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CHECK report for HelloRanges on malbec2

This page was generated on 2018-10-17 08:29:34 -0400 (Wed, 17 Oct 2018).

Package 678/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
HelloRanges 1.6.0
Michael Lawrence
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/HelloRanges
Branch: RELEASE_3_7
Last Commit: 94962db
Last Changed Date: 2018-04-30 10:35:44 -0400 (Mon, 30 Apr 2018)
malbec2 Linux (Ubuntu 16.04.1 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
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: HelloRanges
Version: 1.6.0
Command: /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:HelloRanges.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings HelloRanges_1.6.0.tar.gz
StartedAt: 2018-10-16 01:07:46 -0400 (Tue, 16 Oct 2018)
EndedAt: 2018-10-16 01:11:31 -0400 (Tue, 16 Oct 2018)
EllapsedTime: 225.0 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: HelloRanges.Rcheck
Warnings: 1

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:HelloRanges.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings HelloRanges_1.6.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.7-bioc/meat/HelloRanges.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘HelloRanges/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘HelloRanges’ version ‘1.6.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  ‘BiocGenerics’ ‘S4Vectors’ ‘IRanges’ ‘GenomicRanges’ ‘Biostrings’
  ‘BSgenome’ ‘GenomicFeatures’ ‘VariantAnnotation’ ‘Rsamtools’
  ‘GenomicAlignments’ ‘rtracklayer’ ‘GenomeInfoDb’
  ‘SummarizedExperiment’
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 ‘HelloRanges’ 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
Packages in Depends field not imported from:
  ‘BSgenome’ ‘GenomicAlignments’ ‘GenomicFeatures’ ‘VariantAnnotation’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Unexported objects imported by ':::' calls:
  ‘BiocGenerics:::testPackage’ ‘IRanges:::subgrouping’
  ‘S4Vectors:::make_zero_col_DataFrame’
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... WARNING
Missing link or links in documentation object 'bedtools_shift.Rd':
  ‘[GenomicRanges]{shift}’

See section 'Cross-references' in the 'Writing R Extensions' manual.

* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘HelloRanges_unit_tests.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
  ‘/home/biocbuild/bbs-3.7-bioc/meat/HelloRanges.Rcheck/00check.log’
for details.



Installation output

HelloRanges.Rcheck/00install.out

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### Running command:
###
###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD INSTALL HelloRanges
###
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* installing to library ‘/home/biocbuild/bbs-3.7-bioc/R/library’
* installing *source* package ‘HelloRanges’ ...
** R
** 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
* DONE (HelloRanges)

Tests output

HelloRanges.Rcheck/tests/HelloRanges_unit_tests.Rout


R version 3.5.1 Patched (2018-07-12 r74967) -- "Feather Spray"
Copyright (C) 2018 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.

> require("HelloRanges") || stop("unable to load HelloRanges package")
Loading required package: HelloRanges
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, 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: GenomicRanges
Loading required package: GenomeInfoDb
Loading required package: Biostrings
Loading required package: XVector

Attaching package: 'Biostrings'

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

    strsplit

Loading required package: BSgenome
Loading required package: rtracklayer
Loading required package: GenomicFeatures
Loading required package: AnnotationDbi
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: VariantAnnotation
Loading required package: SummarizedExperiment
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 object is masked from 'package:Biostrings':

    type

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

    aperm, apply

Loading required package: Rsamtools

Attaching package: 'VariantAnnotation'

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

    tabulate

Loading required package: GenomicAlignments
[1] TRUE
> HelloRanges:::.test()


RUNIT TEST PROTOCOL -- Tue Oct 16 01:11:27 2018 
*********************************************** 
Number of test functions: 17 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
HelloRanges RUnit Tests - 17 test functions, 0 errors, 0 failures
Number of test functions: 17 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
 39.608   0.388  40.379 

Example timings

HelloRanges.Rcheck/HelloRanges-Ex.timings

nameusersystemelapsed
bedtools_closest0.2560.0000.259
bedtools_complement0.0160.0000.016
bedtools_coverage0.0960.0160.114
bedtools_flank0.0840.0040.086
bedtools_genomecov0.1320.0080.139
bedtools_getfasta0.0440.0000.045
bedtools_groupby0.0520.0000.053
bedtools_intersect0.4120.0280.441
bedtools_jaccard0.1120.0000.115
bedtools_makewindows0.0760.0000.076
bedtools_map0.1440.0000.147
bedtools_merge0.1600.0000.161
bedtools_multiinter0.0640.0000.064
bedtools_nuc0.0440.0000.044
bedtools_shift0.0520.0000.054
bedtools_slop0.0520.0000.052
bedtools_subtract0.7480.0000.750
bedtools_unionbedg0.0400.0040.044
distmode0.0040.0000.002