Paul Shannon
| Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021) |
| git_url: https://git.bioconductor.org/packages/MotifDb |
| git_branch: RELEASE_3_13 |
| git_last_commit: ed81ab9 |
| git_last_commit_date: 2021-05-19 11:53:25 -0400 (Wed, 19 May 2021) |
| Back to Multiple platform build/check report for BioC 3.13 |
|
This page was generated on 2021-10-15 15:06:12 -0400 (Fri, 15 Oct 2021).
|
To the developers/maintainers of the MotifDb package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/MotifDb.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1183/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| MotifDb 1.34.0 (landing page) Paul Shannon
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| Package: MotifDb |
| Version: 1.34.0 |
| Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MotifDb.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings MotifDb_1.34.0.tar.gz |
| StartedAt: 2021-10-15 02:13:26 -0400 (Fri, 15 Oct 2021) |
| EndedAt: 2021-10-15 02:22:49 -0400 (Fri, 15 Oct 2021) |
| EllapsedTime: 563.3 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: MotifDb.Rcheck |
| Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:MotifDb.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings MotifDb_1.34.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/MotifDb.Rcheck' * using R version 4.1.1 (2021-08-10) * 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 '1.34.0' * package encoding: UTF-8 * 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' ... WARNING Found 'inst/doc/makefile': should be 'Makefile' and will be ignored * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 1 WARNING See 'C:/Users/biocbuild/bbs-3.13-bioc/meat/MotifDb.Rcheck/00check.log' for details.
MotifDb.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/MotifDb_1.34.0.tar.gz && rm -rf MotifDb.buildbin-libdir && mkdir MotifDb.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=MotifDb.buildbin-libdir MotifDb_1.34.0.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL MotifDb_1.34.0.zip && rm MotifDb_1.34.0.tar.gz MotifDb_1.34.0.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
56 2885k 56 1633k 0 0 1842k 0 0:00:01 --:--:-- 0:00:01 1843k
100 2885k 100 2885k 0 0 2156k 0 0:00:01 0:00:01 --:--:-- 2158k
install for i386
* installing *source* package 'MotifDb' ...
** using staged installation
** 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_1.34.0.zip
* DONE (MotifDb)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'MotifDb' successfully unpacked and MD5 sums checked
|
MotifDb.Rcheck/tests_i386/runTests.Rout
R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 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, 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, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unsplit, which.max, which.min
Loading required package: S4Vectors
Loading required package: stats4
Attaching package: 'S4Vectors'
The following objects are masked from 'package:base':
I, expand.grid, unname
Loading required package: IRanges
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
Loading required package: GenomicRanges
Loading required package: GenomeInfoDb
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')
Loading required package: grid
Attaching package: 'grid'
The following object is masked from 'package:Biostrings':
pattern
[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.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.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.hocomoco11.with.reliabilityScores
[1] "--- test.MotifDb.emptyMode"
See system.file("LICENSE", package="MotifDb") for use restrictions.
[1] "--- test.MotifDb.normalMode"
[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.hocomoco11.with.reliabilityScores
[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.sequenceCount"
[1] "--- test.tfFamilies"
[1] "--- test.transformMatrixToMemeRepresentation"
RUNIT TEST PROTOCOL -- Fri Oct 15 02:20:47 2021
***********************************************
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
There were 26 warnings (use warnings() to see them)
>
> proc.time()
user system elapsed
104.15 1.39 105.53
|
MotifDb.Rcheck/tests_x64/runTests.Rout
R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 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, 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, rownames, sapply, setdiff, sort, table,
tapply, union, unique, unsplit, which.max, which.min
Loading required package: S4Vectors
Loading required package: stats4
Attaching package: 'S4Vectors'
The following objects are masked from 'package:base':
I, expand.grid, unname
Loading required package: IRanges
Attaching package: 'IRanges'
The following object is masked from 'package:grDevices':
windows
Loading required package: GenomicRanges
Loading required package: GenomeInfoDb
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')
Loading required package: grid
Attaching package: 'grid'
The following object is masked from 'package:Biostrings':
pattern
[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.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.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.hocomoco11.with.reliabilityScores
[1] "--- test.MotifDb.emptyMode"
See system.file("LICENSE", package="MotifDb") for use restrictions.
[1] "--- test.MotifDb.normalMode"
[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.hocomoco11.with.reliabilityScores
[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.sequenceCount"
[1] "--- test.tfFamilies"
[1] "--- test.transformMatrixToMemeRepresentation"
RUNIT TEST PROTOCOL -- Fri Oct 15 02:22:43 2021
***********************************************
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
There were 26 warnings (use warnings() to see them)
>
> proc.time()
user system elapsed
115.20 0.53 115.73
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MotifDb.Rcheck/examples_i386/MotifDb-Ex.timings
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MotifDb.Rcheck/examples_x64/MotifDb-Ex.timings
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