Back to Multiple platform build/check report for BioC 3.18: simplified long |
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This page was generated on 2024-04-17 11:37:58 -0400 (Wed, 17 Apr 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" | 4676 |
palomino4 | Windows Server 2022 Datacenter | x64 | 4.3.3 (2024-02-29 ucrt) -- "Angel Food Cake" | 4414 |
merida1 | macOS 12.7.1 Monterey | x86_64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4437 |
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 1315/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
MouseFM 1.12.0 (landing page) Matthias Munz
| 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 MouseFM package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/MouseFM.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: MouseFM |
Version: 1.12.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:MouseFM.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings MouseFM_1.12.0.tar.gz |
StartedAt: 2024-04-16 05:43:27 -0400 (Tue, 16 Apr 2024) |
EndedAt: 2024-04-16 05:52:43 -0400 (Tue, 16 Apr 2024) |
EllapsedTime: 555.3 seconds |
RetCode: 0 |
Status: OK |
CheckDir: MouseFM.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:MouseFM.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings MouseFM_1.12.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.18-bioc/meat/MouseFM.Rcheck’ * using R version 4.3.3 (2024-02-29) * using platform: x86_64-apple-darwin20 (64-bit) * R was compiled by Apple clang version 14.0.0 (clang-1400.0.29.202) GNU Fortran (GCC) 12.2.0 * running under: macOS Monterey 12.7.1 * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘MouseFM/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘MouseFM’ version ‘1.12.0’ * 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 ‘MouseFM’ 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 startup messages can be suppressed ... 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 ... NOTE File ‘MouseFM/R/zzz.R’: .onLoad calls: packageStartupMessage("\n ---------\n \n For example usage please run: vignette('MouseFM')\n \n Github Repo: https://github.com/matmu/MouseFM\n MouseFM Backend: https://github.com/matmu/MouseFM-Backend \n\n Citation appreciated:\n Munz M, Khodaygani M, Aherrahrou Z, Busch H, Wohlers I (2021) In silico candidate variant and gene identification using inbred mouse strains. PeerJ. doi:10.7717/peerj.11017\n \n ---------", domain = NULL, appendLF = TRUE) See section ‘Good practice’ in '?.onAttach'. * 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 vis_reduction_factors 64.186 0.502 70.659 get_top 21.975 0.293 23.858 prio 21.460 0.096 23.255 fetch 3.781 0.119 6.230 annotate_mouse_genes 2.468 0.056 5.682 annotate_consequences 0.614 0.013 13.585 GRanges2df 0.392 0.015 7.337 * 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 ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 1 NOTE See ‘/Users/biocbuild/bbs-3.18-bioc/meat/MouseFM.Rcheck/00check.log’ for details.
MouseFM.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL MouseFM ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library’ * installing *source* package ‘MouseFM’ ... ** 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 (MouseFM)
MouseFM.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-apple-darwin20 (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. > library(testthat) > library(MouseFM) --------- For example usage please run: vignette('MouseFM') Github Repo: https://github.com/matmu/MouseFM MouseFM Backend: https://github.com/matmu/MouseFM-Backend Citation appreciated: Munz M, Khodaygani M, Aherrahrou Z, Busch H, Wohlers I (2021) In silico candidate variant and gene identification using inbred mouse strains. PeerJ. doi:10.7717/peerj.11017 --------- > > test_check("MouseFM") [ FAIL 0 | WARN 0 | SKIP 0 | PASS 9 ] > > proc.time() user system elapsed 128.081 1.542 140.175
MouseFM.Rcheck/MouseFM-Ex.timings
name | user | system | elapsed | |
GRanges2df | 0.392 | 0.015 | 7.337 | |
annotate_consequences | 0.614 | 0.013 | 13.585 | |
annotate_mouse_genes | 2.468 | 0.056 | 5.682 | |
avail_chromosomes | 0.005 | 0.001 | 0.006 | |
avail_consequences | 0.004 | 0.001 | 0.005 | |
avail_strains | 0.003 | 0.002 | 0.004 | |
df2GRanges | 0.146 | 0.005 | 0.522 | |
fetch | 3.781 | 0.119 | 6.230 | |
finemap | 0.111 | 0.004 | 0.336 | |
getURL | 0 | 0 | 0 | |
get_top | 21.975 | 0.293 | 23.858 | |
prio | 21.460 | 0.096 | 23.255 | |
ref_genome | 0.000 | 0.000 | 0.001 | |
setURL | 0.001 | 0.001 | 0.001 | |
vis_reduction_factors | 64.186 | 0.502 | 70.659 | |