Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-06-11 15:43 -0400 (Tue, 11 Jun 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.0 RC (2024-04-16 r86468) -- "Puppy Cup" | 4679 |
palomino4 | Windows Server 2022 Datacenter | x64 | 4.4.0 RC (2024-04-16 r86468 ucrt) -- "Puppy Cup" | 4414 |
merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4441 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" | 4394 |
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 2165/2239 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
txcutr 1.11.0 (landing page) Mervin Fansler
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | TIMEOUT | OK | |||||||||
merida1 | macOS 12.7.4 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | ![]() | ||||||||
To the developers/maintainers of the txcutr package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/txcutr.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: txcutr |
Version: 1.11.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:txcutr.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings txcutr_1.11.0.tar.gz |
StartedAt: 2024-06-11 11:32:12 -0400 (Tue, 11 Jun 2024) |
EndedAt: 2024-06-11 11:40:12 -0400 (Tue, 11 Jun 2024) |
EllapsedTime: 479.6 seconds |
RetCode: 0 |
Status: OK |
CheckDir: txcutr.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:txcutr.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings txcutr_1.11.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/txcutr.Rcheck’ * using R version 4.4.0 Patched (2024-04-24 r86482) * using platform: aarch64-apple-darwin20 * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Ventura 13.6.6 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘txcutr/DESCRIPTION’ ... OK * this is package ‘txcutr’ version ‘1.11.0’ * package encoding: UTF-8 * 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 ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘txcutr’ 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 ... 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 truncateTxome 55.618 13.720 26.753 generateMergeTable 54.873 13.681 26.355 exportGTF 42.847 12.336 22.936 exportFASTA 41.936 5.510 30.517 exportMergeTable 21.917 6.586 11.979 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.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: OK
txcutr.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL txcutr ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’ * installing *source* package ‘txcutr’ ... ** using staged installation ** R ** 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 (txcutr)
txcutr.Rcheck/tests/testthat.Rout
R version 4.4.0 Patched (2024-04-24 r86482) -- "Puppy Cup" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: aarch64-apple-darwin20 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) > library(txcutr) > > test_check("txcutr") 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 Loading required package: S4Vectors 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: 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")'. Attaching package: 'txdbmaker' The following objects are masked from 'package:GenomicFeatures': UCSCFeatureDbTableSchema, browseUCSCtrack, getChromInfoFromBiomart, makeFDbPackageFromUCSC, makeFeatureDbFromUCSC, makePackageName, makeTxDb, makeTxDbFromBiomart, makeTxDbFromEnsembl, makeTxDbFromGFF, makeTxDbFromGRanges, makeTxDbFromUCSC, makeTxDbPackage, makeTxDbPackageFromBiomart, makeTxDbPackageFromUCSC, supportedMiRBaseBuildValues, supportedUCSCFeatureDbTables, supportedUCSCFeatureDbTracks, supportedUCSCtables 'select()' returned 1:1 mapping between keys and columns Truncating transcripts... Done. Checking for duplicate transcripts... Removed 1 duplicates. Creating exon ranges... Done. Creating tx ranges... Done. Creating gene ranges... Done. 'select()' returned 1:1 mapping between keys and columns Truncating transcripts... Done. Checking for duplicate transcripts... Removed 1 duplicates. Creating exon ranges... Done. Creating tx ranges... Done. Creating gene ranges... Done. 'select()' returned 1:1 mapping between keys and columns Truncating transcripts... Done. Checking for duplicate transcripts... Removed 1 duplicates. Creating exon ranges... Done. Creating tx ranges... Done. Creating gene ranges... Done. 'select()' returned 1:1 mapping between keys and columns Truncating transcripts... Done. Checking for duplicate transcripts... Removed 1 duplicates. Creating exon ranges... Done. Creating tx ranges... Done. Creating gene ranges... Done. 