Back to Multiple platform build/check report for BioC 3.6 |
|
This page was generated on 2018-04-12 13:10:48 -0400 (Thu, 12 Apr 2018).
Package 168/1472 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
bumphunter 1.20.0 Rafael A. Irizarry
| malbec1 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | [ OK ] | ![]() | ||||||
tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | ![]() | ||||||
veracruz1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | ![]() |
Package: bumphunter |
Version: 1.20.0 |
Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings bumphunter_1.20.0.tar.gz |
StartedAt: 2018-04-11 21:56:31 -0400 (Wed, 11 Apr 2018) |
EndedAt: 2018-04-11 22:03:33 -0400 (Wed, 11 Apr 2018) |
EllapsedTime: 421.3 seconds |
RetCode: 0 |
Status: OK |
CheckDir: bumphunter.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings bumphunter_1.20.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/bumphunter.Rcheck’ * using R version 3.4.4 (2018-03-15) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘bumphunter/DESCRIPTION’ ... OK * this is package ‘bumphunter’ version ‘1.20.0’ * 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 installed files from ‘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 ‘/home/biocbuild/bbs-3.6-bioc/meat/bumphunter.Rcheck/00check.log’ for details.
bumphunter.Rcheck/00install.out
* installing *source* package ‘bumphunter’ ... ** R ** data *** moving datasets to lazyload DB ** inst ** preparing 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 3.4.4 (2018-03-15) -- "Someone to Lean On" Copyright (C) 2018 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu (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, cbind, colMeans, colSums, colnames, 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': isNamespaceLoaded [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: 1.0.11). [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: 1.0.11). [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 Apr 11 21:59:58 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 17.636 0.928 29.809
bumphunter.Rcheck/tests/test-all.Rout
R version 3.4.4 (2018-03-15) -- "Someone to Lean On" Copyright (C) 2018 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu (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, cbind, colMeans, colSums, colnames, 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 182.508 1.392 211.489
bumphunter.Rcheck/bumphunter-Ex.timings
name | user | system | elapsed | |
annotateNearest | 1.024 | 0.004 | 1.028 | |
annotateTranscripts | 0 | 0 | 0 | |
bumphunter | 2.884 | 0.820 | 2.402 | |
clusterMaker | 0.024 | 0.000 | 0.023 | |
dummyData | 0.024 | 0.008 | 0.032 | |
getSegments | 0.044 | 0.012 | 0.056 | |
locfitByCluster | 0.320 | 0.012 | 0.330 | |
loessByCluster | 0.232 | 0.004 | 0.235 | |
matchGenes | 0 | 0 | 0 | |
regionFinder | 0.112 | 0.000 | 0.110 | |
runmedByCluster | 0.004 | 0.000 | 0.004 | |
smoother | 0.140 | 0.084 | 0.167 | |