Paul Shannon
| Snapshot Date: 2024-11-24 13:40 -0500 (Sun, 24 Nov 2024) |
| git_url: https://git.bioconductor.org/packages/MotifDb |
| git_branch: devel |
| git_last_commit: c4cd303 |
| git_last_commit_date: 2024-10-29 09:42:14 -0500 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2024-11-25 11:38 -0500 (Mon, 25 Nov 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" | 4748 |
| palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4459 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4349 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 1308/2272 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| MotifDb 1.49.0 (landing page) Paul Shannon
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
|
To the developers/maintainers of the MotifDb package: - 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 Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: MotifDb |
| Version: 1.49.0 |
| Command: E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:MotifDb.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings MotifDb_1.49.0.tar.gz |
| StartedAt: 2024-11-25 02:44:02 -0500 (Mon, 25 Nov 2024) |
| EndedAt: 2024-11-25 02:50:12 -0500 (Mon, 25 Nov 2024) |
| EllapsedTime: 369.6 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: MotifDb.Rcheck |
| Warnings: 2 |
##############################################################################
##############################################################################
###
### Running command:
###
### E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:MotifDb.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings MotifDb_1.49.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'E:/biocbuild/bbs-3.21-bioc/meat/MotifDb.Rcheck'
* using R Under development (unstable) (2024-10-26 r87273 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
gcc.exe (GCC) 13.2.0
GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 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 '1.49.0'
* 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 ... INFO
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 code 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 whether startup messages can be suppressed ... NOTE
See system.file("LICENSE", package="MotifDb") for use restrictions.
It looks like this package (or a package it requires) has a startup
message which cannot be suppressed: see ?packageStartupMessage.
* 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 ... 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
'E:/biocbuild/bbs-3.21-bioc/meat/MotifDb.Rcheck/00check.log'
for details.
MotifDb.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD INSTALL MotifDb
###
##############################################################################
##############################################################################
* installing to library 'E:/biocbuild/bbs-3.21-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)
MotifDb.Rcheck/tests/runTests.Rout
R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64
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: generics
Attaching package: 'generics'
The following objects are masked from 'package:base':
as.difftime, as.factor, as.ordered, intersect, is.element, setdiff,
setequal, union
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, is.unsorted, lapply,
mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
rank, rbind, rownames, sapply, saveRDS, table, tapply, unique,
unsplit, which.max, which.min
Loading required package: S4Vectors
Loading required package: stats4
Attaching package: 'S4Vectors'
The following object is masked from 'package:utils':
findMatches
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 -- Mon Nov 25 02:50:02 2024
***********************************************
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
29.12 0.87 30.31
MotifDb.Rcheck/MotifDb-Ex.timings
| name | user | system | elapsed | |
| MotifDb | 0.17 | 0.02 | 0.19 | |
| MotifList-class | 0 | 0 | 0 | |
| associateTranscriptionFactors | 0.09 | 0.00 | 0.10 | |
| export | 0.06 | 0.01 | 0.07 | |
| geneToMotif | 0.08 | 0.00 | 0.08 | |
| motifToGene | 0.03 | 0.00 | 0.03 | |
| query | 1.33 | 0.02 | 1.34 | |
| subset | 0 | 0 | 0 | |