Panagiotis Moulos
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/recoup |
| Branch: RELEASE_3_9 |
| Last Commit: f4d0498 |
| Last Changed Date: 2019-05-02 11:54:01 -0400 (Thu, 02 May 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 12:08:37 -0400 (Wed, 16 Oct 2019).
| Package 1346/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| recoup 1.12.0 Panagiotis Moulos
| 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: recoup |
| Version: 1.12.0 |
| Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:recoup.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings recoup_1.12.0.tar.gz |
| StartedAt: 2019-10-16 04:24:28 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 04:30:57 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 389.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: recoup.Rcheck |
| Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:recoup.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings recoup_1.12.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/recoup.Rcheck’ * using R version 3.6.1 (2019-07-05) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘recoup/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘recoup’ version ‘1.12.0’ * 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 for sufficient/correct file permissions ... OK * checking whether package ‘recoup’ 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 ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE baseCoverageMatrix: no visible global function definition for ‘runValue’ baseCoverageMatrix :: no visible global function definition for ‘runValue’ binCoverageMatrix : : no visible global function definition for ‘runValue’ buildAnnotationStore: no visible global function definition for ‘Seqinfo’ calcCoverage: no visible global function definition for ‘runValue’ cleanRanges: no visible global function definition for ‘seqlevels’ cleanRanges: no visible global function definition for ‘seqlevels<-’ cmclapply: no visible global function definition for ‘mclapply’ cmcmapply: no visible global function definition for ‘mcmapply’ coverageFromBam: no visible global function definition for ‘ScanBamParam’ coverageFromBam: no visible global function definition for ‘seqlevels<-’ coverageFromBigWig : : : no visible global function definition for ‘Rle’ coverageFromBigWig: no visible global function definition for ‘Rle’ coverageFromBigWig : : no visible global function definition for ‘Rle’ coverageFromRanges: no visible global function definition for ‘subjectHits’ coverageFromRanges : : : no visible global function definition for ‘Rle’ coverageFromRanges: no visible global function definition for ‘Rle’ coverageFromRangesOld: no visible global function definition for ‘subjectHits’ getEnsemblAnnotation: no visible global function definition for ‘get.transcript.utr.attributes’ getGcContent: no visible global function definition for ‘Rle’ getGcContent: no visible global function definition for ‘IRanges’ getGcContent: no visible global function definition for ‘alphabetFrequency’ getMainRnaRangesOnTheFly: no visible binding for global variable ‘f’ getUcscAnnotation: no visible global function definition for ‘warnwrap’ getUcscAnnotation: no visible global function definition for ‘dbDriver’ getUcscAnnotation: no visible global function definition for ‘dbConnect’ getUcscAnnotation: no visible global function definition for ‘dbGetQuery’ getUcscAnnotation: no visible global function definition for ‘dbDisconnect’ getUcscDbl: no visible global function definition for ‘dbDriver’ getUcscDbl: no visible global function definition for ‘dbConnect’ getUcscDbl: no visible global function definition for ‘dbWriteTable’ getUcscDbl: no visible global function definition for ‘dbDisconnect’ loadBsGenome: no visible global function definition for ‘installed.genomes’ loadBsGenome: no visible global function definition for ‘getBSgenome’ prepareBam: no visible global function definition for ‘indexBam’ prepareBam : : no visible global function definition for ‘sortBam’ prepareBam : : no visible global function definition for ‘indexBam’ preprocessRanges: no visible global function definition for ‘ScanBamParam’ preprocessRanges: no visible global function definition for ‘bamWhich<-’ readBed: no visible global function definition for ‘seqlevels’ readBed: no visible global function definition for ‘Seqinfo’ recoup: no visible binding for global variable ‘gene’ recoup: no visible binding for global variable ‘sexon’ recoup: no visible binding for global variable ‘flankedSexon’ recoup : : no visible global function definition for ‘runValue’ recoupCorrelation: no visible binding for global variable ‘Index’ recoupCorrelation: no visible binding for global variable ‘Coverage’ recoupCorrelation: no visible binding for global variable ‘Condition’ recoupCorrelation: no visible binding for global variable ‘Design’ recoupHeatmap : : no visible global function definition for ‘grid.text’ recoupProfile: no visible binding for global variable ‘Signal’ recoupProfile: no visible binding for global variable ‘Condition’ recoupProfile: no visible binding for global variable ‘Design’ reduceExons : : no visible global function definition for ‘DataFrame’ splitVector: no visible global function definition for ‘Rle’ Undefined global functions or variables: Condition Coverage DataFrame Design IRanges Index Rle ScanBamParam Seqinfo Signal alphabetFrequency bamWhich<- dbConnect dbDisconnect dbDriver dbGetQuery dbWriteTable f flankedSexon gene get.transcript.utr.attributes getBSgenome grid.text indexBam installed.genomes mclapply mcmapply runValue seqlevels seqlevels<- sexon sortBam subjectHits warnwrap * 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 files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU or elapsed time > 5s user system elapsed profileMatrix 25.756 20.369 15.400 mergeRuns 15.635 13.371 18.606 recoupPlot 6.380 7.880 8.540 recoup 6.207 7.289 8.184 simpleGetSet 4.771 7.620 6.742 sliceObj 4.956 7.377 6.911 kmeansDesign 5.016 5.636 6.433 recoupProfile 3.004 3.791 4.530 recoupCorrelation 2.729 3.640 4.239 recoupHeatmap 2.457 3.535 3.868 coverageRef 4.625 0.468 5.095 getAnnotation 1.115 0.032 5.731 * 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: 1 NOTE See ‘/home/biocbuild/bbs-3.9-bioc/meat/recoup.Rcheck/00check.log’ for details.
