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CHECK report for mdgsa on merida1

This page was generated on 2019-04-16 11:58:13 -0400 (Tue, 16 Apr 2019).

Package 899/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
mdgsa 1.14.0
David Montaner
Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019)
URL: https://git.bioconductor.org/packages/mdgsa
Branch: RELEASE_3_8
Last Commit: 93627c0
Last Changed Date: 2018-10-30 11:41:56 -0400 (Tue, 30 Oct 2018)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: mdgsa
Version: 1.14.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:mdgsa.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings mdgsa_1.14.0.tar.gz
StartedAt: 2019-04-16 01:03:56 -0400 (Tue, 16 Apr 2019)
EndedAt: 2019-04-16 01:06:04 -0400 (Tue, 16 Apr 2019)
EllapsedTime: 127.9 seconds
RetCode: 0
Status:  OK 
CheckDir: mdgsa.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:mdgsa.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings mdgsa_1.14.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/mdgsa.Rcheck’
* using R version 3.5.3 (2019-03-11)
* 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 ‘1.14.0’
* 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 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 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
  ‘/Users/biocbuild/bbs-3.8-bioc/meat/mdgsa.Rcheck/00check.log’
for details.



Installation output

mdgsa.Rcheck/00install.out

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL mdgsa
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘mdgsa’ ...
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (mdgsa)

Tests output

mdgsa.Rcheck/tests/runTests.Rout


R version 3.5.3 (2019-03-11) -- "Great Truth"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> BiocGenerics:::testPackage ("mdgsa")


KEGG.db contains mappings based on older data because the original
  resource was removed from the the public domain before the most
  recent update was produced. This package should now be considered
  deprecated and future versions of Bioconductor may not have it
  available.  Users who want more current data are encouraged to look
  at the KEGGREST or reactome.db packages

Warning: The annotation list has no names.
List position will be used instead.
Warning: Some blocks in the annot list have duplicated genes.
Duplicated will be removed.
Warning: Some blocks in the annot gene IDs are missing or "".
Those will be removed.
Filtering annotation by size:
   1 small blocks removed.
   0 big blocks removed.
   3 blocks remain in the annotation.
Warning: The annotation list has no names.
List position will be used instead.
Warning: Some blocks in the annot list have duplicated genes.
Duplicated will be removed.
Warning: Some blocks in the annot gene IDs are missing or "".
Those will be removed.
Warning: There are genes in the annotation list which are not
part of the gene universe defined by the ranking index;
they will be eliminated form the annotation.
60% of the genes in the index are annotated in the list.
Filtering annotation by size:
   1 small blocks removed.
   0 big blocks removed.
   3 blocks remain in the annotation.
Loading required package: GO.db
Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colMeans, colSums, colnames,
    dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, lengths, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
    rowMeans, rowSums, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which, which.max, which.min

Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: IRanges
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid

Using GO.db version: 3.7.0
Using GO.db version: 3.7.0
Loading required package: KEGG.db
Using KEGG.db version: 3.2.3
Using GO.db version: 3.7.0
Analyzed blocks:
time in seconds:
   user  system elapsed 
  0.045   0.009   0.054 
Using GO.db version: 3.7.0
  3miRNAs with annotated targets
  2miRNAs without targets
  0miRNAs with targets but not in the ranking index
Analyzed blocks:
time in seconds:
   user  system elapsed 
  0.012   0.004   0.016 
Analyzed blocks:
time in seconds:
   user  system elapsed 
  0.013   0.003   0.017 


RUNIT TEST PROTOCOL -- Tue Apr 16 01:05:56 2019 
*********************************************** 
Number of test functions: 18 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
mdgsa RUnit Tests - 18 test functions, 0 errors, 0 failures
Number of test functions: 18 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
 11.685   0.497  12.271 

Example timings

mdgsa.Rcheck/mdgsa-Ex.timings

nameusersystemelapsed
annotFilter0.0080.0010.009
annotList2mat0.0000.0000.001
annotMat2list0.0010.0000.001
getGOnames0.2530.0410.296
getKEGGnames0.0230.0010.024
getOntology0.1890.0030.192
goLeaves3.3190.1013.450
indexTransform0.0080.0010.009
mdGsa0.0350.0060.042
mdPat0.0180.0020.020
plotMdGsa0.0010.0000.000
propagateGO4.7600.0934.936
pval2index0.0060.0020.007
revList0.0010.0000.001
splitOntologies0.3750.0140.388
transferIndex0.0430.0020.044
uvGsa0.0540.0060.060
uvPat0.0040.0000.004
uvSignif0.0030.0000.004