Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-12-23 12:07 -0500 (Mon, 23 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4744 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4487 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4515 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4467 |
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 603/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
doubletrouble 1.6.0 (landing page) Fabrício Almeida-Silva
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | |||||||||
To the developers/maintainers of the doubletrouble package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/doubletrouble.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: doubletrouble |
Version: 1.6.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:doubletrouble.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings doubletrouble_1.6.0.tar.gz |
StartedAt: 2024-12-20 18:09:04 -0500 (Fri, 20 Dec 2024) |
EndedAt: 2024-12-20 18:14:49 -0500 (Fri, 20 Dec 2024) |
EllapsedTime: 344.9 seconds |
RetCode: 0 |
Status: OK |
CheckDir: doubletrouble.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:doubletrouble.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings doubletrouble_1.6.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/doubletrouble.Rcheck’ * using R version 4.4.2 (2024-10-31) * 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 13.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘doubletrouble/DESCRIPTION’ ... OK * this is package ‘doubletrouble’ version ‘1.6.0’ * 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 ‘doubletrouble’ 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 contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... OK * 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 classify_gene_pairs 6.657 0.221 6.935 * 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
doubletrouble.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL doubletrouble ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’ * installing *source* package ‘doubletrouble’ ... ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** 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 (doubletrouble)
doubletrouble.Rcheck/tests/testthat.Rout
R version 4.4.2 (2024-10-31) -- "Pile of Leaves" 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. > # This file is part of the standard setup for testthat. > # It is recommended that you do not modify it. > # > # Where should you do additional test configuration? > # Learn more about the roles of various files in: > # * https://r-pkgs.org/tests.html > # * https://testthat.r-lib.org/reference/test_package.html#special-files > > library(testthat) > library(doubletrouble) > > test_check("doubletrouble") 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, saveRDS, 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: GenomeInfoDb Loading required package: IRanges Loading required package: GenomicRanges 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 Calculating rates for species 'Scerevisiae' For species Scerevisiae, the lengths of 1 CDS are not multiples of 3. Removing them... Bayesian Information Criterion (BIC): E V 1 -5627.215 -5627.215 2 -4833.369 -4312.906 Top 3 models based on the BIC criterion: V,2 E,2 E,1 -4312.906 -4833.369 -5627.215 [ FAIL 0 | WARN 0 | SKIP 0 | PASS 69 ] > > proc.time() user system elapsed 26.928 1.856 28.783
doubletrouble.Rcheck/doubletrouble-Ex.timings
name | user | system | elapsed | |
cds_scerevisiae | 0.006 | 0.002 | 0.007 | |
classify_gene_pairs | 6.657 | 0.221 | 6.935 | |
classify_genes | 0.037 | 0.002 | 0.040 | |
diamond_inter | 0.057 | 0.002 | 0.060 | |
diamond_intra | 0.061 | 0.003 | 0.065 | |
duplicates2counts | 0.047 | 0.002 | 0.050 | |
find_ks_peaks | 0.124 | 0.003 | 0.128 | |
fungi_kaks | 0.030 | 0.002 | 0.032 | |
get_anchors_list | 1.413 | 0.037 | 1.468 | |
get_intron_counts | 2.845 | 0.047 | 2.892 | |
get_segmental | 1.231 | 0.041 | 1.271 | |
get_tandem_proximal | 1.047 | 0.027 | 1.073 | |
get_transposed | 1.491 | 0.054 | 1.551 | |
get_transposed_classes | 3.032 | 0.110 | 3.142 | |
gmax_ks | 0.325 | 0.006 | 0.331 | |
pairs2kaks | 1.852 | 0.126 | 3.776 | |
plot_duplicate_freqs | 1.828 | 0.486 | 0.524 | |
plot_ks_distro | 0.476 | 0.096 | 0.571 | |
plot_ks_peaks | 0.253 | 0.028 | 0.281 | |
plot_rates_by_species | 1.470 | 0.192 | 1.662 | |
split_pairs_by_peak | 0.262 | 0.006 | 0.268 | |
yeast_annot | 0.259 | 0.007 | 0.265 | |
yeast_seq | 0.391 | 0.008 | 0.404 | |