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CHECK report for genoset on malbec2

This page was generated on 2018-10-17 08:23:33 -0400 (Wed, 17 Oct 2018).

Package 601/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
genoset 1.36.0
Peter M. Haverty
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/genoset
Branch: RELEASE_3_7
Last Commit: 0ff7c06
Last Changed Date: 2018-04-30 10:35:17 -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: genoset
Version: 1.36.0
Command: /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:genoset.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings genoset_1.36.0.tar.gz
StartedAt: 2018-10-16 00:46:57 -0400 (Tue, 16 Oct 2018)
EndedAt: 2018-10-16 00:49:04 -0400 (Tue, 16 Oct 2018)
EllapsedTime: 127.2 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: genoset.Rcheck
Warnings: 1

Command output

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###
### Running command:
###
###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:genoset.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings genoset_1.36.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.7-bioc/meat/genoset.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 ‘genoset/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘genoset’ version ‘1.36.0’
* 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 ... WARNING
Found the following significant warnings:
  Warning: subclass "GenomicPos" of class "GenomicRanges" is not local and cannot be updated for new inheritance information; consider setClassUnion()
See ‘/home/biocbuild/bbs-3.7-bioc/meat/genoset.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 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 WARNING, 1 NOTE
See
  ‘/home/biocbuild/bbs-3.7-bioc/meat/genoset.Rcheck/00check.log’
for details.



Installation output

genoset.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD INSTALL genoset
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.7-bioc/R/library’
* installing *source* package ‘genoset’ ...
** libs
gcc -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c bounds.c -o bounds.o
gcc -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c init.c -o init.o
gcc -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c rangeSummaries.c -o rangeSummaries.o
gcc -I"/home/biocbuild/bbs-3.7-bioc/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -Wall -c utils.c -o utils.o
gcc -shared -L/home/biocbuild/bbs-3.7-bioc/R/lib -L/usr/local/lib -o genoset.so bounds.o init.o rangeSummaries.o utils.o -L/home/biocbuild/bbs-3.7-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.7-bioc/R/library/genoset/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Warning: subclass "GenomicPos" of class "GenomicRanges" is not local and cannot be updated for new inheritance information; consider setClassUnion()
** 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 3.5.1 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.

> 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 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 1 : a1
Working on segmentation for sample number 2 : a2
══ testthat results  ═══════════════════════════════════════════════════════════
OK: 162 SKIPPED: 0 FAILED: 0
> 
> proc.time()
   user  system elapsed 
 12.952   0.556  10.725 

Example timings

genoset.Rcheck/genoset-Ex.timings

nameusersystemelapsed
GenoSet-class0.1360.0000.136
RleDataFrame-class0.2320.0120.244
RleDataFrame-views0.0480.0000.047
baf2mbaf0.0560.0000.053
boundingIndices0.0000.0000.001
calcGC000
calcGC20.0000.0000.001
chr-methods0.0200.0000.018
chrIndices-methods0.0120.0040.015
chrInfo-methods0.0280.0000.028
chrNames-methods0.0200.0000.018
chrOrder0.0000.0000.001
gcCorrect0.0040.0000.003
genoPlot-methods0.0760.0080.081
genoPos-methods0.0200.0000.023
genome0.0080.0040.015
genomeAxis0.0320.0000.033
genoset-methods0.0360.0000.037
genoset-subset0.1520.0000.153
isGenomeOrder0.0160.0040.018
modeCenter0.0040.0040.007
pos-methods0.0120.0040.017
rangeSampleMeans0.0280.0000.031
readGenoSet000
runCBS1.5080.0001.509
segPairTable-methods0.0120.0000.009
segTable-methods0.9200.0000.924
segs2Rle1.2440.0001.247
segs2RleDataFrame0.8800.0000.881
toGenomeOrder0.0320.0000.033