Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2024-12-24 11:47 -0500 (Tue, 24 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2024-10-21 r87258) -- "Unsuffered Consequences" | 4754 |
palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" | 4472 |
lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4426 |
kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2024-11-20 r87352) -- "Unsuffered Consequences" | 4381 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" | 4373 |
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 1315/2274 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
MouseFM 1.17.0 (landing page) Matthias Munz
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | |||||||||
kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | OK | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | WARNINGS | ||||||||||
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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
Package: MouseFM |
Version: 1.17.0 |
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:MouseFM.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings MouseFM_1.17.0.tar.gz |
StartedAt: 2024-12-24 08:53:52 -0000 (Tue, 24 Dec 2024) |
EndedAt: 2024-12-24 08:59:31 -0000 (Tue, 24 Dec 2024) |
EllapsedTime: 339.4 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: MouseFM.Rcheck |
Warnings: 5 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD check --install=check:MouseFM.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings MouseFM_1.17.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/MouseFM.Rcheck’ * using R Under development (unstable) (2024-11-24 r87369) * using platform: aarch64-unknown-linux-gnu * R was compiled by aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0 GNU Fortran (GCC) 14.2.0 * running under: openEuler 24.03 (LTS) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘MouseFM/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘MouseFM’ version ‘1.17.0’ * 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 ... WARNING Found the following significant warnings: Warning: program compiled against libxml 212 using older 211 See ‘/home/biocbuild/bbs-3.21-bioc/meat/MouseFM.Rcheck/00install.out’ for details. * 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 ... NOTE Warning: program compiled against libxml 212 using older 211 A namespace must be able to be loaded with just the base namespace loaded: otherwise if the namespace gets loaded by a saved object, the session will be unable to start. Probably some imports need to be declared in the NAMESPACE file. * checking whether the namespace can be unloaded cleanly ... OK * checking loading without being on the library search path ... OK * checking whether startup messages can be suppressed ... NOTE Warning: program compiled against libxml 212 using older 211 It looks like this package (or a package it requires) has a startup message which cannot be suppressed: see ?packageStartupMessage. * checking dependencies in R code ... NOTE Warning: program compiled against libxml 212 using older 211 * checking S3 generic/method consistency ... WARNING Warning: program compiled against libxml 212 using older 211 See section ‘Generic functions and methods’ in the ‘Writing R Extensions’ manual. * checking replacement functions ... WARNING Warning: program compiled against libxml 212 using older 211 The argument of a replacement function which corresponds to the right hand side must be named ‘value’. * checking foreign function calls ... NOTE Warning: program compiled against libxml 212 using older 211 See chapter ‘System and foreign language interfaces’ in the ‘Writing R Extensions’ manual. * checking R code for possible problems ... NOTE File ‘MouseFM/R/zzz.R’: .onLoad calls: packageStartupMessage("\n ---------\n For example usage please run: vignette('MouseFM')\n \n Support me: http://matthiasmunz.de/support_me\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 Github Repo: https://github.com/matmu/MouseFM\n MouseFM Backend: https://github.com/matmu/MouseFM-Backend\n ---------", domain = NULL, appendLF = TRUE) See section ‘Good practice’ in '?.onAttach'. Warning: program compiled against libxml 212 using older 211 * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... WARNING Warning: program compiled against libxml 212 using older 211 All user-level objects in a package should have documentation entries. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. * checking for code/documentation mismatches ... WARNING Warning: program compiled against libxml 212 using older 211 Warning: program compiled against libxml 212 using older 211 Warning: program compiled against libxml 212 using older 211 * checking Rd \usage sections ... NOTE Warning: program compiled against libxml 212 using older 211 The \usage entries for S3 methods should use the \method markup and not their full name. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. * 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 40.019 0.211 42.267 get_top 15.337 0.084 16.029 prio 14.580 0.076 15.769 annotate_mouse_genes 2.173 0.139 6.618 * 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: 5 WARNINGs, 6 NOTEs See ‘/home/biocbuild/bbs-3.21-bioc/meat/MouseFM.Rcheck/00check.log’ for details.
MouseFM.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL MouseFM ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library’ * installing *source* package ‘MouseFM’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading Warning: program compiled against libxml 212 using older 211 ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location Warning: program compiled against libxml 212 using older 211 ** testing if installed package can be loaded from final location Warning: program compiled against libxml 212 using older 211 ** testing if installed package keeps a record of temporary installation path * DONE (MouseFM)
MouseFM.Rcheck/tests/testthat.Rout
R Under development (unstable) (2024-11-24 r87369) -- "Unsuffered Consequences" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: aarch64-unknown-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. > library(testthat) > library(MouseFM) Warning: program compiled against libxml 212 using older 211 --------- For example usage please run: vignette('MouseFM') Support me: http://matthiasmunz.de/support_me 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 Github Repo: https://github.com/matmu/MouseFM MouseFM Backend: https://github.com/matmu/MouseFM-Backend --------- > > test_check("MouseFM") [ FAIL 0 | WARN 0 | SKIP 0 | PASS 9 ] > > proc.time() user system elapsed 84.713 2.127 95.355
MouseFM.Rcheck/MouseFM-Ex.timings
name | user | system | elapsed | |
GRanges2df | 0.258 | 0.004 | 1.557 | |
annotate_consequences | 0.399 | 0.001 | 4.942 | |
annotate_mouse_genes | 2.173 | 0.139 | 6.618 | |
avail_chromosomes | 0.003 | 0.000 | 0.004 | |
avail_consequences | 0.002 | 0.000 | 0.002 | |
avail_strains | 0.002 | 0.000 | 0.001 | |
df2GRanges | 0.070 | 0.015 | 1.135 | |
fetch | 2.393 | 0.100 | 4.810 | |
finemap | 0.055 | 0.004 | 0.618 | |
getURL | 0 | 0 | 0 | |
get_top | 15.337 | 0.084 | 16.029 | |
prio | 14.580 | 0.076 | 15.769 | |
ref_genome | 0 | 0 | 0 | |
setURL | 0 | 0 | 0 | |
vis_reduction_factors | 40.019 | 0.211 | 42.267 | |