This page was generated on 2018-04-12 13:35:55 -0400 (Thu, 12 Apr 2018).
MotifDb 1.20.0 Paul Shannon
Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018) |
URL: https://git.bioconductor.org/packages/MotifDb |
Branch: RELEASE_3_6 |
Last Commit: 704c856 |
Last Changed Date: 2017-10-30 12:39:49 -0400 (Mon, 30 Oct 2017) |
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | | ![UNNEEDED, same version exists in internal repository UNNEEDED, same version exists in internal repository](../120px-Blue_Light_Icon.svg.png) |
tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | ![UNNEEDED, same version exists in internal repository UNNEEDED, same version exists in internal repository](../120px-Blue_Light_Icon.svg.png) |
veracruz1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | ![UNNEEDED, same version exists in internal repository UNNEEDED, same version exists in internal repository](../120px-Blue_Light_Icon.svg.png) |
R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
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, cbind, colMeans, colSums, colnames, 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.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 -- Thu Apr 12 06:44:13 2018
***********************************************
Number of test functions: 37
Number of errors: 0
Number of failures: 0
1 Test Suite :
MotifDb RUnit Tests - 37 test functions, 0 errors, 0 failures
Number of test functions: 37
Number of errors: 0
Number of failures: 0
>
> proc.time()
user system elapsed
30.041 0.424 30.855