Back to Multiple platform build/check report for BioC 3.19: simplified long |
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This page was generated on 2024-06-07 20:24 -0400 (Fri, 07 Jun 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4755 |
palomino3 | Windows Server 2022 Datacenter | x64 | 4.4.0 (2024-04-24 ucrt) -- "Puppy Cup" | 4489 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4520 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4466 |
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 832/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
GenomicFeatures 1.56.0 (landing page) H. Pagès
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | OK | OK | |||||||||
To the developers/maintainers of the GenomicFeatures package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/GenomicFeatures.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: GenomicFeatures |
Version: 1.56.0 |
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:GenomicFeatures.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings GenomicFeatures_1.56.0.tar.gz |
StartedAt: 2024-06-05 23:22:14 -0400 (Wed, 05 Jun 2024) |
EndedAt: 2024-06-05 23:31:26 -0400 (Wed, 05 Jun 2024) |
EllapsedTime: 552.2 seconds |
RetCode: 0 |
Status: OK |
CheckDir: GenomicFeatures.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:GenomicFeatures.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings GenomicFeatures_1.56.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/GenomicFeatures.Rcheck’ * using R version 4.4.0 (2024-04-24) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 * running under: Ubuntu 22.04.4 LTS * using session charset: UTF-8 * checking for file ‘GenomicFeatures/DESCRIPTION’ ... OK * this is package ‘GenomicFeatures’ version ‘1.56.0’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... NOTE Depends: includes the non-default packages: 'BiocGenerics', 'S4Vectors', 'IRanges', 'GenomeInfoDb', 'GenomicRanges', 'AnnotationDbi' 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 ‘GenomicFeatures’ 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 loading without being on the library search path ... OK * checking dependencies in R code ... NOTE Unexported objects imported by ':::' calls: ‘AnnotationDbi:::.getMetaValue’ ‘AnnotationDbi:::.valid.colnames’ ‘AnnotationDbi:::.valid.metadata.table’ ‘AnnotationDbi:::.valid.table.colnames’ ‘AnnotationDbi:::dbEasyQuery’ ‘AnnotationDbi:::dbQuery’ ‘AnnotationDbi:::smartKeys’ ‘BiocGenerics:::testPackage’ ‘GenomeInfoDb:::getSeqlevelsReplacementMode’ ‘GenomeInfoDb:::normarg_new2old’ ‘GenomicRanges:::unsafe.transcriptLocs2refLocs’ ‘GenomicRanges:::unsafe.transcriptWidths’ ‘IRanges:::regroupBySupergroup’ ‘S4Vectors:::V_recycle’ ‘S4Vectors:::decodeRle’ ‘S4Vectors:::extract_data_frame_rows’ 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) coordinate-mapping-methods.Rd:144-168: Lost braces in \itemize; meant \describe ? checkRd: (-1) coordinate-mapping-methods.Rd:169-194: Lost braces in \itemize; meant \describe ? checkRd: (-1) nearest-methods.Rd:43-61: Lost braces in \itemize; meant \describe ? * 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 coverageByTranscript 72.541 3.776 76.317 coordinate-mapping-methods 46.893 3.657 52.014 exonicParts 37.867 0.767 38.637 extractTranscriptSeqs 12.486 0.472 12.966 transcriptLocs2refLocs 5.222 0.412 5.642 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘run_unitTests.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 3 NOTEs See ‘/home/biocbuild/bbs-3.19-bioc/meat/GenomicFeatures.Rcheck/00check.log’ for details.
