Back to Multiple platform build/check report for BioC 3.18: simplified long |
|
This page was generated on 2024-03-29 11:35:55 -0400 (Fri, 29 Mar 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4669 |
palomino4 | Windows Server 2022 Datacenter | x64 | 4.3.3 (2024-02-29 ucrt) -- "Angel Food Cake" | 4404 |
merida1 | macOS 12.7.1 Monterey | x86_64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4427 |
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 595/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
doubletrouble 1.2.5 (landing page) Fabrício Almeida-Silva
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson1 | macOS 13.6.1 Ventura / arm64 | see weekly results here | ||||||||||||
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: 1.2.5 |
Command: /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:doubletrouble.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings doubletrouble_1.2.5.tar.gz |
StartedAt: 2024-03-27 22:04:16 -0400 (Wed, 27 Mar 2024) |
EndedAt: 2024-03-27 22:10:14 -0400 (Wed, 27 Mar 2024) |
EllapsedTime: 358.0 seconds |
RetCode: 0 |
Status: OK |
CheckDir: doubletrouble.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:doubletrouble.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings doubletrouble_1.2.5.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/doubletrouble.Rcheck’ * using R version 4.3.3 (2024-02-29) * using platform: x86_64-pc-linux-gnu (64-bit) * 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 ‘doubletrouble/DESCRIPTION’ ... OK * this is package ‘doubletrouble’ version ‘1.2.5’ * 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 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 loading without being on the library search path ... 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 5.688 0.324 6.013 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... ‘doubletrouble_vignette.Rmd’ using ‘UTF-8’... OK NONE * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: OK
doubletrouble.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD INSTALL doubletrouble ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.18-bioc/R/site-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 4.3.3 (2024-02-29) -- "Angel Food Cake" Copyright (C) 2024 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. > # 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") 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 68 ] > > proc.time() user system elapsed 25.359 3.010 28.079
doubletrouble.Rcheck/doubletrouble-Ex.timings
name | user | system | elapsed | |
cds_scerevisiae | 0.004 | 0.000 | 0.005 | |
classify_gene_pairs | 5.688 | 0.324 | 6.013 | |
classify_genes | 0.026 | 0.000 | 0.026 | |
diamond_inter | 0.038 | 0.000 | 0.038 | |
diamond_intra | 0.036 | 0.004 | 0.040 | |
duplicates2counts | 0.034 | 0.004 | 0.037 | |
find_ks_peaks | 0.127 | 0.012 | 0.139 | |
fungi_kaks | 0.019 | 0.000 | 0.019 | |
get_anchors_list | 0.986 | 0.024 | 1.011 | |
get_intron_counts | 2.241 | 0.092 | 2.333 | |
get_segmental | 0.956 | 0.036 | 0.991 | |
get_tandem_proximal | 0.802 | 0.012 | 0.814 | |
get_transposed | 1.119 | 0.028 | 1.147 | |
get_transposed_classes | 2.222 | 0.044 | 2.266 | |
gmax_ks | 0.210 | 0.000 | 0.209 | |
pairs2kaks | 3.283 | 0.629 | 4.628 | |
plot_duplicate_freqs | 1.064 | 0.316 | 0.496 | |
plot_ks_distro | 0.496 | 0.112 | 0.607 | |
plot_ks_peaks | 0.295 | 0.052 | 0.347 | |
plot_rates_by_species | 0.235 | 0.052 | 0.286 | |
split_pairs_by_peak | 0.47 | 0.08 | 0.55 | |
yeast_annot | 0.183 | 0.020 | 0.204 | |
yeast_seq | 0.237 | 0.012 | 0.249 | |