'select()' returned 1:1 mapping between keys and columns Truncating transcripts... Done. Checking for duplicate transcripts... Removed 0 duplicates. Creating exon ranges... Done. Creating tx ranges... Done. Creating gene ranges... Done. 'select()' returned 1:1 mapping between keys and columns Truncating transcripts... Done. Checking for duplicate transcripts... Removed 0 duplicates. Creating exon ranges... Done. Creating tx ranges... Done. Creating gene ranges... Done. 'select()' returned 1:1 mapping between keys and columns Truncating transcripts... Done. Checking for duplicate transcripts... Removed 0 duplicates. Creating exon ranges... Done. Creating tx ranges... Done. Creating gene ranges... Done. 'select()' returned 1:1 mapping between keys and columns Truncating transcripts... Done. Checking for duplicate transcripts... Removed 0 duplicates. Creating exon ranges... Done. Creating tx ranges... Done. Creating gene ranges... Done. 'select()' returned 1:1 mapping between keys and columns Truncating transcripts... Done. Checking for duplicate transcripts... Removed 0 duplicates. Creating exon ranges... Done. Creating tx ranges... Done. Creating gene ranges... Done. 'select()' returned 1:1 mapping between keys and columns Truncating transcripts... Done. Checking for duplicate transcripts... Removed 0 duplicates. Creating exon ranges... Done. Creating tx ranges... Done. Creating gene ranges... Done. 'select()' returned 1:1 mapping between keys and columns Truncating transcripts... Done. Checking for duplicate transcripts... Removed 0 duplicates. Creating exon ranges... Done. Creating tx ranges... Done. Creating gene ranges... Done. 'select()' returned 1:1 mapping between keys and columns Truncating transcripts... Done. Checking for duplicate transcripts... Removed 0 duplicates. Creating exon ranges... Done. Creating tx ranges... Done. Creating gene ranges... Done. 'select()' returned 1:1 mapping between keys and columns Truncating transcripts... Done. Checking for duplicate transcripts... Removed 0 duplicates. Creating exon ranges... Done. Creating tx ranges... Done. Creating gene ranges... Done. 'select()' returned 1:1 mapping between keys and columns Truncating transcripts... Done. Checking for duplicate transcripts... Removed 0 duplicates. Creating exon ranges... Done. Creating tx ranges... Done. Creating gene ranges... Done. 'select()' returned 1:1 mapping between keys and columns Truncating transcripts... Done. Checking for duplicate transcripts... Removed 0 duplicates. Creating exon ranges... Done. Creating tx ranges... Done. Creating gene ranges... Done. 'select()' returned 1:1 mapping between keys and columns Truncating transcripts... Done. Checking for duplicate transcripts... Removed 0 duplicates. Creating exon ranges... Done. Creating tx ranges... Done. Creating gene ranges... Done. 'select()' returned 1:1 mapping between keys and columns Truncating transcripts... Done. Checking for duplicate transcripts... Removed 0 duplicates. Creating exon ranges... Done. Creating tx ranges... Done. Creating gene ranges... Done. 'select()' returned 1:1 mapping between keys and columns Truncating transcripts... Done. Checking for duplicate transcripts... Removed 0 duplicates. Creating exon ranges... Done. Creating tx ranges... Done. Creating gene ranges... Done. 'select()' returned 1:1 mapping between keys and columns Truncating transcripts... Done. Checking for duplicate transcripts... Removed 0 duplicates. Creating exon ranges... Done. Creating tx ranges... Done. Creating gene ranges... Done. 'select()' returned 1:1 mapping between keys and columns Truncating transcripts... Done. Checking for duplicate transcripts... Removed 0 duplicates. Creating exon ranges... Done. Creating tx ranges... Done. Creating gene ranges... Done. 'select()' returned 1:1 mapping between keys and columns Truncating transcripts... Done. Checking for duplicate transcripts... Removed 0 duplicates. Creating exon ranges... Done. Creating tx ranges... Done. Creating gene ranges... Done. [ FAIL 0 | WARN 0 | SKIP 0 | PASS 117 ] > > proc.time() user system elapsed 75.342 19.041 89.829
txcutr.Rcheck/txcutr-Ex.timings
name | user | system | elapsed | |
exportFASTA | 41.936 | 5.510 | 30.517 | |
exportGTF | 42.847 | 12.336 | 22.936 | |
exportMergeTable | 21.917 | 6.586 | 11.979 | |
generateMergeTable | 54.873 | 13.681 | 26.355 | |
truncateTxome | 55.618 | 13.720 | 26.753 | |
txdbToGRangesList | 0.891 | 0.135 | 1.026 | |