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CHECK report for soGGi on celaya2

This page was generated on 2019-04-09 13:13:58 -0400 (Tue, 09 Apr 2019).

Package 1524/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
soGGi 1.15.1
Tom Carroll
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/soGGi
Branch: master
Last Commit: b64fd3b
Last Changed Date: 2019-03-27 18:59:15 -0400 (Wed, 27 Mar 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK 

Summary

Package: soGGi
Version: 1.15.1
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:soGGi.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings soGGi_1.15.1.tar.gz
StartedAt: 2019-04-09 05:39:52 -0400 (Tue, 09 Apr 2019)
EndedAt: 2019-04-09 05:46:10 -0400 (Tue, 09 Apr 2019)
EllapsedTime: 378.6 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: soGGi.Rcheck
Warnings: 1

Command output

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:soGGi.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings soGGi_1.15.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/soGGi.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘soGGi/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘soGGi’ version ‘1.15.1’
* 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 ‘soGGi’ can be installed ... WARNING
Found the following significant warnings:
  Warning: replacing previous import ‘ggplot2::Position’ by ‘BiocGenerics::Position’ when loading ‘soGGi’
See ‘/Users/biocbuild/bbs-3.9-bioc/meat/soGGi.Rcheck/00install.out’ for details.
* 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 ... NOTE
Foreign function call to a different package:
  .Call("rle_sum_any", ..., PACKAGE = "chipseq")
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
* checking R code for possible problems ... NOTE
plotCuts: warning in ggsave(myP, file = outName): partial argument
  match of 'file' to 'filename'
GetGRanges: no visible global function definition for ‘read.delim’
GetGRanges: possible error in `seqlevels<-`(RegionRanges, force = TRUE,
  value = `*tmpv*`): unused argument (force = TRUE)
findconsensusRegions : <anonymous>: no visible global function
  definition for ‘weighted.mean’
getShifts: no visible global function definition for
  ‘readGAlignmentsFromBam’
getSummitScore: no visible global function definition for
  ‘readGAlignmentsFromBam’
plotHeatmap: no visible global function definition for ‘heat.colors’
plotHeatmap: no visible global function definition for ‘layout’
plotHeatmap: no visible global function definition for ‘par’
plotRegion.ChIPprofile: no visible global function definition for
  ‘formula’
runFindSummit: no visible global function definition for
  ‘readGAlignmentsFromBam’
runRegionPlot : <anonymous>: no visible global function definition for
  ‘spline’
summitPipeline: no visible global function definition for
  ‘readGAlignmentsFromBam’
plotRegion,ChIPprofile: no visible global function definition for
  ‘formula’
Undefined global functions or variables:
  formula heat.colors layout par read.delim readGAlignmentsFromBam
  spline weighted.mean
Consider adding
  importFrom("grDevices", "heat.colors")
  importFrom("graphics", "layout", "par")
  importFrom("stats", "formula", "spline", "weighted.mean")
  importFrom("utils", "read.delim")
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
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.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 WARNING, 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.9-bioc/meat/soGGi.Rcheck/00check.log’
for details.



Installation output

soGGi.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL soGGi
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘soGGi’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Warning: replacing previous import ‘ggplot2::Position’ by ‘BiocGenerics::Position’ when loading ‘soGGi’
** help
*** installing help indices
** building package indices
** installing vignettes
   ‘soggi.Rnw’ 
** testing if installed package can be loaded from temporary location
Warning: replacing previous import ‘ggplot2::Position’ by ‘BiocGenerics::Position’ when loading ‘soGGi’
** testing if installed package can be loaded from final location
Warning: replacing previous import ‘ggplot2::Position’ by ‘BiocGenerics::Position’ when loading ‘soGGi’
** testing if installed package keeps a record of temporary installation path
* DONE (soGGi)

Tests output

soGGi.Rcheck/tests/testthat.Rout


R Under development (unstable) (2019-03-18 r76245) -- "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(soGGi)
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, colMeans, colSums, 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, rowMeans, rowSums,
    rownames, sapply, setdiff, sort, table, tapply, union, unique,
    unsplit, which, which.max, which.min

Loading required package: SummarizedExperiment
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid

Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: DelayedArray
Loading required package: matrixStats

Attaching package: 'matrixStats'

The following objects are masked from 'package:Biobase':

    anyMissing, rowMedians

Loading required package: BiocParallel

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

Warning message:
replacing previous import 'ggplot2::Position' by 'BiocGenerics::Position' when loading 'soGGi' 
> 
> test_check("soGGi")
══ testthat results  ═══════════════════════════════════════════════════════════
OK: 4 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
 17.692   1.419  19.063 

Example timings

soGGi.Rcheck/soGGi-Ex.timings

nameusersystemelapsed
ChIPprofile0.3040.0310.336
Ops0.7550.0550.810
groupByOverlaps0.6610.0360.697
manipulateObjects0.8950.0500.946
normalise1.5130.1591.658
normaliseQuantiles0.7370.1380.864
orientBy0.3540.0160.369
plotRegion0.6990.0280.728
pwmToCoverage0.0050.0120.018