Vanja Haberle
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/seqPattern |
| Branch: RELEASE_3_9 |
| Last Commit: 1858497 |
| Last Changed Date: 2019-05-02 11:53:52 -0400 (Thu, 02 May 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 12:54:51 -0400 (Wed, 16 Oct 2019).
| Package 1497/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| seqPattern 1.16.0 Vanja Haberle
| malbec2 | Linux (Ubuntu 18.04.2 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: seqPattern |
| Version: 1.16.0 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:seqPattern.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings seqPattern_1.16.0.tar.gz |
| StartedAt: 2019-10-16 06:47:19 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 06:52:19 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 300.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: seqPattern.Rcheck |
| Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:seqPattern.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings seqPattern_1.16.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/seqPattern.Rcheck’ * using R version 3.6.1 (2019-07-05) * using platform: x86_64-apple-darwin15.6.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘seqPattern/DESCRIPTION’ ... OK * this is package ‘seqPattern’ version ‘1.16.0’ * 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 ‘seqPattern’ 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' call to ‘parallel’ in package code. 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 .pattern.smoothscatter: no visible global function definition for ‘mclapply’ .pattern.smoothscatter :: no visible global function definition for ‘png’ .pattern.smoothscatter : : no visible global function definition for ‘par’ .pattern.smoothscatter : : no visible global function definition for ‘colorRampPalette’ .pattern.smoothscatter : : no visible global function definition for ‘axis’ .pattern.smoothscatter : : no visible global function definition for ‘box’ .pattern.smoothscatter : : no visible global function definition for ‘lines’ .pattern.smoothscatter : : no visible global function definition for ‘text’ .pattern.smoothscatter : : no visible global function definition for ‘abline’ .pattern.smoothscatter : : no visible global function definition for ‘dev.off’ .pattern.smoothscatter: no visible global function definition for ‘png’ .pattern.smoothscatter: no visible global function definition for ‘par’ .pattern.smoothscatter: no visible global function definition for ‘colorRampPalette’ .pattern.smoothscatter: no visible global function definition for ‘axis’ .pattern.smoothscatter: no visible global function definition for ‘box’ .pattern.smoothscatter: no visible global function definition for ‘lines’ .pattern.smoothscatter: no visible global function definition for ‘text’ .pattern.smoothscatter: no visible global function definition for ‘abline’ .pattern.smoothscatter: no visible global function definition for ‘dev.off’ .pattern.smoothscatter: no visible global function definition for ‘plot’ .plot.motif.heatmap: no visible global function definition for ‘par’ .plot.motif.heatmap: no visible global function definition for ‘image’ .plot.motif.heatmap: no visible global function definition for ‘axis’ .plot.motif.heatmap: no visible global function definition for ‘box’ .plot.motif.heatmap: no visible global function definition for ‘lines’ .plot.motif.heatmap: no visible global function definition for ‘text’ .plot.motif.heatmap: no visible global function definition for ‘abline’ .plot.windowed.average: no visible global function definition for ‘rainbow’ .plot.windowed.average: no visible global function definition for ‘plot’ .plot.windowed.average : : no visible global function definition for ‘lines’ .plot.windowed.average: no visible global function definition for ‘legend’ .plot.windowed.average: no visible global function definition for ‘abline’ .smoothScatter: no visible global function definition for ‘colorRampPalette’ .smoothScatter: no visible binding for global variable ‘blues9’ .smoothScatter: no visible binding for global variable ‘box’ .smoothScatter: no visible global function definition for ‘par’ .smoothScatter: no visible global function definition for ‘xy.coords’ .smoothScatter: no visible global function definition for ‘image’ .smoothScatter: no visible global function definition for ‘points’ plotPatternOccurrenceAverage: no visible global function definition for ‘rainbow’ getPatternOccurrenceList,DNAStringSet: no visible global function definition for ‘installed.packages’ getPatternOccurrenceList,DNAStringSet: no visible global function definition for ‘detectCores’ getPatternOccurrenceList,DNAStringSet: no visible global function definition for ‘mclapply’ plotMotifScanScores,DNAStringSet-matrix: no visible global function definition for ‘png’ plotMotifScanScores,DNAStringSet-matrix: no visible global function definition for ‘colorRampPalette’ plotMotifScanScores,DNAStringSet-matrix: no visible global function definition for ‘layout’ plotMotifScanScores,DNAStringSet-matrix: no visible global function definition for ‘par’ plotMotifScanScores,DNAStringSet-matrix: no visible global function definition for ‘plot’ plotMotifScanScores,DNAStringSet-matrix: no visible global function definition for ‘box’ plotMotifScanScores,DNAStringSet-matrix: no visible global function definition for ‘dev.off’ plotPatternDensityMap,DNAStringSet: no visible global function definition for ‘installed.packages’ plotPatternDensityMap,DNAStringSet: no visible global function definition for ‘detectCores’ plotPatternOccurrenceAverage,DNAStringSet: no visible global function definition for ‘rainbow’ Undefined global functions or variables: abline axis blues9 box colorRampPalette detectCores dev.off image installed.packages layout legend lines mclapply par plot png points rainbow text xy.coords Consider adding importFrom("grDevices", "blues9", "colorRampPalette", "dev.off", "png", "rainbow", "xy.coords") importFrom("graphics", "abline", "axis", "box", "image", "layout", "legend", "lines", "par", "plot", "points", "text") importFrom("utils", "installed.packages") 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 contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... OK * checking data for ASCII and uncompressed saves ... OK * checking sizes of PDF files under ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU or elapsed time > 5s user system elapsed plotPatternDensityMap 70.176 1.138 71.159 plotMotifDensityMap 34.240 0.498 34.927 plotMotifScanScores 22.468 0.185 22.623 * 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’ ... 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-3.9-bioc/meat/seqPattern.Rcheck/00check.log’ for details.
seqPattern.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL seqPattern ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’ * installing *source* package ‘seqPattern’ ... ** using staged installation ** R ** data ** 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 (seqPattern)
seqPattern.Rcheck/tests/runTests.Rout
R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 The R Foundation for Statistical Computing
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> BiocGenerics:::testPackage("seqPattern")
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: 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
RUNIT TEST PROTOCOL -- Wed Oct 16 06:52:12 2019
***********************************************
Number of test functions: 6
Number of errors: 0
Number of failures: 0
1 Test Suite :
seqPattern RUnit Tests - 6 test functions, 0 errors, 0 failures
Number of test functions: 6
Number of errors: 0
Number of failures: 0
>
> proc.time()
user system elapsed
6.425 0.722 7.101
seqPattern.Rcheck/seqPattern-Ex.timings
| name | user | system | elapsed | |
| getPatternOccurrenceList | 2.678 | 0.124 | 2.804 | |
| motifScanHits | 4.373 | 0.039 | 4.414 | |
| motifScanScores | 3.598 | 0.112 | 3.721 | |
| plotMotifDensityMap | 34.240 | 0.498 | 34.927 | |
| plotMotifOccurrenceAverage | 4.015 | 0.069 | 4.085 | |
| plotMotifScanScores | 22.468 | 0.185 | 22.623 | |
| plotPatternDensityMap | 70.176 | 1.138 | 71.159 | |
| plotPatternOccurrenceAverage | 3.443 | 0.185 | 3.628 | |