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CHECK report for genoset on celaya2

This page was generated on 2020-01-16 13:33:27 -0500 (Thu, 16 Jan 2020).

Package 687/1818HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
genoset 1.43.0
Peter M. Haverty
Snapshot Date: 2020-01-15 16:46:30 -0500 (Wed, 15 Jan 2020)
URL: https://git.bioconductor.org/packages/genoset
Branch: master
Last Commit: df8eb30
Last Changed Date: 2019-10-29 13:35:27 -0500 (Tue, 29 Oct 2019)
malbec2 Linux (Ubuntu 18.04.3 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

Summary

Package: genoset
Version: 1.43.0
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_1.43.0.tar.gz
StartedAt: 2020-01-16 04:51:51 -0500 (Thu, 16 Jan 2020)
EndedAt: 2020-01-16 04:57:03 -0500 (Thu, 16 Jan 2020)
EllapsedTime: 311.4 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: genoset.Rcheck
Warnings: 1

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_1.43.0.tar.gz
###
##############################################################################
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/genoset.Rcheck’
* using R Under development (unstable) (2019-12-14 r77572)
* 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 ‘1.43.0’
* 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 ... WARNING
Undocumented code objects:
  ‘lengths’
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 ... NOTE
Note: information on .o files is not available
* 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-3.11-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/4.0/Resources/library’
* installing *source* package ‘genoset’ ...
** using staged installation
** libs
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC  -Wall -g -O2  -c bounds.c -o bounds.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC  -Wall -g -O2  -c init.c -o init.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -I/usr/local/include   -fPIC  -Wall -g -O2  -c rangeSummaries.c -o rangeSummaries.o
clang -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk -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/4.0/Resources/library/00LOCK-genoset/00new/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: 0x7fc494028e78>, where2=<environment: namespace:genoset>]
From .checkSubclasses(): subclass "UnstitchedGPos" of class "GenomicRanges" is not local and is not updated for new inheritance information currently; 
[where=<environment: 0x7fc494028e78>, where2=<environment: namespace:genoset>]
From .checkSubclasses(): subclass "StitchedGPos" of class "GenomicRanges" is not local and is not updated for new inheritance information currently; 
[where=<environment: 0x7fc494028e78>, where2=<environment: namespace:genoset>]
From .checkSubclasses(): subclass "UnstitchedGPos" of class "GenomicRanges" is not local and is not updated for new inheritance information currently; 
[where=<environment: 0x7fc494028e78>, where2=<environment: namespace:genoset>]
From .checkSubclasses(): subclass "StitchedGPos" of class "GenomicRanges" is not local and is not updated for new inheritance information currently; 
[where=<environment: 0x7fc494028e78>, where2=<environment: namespace:genoset>]
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (genoset)

Tests output

genoset.Rcheck/tests/testthat.Rout


R Under development (unstable) (2019-12-14 r77572) -- "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(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, 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

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, rowsum

> 
> test_check("genoset")
Working on segmentation for sample number 1 : a1
Working on segmentation for sample number 2 : a2
Working on segmentation for sample number 1 : a1
Working on segmentation for sample number 2 : a2
Working on segmentation for sample number 1 : a1
Working on segmentation for sample number 2 : a2
Working on segmentation for sample number 1 : a1
Working on segmentation for sample number 2 : a2
Working on segmentation for sample number 1 : a1
Working on segmentation for sample number 2 : a2
══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 162 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
 21.960   1.339  23.278 

Example timings

genoset.Rcheck/genoset-Ex.timings

nameusersystemelapsed
GenoSet-class0.1700.0020.172
RleDataFrame-class0.7320.0700.802
RleDataFrame-views0.1020.0030.105
baf2mbaf0.1210.0060.128
boundingIndices0.0020.0010.002
calcGC0.0000.0000.001
calcGC2000
chr-methods0.0430.0270.071
chrIndices-methods0.0210.0060.027
chrInfo-methods0.0630.0080.071
chrNames-methods0.0290.0050.034
chrOrder0.0010.0000.001
gcCorrect0.0030.0010.005
genoPlot-methods0.1790.0100.189
genoPos-methods0.0760.0050.081
genome0.0240.0080.032
genomeAxis0.0780.0070.085
genoset-methods0.1010.0000.101
genoset-subset0.4140.0170.432
isGenomeOrder0.0290.0060.035
modeCenter0.0090.0020.011
pos-methods0.0340.0270.062
rangeSampleMeans0.0630.0090.072
readGenoSet000
runCBS1.3440.0111.356
segPairTable-methods0.0250.0010.026
segTable-methods1.3510.0181.414
segs2Rle1.2630.0131.276
segs2RleDataFrame1.2170.0091.227
toGenomeOrder0.0880.0060.094