recoup.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL recoup ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’ * installing *source* package ‘recoup’ ... ** using staged installation ** R ** data *** moving datasets to lazyload DB ** 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 (recoup)
recoup.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
Platform: x86_64-pc-linux-gnu (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("recoup")
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
Attaching package: 'S4Vectors'
The following object is masked from 'package:base':
expand.grid
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Attaching package: 'matrixStats'
The following objects are masked from 'package:Biobase':
anyMissing, rowMedians
Attaching package: 'DelayedArray'
The following objects are masked from 'package:matrixStats':
colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges
The following objects are masked from 'package:base':
aperm, apply, rowsum
Attaching package: 'Biostrings'
The following object is masked from 'package:DelayedArray':
type
The following object is masked from 'package:base':
strsplit
========================================
ComplexHeatmap version 2.0.0
Bioconductor page: http://bioconductor.org/packages/ComplexHeatmap/
Github page: https://github.com/jokergoo/ComplexHeatmap
Documentation: http://jokergoo.github.io/ComplexHeatmap-reference
If you use it in published research, please cite:
Gu, Z. Complex heatmaps reveal patterns and correlations in multidimensional
genomic data. Bioinformatics 2016.
========================================
Getting main ranges for measurements
measurement type: chipseq
genomic region type: tss
Calculating requested regions coverage for WT H4K20me1
processing chr12
Calculating requested regions coverage for Set8KO H4K20me1
processing chr12
Calculating profile for WT H4K20me1
Calculating profile for Set8KO H4K20me1
Constructing genomic coverage profile curve(s)
The resolution of the requested profiles will be lowered to avoid
increased computation time and/or storage space for heatmap profiles...
Calculating tss profile for WT H4K20me1
Calculating tss profile for Set8KO H4K20me1
Constructing genomic coverage heatmap(s)
Constructing coverage correlation profile curve(s)
dev.new(): using pdf(file="Rplots1.pdf")
dev.new(): using pdf(file="Rplots2.pdf")
Getting main ranges for measurements
measurement type: chipseq
genomic region type: genebody
Calculating requested regions coverage for WT H4K20me1
processing chr12
Calculating requested regions coverage for Set8KO H4K20me1
processing chr12
Calculating profile for WT H4K20me1
center
upstream
downstream
Calculating profile for Set8KO H4K20me1
center
upstream
downstream
Constructing genomic coverage profile curve(s)
Using provided design to facet the coverage profiles
Constructing genomic coverage heatmap(s)
Using provided design to facet the coverage profiles
Constructing coverage correlation profile curve(s)
Using provided design to facet the coverage profiles
dev.new(): using pdf(file="Rplots3.pdf")
dev.new(): using pdf(file="Rplots4.pdf")
dev.new(): using pdf(file="Rplots5.pdf")
RUNIT TEST PROTOCOL -- Wed Oct 16 04:30:53 2019
***********************************************
Number of test functions: 1
Number of errors: 0
Number of failures: 0
1 Test Suite :
recoup RUnit Tests - 1 test function, 0 errors, 0 failures
Number of test functions: 1
Number of errors: 0
Number of failures: 0
Warning messages:
1: `panel.margin` is deprecated. Please use `panel.spacing` property instead
2: `panel.margin` is deprecated. Please use `panel.spacing` property instead
>
> proc.time()
user system elapsed
42.805 25.820 40.825
recoup.Rcheck/recoup-Ex.timings
| name | user | system | elapsed | |
| buildAnnotationStore | 0.001 | 0.000 | 0.000 | |
| calcCoverage | 3.240 | 0.303 | 3.556 | |
| coverageRef | 4.625 | 0.468 | 5.095 | |
| coverageRnaRef | 2.554 | 0.427 | 2.978 | |
| getAnnotation | 1.115 | 0.032 | 5.731 | |
| getBiotypes | 0.000 | 0.000 | 0.001 | |
| kmeansDesign | 5.016 | 5.636 | 6.433 | |
| mergeRuns | 15.635 | 13.371 | 18.606 | |
| preprocessRanges | 0.453 | 0.072 | 0.566 | |
| profileMatrix | 25.756 | 20.369 | 15.400 | |
| recoup | 6.207 | 7.289 | 8.184 | |
| recoupCorrelation | 2.729 | 3.640 | 4.239 | |
| recoupHeatmap | 2.457 | 3.535 | 3.868 | |
| recoupPlot | 6.38 | 7.88 | 8.54 | |
| recoupProfile | 3.004 | 3.791 | 4.530 | |
| removeData | 0.026 | 0.000 | 0.025 | |
| simpleGetSet | 4.771 | 7.620 | 6.742 | |
| sliceObj | 4.956 | 7.377 | 6.911 | |