Back to Multiple platform build/check report for BioC 3.13 |
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This page was generated on 2021-10-15 15:06:28 -0400 (Fri, 15 Oct 2021).
To the developers/maintainers of the BaalChIP package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/BaalChIP.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 106/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
BaalChIP 1.18.0 (landing page) Ines de Santiago
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | WARNINGS | OK | |||||||||
machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | WARNINGS | OK | |||||||||
Package: BaalChIP |
Version: 1.18.0 |
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:BaalChIP.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings BaalChIP_1.18.0.tar.gz |
StartedAt: 2021-10-14 16:25:43 -0400 (Thu, 14 Oct 2021) |
EndedAt: 2021-10-14 16:41:47 -0400 (Thu, 14 Oct 2021) |
EllapsedTime: 964.2 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: BaalChIP.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:BaalChIP.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings BaalChIP_1.18.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/BaalChIP.Rcheck’ * using R version 4.1.1 (2021-08-10) * using platform: x86_64-apple-darwin17.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘BaalChIP/DESCRIPTION’ ... OK * this is package ‘BaalChIP’ version ‘1.18.0’ * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for hidden files and directories ... NOTE Found the following hidden files and directories: .git_fetch_output.txt .git_merge_output.txt These were most likely included in error. See section ‘Package structure’ in the ‘Writing R Extensions’ manual. * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘BaalChIP’ can be installed ... OK * checking installed package size ... NOTE installed size is 198.4Mb sub-directories of 1Mb or more: data 96.0Mb test 101.9Mb * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... OK * 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 ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... OK * 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 ... WARNING LazyData DB of 95.7 MB without LazyDataCompression set See §1.1.6 of 'Writing R Extensions' * checking data for ASCII and uncompressed saves ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed BaalChIP.run 22.094 0.925 275.169 mergePerGroup 16.119 0.369 16.498 filter1allele 14.726 0.346 15.153 QCfilter 14.541 0.519 15.085 filterIntbias 9.699 1.277 10.997 getASB 7.804 0.372 285.031 alleleCounts 5.479 0.058 5.566 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘runTests.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: 1 WARNING, 2 NOTEs See ‘/Users/biocbuild/bbs-3.13-bioc/meat/BaalChIP.Rcheck/00check.log’ for details.
BaalChIP.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL BaalChIP ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’ * installing *source* package ‘BaalChIP’ ... ** 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 (BaalChIP)
BaalChIP.Rcheck/tests/runTests.Rout
R version 4.1.1 (2021-08-10) -- "Kick Things" Copyright (C) 2021 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. > BiocGenerics:::testPackage("BaalChIP") 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 objects are masked from 'package:base': I, expand.grid, unname Attaching package: 'Biostrings' The following object is masked from 'package:base': strsplit RUNIT TEST PROTOCOL -- Thu Oct 14 16:41:35 2021 *********************************************** Number of test functions: 1 Number of errors: 0 Number of failures: 0 1 Test Suite : BaalChIP RUnit Tests - 1 test function, 0 errors, 0 failures Number of test functions: 1 Number of errors: 0 Number of failures: 0 > > proc.time() user system elapsed 11.960 0.538 12.501
BaalChIP.Rcheck/BaalChIP-Ex.timings
name | user | system | elapsed | |
BaalChIP | 0.048 | 0.006 | 0.056 | |
BaalChIP.get | 0.129 | 0.009 | 0.138 | |
BaalChIP.report | 0.027 | 0.005 | 0.031 | |
BaalChIP.run | 22.094 | 0.925 | 275.169 | |
QCfilter | 14.541 | 0.519 | 15.085 | |
adjustmentBaalPlot | 1.061 | 0.029 | 1.092 | |
alleleCounts | 5.479 | 0.058 | 5.566 | |
filter1allele | 14.726 | 0.346 | 15.153 | |
filterIntbias | 9.699 | 1.277 | 10.997 | |
getASB | 7.804 | 0.372 | 285.031 | |
mergePerGroup | 16.119 | 0.369 | 16.498 | |
plotQC | 1.298 | 0.009 | 1.311 | |
plotSimul | 0.160 | 0.003 | 0.161 | |
summaryASB | 0.002 | 0.002 | 0.003 | |
summaryQC | 0.053 | 0.002 | 0.055 | |