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 1260/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
midasHLA 1.14.0 (landing page) Maciej Migdał
| 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 | ERROR | OK | |||||||||
To the developers/maintainers of the midasHLA package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/midasHLA.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: midasHLA |
Version: 1.14.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:midasHLA.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings midasHLA_1.14.0.tar.gz |
StartedAt: 2024-12-21 01:16:50 -0500 (Sat, 21 Dec 2024) |
EndedAt: 2024-12-21 01:22:46 -0500 (Sat, 21 Dec 2024) |
EllapsedTime: 355.7 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: midasHLA.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:midasHLA.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings midasHLA_1.14.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/midasHLA.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 ‘midasHLA/DESCRIPTION’ ... OK * this is package ‘midasHLA’ version ‘1.14.0’ * 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 ... NOTE Found the following hidden files and directories: .BBSoptions These were most likely included in error. See section ‘Package structure’ in the ‘Writing R Extensions’ manual. * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘midasHLA’ can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... NOTE License stub is invalid DCF. * 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 ... NOTE checkRd: (-1) omnibusTest.Rd:39: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) omnibusTest.Rd:40: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) omnibusTest.Rd:41: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) omnibusTest.Rd:42: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) omnibusTest.Rd:43: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) omnibusTest.Rd:44: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) omnibusTest.Rd:45: Lost braces in \itemize; \value handles \item{}{} directly checkRd: (-1) runMiDAS.Rd:151-154: Lost braces in \itemize; meant \describe ? checkRd: (-1) runMiDAS.Rd:155-158: Lost braces in \itemize; meant \describe ? checkRd: (-1) runMiDAS.Rd:159-163: Lost braces in \itemize; meant \describe ? checkRd: (-1) runMiDAS.Rd:164-168: Lost braces in \itemize; meant \describe ? * 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 'kableResults.Rd': kableResults Code: function(results, colnames = NULL, header = "MiDAS analysis results", pvalue_cutoff = NULL, format = "html", scroll_box_height = "400px") Docs: function(results, colnames = NULL, header = "MiDAS analysis results", pvalue_cutoff = NULL, format = getOption("knitr.table.format"), scroll_box_height = "400px") Mismatches in argument default values: Name: 'format' Code: "html" Docs: getOption("knitr.table.format") * 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 ... NOTE Note: found 1180 marked UTF-8 strings * 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 runMiDAS 12.312 0.196 13.297 omnibusTest 6.923 0.153 7.854 getAAFrequencies 6.640 0.163 6.812 kableResults 6.384 0.138 6.929 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ ERROR Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output: anyMissing, rowMedians > > test_check("midasHLA") [ FAIL 1 | WARN 20 | SKIP 0 | PASS 308 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Failure ('test_utils.R:166:3'): LRTest ────────────────────────────────────── `lrt_res` not equal to data.frame(...). Component "logLik": Mean relative difference: 0.005254902 Component "statistic": Mean relative difference: 0.005254902 [ FAIL 1 | WARN 20 | SKIP 0 | PASS 308 ] Error: Test failures Execution halted * 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 ERROR, 1 WARNING, 4 NOTEs See ‘/Users/biocbuild/bbs-3.20-bioc/meat/midasHLA.Rcheck/00check.log’ for details.
