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CHECK report for recoup on malbec2

This page was generated on 2019-10-16 12:08:37 -0400 (Wed, 16 Oct 2019).

Package 1346/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
recoup 1.12.0
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)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

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

Command output

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### 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
###
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##############################################################################


* 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.



Installation output

recoup.Rcheck/00install.out

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###
### 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)

Tests output

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 

Example timings

recoup.Rcheck/recoup-Ex.timings

nameusersystemelapsed
buildAnnotationStore0.0010.0000.000
calcCoverage3.2400.3033.556
coverageRef4.6250.4685.095
coverageRnaRef2.5540.4272.978
getAnnotation1.1150.0325.731
getBiotypes0.0000.0000.001
kmeansDesign5.0165.6366.433
mergeRuns15.63513.37118.606
preprocessRanges0.4530.0720.566
profileMatrix25.75620.36915.400
recoup6.2077.2898.184
recoupCorrelation2.7293.6404.239
recoupHeatmap2.4573.5353.868
recoupPlot6.387.888.54
recoupProfile3.0043.7914.530
removeData0.0260.0000.025
simpleGetSet4.7717.6206.742
sliceObj4.9567.3776.911