Robert Stojnic
| Snapshot Date: 2020-01-15 16:46:30 -0500 (Wed, 15 Jan 2020) |
| URL: https://git.bioconductor.org/packages/PWMEnrich |
| Branch: master |
| Last Commit: 324f5a9 |
| Last Changed Date: 2019-10-29 13:36:15 -0500 (Tue, 29 Oct 2019) |
| Back to Multiple platform build/check report for BioC 3.11 |
|
This page was generated on 2020-01-16 13:35:06 -0500 (Thu, 16 Jan 2020).
| Package 1332/1818 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| PWMEnrich 4.23.0 Robert Stojnic
| malbec2 | Linux (Ubuntu 18.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | |
| Package: PWMEnrich |
| Version: 4.23.0 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:PWMEnrich.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings PWMEnrich_4.23.0.tar.gz |
| StartedAt: 2020-01-16 07:48:45 -0500 (Thu, 16 Jan 2020) |
| EndedAt: 2020-01-16 07:51:53 -0500 (Thu, 16 Jan 2020) |
| EllapsedTime: 188.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: PWMEnrich.Rcheck |
| Warnings: 0 |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:PWMEnrich.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings PWMEnrich_4.23.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/PWMEnrich.Rcheck’
* using R Under development (unstable) (2019-12-14 r77572)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘PWMEnrich/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘PWMEnrich’ version ‘4.23.0’
* 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 for sufficient/correct file permissions ... 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
* 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 ... NOTE
'library' or 'require' calls in package code:
‘PWMEnrich.Dmelanogaster.background’ ‘PWMEnrich.Hsapiens.background’
‘PWMEnrich.Mmusculus.background’ ‘parallel’
Please use :: or requireNamespace() instead.
See section 'Suggested packages' in the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
colMedians: no visible binding for global variable ‘median’
getPromoters: no visible global function definition for
‘providerVersion’
getPromoters: no visible global function definition for ‘data’
gevPerSequence: no visible global function definition for ‘predict.lm’
logNormPval: no visible global function definition for ‘plnorm’
makePWMGEVBackground : <anonymous>: no visible global function
definition for ‘lm’
makePWMLognBackground : dlnorm.lcen: no visible global function
definition for ‘dlnorm’
makePWMLognBackground : dlnorm.lcen: no visible global function
definition for ‘plnorm’
makePWMLognBackground: no visible global function definition for
‘quantile’
makePWMLognBackground: no visible global function definition for
‘median’
makePWMLognBackground: no visible global function definition for
‘optimize’
makePWMPvalCutoffBackground: no visible global function definition for
‘quantile’
makePWMPvalCutoffBackground: no visible global function definition for
‘ecdf’
makePWMPvalCutoffBackgroundFromSeq: no visible global function
definition for ‘na.omit’
makePWMPvalCutoffBackgroundFromSeq: no visible global function
definition for ‘quantile’
makePWMPvalCutoffBackgroundFromSeq: no visible global function
definition for ‘ecdf’
motifEcdf : <anonymous>: no visible global function definition for
‘na.omit’
motifEcdf: no visible binding for global variable ‘ecdf’
motifEnrichment: no visible binding for global variable ‘qlnorm’
motifEnrichment : <anonymous>: no visible global function definition
for ‘pchisq’
motifScores: no visible global function definition for ‘mclapply’
motifScoresBigMemory: no visible global function definition for
‘mclapply’
plotMotifScores: no visible global function definition for ‘palette’
plotMotifScores: no visible global function definition for ‘col2rgb’
plotMotifScores: no visible global function definition for ‘rgb’
plotMotifScores: no visible global function definition for ‘par’
plotMotifScores: no visible global function definition for ‘lines’
plotMotifScores: no visible global function definition for ‘polygon’
plotMotifScores: no visible global function definition for ‘rect’
plotMotifScores: no visible global function definition for ‘text’
registerCoresPWMEnrich: no visible global function definition for
‘detectCores’
tryAllMotifAlignments : <anonymous>: no visible global function
definition for ‘cor’
Undefined global functions or variables:
col2rgb cor data detectCores dlnorm ecdf lines lm mclapply median
na.omit optimize palette par pchisq plnorm polygon predict.lm
providerVersion qlnorm quantile rect rgb text
Consider adding
importFrom("grDevices", "col2rgb", "palette", "rgb")
importFrom("graphics", "lines", "par", "polygon", "rect", "text")
importFrom("stats", "cor", "dlnorm", "ecdf", "lm", "median", "na.omit",
"optimize", "pchisq", "plnorm", "predict.lm", "qlnorm",
"quantile")
importFrom("utils", "data")
to your NAMESPACE file.
