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CHECK report for MotifDb on tokay2

This page was generated on 2019-04-09 12:00:59 -0400 (Tue, 09 Apr 2019).

Package 1023/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MotifDb 1.25.0
Paul Shannon
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/MotifDb
Branch: master
Last Commit: f118237
Last Changed Date: 2018-10-30 11:54:30 -0400 (Tue, 30 Oct 2018)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK 

Summary

Package: MotifDb
Version: 1.25.0
Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MotifDb.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings MotifDb_1.25.0.tar.gz
StartedAt: 2019-04-09 04:23:17 -0400 (Tue, 09 Apr 2019)
EndedAt: 2019-04-09 04:29:42 -0400 (Tue, 09 Apr 2019)
EllapsedTime: 385.4 seconds
RetCode: 0
Status:  OK  
CheckDir: MotifDb.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MotifDb.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings MotifDb_1.25.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/MotifDb.Rcheck'
* using R Under development (unstable) (2019-03-09 r76216)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'MotifDb/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'MotifDb' version '1.25.0'
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runTests.R'
 OK
** running tests for arch 'x64' ...
  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

Installation output

MotifDb.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/MotifDb_1.25.0.tar.gz && rm -rf MotifDb.buildbin-libdir && mkdir MotifDb.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=MotifDb.buildbin-libdir MotifDb_1.25.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL MotifDb_1.25.0.zip && rm MotifDb_1.25.0.tar.gz MotifDb_1.25.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 3199k  100 3199k    0     0  18.5M      0 --:--:-- --:--:-- --:--:-- 19.4M

install for i386

* installing *source* package 'MotifDb' ...
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'MotifDb'
    finding HTML links ... done
    MotifDb                                 html  
    MotifList-class                         html  
    associateTranscriptionFactors           html  
    export                                  html  
    geneToMotif                             html  
    motifToGene                             html  
    query                                   html  
    subset                                  html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
See system.file("LICENSE", package="MotifDb") for use restrictions.
** testing if installed package can be loaded from final location
See system.file("LICENSE", package="MotifDb") for use restrictions.
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'MotifDb' ...
** testing if installed package can be loaded
See system.file("LICENSE", package="MotifDb") for use restrictions.
* MD5 sums
packaged installation of 'MotifDb' as MotifDb_1.25.0.zip
* DONE (MotifDb)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'MotifDb' successfully unpacked and MD5 sums checked

Tests output

MotifDb.Rcheck/tests_i386/runTests.Rout


R Under development (unstable) (2019-03-09 r76216) -- "Unsuffered Consequences"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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, 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

Attaching package: 'IRanges'

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

    windows

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.emptyCtor"
[1] "--- test.nonEmptyCtor"
[1] "--- test.MotifDb.normalMode"
[1] "--- test.MotifDb.emptyMode"
See system.file("LICENSE", package="MotifDb") for use restrictions.
[1] "--- test.allMatricesAreNormalized"
[1] "--- test.getProviderNames"
[1] "--- test.getGeneSymbols"
[1] "--- test.getGeneIdsAndTypes"
[1] "--- test.proteinIds"
[1] "--- test.sequenceCount"
[1] "--- test.longNames"
[1] "--- test.organisms"
[1] "--- test.bindingDomains"
[1] "--- test.experimentTypes"
[1] "--- test.tfFamilies"
[1] "--- test.bindingSequences"
[1] "--- test.flyBindingDomains"
[1] "--- test.pubmedIDs"
[1] "--- test.allFullNames"
[1] "--- test.queryOldStyle"
[1] "--- test.query"
[1] "--- test.transformMatrixToMemeRepresentation"
[1] "--- test.matrixToMemeText"
[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.MotIVtoTable"

	Ungapped Alignment
	Scores read
	Database read
	Motif matches : 5
[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.flyFactorGeneSymbols"
[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.geneToMotif
[1] --- test.geneToMotif.ignore.jasparSuffixes
[1] --- test.motifToGene
[1] --- test.associateTranscriptionFactors
[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] "--- test.noNAorganisms"
[1] "--- test.nonEmptyCtor"
[1] "--- test.organisms"
[1] "--- test.proteinIds"
[1] "--- test.getProviderNames"
[1] "--- test.pubmedIDs"
[1] "--- test.query"
[1] "--- test.queryOldStyle"
[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 Apr 09 04:29:06 2019 
*********************************************** 
Number of test functions: 41 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
MotifDb RUnit Tests - 41 test functions, 0 errors, 0 failures
Number of test functions: 41 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
  24.76    1.09   25.86

MotifDb.Rcheck/tests_x64/runTests.Rout


R Under development (unstable) (2019-03-09 r76216) -- "Unsuffered Consequences"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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, 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

Attaching package: 'IRanges'

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

    windows

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.emptyCtor"
[1] "--- test.nonEmptyCtor"
[1] "--- test.MotifDb.normalMode"
[1] "--- test.MotifDb.emptyMode"
See system.file("LICENSE", package="MotifDb") for use restrictions.
[1] "--- test.allMatricesAreNormalized"
[1] "--- test.getProviderNames"
[1] "--- test.getGeneSymbols"
[1] "--- test.getGeneIdsAndTypes"
[1] "--- test.proteinIds"
[1] "--- test.sequenceCount"
[1] "--- test.longNames"
[1] "--- test.organisms"
[1] "--- test.bindingDomains"
[1] "--- test.experimentTypes"
[1] "--- test.tfFamilies"
[1] "--- test.bindingSequences"
[1] "--- test.flyBindingDomains"
[1] "--- test.pubmedIDs"
[1] "--- test.allFullNames"
[1] "--- test.queryOldStyle"
[1] "--- test.query"
[1] "--- test.transformMatrixToMemeRepresentation"
[1] "--- test.matrixToMemeText"
[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.MotIVtoTable"

	Ungapped Alignment
	Scores read
	Database read
	Motif matches : 5
[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.flyFactorGeneSymbols"
[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.geneToMotif
[1] --- test.geneToMotif.ignore.jasparSuffixes
[1] --- test.motifToGene
[1] --- test.associateTranscriptionFactors
[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] "--- test.noNAorganisms"
[1] "--- test.nonEmptyCtor"
[1] "--- test.organisms"
[1] "--- test.proteinIds"
[1] "--- test.getProviderNames"
[1] "--- test.pubmedIDs"
[1] "--- test.query"
[1] "--- test.queryOldStyle"
[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 Apr 09 04:29:37 2019 
*********************************************** 
Number of test functions: 41 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
MotifDb RUnit Tests - 41 test functions, 0 errors, 0 failures
Number of test functions: 41 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
   30.0     0.4    30.4

Example timings

MotifDb.Rcheck/examples_i386/MotifDb-Ex.timings

nameusersystemelapsed
MotifDb0.140.060.20
MotifList-class000
associateTranscriptionFactors0.190.000.19
export0.110.000.25
geneToMotif0.070.000.08
motifToGene0.030.000.03
query1.720.031.75
subset000

MotifDb.Rcheck/examples_x64/MotifDb-Ex.timings

nameusersystemelapsed
MotifDb0.170.000.17
MotifList-class000
associateTranscriptionFactors0.200.000.21
export0.050.010.06
geneToMotif0.040.000.05
motifToGene0.020.000.01
query1.690.001.69
subset000