Back to Multiple platform build/check report for BioC 3.13 |
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This page was generated on 2021-10-15 15:05:41 -0400 (Fri, 15 Oct 2021).
To the developers/maintainers of the GenomicFiles package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/GenomicFiles.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 743/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
GenomicFiles 1.28.0 (landing page) Bioconductor Package Maintainer
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | OK | |||||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |||||||||
machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |||||||||
Package: GenomicFiles |
Version: 1.28.0 |
Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:GenomicFiles.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings GenomicFiles_1.28.0.tar.gz |
StartedAt: 2021-10-14 09:58:35 -0400 (Thu, 14 Oct 2021) |
EndedAt: 2021-10-14 10:04:02 -0400 (Thu, 14 Oct 2021) |
EllapsedTime: 327.5 seconds |
RetCode: 0 |
Status: OK |
CheckDir: GenomicFiles.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:GenomicFiles.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings GenomicFiles_1.28.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/GenomicFiles.Rcheck’ * using R version 4.1.1 (2021-08-10) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘GenomicFiles/DESCRIPTION’ ... OK * this is package ‘GenomicFiles’ version ‘1.28.0’ * checking package namespace information ... OK * checking package dependencies ... NOTE Depends: includes the non-default packages: 'BiocGenerics', 'MatrixGenerics', 'GenomicRanges', 'SummarizedExperiment', 'BiocParallel', 'Rsamtools', 'rtracklayer' 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 ‘GenomicFiles’ 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 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 files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed reduceByFile-methods 14.373 4.373 5.131 reduceByRange-methods 10.579 4.259 6.519 VcfStack-class 8.795 2.008 8.824 GenomicFiles-class 6.834 1.546 5.588 reduceByYield 3.785 1.393 23.359 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘GenomicFiles_unit_tests.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 NOTE See ‘/home/biocbuild/bbs-3.13-bioc/meat/GenomicFiles.Rcheck/00check.log’ for details.
GenomicFiles.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL GenomicFiles ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.13-bioc/R/library’ * installing *source* package ‘GenomicFiles’ ... ** 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 (GenomicFiles)
GenomicFiles.Rcheck/tests/GenomicFiles_unit_tests.Rout
R version 4.1.1 (2021-08-10) -- "Kick Things" Copyright (C) 2021 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. > BiocGenerics:::testPackage("GenomicFiles") 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: '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 Attaching package: 'S4Vectors' The following objects are masked from 'package:base': I, expand.grid, unname Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. Attaching package: 'Biobase' The following object is masked from 'package:MatrixGenerics': rowMedians The following objects are masked from 'package:matrixStats': anyMissing, rowMedians Attaching package: 'Biostrings' The following object is masked from 'package:base': strsplit RUNIT TEST PROTOCOL -- Thu Oct 14 10:03:59 2021 *********************************************** Number of test functions: 20 Number of errors: 0 Number of failures: 0 1 Test Suite : GenomicFiles RUnit Tests - 20 test functions, 0 errors, 0 failures Number of test functions: 20 Number of errors: 0 Number of failures: 0 Warning message: In valid.GenomicRanges.seqinfo(x, suggest.trim = TRUE) : GRanges object contains 1 out-of-bound range located on sequence 19. Note that ranges located on a sequence whose length is unknown (NA) or on a circular sequence are not considered out-of-bound (use seqlengths() and isCircular() to get the lengths and circularity flags of the underlying sequences). You can use trim() to trim these ranges. See ?`trim,GenomicRanges-method` for more information. > > proc.time() user system elapsed 51.949 4.291 53.351
GenomicFiles.Rcheck/GenomicFiles-Ex.timings
name | user | system | elapsed | |
GenomicFiles-class | 6.834 | 1.546 | 5.588 | |
VcfStack-class | 8.795 | 2.008 | 8.824 | |
pack-methods | 1.035 | 0.068 | 1.103 | |
reduceByFile-methods | 14.373 | 4.373 | 5.131 | |
reduceByRange-methods | 10.579 | 4.259 | 6.519 | |
reduceByYield | 3.785 | 1.393 | 23.359 | |
registry-utils | 0.000 | 0.000 | 0.001 | |
unpack-methods | 0.874 | 0.553 | 0.748 | |