Vanja Haberle
| Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018) |
| URL: https://git.bioconductor.org/packages/seqPattern |
| Branch: RELEASE_3_6 |
| Last Commit: aec9d48 |
| Last Changed Date: 2017-10-30 12:40:48 -0400 (Mon, 30 Oct 2017) |
| Back to Multiple platform build/check report for BioC 3.6 |
|
This page was generated on 2018-04-12 13:40:11 -0400 (Thu, 12 Apr 2018).
| Package 1278/1472 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| seqPattern 1.10.0 Vanja Haberle
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | | ||||||
| veracruz1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | |
| Package: seqPattern |
| Version: 1.10.0 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings seqPattern_1.10.0.tar.gz |
| StartedAt: 2018-04-12 09:29:51 -0400 (Thu, 12 Apr 2018) |
| EndedAt: 2018-04-12 09:33:00 -0400 (Thu, 12 Apr 2018) |
| EllapsedTime: 189.0 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: seqPattern.Rcheck |
| Warnings: 0 |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings seqPattern_1.10.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/seqPattern.Rcheck’
* using R version 3.4.4 (2018-03-15)
* 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 ‘1.10.0’
* 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 : <anonymous>: no visible global function
definition for ‘png’
.pattern.smoothscatter : <anonymous>: no visible global function
definition for ‘par’
.pattern.smoothscatter : <anonymous>: no visible global function
definition for ‘colorRampPalette’
.pattern.smoothscatter : <anonymous>: no visible global function
definition for ‘axis’
.pattern.smoothscatter : <anonymous>: no visible global function
definition for ‘box’
.pattern.smoothscatter : <anonymous>: no visible global function
definition for ‘lines’
.pattern.smoothscatter : <anonymous>: no visible global function
definition for ‘text’
.pattern.smoothscatter : <anonymous>: no visible global function
definition for ‘abline’
.pattern.smoothscatter : <anonymous>: 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 : <anonymous>: 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
plotPatternDensityMap 47.937 0.519 49.206
plotMotifDensityMap 20.080 0.189 20.597
plotMotifScanScores 12.898 0.074 13.149
* 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-3.6-bioc/meat/seqPattern.Rcheck/00check.log’
for details.
seqPattern.Rcheck/00install.out
* installing *source* package ‘seqPattern’ ... ** R ** data ** inst ** preparing package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded * DONE (seqPattern)
seqPattern.Rcheck/tests/runTests.Rout
R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 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.
> 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, cbind, colMeans, colSums, colnames, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
pmin, pmin.int, rank, rbind, rowMeans, rowSums, 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 -- Thu Apr 12 09:32:55 2018
***********************************************
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
5.258 0.204 5.519
seqPattern.Rcheck/seqPattern-Ex.timings
| name | user | system | elapsed | |
| getPatternOccurrenceList | 2.163 | 0.066 | 2.254 | |
| motifScanHits | 2.751 | 0.029 | 2.823 | |
| motifScanScores | 1.888 | 0.043 | 1.960 | |
| plotMotifDensityMap | 20.080 | 0.189 | 20.597 | |
| plotMotifOccurrenceAverage | 2.421 | 0.029 | 2.497 | |
| plotMotifScanScores | 12.898 | 0.074 | 13.149 | |
| plotPatternDensityMap | 47.937 | 0.519 | 49.206 | |
| plotPatternOccurrenceAverage | 2.226 | 0.066 | 2.316 | |