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 12:05 -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 1829/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
RVS 1.28.0 (landing page) Alexandre Bureau
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | |||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | WARNINGS | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | WARNINGS | OK | |||||||||
To the developers/maintainers of the RVS package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/RVS.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: RVS |
Version: 1.28.0 |
Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:RVS.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings RVS_1.28.0.tar.gz |
StartedAt: 2024-12-20 05:32:33 -0500 (Fri, 20 Dec 2024) |
EndedAt: 2024-12-20 05:36:38 -0500 (Fri, 20 Dec 2024) |
EllapsedTime: 244.5 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: RVS.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:RVS.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings RVS_1.28.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/RVS.Rcheck' * using R version 4.4.2 (2024-10-31 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 13.3.0 GNU Fortran (GCC) 13.3.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * using option '--no-vignettes' * checking for file 'RVS/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'RVS' version '1.28.0' * 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 whether package 'RVS' 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 ... WARNING Codoc mismatches from Rd file 'RVsharing-methods.Rd': RVsharing Code: function(ped, carriers = NULL, alleleFreq = NA, kinshipCoeff = NA, nSim = NA, founderDist = NULL, useAffected = FALSE, kinshipOrder = 5, splitPed = FALSE, useFounderCouples = TRUE, distinguishHomo = FALSE, ...) Docs: function(ped, carriers = NULL, alleleFreq = NA, kinshipCoeff = NA, nSim = NA, founderDist = NULL, useAffected = FALSE, kinshipOrder = 5, splitPed = FALSE, useFounderCouples = TRUE, ...) Argument names in code not in docs: distinguishHomo Mismatches in argument names: Position: 11 Code: distinguishHomo Docs: ... \S4method{RVsharing}{pedigree} Code: function(ped, carriers = NULL, alleleFreq = NA, kinshipCoeff = NA, nSim = NA, founderDist = NULL, useAffected = FALSE, kinshipOrder = 5, splitPed = FALSE, useFounderCouples = TRUE, distinguishHomo = FALSE, ...) Docs: function(ped, carriers = NULL, alleleFreq = NA, kinshipCoeff = NA, nSim = NA, founderDist = NULL, useAffected = FALSE, kinshipOrder = 5, splitPed = FALSE, useFounderCouples = TRUE, ...) Argument names in code not in docs: distinguishHomo Mismatches in argument names: Position: 11 Code: distinguishHomo Docs: ... \S4method{RVsharing}{list} Code: function(ped, carriers = NULL, alleleFreq = NA, kinshipCoeff = NA, nSim = NA, founderDist = NULL, useAffected = FALSE, kinshipOrder = 5, splitPed = FALSE, useFounderCouples = TRUE, distinguishHomo = FALSE, ...) Docs: function(ped, carriers = NULL, alleleFreq = NA, kinshipCoeff = NA, nSim = NA, founderDist = NULL, useAffected = FALSE, kinshipOrder = 5, splitPed = FALSE, useFounderCouples = TRUE, ...) Argument names in code not in docs: distinguishHomo Mismatches in argument names: Position: 11 Code: distinguishHomo Docs: ... Codoc mismatches from Rd file 'oneFounderSharingProb.Rd': oneFounderSharingProb Code: function(procPed, distinguishHomo = FALSE) Docs: function(procPed) Argument names in code not in docs: distinguishHomo Codoc mismatches from Rd file 'twoFounderSharingProb.Rd': twoFounderSharingProb Code: function(procPed, kinshipCoeff, kinshipOrder, distinguishHomo = FALSE) Docs: function(procPed, kinshipCoeff, kinshipOrder) Argument names in code not in docs: distinguishHomo * checking Rd \usage sections ... NOTE Documented arguments not in \usage in Rd file 'denomProb.Rd': 'gRain' Documented arguments not in \usage in Rd file 'numerProb.Rd': 'gRain' Functions with \usage entries need to have the appropriate \alias entries, and all their arguments documented. The \usage entries must correspond to syntactically valid R code. See chapter 'Writing R documentation files' in the 'Writing R Extensions' manual. * 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 LazyData ... 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 RVgene 14.74 0.57 15.33 * 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: 1 WARNING, 1 NOTE See 'F:/biocbuild/bbs-3.20-bioc/meat/RVS.Rcheck/00check.log' for details.
RVS.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL RVS ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.20-bioc/R/library' * installing *source* package 'RVS' ... ** using staged installation ** R ** data *** moving datasets to lazyload DB ** 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 (RVS)
RVS.Rcheck/tests/testthat.Rout
R version 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-w64-mingw32/x64 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(RVS) > > test_check('RVS') Founder 2 subped size 20 Founder 4 subped size 11 Founder 5 subped size 16 Founder 9 subped size 5 Founder 13 subped size 5 Founder 14 subped size 3 Founder 16 subped size 5 [1] 0.01873 0.49970 0.48150 [ FAIL 0 | WARN 0 | SKIP 2 | PASS 113 ] ══ Skipped tests (2) ═══════════════════════════════════════════════════════════ • empty test (2): 'test_multipleFamilyCalculations.R:19:1', 'test_multipleFamilyCalculations.R:42:1' [ FAIL 0 | WARN 0 | SKIP 2 | PASS 113 ] > > proc.time() user system elapsed 105.18 1.89 107.59
RVS.Rcheck/RVS-Ex.timings
name | user | system | elapsed | |
ComputeKinshipPropCoef-methods | 0.25 | 0.01 | 0.27 | |
GeneDrop | 0 | 0 | 0 | |
RVgene | 14.74 | 0.57 | 15.33 | |
RVsharing-methods | 0.11 | 0.01 | 0.12 | |
SnpMatrixToCount | 0.00 | 0.02 | 0.02 | |
get.psubset | 2.78 | 0.18 | 2.97 | |
multipleFamilyPValue | 1.39 | 0.05 | 1.43 | |
ped2trio | 0 | 0 | 0 | |
processPedigree-methods | 0 | 0 | 0 | |