global function definition for ‘glm.fit’
mdGsa: no visible global function definition for ‘summary.glm’
mdGsa: no visible global function definition for ‘p.adjust’
mdPat: no visible global function definition for ‘read.table’
plotMdGsa: no visible global function definition for ‘plot’
plotMdGsa: no visible global function definition for ‘points’
plotMdGsa: no visible global function definition for ‘cov’
plotMdGsa: no visible global function definition for ‘qchisq’
plotMdGsa: no visible global function definition for ‘lines’
plotMdGsa: no visible global function definition for ‘abline’
propagateGO.matrix: no visible global function definition for
  ‘packageDescription’
splitOntologies: no visible global function definition for
  ‘packageDescription’
uvGsa: no visible global function definition for ‘quasibinomial’
uvGsa: no visible global function definition for ‘glm.fit’
uvGsa: no visible global function definition for ‘summary.glm’
uvGsa: no visible global function definition for ‘p.adjust’
Undefined global functions or variables:
  abline cov glm.fit lines p.adjust packageDescription plot points
  qchisq qqnorm quasibinomial read.table sd summary.glm
Consider adding
  importFrom("graphics", "abline", "lines", "plot", "points")
  importFrom("stats", "cov", "glm.fit", "p.adjust", "qchisq", "qqnorm",
             "quasibinomial", "sd", "summary.glm")
  importFrom("utils", "packageDescription", "read.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
Examples with CPU or elapsed time > 5s
             user system elapsed
propagateGO 5.775  0.087   6.088
* 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
  ‘/Users/biocbuild/bbs-3.5-bioc/meat/mdgsa.Rcheck/00check.log’
for details.


mdgsa.Rcheck/00install.out:

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

mdgsa.Rcheck/mdgsa-Ex.timings:

nameusersystemelapsed
annotFilter0.0640.0110.076
annotList2mat0.0000.0000.001
annotMat2list0.0010.0000.002
getGOnames0.4910.0350.543
getKEGGnames0.0220.0010.028
getOntology0.3840.0040.391
goLeaves3.0310.1183.252
indexTransform0.0060.0010.008
mdGsa0.0370.0050.042
mdPat0.0160.0010.017
plotMdGsa0.0000.0000.001
propagateGO5.7750.0876.088
pval2index0.0310.0020.033
revList0.0020.0000.002
splitOntologies0.4070.0060.465
transferIndex0.3210.0080.340
uvGsa0.0140.0010.021
uvPat0.0050.0000.006
uvSignif0.0050.0010.004