BioC 3.5: CHECK report for mdgsa on veracruz2

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

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

* 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)

name	user	system	elapsed
annotFilter	0.064	0.011	0.076
annotList2mat	0.000	0.000	0.001
annotMat2list	0.001	0.000	0.002
getGOnames	0.491	0.035	0.543
getKEGGnames	0.022	0.001	0.028
getOntology	0.384	0.004	0.391
goLeaves	3.031	0.118	3.252
indexTransform	0.006	0.001	0.008
mdGsa	0.037	0.005	0.042
mdPat	0.016	0.001	0.017
plotMdGsa	0.000	0.000	0.001
propagateGO	5.775	0.087	6.088
pval2index	0.031	0.002	0.033
revList	0.002	0.000	0.002
splitOntologies	0.407	0.006	0.465
transferIndex	0.321	0.008	0.340
uvGsa	0.014	0.001	0.021
uvPat	0.005	0.000	0.006
uvSignif	0.005	0.001	0.004