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
motifScores 7.160 0.096 7.258
motifEnrichment 6.491 0.024 6.516
PFMtoPWM 3.990 1.158 5.210
sequenceReport-commaMotifEnrichmentResults-method 4.916 0.166 5.090
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
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: 2 NOTEs
See
‘/Users/biocbuild/bbs-3.11-bioc/meat/PWMEnrich.Rcheck/00check.log’
for details.
PWMEnrich.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL PWMEnrich ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’ * installing *source* package ‘PWMEnrich’ ... ** 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 ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (PWMEnrich)
PWMEnrich.Rcheck/tests/test-all.Rout
R Under development (unstable) (2019-12-14 r77572) -- "Unsuffered Consequences"
Copyright (C) 2019 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.
> 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, which.max, which.min
Loading required package: Biostrings
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: XVector
Attaching package: 'Biostrings'
The following object is masked from 'package:base':
strsplit
>
> test_package("PWMEnrich")
Calculating motif enrichment scores ...
Calculating motif enrichment scores ...
NOTE: Using the 'default' algorithm to infer background parameters,
appropriate for all organisms except human.
Calculating motif enrichment scores ...
Calculating motif enrichment scores ...
Calculating motif enrichment scores ...
Calculating motif enrichment scores ...
Calculating motif enrichment scores ...
Calculating motif enrichment scores ...
Calculating motif enrichment scores ...
Calculating motif enrichment scores ...
NOTE: Using the 'default' algorithm to infer background parameters,
appropriate for all organisms except human.
Calculating motif enrichment scores ...
Calculating motif enrichment scores ...
══ testthat results ═══════════════════════════════════════════════════════════
[ OK: 48 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
Warning message:
Placing tests in `inst/tests` is deprecated. Please use `tests/testthat` instead
>
>
> proc.time()
user system elapsed
8.164 0.726 8.844
PWMEnrich.Rcheck/PWMEnrich-Ex.timings
| name | user | system | elapsed | |
| PFMtoPWM | 3.990 | 1.158 | 5.210 | |
| PWMUnscaled | 0.369 | 0.020 | 0.388 | |
| getBackgroundFrequencies | 0.000 | 0.001 | 0.001 | |
| groupReport-commaMotifEnrichmentResults-method | 4.153 | 0.127 | 4.282 | |
| makeBackground | 0.006 | 0.002 | 0.009 | |
| makePWMCutoffBackground | 0 | 0 | 0 | |
| makePWMEmpiricalBackground | 0 | 0 | 0 | |
| makePWMGEVBackground | 0.001 | 0.001 | 0.000 | |
| makePWMLognBackground | 0.000 | 0.000 | 0.001 | |
| makePWMPvalCutoffBackground | 0.001 | 0.000 | 0.001 | |
| makePWMPvalCutoffBackgroundFromSeq | 0.000 | 0.000 | 0.001 | |
| makePriors | 0.002 | 0.000 | 0.003 | |
| motifDiffEnrichment | 4.261 | 0.037 | 4.299 | |
| motifEnrichment | 6.491 | 0.024 | 6.516 | |
| motifIC | 0.068 | 0.009 | 0.080 | |
| motifRankingForGroup-commaMotifEnrichmentResults-method | 3.306 | 0.022 | 3.328 | |
| motifRankingForSequence-commaMotifEnrichmentResults-method | 3.532 | 0.074 | 3.606 | |
| motifScores | 7.160 | 0.096 | 7.258 | |
| motifSimilarity | 0.117 | 0.004 | 0.122 | |
| plot | 0.268 | 0.011 | 0.282 | |
| plotMotifScores | 0.109 | 0.007 | 0.116 | |
| plotTopMotifsGroup-commaMotifEnrichmentResults-method | 3.608 | 0.031 | 3.641 | |
| plotTopMotifsSequence-commaMotifEnrichmentResults-method | 3.835 | 0.048 | 3.889 | |
| readMotifs | 0.199 | 0.046 | 0.246 | |
| registerCoresPWMEnrich | 0.000 | 0.000 | 0.001 | |
| reverseComplement | 0.031 | 0.004 | 0.034 | |
| scanWithPWM | 0.065 | 0.004 | 0.070 | |
| sequenceReport-commaMotifEnrichmentResults-method | 4.916 | 0.166 | 5.090 | |
| toPWM | 3.888 | 0.950 | 4.837 | |
| useBigMemoryPWMEnrich | 0.000 | 0.001 | 0.000 | |