Diego Diez
| Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021) |
| git_url: https://git.bioconductor.org/packages/PWMEnrich |
| git_branch: RELEASE_3_13 |
| git_last_commit: 7ca4ee9 |
| git_last_commit_date: 2021-05-25 08:26:57 -0400 (Tue, 25 May 2021) |
| Back to Multiple platform build/check report for BioC 3.13 |
|
This page was generated on 2021-10-15 15:06:17 -0400 (Fri, 15 Oct 2021).
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To the developers/maintainers of the PWMEnrich package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/PWMEnrich.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 1465/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| PWMEnrich 4.28.1 (landing page) Diego Diez
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||||
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | | ||||||||
| Package: PWMEnrich |
| Version: 4.28.1 |
| Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:PWMEnrich.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings PWMEnrich_4.28.1.tar.gz |
| StartedAt: 2021-10-15 03:54:03 -0400 (Fri, 15 Oct 2021) |
| EndedAt: 2021-10-15 03:56:53 -0400 (Fri, 15 Oct 2021) |
| EllapsedTime: 169.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: PWMEnrich.Rcheck |
| Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:PWMEnrich.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings PWMEnrich_4.28.1.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/PWMEnrich.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 'PWMEnrich/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'PWMEnrich' version '4.28.1' * 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 'PWMEnrich' 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 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 'test-all.R' OK ** running tests for arch 'x64' ... Running 'test-all.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
PWMEnrich.Rcheck/00install.out
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###
### Running command:
###
### C:\cygwin\bin\curl.exe -O http://155.52.207.165/BBS/3.13/bioc/src/contrib/PWMEnrich_4.28.1.tar.gz && rm -rf PWMEnrich.buildbin-libdir && mkdir PWMEnrich.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=PWMEnrich.buildbin-libdir PWMEnrich_4.28.1.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL PWMEnrich_4.28.1.zip && rm PWMEnrich_4.28.1.tar.gz PWMEnrich_4.28.1.zip
###
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% Total % Received % Xferd Average Speed Time Time Time Current
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install for i386
* installing *source* package 'PWMEnrich' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'PWMEnrich'
finding HTML links ... done
DNAStringSetToList html
MotifEnrichmentReport-class html
MotifEnrichmentResults-class html
PFMtoPWM html
PWM-class html
PWMCutoffBackground-class html
PWMEmpiricalBackground-class html
PWMEnrich-package html
PWMGEVBackground-class html
PWMLognBackground-class html
PWMUnscaled html
affinitySequenceSet html
as.data.frame-MotifEnrichmentReport-method
html
cloverPvalue1seq html
cloverScore html
colMedians html
colSds html
concatenateSequences html
cutoffZscore html
cutoffZscoreSequenceSet html
divideRows html
dot-inputPFMfromMatrixOrPWM html
dot-inputParamMotifs html
dot-inputParamSequences html
dot-normalize.bg.seq html
dot-normargPfm html
dot-normargPriorParams html
empiricalPvalue html
empiricalPvalueSequenceSet html
getBackgroundFrequencies html
getPromoters html
gevPerSequence html
groupReport-MotifEnrichmentResults-method
html
keepFinite html
logNormPval html
logNormPvalSequenceSet html
makeBackground html
makePWMCutoffBackground html
makePWMEmpiricalBackground html
makePWMGEVBackground html
makePWMLognBackground html
makePWMPvalCutoffBackground html
makePWMPvalCutoffBackgroundFromSeq html
makePriors html
makeStartEndPos html
matrixShuffleZscorePerSequence html
maxAligned html
motifDiffEnrichment html
motifEcdf html
motifEnrichment html
motifIC html
motifPrAUC html
motifRankingForGroup-MotifEnrichmentResults-method
html
motifRankingForSequence-MotifEnrichmentResults-method
html
motifRecoveryAUC html
motifScores html
motifScoresBigMemory html
motifSimilarity html
operators-MotifEnrichmentReport html
operators-MotifEnrichmentResults html
operators-PWM html
operators-PWMCutoffBackground html
operators-PWMEmpiricalBackground html
operators-PWMGEVBackground html
operators-PWMLognBackground html
plot-MotifEnrichmentReport-missing-method
html
plot-PWM-missing-method html
plotMotifScores html
plotMultipleMotifs html
plotPFM html
plotTopMotifsGroup-MotifEnrichmentResults-method
html
plotTopMotifsSequence-MotifEnrichmentResults-method
html
rankingProcessAndReturn html
readJASPAR html
readMotifs html
readTRANSFAC html
registerCoresPWMEnrich html
reverseComplement-PWM-method html
scanWithPWM html
seqLogoGrid html
sequenceReport-MotifEnrichmentResults-method
html
show-MotifEnrichmentReport-method html
show-MotifEnrichmentResults-method html
show-PWM-method html
show-PWMCutoffBackground-method html
show-PWMEmpiricalBackground-method html
show-PWMGEVBackground-method html
show-PWMLognBackground-method html
subsetting-PWMCutoffBackground html
subsetting-PWMEmpiricalBackground html
subsetting-PWMGEVBackground html
subsetting-PWMLognBackground html
toPWM html
tryAllMotifAlignments html
useBigMemoryPWMEnrich html
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
install for x64
* installing *source* package 'PWMEnrich' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'PWMEnrich' as PWMEnrich_4.28.1.zip
* DONE (PWMEnrich)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'PWMEnrich' successfully unpacked and MD5 sums checked
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PWMEnrich.Rcheck/tests_i386/test-all.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.
> library(testthat)
> library(PWMEnrich)
Loading required package: grid
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: Biostrings
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: XVector
Loading required package: GenomeInfoDb
Attaching package: 'Biostrings'
The following object is masked from 'package:grid':
pattern
The following object is masked from 'package:base':
strsplit
>
> test_package("PWMEnrich")
No installed testthat tests found for PWMEnrich
>
>
> proc.time()
user system elapsed
3.28 0.26 3.53
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PWMEnrich.Rcheck/tests_x64/test-all.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.
> library(testthat)
> library(PWMEnrich)
Loading required package: grid
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: Biostrings
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: XVector
Loading required package: GenomeInfoDb
Attaching package: 'Biostrings'
The following object is masked from 'package:grid':
pattern
The following object is masked from 'package:base':
strsplit
>
> test_package("PWMEnrich")
No installed testthat tests found for PWMEnrich
>
>
> proc.time()
user system elapsed
3.53 0.23 3.73
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PWMEnrich.Rcheck/examples_i386/PWMEnrich-Ex.timings
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PWMEnrich.Rcheck/examples_x64/PWMEnrich-Ex.timings
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