Back to Multiple platform build/check report for BioC 3.12
A[B]CDEFGHIJKLMNOPQRSTUVWXYZ

CHECK report for bumphunter on merida1

This page was generated on 2020-08-12 11:55:34 -0400 (Wed, 12 Aug 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE bumphunter PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 208/1885HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
bumphunter 1.31.0
Rafael A. Irizarry
Snapshot Date: 2020-08-11 14:50:16 -0400 (Tue, 11 Aug 2020)
URL: https://git.bioconductor.org/packages/bumphunter
Branch: master
Last Commit: 1d0ee5b
Last Changed Date: 2020-04-27 14:32:19 -0400 (Mon, 27 Apr 2020)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
nebbiolo1 Linux (Ubuntu 20.04.1 LTS) / x86_64  OK  OK  OK 
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
merida1 macOS 10.14.6 Mojave / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: bumphunter
Version: 1.31.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:bumphunter.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings bumphunter_1.31.0.tar.gz
StartedAt: 2020-08-12 00:03:58 -0400 (Wed, 12 Aug 2020)
EndedAt: 2020-08-12 00:12:31 -0400 (Wed, 12 Aug 2020)
EllapsedTime: 513.3 seconds
RetCode: 0
Status:  OK 
CheckDir: bumphunter.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:bumphunter.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings bumphunter_1.31.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.12-bioc/meat/bumphunter.Rcheck’
* using R version 4.0.2 (2020-06-22)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘bumphunter/DESCRIPTION’ ... OK
* this is package ‘bumphunter’ version ‘1.31.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  'S4Vectors', 'IRanges', 'GenomeInfoDb', 'GenomicRanges', 'foreach',
  'iterators', 'parallel', 'locfit'
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 ‘bumphunter’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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 object imported by a ':::' call: ‘doParallel:::.options’
  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 ... NOTE
bumphunterEngine: no visible binding for global variable ‘bootstraps’
Undefined global functions or variables:
  bootstraps
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
            user system elapsed
bumphunter 3.782  1.416   2.886
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
  Running ‘test-all.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: 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.12-bioc/meat/bumphunter.Rcheck/00check.log’
for details.



Installation output

bumphunter.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘bumphunter’ ...
** using staged installation
** 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 from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (bumphunter)

Tests output

bumphunter.Rcheck/tests/runTests.Rout


R version 4.0.2 (2020-06-22) -- "Taking Off Again"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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("bumphunter") || stop("unable to load bumphunter")
Loading required package: bumphunter
Loading required package: S4Vectors
Loading required package: stats4
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.max, which.min


Attaching package: 'S4Vectors'

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

    expand.grid

Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: GenomicRanges
Loading required package: foreach
Loading required package: iterators
Loading required package: locfit
locfit 1.5-9.4 	 2020-03-24
[1] TRUE
> BiocGenerics:::testPackage("bumphunter")
[bumphunterEngine] Using a single core (backend: doSEQ, version: 1.5.0).
[bumphunterEngine] Computing coefficients.
[bumphunterEngine] Smoothing coefficients.
Loading required package: rngtools
[bumphunterEngine] Performing 500 permutations.
[bumphunterEngine] Computing marginal permutation p-values.
[bumphunterEngine] Smoothing permutation coefficients.
[bumphunterEngine] cutoff: 0.28
[bumphunterEngine] Finding regions.
[bumphunterEngine] Found 2 bumps.
[bumphunterEngine] Computing regions for each permutation.
[bumphunterEngine] Estimating p-values and FWER.
[bumphunterEngine] Using a single core (backend: doSEQ, version: 1.5.0).
[bumphunterEngine] Computing coefficients.
[bumphunterEngine] Smoothing coefficients.
[bumphunterEngine] Performing 500 permutations.
[bumphunterEngine] Computing marginal permutation p-values.
[bumphunterEngine] Smoothing permutation coefficients.
[bumphunterEngine] cutoff: 0.28
[bumphunterEngine] Finding regions.
[bumphunterEngine] Found 2 bumps.
[bumphunterEngine] Computing regions for each permutation.
[bumphunterEngine] Estimating p-values and FWER.
Loading required package: doParallel
[bumphunterEngine] Parallelizing using 2 workers/cores (backend: doParallelMC, version: 1.0.15).
[bumphunterEngine] Computing coefficients.
[bumphunterEngine] Smoothing coefficients.
[bumphunterEngine] Performing 500 permutations.
[bumphunterEngine] Computing marginal permutation p-values.
[bumphunterEngine] Smoothing permutation coefficients.
[bumphunterEngine] cutoff: 0.28
[bumphunterEngine] Finding regions.
[bumphunterEngine] Found 2 bumps.
[bumphunterEngine] Computing regions for each permutation.
[bumphunterEngine] Estimating p-values and FWER.
[bumphunterEngine] Parallelizing using 2 workers/cores (backend: doParallelSNOW, version: 1.0.15).
[bumphunterEngine] Computing coefficients.
[bumphunterEngine] Smoothing coefficients.
[bumphunterEngine] Performing 500 permutations.
[bumphunterEngine] Computing marginal permutation p-values.
[bumphunterEngine] Smoothing permutation coefficients.
[bumphunterEngine] cutoff: 0.28
[bumphunterEngine] Finding regions.
[bumphunterEngine] Found 2 bumps.
[bumphunterEngine] Computing regions for each permutation.
[bumphunterEngine] Estimating p-values and FWER.


RUNIT TEST PROTOCOL -- Wed Aug 12 00:09:27 2020 
*********************************************** 
Number of test functions: 5 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
bumphunter RUnit Tests - 5 test functions, 0 errors, 0 failures
Number of test functions: 5 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
 26.635   2.731  46.140 

bumphunter.Rcheck/tests/test-all.Rout


R version 4.0.2 (2020-06-22) -- "Taking Off Again"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (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')
> test_check('bumphunter')
Loading required package: bumphunter
Loading required package: S4Vectors
Loading required package: stats4
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.max, which.min


Attaching package: 'S4Vectors'

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

    expand.grid

Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: GenomicRanges
Loading required package: foreach
Loading required package: iterators
Loading required package: locfit
locfit 1.5-9.4 	 2020-03-24
trying URL 'ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_25/gencode.v25.annotation.gtf.gz'
Content type 'unknown' length 38817086 bytes (37.0 MB)
==================================================
══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 15 | SKIPPED: 0 | WARNINGS: 2 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
166.193   2.772 174.976 

Example timings

bumphunter.Rcheck/bumphunter-Ex.timings

nameusersystemelapsed
annotateNearest0.8420.0850.928
annotateTranscripts000
bumphunter3.7821.4162.886
clusterMaker0.0150.0030.018
dummyData0.0030.0010.004
getSegments0.0230.0050.028
locfitByCluster0.0670.0230.091
loessByCluster0.3290.0340.364
matchGenes0.0000.0000.001
regionFinder0.0330.0040.038
runmedByCluster0.0060.0010.007
smoother0.1210.1020.196