midasHLA.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL midasHLA ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library’ * installing *source* package ‘midasHLA’ ... ** 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 (midasHLA)
midasHLA.Rcheck/tests/testthat.Rout.fail
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. > library(testthat) > library(midasHLA) Loading required package: MultiAssayExperiment Loading required package: SummarizedExperiment Loading required package: MatrixGenerics Loading required package: matrixStats Attaching package: 'MatrixGenerics' The following objects are masked from 'package:matrixStats': colAlls, colAnyNAs, colAnys, colAvgsPerRowSet, colCollapse, colCounts, colCummaxs, colCummins, colCumprods, colCumsums, colDiffs, colIQRDiffs, colIQRs, colLogSumExps, colMadDiffs, colMads, colMaxs, colMeans2, colMedians, colMins, colOrderStats, colProds, colQuantiles, colRanges, colRanks, colSdDiffs, colSds, colSums2, colTabulates, colVarDiffs, colVars, colWeightedMads, colWeightedMeans, colWeightedMedians, colWeightedSds, colWeightedVars, rowAlls, rowAnyNAs, rowAnys, rowAvgsPerColSet, rowCollapse, rowCounts, rowCummaxs, rowCummins, rowCumprods, rowCumsums, rowDiffs, rowIQRDiffs, rowIQRs, rowLogSumExps, rowMadDiffs, rowMads, rowMaxs, rowMeans2, rowMedians, rowMins, rowOrderStats, rowProds, rowQuantiles, rowRanges, rowRanks, rowSdDiffs, rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars, rowWeightedMads, rowWeightedMeans, rowWeightedMedians, rowWeightedSds, rowWeightedVars Loading required package: GenomicRanges Loading required package: stats4 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 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: IRanges Loading required package: GenomeInfoDb 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: 'Biobase' The following object is masked from 'package:MatrixGenerics': rowMedians The following objects are masked from 'package:matrixStats': anyMissing, rowMedians > > test_check("midasHLA") [ FAIL 1 | WARN 20 | SKIP 0 | PASS 308 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Failure ('test_utils.R:166:3'): LRTest ────────────────────────────────────── `lrt_res` not equal to data.frame(...). Component "logLik": Mean relative difference: 0.005254902 Component "statistic": Mean relative difference: 0.005254902 [ FAIL 1 | WARN 20 | SKIP 0 | PASS 308 ] Error: Test failures Execution halted
midasHLA.Rcheck/midasHLA-Ex.timings
name | user | system | elapsed | |
HWETest | 2.010 | 0.046 | 2.083 | |
analyzeAssociations | 0.532 | 0.012 | 0.543 | |
analyzeConditionalAssociations | 0.459 | 0.013 | 0.470 | |
checkAlleleFormat | 0.001 | 0.000 | 0.000 | |
checkKirGenesFormat | 0 | 0 | 0 | |
convertAlleleToVariable | 0.005 | 0.001 | 0.007 | |
countsToVariables | 0.020 | 0.031 | 0.051 | |
filterByFrequency | 0.201 | 0.017 | 0.219 | |
filterByOmnibusGroups | 0.084 | 0.005 | 0.089 | |
filterByVariables | 0.191 | 0.002 | 0.193 | |
formatResults | 0 | 0 | 0 | |
getAAFrequencies | 6.640 | 0.163 | 6.812 | |
getAlleleResolution | 0.000 | 0.000 | 0.001 | |
getAllelesForAA | 0.834 | 0.011 | 0.845 | |
getExperiments | 0 | 0 | 0 | |
getFrequencies | 0.271 | 0.054 | 0.327 | |
getHlaCalls | 0.094 | 0.086 | 0.186 | |
getHlaFrequencies | 0.173 | 0.020 | 0.196 | |
getHlaKirInteractions | 3.104 | 0.239 | 3.383 | |
getKIRFrequencies | 0.005 | 0.001 | 0.006 | |
getKirCalls | 0.032 | 0.071 | 0.102 | |
getOmnibusGroups | 0.046 | 0.016 | 0.063 | |
getPlaceholder | 0.000 | 0.001 | 0.001 | |
getVariableAAPos | 0.018 | 0.001 | 0.020 | |
hlaCallsGranthamDistance | 1.247 | 0.132 | 1.380 | |
hlaToAAVariation | 3.149 | 0.489 | 3.640 | |
hlaToVariable | 0.276 | 0.026 | 0.302 | |
kableResults | 6.384 | 0.138 | 6.929 | |
omnibusTest | 6.923 | 0.153 | 7.854 | |
prepareMiDAS | 0.255 | 0.009 | 0.293 | |
readHlaAlignments | 0.654 | 0.015 | 0.741 | |
readHlaCalls | 0.129 | 0.003 | 0.146 | |
readKirCalls | 0.038 | 0.072 | 0.124 | |
reduceAlleleResolution | 0.000 | 0.001 | 0.001 | |
reduceHlaCalls | 0.223 | 0.081 | 0.334 | |
runMiDAS | 12.312 | 0.196 | 13.297 | |
summariseAAPosition | 0.709 | 0.010 | 0.727 | |