Rafael A. Irizarry
| Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019) |
| URL: https://git.bioconductor.org/packages/bumphunter |
| Branch: RELEASE_3_8 |
| Last Commit: 29b8740 |
| Last Changed Date: 2018-11-30 13:46:10 -0400 (Fri, 30 Nov 2018) |
| Back to Multiple platform build/check report for BioC 3.8 |
|
This page was generated on 2019-04-16 11:56:39 -0400 (Tue, 16 Apr 2019).
| Package 186/1649 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| bumphunter 1.24.5 Rafael A. Irizarry
| malbec1 | Linux (Ubuntu 16.04.6 LTS) / x86_64 | OK | OK | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | |
| Package: bumphunter |
| Version: 1.24.5 |
| 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_1.24.5.tar.gz |
| StartedAt: 2019-04-15 22:42:51 -0400 (Mon, 15 Apr 2019) |
| EndedAt: 2019-04-15 22:50:21 -0400 (Mon, 15 Apr 2019) |
| EllapsedTime: 449.8 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: bumphunter.Rcheck |
| Warnings: 0 |
##############################################################################
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### 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_1.24.5.tar.gz
###
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##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/bumphunter.Rcheck’
* using R version 3.5.3 (2019-03-11)
* 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 ‘1.24.5’
* 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 or elapsed time > 5s
user system elapsed
bumphunter 6.621 4.784 5.828
* 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-3.8-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 3.5.3 (2019-03-11) -- "Great Truth"
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.
> 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 -- Mon Apr 15 22:47:20 2019
***********************************************
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
22.695 2.947 38.610
bumphunter.Rcheck/tests/test-all.Rout
R version 3.5.3 (2019-03-11) -- "Great Truth"
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')
> 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
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: 16 SKIPPED: 0 FAILED: 0
>
> proc.time()
user system elapsed
159.594 3.297 174.481
bumphunter.Rcheck/bumphunter-Ex.timings
| name | user | system | elapsed | |
| annotateNearest | 0.745 | 0.059 | 0.805 | |
| annotateTranscripts | 0.000 | 0.001 | 0.000 | |
| bumphunter | 6.621 | 4.784 | 5.828 | |
| clusterMaker | 0.019 | 0.003 | 0.022 | |
| dummyData | 0.004 | 0.001 | 0.005 | |
| getSegments | 0.024 | 0.004 | 0.029 | |
| locfitByCluster | 0.765 | 0.175 | 0.947 | |
| loessByCluster | 0.200 | 0.005 | 0.207 | |
| matchGenes | 0 | 0 | 0 | |
| regionFinder | 0.022 | 0.000 | 0.022 | |
| runmedByCluster | 0.003 | 0.001 | 0.004 | |
| smoother | 0.115 | 0.072 | 0.160 | |