Package: MotifDb

Version: 1.22.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:MotifDb.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings MotifDb_1.22.0.tar.gz

StartedAt: 2018-10-16 22:45:18 -0400 (Tue, 16 Oct 2018)

EndedAt: 2018-10-16 22:50:36 -0400 (Tue, 16 Oct 2018)

EllapsedTime: 317.8 seconds

RetCode: 0

Status:  OK

CheckDir: MotifDb.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:MotifDb.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings MotifDb_1.22.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/MotifDb.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MotifDb/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MotifDb’ version ‘1.22.0’
* 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 ‘MotifDb’ 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 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 ... OK
* 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 include directives in Makefiles ... 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: OK

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL MotifDb
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘MotifDb’ ...
** 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
See system.file("LICENSE", package="MotifDb") for use restrictions.
* DONE (MotifDb)

R version 3.5.1 Patched (2018-07-12 r74967) -- "Feather Spray"
Copyright (C) 2018 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.

> require(MotifDb) || stop("unable to load MyPackage")
Loading required package: MotifDb
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: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

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

    expand.grid

Loading required package: IRanges
Loading required package: Biostrings
Loading required package: XVector

Attaching package: 'Biostrings'

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

    strsplit

See system.file("LICENSE", package="MotifDb") for use restrictions.
[1] TRUE
> BiocGenerics:::testPackage('MotifDb')

Attaching package: 'MotIV'

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

    filter

Loading required package: grid

Attaching package: 'seqLogo'

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

    makePWM

[1] "--- test.MotIVtoTable"

	Ungapped Alignment
	Scores read
	Database read
	Motif matches : 5
[1] "--- test.MotifDb.emptyMode"
See system.file("LICENSE", package="MotifDb") for use restrictions.
[1] "--- test.MotifDb.normalMode"
[1] "--- test.allFullNames"
[1] "--- test.allMatricesAreNormalized"
[1] --- test.associateTranscriptionFactors
[1] "--- test.bindingDomains"
[1] "--- test.bindingSequences"
[1] "--- test.emptyCtor"
[1] "--- test.experimentTypes"
[1] "--- test.export_jasparFormatStdOut"
>Gallus-JASPAR_CORE-NFE2L1::MafG-MA0089.1
A [ 0.205882352941176 0.852941176470588 0 0.0294117647058824 1 0 ]
C [ 0.323529411764706 0.0588235294117647 0 0 0 0.764705882352941 ]
G [ 0.294117647058824 0.0882352941176471 0 0.941176470588235 0 0.0588235294117647 ]
T [ 0.176470588235294 0 1 0.0294117647058824 0 0.176470588235294 ]

>Gallus-JASPAR_CORE-ZEB1-MA0103.1
A [ 0.024390243902439 0.926829268292683 0 0 0 0.24390243902439 ]
C [ 0.829268292682927 0 0.975609756097561 0.926829268292683 0.024390243902439 0.024390243902439 ]
G [ 0.024390243902439 0.0487804878048781 0.024390243902439 0.0731707317073171 0 0.390243902439024 ]
T [ 0.121951219512195 0.024390243902439 0 0 0.975609756097561 0.341463414634146 ]

>Gallus-JASPAR_2014-NFE2L1::MafG-MA0089.1
A [ 0.205882352941176 0.852941176470588 0 0.0294117647058824 1 0 ]
C [ 0.323529411764706 0.0588235294117647 0 0 0 0.764705882352941 ]
G [ 0.294117647058824 0.0882352941176471 0 0.941176470588235 0 0.0588235294117647 ]
T [ 0.176470588235294 0 1 0.0294117647058824 0 0.176470588235294 ][1] "--- test.export_jasparFormatToFile"
[1] "--- test.export_memeFormatStdOut"
MEME version 4

ALPHABET= ACGT

strands: + -

Background letter frequencies
A 0.250 C 0.250 G 0.250 T 0.250 

MOTIF Gallus-JASPAR_CORE-NFE2L1::MafG-MA0089.1
letter-probability matrix: alength= 4 w= 6 nsites= 45 E=8.1e-020
 0.2058823529  0.3235294118  0.2941176471  0.1764705882
 0.8529411765  0.0588235294  0.0882352941  0.0000000000
 0.0000000000  0.0000000000  0.0000000000  1.0000000000
 0.0294117647  0.0000000000  0.9411764706  0.0294117647
 1.0000000000  0.0000000000  0.0000000000  0.0000000000
 0.0000000000  0.7647058824  0.0588235294  0.1764705882

MOTIF Gallus-JASPAR_CORE-ZEB1-MA0103.1
letter-probability matrix: alength= 4 w= 6 nsites= 45 E=8.1e-020
 0.0243902439  0.8292682927  0.0243902439  0.1219512195
 0.9268292683  0.0000000000  0.0487804878  0.0243902439
 0.0000000000  0.9756097561  0.0243902439  0.0000000000
 0.0000000000  0.9268292683  0.0731707317  0.0000000000
 0.0000000000  0.0243902439  0.0000000000  0.9756097561
 0.2439024390  0.0243902439  0.3902439024  0.3414634146

MOTIF Gallus-JASPAR_2014-NFE2L1::MafG-MA0089.1
letter-probability matrix: alength= 4 w= 6 nsites= 45 E=8.1e-020
 0.2058823529  0.3235294118  0.2941176471  0.1764705882
 0.8529411765  0.0588235294  0.0882352941  0.0000000000
 0.0000000000  0.0000000000  0.0000000000  1.0000000000
 0.0294117647  0.0000000000  0.9411764706  0.0294117647
 1.0000000000  0.0000000000  0.0000000000  0.0000000000
 0.0000000000  0.7647058824  0.0588235294  0.1764705882



[1] "--- test.export_memeFormatToFile"
[1] "--- test.export_memeFormatToFileDuplication"
[1] "--- test.flyBindingDomains"
[1] "--- test.flyFactorGeneSymbols"
[1] "--- test.getGeneIdsAndTypes"
[1] "--- test.getGeneSymbols"
[1] --- test.geneToMotif
[1] --- test.geneToMotif.ignore.jasparSuffixes
[1] "--- test.longNames"
[1] "--- test.matrixToMemeText"
[1] --- test.motifToGene
[1] Sys.getlocale: C/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
[1] "--- test.noNAorganisms"
[1] "--- test.nonEmptyCtor"
[1] "--- test.organisms"
[1] "--- test.proteinIds"
[1] "--- test.getProviderNames"
[1] "--- test.pubmedIDs"
[1] "--- test.query"
[1] "--- test.run_MotIV.motifMatch"

	Ungapped Alignment
	Scores read
	Database read
	Motif matches : 5

	Ungapped Alignment
	Scores read
	Database read
	Motif matches : 50
[1] "--- test.sequenceCount"
[1] "--- test.tfFamilies"
[1] "--- test.transformMatrixToMemeRepresentation"


RUNIT TEST PROTOCOL -- Tue Oct 16 22:50:31 2018 
*********************************************** 
Number of test functions: 39 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
MotifDb RUnit Tests - 39 test functions, 0 errors, 0 failures
Number of test functions: 39 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
 24.586   0.852  25.578 

name	user	system	elapsed
MotifDb	0.315	0.009	0.327
MotifList-class	0.004	0.001	0.006
associateTranscriptionFactors	0.120	0.005	0.125
export	0.104	0.015	0.120
geneToMotif	0.330	0.006	0.337
motifToGene	0.02	0.00	0.02
query	0.576	0.001	0.579
subset	0.004	0.001	0.003