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This page was generated on 2023-01-02 09:00:39 -0500 (Mon, 02 Jan 2023).

HostnameOSArch (*)R versionInstalled pkgs
palomino5Windows Server 2022 Datacenterx64R Under development (unstable) (2022-12-25 r83502 ucrt) -- "Unsuffered Consequences" 4165
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CHECK results for MotifDb on palomino5


To the developers/maintainers of the MotifDb package:
Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1240/2158HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MotifDb 1.41.0  (landing page)
Paul Shannon
Snapshot Date: 2022-12-28 11:00:06 -0500 (Wed, 28 Dec 2022)
git_url: https://git.bioconductor.org/packages/MotifDb
git_branch: master
git_last_commit: 113732b
git_last_commit_date: 2022-11-01 11:07:15 -0500 (Tue, 01 Nov 2022)
palomino5Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  

Summary

Package: MotifDb
Version: 1.41.0
Command: F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:MotifDb.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings MotifDb_1.41.0.tar.gz
StartedAt: 2022-12-29 01:34:31 -0500 (Thu, 29 Dec 2022)
EndedAt: 2022-12-29 01:38:27 -0500 (Thu, 29 Dec 2022)
EllapsedTime: 235.2 seconds
RetCode: 0
Status:   WARNINGS  
CheckDir: MotifDb.Rcheck
Warnings: 2

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:MotifDb.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings MotifDb_1.41.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/MotifDb.Rcheck'
* using R Under development (unstable) (2022-12-25 r83502 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
    gcc.exe (GCC) 10.4.0
    GNU Fortran (GCC) 10.4.0
* running under: Windows Server x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'MotifDb/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'MotifDb' version '1.41.0'
* 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 ... NOTE
  installed size is  7.0Mb
  sub-directories of 1Mb or more:
    extdata   3.3Mb
    scripts   3.1Mb
* 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 ... WARNING
checkRd: (5) MotifList-class.Rd:29-31: \item in \describe must have non-empty label
checkRd: (5) MotifList-class.Rd:32-34: \item in \describe must have non-empty label
checkRd: (5) MotifList-class.Rd:35-37: \item in \describe must have non-empty label
checkRd: (5) MotifList-class.Rd:38-40: \item in \describe must have non-empty label
* 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 ... 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' ... 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: 2 WARNINGs, 1 NOTE
See
  'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/MotifDb.Rcheck/00check.log'
for details.

Installation output

MotifDb.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD INSTALL MotifDb
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.17-bioc/R/library'
* installing *source* package 'MotifDb' ...
** using staged installation
** 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 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
* DONE (MotifDb)

Tests output

MotifDb.Rcheck/tests/runTests.Rout


R Under development (unstable) (2022-12-25 r83502 ucrt) -- "Unsuffered Consequences"
Copyright (C) 2022 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

Attaching package: 'BiocGenerics'

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, aperm, 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=0.000000
 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=0.000000
 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=0.000000
 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=0.000000
 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=0.000000
 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=0.000000
 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 -- Thu Dec 29 01:38:15 2022 
*********************************************** 
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 
  20.25    0.51   20.79

Example timings

MotifDb.Rcheck/MotifDb-Ex.timings

nameusersystemelapsed
MotifDb0.090.010.11
MotifList-class0.040.000.03
associateTranscriptionFactors0.050.020.07
export0.080.010.09
geneToMotif0.060.000.06
motifToGene0.030.000.03
query1.590.001.59
subset000