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 11:41 -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 932/2255 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
HelloRanges 1.31.0 (landing page) Michael Lawrence
| 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 | ERROR | skipped | skipped | |||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | ERROR | skipped | skipped | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
To the developers/maintainers of the HelloRanges package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/HelloRanges.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: HelloRanges |
Version: 1.31.0 |
Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:HelloRanges.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings HelloRanges_1.31.0.tar.gz |
StartedAt: 2024-08-21 01:36:14 -0400 (Wed, 21 Aug 2024) |
EndedAt: 2024-08-21 01:42:05 -0400 (Wed, 21 Aug 2024) |
EllapsedTime: 351.4 seconds |
RetCode: 0 |
Status: OK |
CheckDir: HelloRanges.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:HelloRanges.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings HelloRanges_1.31.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/HelloRanges.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 'HelloRanges/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'HelloRanges' version '1.31.0' * checking package namespace information ... OK * checking package dependencies ... NOTE Depends: includes the non-default packages: 'BiocGenerics', 'S4Vectors', 'IRanges', 'GenomicRanges', 'Biostrings', 'BSgenome', 'GenomicFeatures', 'VariantAnnotation', 'Rsamtools', 'GenomicAlignments', 'rtracklayer', 'GenomeInfoDb', 'SummarizedExperiment', 'BiocIO' 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 'HelloRanges' can be installed ... OK * checking installed package size ... OK * 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 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 Packages in Depends field not imported from: 'BSgenome' 'GenomicAlignments' 'GenomicFeatures' 'VariantAnnotation' These packages need to be imported from (in the NAMESPACE file) for when this namespace is loaded but not attached. Unexported objects imported by ':::' calls: 'BiocGenerics:::testPackage' 'IRanges:::subgrouping' 'S4Vectors:::make_zero_col_DataFrame' 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 ... OK * checking Rd files ... NOTE checkRd: (-1) bedtools_groupby.Rd:95: Lost braces 95 | \code{freq}{\code{table(X)}} | ^ checkRd: (-1) bedtools_groupby.Rd:96: Lost braces 96 | \code{first}{\code{drop(heads(X, 1L))}} | ^ checkRd: (-1) bedtools_groupby.Rd:97: Lost braces 97 | \code{last}{\code{drop(tails(X, 1L))}} | ^ * 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 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 'HelloRanges_unit_tests.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: 3 NOTEs See 'F:/biocbuild/bbs-3.20-bioc/meat/HelloRanges.Rcheck/00check.log' for details.
HelloRanges.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL HelloRanges ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.20-bioc/R/library' * installing *source* package 'HelloRanges' ... ** using staged installation ** R ** 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 (HelloRanges)
HelloRanges.Rcheck/tests/HelloRanges_unit_tests.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("HelloRanges") || stop("unable to load HelloRanges package") Loading required package: HelloRanges 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 Loading required package: S4Vectors Loading required package: stats4 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: GenomicRanges Loading required package: GenomeInfoDb Loading required package: Biostrings Loading required package: XVector Attaching package: 'Biostrings' The following object is masked from 'package:base': strsplit Loading required package: BSgenome Loading required package: BiocIO Loading required package: rtracklayer Attaching package: 'rtracklayer' The following object is masked from 'package:BiocIO': FileForFormat Loading required package: GenomicFeatures Loading required package: AnnotationDbi Loading required package: Biobase Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Loading required package: VariantAnnotation Loading required package: MatrixGenerics Loading required package: matrixStats Attaching package: 'matrixStats' The following objects are masked from 'package:Biobase': anyMissing, rowMedians Attaching package: 'MatrixGenerics' The following objects are masked from 'package:matrixStats': colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse, colCounts, colCummaxs, colCummins, colCumprods, colCumsums, colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs, colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats, colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds, colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads, colWeightedMeans, colWeightedMedians, colWeightedSds, colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet, rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods, rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps, rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins, rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks, rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars, rowWeightedMads, rowWeightedMeans, rowWeightedMedians, rowWeightedSds, rowWeightedVars The following object is masked from 'package:Biobase': rowMedians Loading required package: SummarizedExperiment Loading required package: Rsamtools Attaching package: 'VariantAnnotation' The following object is masked from 'package:base': tabulate Loading required package: GenomicAlignments [1] TRUE > HelloRanges:::.test() RUNIT TEST PROTOCOL -- Wed Aug 21 01:41:54 2024 *********************************************** Number of test functions: 17 Number of errors: 0 Number of failures: 0 1 Test Suite : HelloRanges RUnit Tests - 17 test functions, 0 errors, 0 failures Number of test functions: 17 Number of errors: 0 Number of failures: 0 > > proc.time() user system elapsed 54.29 1.70 56.29
HelloRanges.Rcheck/HelloRanges-Ex.timings
name | user | system | elapsed | |
bedtools_closest | 0.37 | 0.04 | 0.41 | |
bedtools_complement | 0.02 | 0.00 | 0.02 | |
bedtools_coverage | 0.19 | 0.01 | 0.21 | |
bedtools_flank | 0.12 | 0.00 | 0.12 | |
bedtools_genomecov | 0.19 | 0.00 | 0.19 | |
bedtools_getfasta | 0.06 | 0.00 | 0.06 | |
bedtools_groupby | 0.1 | 0.0 | 0.1 | |
bedtools_intersect | 0.47 | 0.10 | 0.56 | |
bedtools_jaccard | 0.07 | 0.02 | 0.10 | |
bedtools_makewindows | 0.14 | 0.00 | 0.14 | |
bedtools_map | 0.25 | 0.00 | 0.25 | |
bedtools_merge | 0.3 | 0.0 | 0.3 | |
bedtools_multiinter | 0.08 | 0.01 | 0.09 | |
bedtools_nuc | 0.06 | 0.00 | 0.06 | |
bedtools_shift | 0.08 | 0.00 | 0.08 | |
bedtools_slop | 0.08 | 0.00 | 0.08 | |
bedtools_subtract | 0.17 | 0.00 | 0.17 | |
bedtools_unionbedg | 0.08 | 0.00 | 0.08 | |
distmode | 0 | 0 | 0 | |