GenomicFeatures.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL GenomicFeatures ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-library’ * installing *source* package ‘GenomicFeatures’ ... ** 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 (GenomicFeatures)
GenomicFeatures.Rcheck/tests/run_unitTests.Rout
R version 4.4.0 (2024-04-24) -- "Puppy Cup" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu 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("GenomicFeatures") || stop("unable to load GenomicFeatures package") Loading required package: GenomicFeatures 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 Loading required package: GenomeInfoDb Loading required package: GenomicRanges 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")'. [1] TRUE > GenomicFeatures:::.test() Loading required package: BSgenome Loading required package: Biostrings Loading required package: XVector Attaching package: 'Biostrings' The following object is masked from 'package:base': strsplit Loading required package: BiocIO Loading required package: rtracklayer Attaching package: 'rtracklayer' The following object is masked from 'package:BiocIO': FileForFormat 'select()' returned 1:1 mapping between keys and columns 'select()' returned 1:many mapping between keys and columns 'select()' returned 1:many mapping between keys and columns 'select()' returned 1:1 mapping between keys and columns 'select()' returned 1:1 mapping between keys and columns 'select()' returned 1:many mapping between keys and columns 'select()' returned 1:many mapping between keys and columns 'select()' returned 1:many mapping between keys and columns 'select()' returned 1:many mapping between keys and columns 'select()' returned 1:many mapping between keys and columns 'select()' returned 1:many mapping between keys and columns 'select()' returned 1:many mapping between keys and columns 'select()' returned 1:many mapping between keys and columns 'select()' returned 1:many mapping between keys and columns 'select()' returned 1:many mapping between keys and columns 'select()' returned 1:1 mapping between keys and columns 'select()' returned 1:many mapping between keys and columns 'select()' returned 1:many mapping between keys and columns 'select()' returned 1:many mapping between keys and columns 'select()' returned 1:1 mapping between keys and columns Import genomic features from the file as a GRanges object ... OK Prepare the 'metadata' data frame ... OK Make the TxDb object ... OK Import genomic features from the file as a GRanges object ... OK Prepare the 'metadata' data frame ... OK Make the TxDb object ... OK RUNIT TEST PROTOCOL -- Wed Jun 5 23:30:38 2024 *********************************************** Number of test functions: 67 Number of errors: 0 Number of failures: 0 1 Test Suite : GenomicFeatures RUnit Tests - 67 test functions, 0 errors, 0 failures Number of test functions: 67 Number of errors: 0 Number of failures: 0 There were 11 warnings (use warnings() to see them) > > proc.time() user system elapsed 67.084 1.476 69.659
GenomicFeatures.Rcheck/GenomicFeatures-Ex.timings
name | user | system | elapsed | |
FeatureDb-class | 0.069 | 0.004 | 0.074 | |
TxDb-class | 2.023 | 0.188 | 2.211 | |
as-format-methods | 1.122 | 0.084 | 1.206 | |
coordinate-mapping-methods | 46.893 | 3.657 | 52.014 | |
coverageByTranscript | 72.541 | 3.776 | 76.317 | |
exonicParts | 37.867 | 0.767 | 38.637 | |
extendExonsIntoIntrons | 2.616 | 0.072 | 2.706 | |
extractTranscriptSeqs | 12.486 | 0.472 | 12.966 | |
extractUpstreamSeqs | 1.294 | 0.112 | 1.406 | |
features | 0.051 | 0.000 | 0.052 | |
getPromoterSeq-methods | 2.582 | 0.986 | 4.042 | |
id2name | 0.189 | 0.010 | 0.198 | |
mapIdsToRanges | 0.658 | 0.056 | 0.714 | |
mapRangesToIds | 0.695 | 0.076 | 0.770 | |
microRNAs | 0 | 0 | 0 | |
nearest-methods | 0.604 | 0.060 | 0.663 | |
proteinToGenome | 1.581 | 0.100 | 1.681 | |
select-methods | 0.183 | 0.016 | 0.200 | |
transcriptLengths | 3.581 | 0.144 | 3.725 | |
transcriptLocs2refLocs | 5.222 | 0.412 | 5.642 | |
transcripts | 2.243 | 0.052 | 2.295 | |
transcriptsBy | 0.810 | 0.052 | 0.862 | |
transcriptsByOverlaps | 0.263 | 0.012 | 0.275 | |