Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-08-21 11:40 -0400 (Wed, 21 Aug 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4703 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4440 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4472 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4421 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4414 |
Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X |
Package 253/2255 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
bumphunter 1.47.0 (landing page) Tamilselvi Guharaj
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | ERROR | OK | |||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
To the developers/maintainers of the bumphunter package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/bumphunter.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
Package: bumphunter |
Version: 1.47.0 |
Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:bumphunter.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings bumphunter_1.47.0.tar.gz |
StartedAt: 2024-08-20 23:00:51 -0400 (Tue, 20 Aug 2024) |
EndedAt: 2024-08-20 23:11:37 -0400 (Tue, 20 Aug 2024) |
EllapsedTime: 646.1 seconds |
RetCode: 0 |
Status: OK |
CheckDir: bumphunter.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:bumphunter.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings bumphunter_1.47.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/bumphunter.Rcheck' * using R version 4.4.1 (2024-06-14 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 13.2.0 GNU Fortran (GCC) 13.2.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * using option '--no-vignettes' * checking for file 'bumphunter/DESCRIPTION' ... OK * this is package 'bumphunter' version '1.47.0' * 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 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 code 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 LazyData ... 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 1.00 0.04 15.61 smoother 0.04 0.02 14.43 * 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 ... 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 'F:/biocbuild/bbs-3.20-bioc/meat/bumphunter.Rcheck/00check.log' for details.
bumphunter.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL bumphunter ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.20-bioc/R/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)
bumphunter.Rcheck/tests/runTests.Rout
R version 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 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 Attaching package: 'BiocGenerics' 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, aperm, 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, table, tapply, union, unique, unsplit, which.max, which.min Attaching package: 'S4Vectors' The following object is masked from 'package:utils': findMatches The following objects are masked from 'package:base': I, expand.grid, unname Loading required package: IRanges Attaching package: 'IRanges' The following object is masked from 'package:grDevices': windows Loading required package: GenomeInfoDb Loading required package: GenomicRanges Loading required package: foreach Loading required package: iterators Loading required package: parallel Loading required package: locfit locfit 1.5-9.10 2024-06-24 [1] TRUE > BiocGenerics:::testPackage("bumphunter") [bumphunterEngine] Using a single core (backend: doSEQ, version: 1.5.2). [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: 1.5.2). [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: doParallelSNOW, version: 1.0.17). [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: 1.0.17). [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 Aug 20 23:06:23 2024 *********************************************** 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 17.29 1.21 50.34
bumphunter.Rcheck/tests/test-all.Rout
R version 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 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 Attaching package: 'BiocGenerics' 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, aperm, 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, table, tapply, union, unique, unsplit, which.max, which.min Attaching package: 'S4Vectors' The following object is masked from 'package:utils': findMatches The following objects are masked from 'package:base': I, expand.grid, unname Loading required package: IRanges Attaching package: 'IRanges' The following object is masked from 'package:grDevices': windows Loading required package: GenomeInfoDb Loading required package: GenomicRanges Loading required package: foreach Loading required package: iterators Loading required package: parallel Loading required package: locfit locfit 1.5-9.10 2024-06-24 trying URL 'http://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_36/gencode.v36.annotation.gtf.gz' Content type 'application/x-gzip' length 44507458 bytes (42.4 MB) ================================================== downloaded 42.4 MB [ FAIL 0 | WARN 1 | SKIP 0 | PASS 15 ] [ FAIL 0 | WARN 1 | SKIP 0 | PASS 15 ] > > proc.time() user system elapsed 239.71 5.07 302.39
bumphunter.Rcheck/bumphunter-Ex.timings
name | user | system | elapsed | |
annotateNearest | 0.60 | 0.06 | 0.66 | |
annotateTranscripts | 0 | 0 | 0 | |
bumphunter | 1.00 | 0.04 | 15.61 | |
clusterMaker | 0.01 | 0.00 | 0.02 | |
dummyData | 0 | 0 | 0 | |
getSegments | 0.02 | 0.00 | 0.01 | |
locfitByCluster | 0.00 | 0.01 | 0.02 | |
loessByCluster | 0.17 | 0.00 | 0.19 | |
matchGenes | 0 | 0 | 0 | |
regionFinder | 0.02 | 0.00 | 0.01 | |
runmedByCluster | 0 | 0 | 0 | |
smoother | 0.04 | 0.02 | 14.43 | |