Rafael A. Irizarry
| Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018) |
| URL: https://git.bioconductor.org/packages/bumphunter |
| Branch: RELEASE_3_7 |
| Last Commit: fb71b19 |
| Last Changed Date: 2018-04-30 10:35:28 -0400 (Mon, 30 Apr 2018) |
| Back to Multiple platform build/check report for BioC 3.7 |
|
This page was generated on 2018-10-17 08:51:05 -0400 (Wed, 17 Oct 2018).
| Package 175/1561 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| bumphunter 1.22.0 Rafael A. Irizarry
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | |
| Package: bumphunter |
| Version: 1.22.0 |
| 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_1.22.0.tar.gz |
| StartedAt: 2018-10-16 20:12:54 -0400 (Tue, 16 Oct 2018) |
| EndedAt: 2018-10-16 20:22:11 -0400 (Tue, 16 Oct 2018) |
| EllapsedTime: 556.9 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: bumphunter.Rcheck |
| Warnings: 0 |
############################################################################## ############################################################################## ### ### 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_1.22.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/bumphunter.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 ‘bumphunter/DESCRIPTION’ ... OK * this is package ‘bumphunter’ version ‘1.22.0’ * 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’ smarterNearest: no visible global function definition for ‘PartitioningByEnd’ Undefined global functions or variables: PartitioningByEnd 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 * 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-3.7-bioc/meat/bumphunter.Rcheck/00check.log’ for details.
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/3.5/Resources/library’ * installing *source* package ‘bumphunter’ ... ** 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 (bumphunter)
bumphunter.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("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, 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
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 1.5-9.1 2013-03-22
[1] TRUE
> BiocGenerics:::testPackage("bumphunter")
[bumphunterEngine] Using a single core (backend: doSEQ, version: 1.4.4).
[bumphunterEngine] Computing coefficients.
[bumphunterEngine] Smoothing coefficients.
Loading required package: rngtools
Loading required package: pkgmaker
Loading required package: registry
Attaching package: 'pkgmaker'
The following object is masked from 'package:S4Vectors':
new2
The following object is masked from 'package:base':
isFALSE
[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: 1.4.4).
[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: 1.0.14).
[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: 1.0.14).
[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 -- Tue Oct 16 20:17:16 2018
***********************************************
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
22.655 3.144 38.416
bumphunter.Rcheck/tests/test-all.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.
> 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, 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
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 1.5-9.1 2013-03-22
Failed with error: 'invalid package name'
trying URL 'ftp://ftp.sanger.ac.uk/pub/gencode/Gencode_human/release_25/gencode.v25.annotation.gtf.gz'
Content type 'unknown' length 38817086 bytes (37.0 MB)
==================================================
══ testthat results ═══════════════════════════════════════════════════════════
OK: 37 SKIPPED: 0 FAILED: 0
>
> proc.time()
user system elapsed
208.482 3.872 234.658
bumphunter.Rcheck/bumphunter-Ex.timings
| name | user | system | elapsed | |
| annotateNearest | 0.635 | 0.060 | 0.697 | |
| annotateTranscripts | 0.001 | 0.000 | 0.001 | |
| bumphunter | 3.158 | 1.017 | 2.369 | |
| clusterMaker | 0.013 | 0.002 | 0.014 | |
| dummyData | 0.003 | 0.001 | 0.005 | |
| getSegments | 0.016 | 0.003 | 0.019 | |
| locfitByCluster | 0.030 | 0.007 | 0.037 | |
| loessByCluster | 0.318 | 0.052 | 0.371 | |
| matchGenes | 0.002 | 0.000 | 0.002 | |
| regionFinder | 0.026 | 0.003 | 0.029 | |
| runmedByCluster | 0.005 | 0.000 | 0.005 | |
| smoother | 0.130 | 0.101 | 0.198 | |