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CHECK report for genoset on merida1

This page was generated on 2019-04-16 11:55:32 -0400 (Tue, 16 Apr 2019).

Package 632/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
genoset 1.38.0
Peter M. Haverty
Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019)
URL: https://git.bioconductor.org/packages/genoset
Branch: RELEASE_3_8
Last Commit: a1f8bdc
Last Changed Date: 2018-10-30 11:41:47 -0400 (Tue, 30 Oct 2018)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: genoset
Version: 1.38.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:genoset.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings genoset_1.38.0.tar.gz
StartedAt: 2019-04-16 00:13:20 -0400 (Tue, 16 Apr 2019)
EndedAt: 2019-04-16 00:16:42 -0400 (Tue, 16 Apr 2019)
EllapsedTime: 201.8 seconds
RetCode: 0
Status:  OK 
CheckDir: genoset.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:genoset.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings genoset_1.38.0.tar.gz
###
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##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/genoset.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘genoset/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘genoset’ version ‘1.38.0’
* 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 ‘genoset’ 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 ... NOTE
Foreign function calls to a different package:
  .Call("RleViews_viewMaxs", ..., PACKAGE = "IRanges")
  .Call("RleViews_viewMeans", ..., PACKAGE = "IRanges")
  .Call("RleViews_viewMins", ..., PACKAGE = "IRanges")
  .Call("RleViews_viewSums", ..., PACKAGE = "IRanges")
  .Call("RleViews_viewWhichMaxs", ..., PACKAGE = "IRanges")
  .Call("RleViews_viewWhichMins", ..., PACKAGE = "IRanges")
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
* checking R code for possible problems ... OK
* 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 line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... 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 NOTE
See
  ‘/Users/biocbuild/bbs-3.8-bioc/meat/genoset.Rcheck/00check.log’
for details.



Installation output

genoset.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘genoset’ ...
** libs
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c bounds.c -o bounds.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c init.c -o init.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c rangeSummaries.c -o rangeSummaries.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/usr/local/include   -fPIC  -Wall -g -O2  -c utils.c -o utils.o
clang -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o genoset.so bounds.o init.o rangeSummaries.o utils.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/3.5/Resources/library/genoset/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
From .checkSubclasses(): subclass "GenomicPos" of class "GenomicRanges" is not local and is  not updated for new inheritance information currently; 
[where=<environment: 0x7fc0928d85e8>, where2=<environment: namespace:genoset>]
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (genoset)

Tests output

genoset.Rcheck/tests/testthat.Rout


R version 3.5.3 (2019-03-11) -- "Great Truth"
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(genoset)
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: 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: SummarizedExperiment
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

> 
> test_check("genoset")
Using mclapply for segmentation ...
Working on segmentation for sample number 1 : a1
Working on segmentation for sample number 2 : a2
Using mclapply for segmentation ...
Working on segmentation for sample number 1 : a1
Working on segmentation for sample number 2 : a2
Using mclapply for segmentation ...
Working on segmentation for sample number 2 : a2
Working on segmentation for sample number 1 : a1
Using mclapply for segmentation ...
Working on segmentation for sample number 1 : a1
Working on segmentation for sample number 2 : a2
Using mclapply for segmentation ...
Working on segmentation for sample number 2 : a2
Working on segmentation for sample number 1 : a1
══ testthat results  ═══════════════════════════════════════════════════════════
OK: 162 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
 24.082  11.709  24.790 

Example timings

genoset.Rcheck/genoset-Ex.timings

nameusersystemelapsed
GenoSet-class0.2420.0030.255
RleDataFrame-class0.4110.0490.469
RleDataFrame-views0.0840.0140.100
baf2mbaf0.0920.0140.113
boundingIndices0.0020.0000.002
calcGC000
calcGC2000
chr-methods0.0370.0160.054
chrIndices-methods0.0190.0050.023
chrInfo-methods0.0340.0060.041
chrNames-methods0.0220.0050.027
chrOrder0.0020.0000.002
gcCorrect0.0050.0010.006
genoPlot-methods0.1080.0190.134
genoPos-methods0.0490.0070.057
genome0.0210.0050.027
genomeAxis0.0520.0050.057
genoset-methods0.0480.0000.049
genoset-subset0.2100.0080.222
isGenomeOrder0.0260.0050.031
modeCenter0.0080.0010.009
pos-methods0.0210.0140.037
rangeSampleMeans0.0360.0050.041
readGenoSet0.0000.0000.001
runCBS1.4560.0121.511
segPairTable-methods0.0150.0010.016
segTable-methods1.1840.0101.229
segs2Rle1.0640.0061.084
segs2RleDataFrame1.0230.0061.043
toGenomeOrder0.0550.0050.061