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CHECK report for bsseq on merida2

This page was generated on 2018-10-17 08:50:37 -0400 (Wed, 17 Oct 2018).

Package 170/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
bsseq 1.16.1
Kasper Daniel Hansen
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/bsseq
Branch: RELEASE_3_7
Last Commit: 8494740
Last Changed Date: 2018-06-12 23:43:44 -0400 (Tue, 12 Jun 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: bsseq
Version: 1.16.1
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:bsseq.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings bsseq_1.16.1.tar.gz
StartedAt: 2018-10-16 20:12:28 -0400 (Tue, 16 Oct 2018)
EndedAt: 2018-10-16 20:17:35 -0400 (Tue, 16 Oct 2018)
EllapsedTime: 306.8 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: bsseq.Rcheck
Warnings: 1

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:bsseq.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings bsseq_1.16.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/bsseq.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘bsseq/DESCRIPTION’ ... OK
* this is package ‘bsseq’ version ‘1.16.1’
* 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 ‘bsseq’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  8.6Mb
  sub-directories of 1Mb or more:
    data   7.7Mb
* 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
Unexported objects imported by ':::' calls:
  ‘DelayedArray:::RealizationSink’
  ‘DelayedArray:::get_max_block_length’
  ‘DelayedArray:::get_spacings_for_linear_capped_length_blocks’
  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 ... OK
* checking for missing documentation entries ... WARNING
Undocumented S4 methods:
  generic 'dimnames' and siglist 'arrayRealizationSink'
All user-level objects in a package (including S4 classes and methods)
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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                user system elapsed
getMeth       13.734  2.715  16.548
getCoverage   12.163  0.829  13.096
BSmooth.tstat  7.439  1.227   8.742
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.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-3.7-bioc/meat/bsseq.Rcheck/00check.log’
for details.



Installation output

bsseq.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL bsseq
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘bsseq’ ...
** R
** data
*** moving datasets to lazyload DB
** 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 (bsseq)

Tests output

bsseq.Rcheck/tests/runTests.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-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.

> require("bsseq") || stop("unable to load bsseq")
Loading required package: bsseq
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

[1] TRUE
> BiocGenerics:::testPackage("bsseq")
Loading required package: rhdf5


RUNIT TEST PROTOCOL -- Tue Oct 16 20:17:29 2018 
*********************************************** 
Number of test functions: 17 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
bsseq 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 
 54.895   1.577  56.913 

Example timings

bsseq.Rcheck/bsseq-Ex.timings

nameusersystemelapsed
BS.chr222.7270.2653.004
BSmooth0.0020.0000.002
BSmooth.fstat0.0010.0000.001
BSmooth.tstat7.4391.2278.742
BSseq-class1.4440.0551.510
BSseq1.1480.0811.241
computeStat0.0020.0010.001
data.frame2GRanges0.0250.0000.025
dmrFinder1.8880.3502.247
fisherTests0.8980.0370.941
getCoverage12.163 0.82913.096
getMeth13.734 2.71516.548
getStats0.4840.1560.644
goodnessOfFit3.3790.7354.156
hasGRanges-class0.0040.0010.004
read.bismark0.7150.0380.755
read.umtab0.0020.0000.002
smoothSds0.0010.0010.002