Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-08-16 11:41 -0400 (Fri, 16 Aug 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4703 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4440 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4472 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4420 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4413 |
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 1245/2255 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
midasHLA 1.13.0 (landing page) Maciej MigdaĆ
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | WARNINGS | ![]() | ||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | ERROR | OK | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | ERROR | ||||||||||
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: 1.13.0 |
Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:midasHLA.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings midasHLA_1.13.0.tar.gz |
StartedAt: 2024-08-16 02:38:55 -0400 (Fri, 16 Aug 2024) |
EndedAt: 2024-08-16 02:44:57 -0400 (Fri, 16 Aug 2024) |
EllapsedTime: 362.4 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: midasHLA.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:midasHLA.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings midasHLA_1.13.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/midasHLA.Rcheck' * using R version 4.4.1 (2024-06-14 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 13.2.0 GNU Fortran (GCC) 13.2.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * using option '--no-vignettes' * checking for file 'midasHLA/DESCRIPTION' ... OK * this is package 'midasHLA' version '1.13.0' * 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 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 12.61 0.24 12.87 getAAFrequencies 6.38 0.25 6.67 kableResults 6.12 0.14 6.29 omnibusTest 5.49 0.18 5.67 * 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, 4 NOTEs See 'F:/biocbuild/bbs-3.20-bioc/meat/midasHLA.Rcheck/00check.log' for details.
midasHLA.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL midasHLA ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.20-bioc/R/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
R version 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 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(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, 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 Attaching package: 'IRanges' The following object is masked from 'package:grDevices': windows 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 0 | WARN 20 | SKIP 0 | PASS 309 ] [ FAIL 0 | WARN 20 | SKIP 0 | PASS 309 ] > > proc.time() user system elapsed 65.34 3.65 69.87
midasHLA.Rcheck/midasHLA-Ex.timings
name | user | system | elapsed | |
HWETest | 2.01 | 0.04 | 2.09 | |
analyzeAssociations | 0.64 | 0.04 | 0.67 | |
analyzeConditionalAssociations | 0.59 | 0.00 | 0.59 | |
checkAlleleFormat | 0 | 0 | 0 | |
checkKirGenesFormat | 0 | 0 | 0 | |
convertAlleleToVariable | 0 | 0 | 0 | |
countsToVariables | 0.06 | 0.01 | 0.08 | |
filterByFrequency | 0.15 | 0.02 | 0.15 | |
filterByOmnibusGroups | 0.06 | 0.00 | 0.06 | |
filterByVariables | 0.19 | 0.00 | 0.19 | |
formatResults | 0 | 0 | 0 | |
getAAFrequencies | 6.38 | 0.25 | 6.67 | |
getAlleleResolution | 0 | 0 | 0 | |
getAllelesForAA | 0.73 | 0.00 | 0.73 | |
getExperiments | 0 | 0 | 0 | |
getFrequencies | 0.23 | 0.00 | 0.23 | |
getHlaCalls | 0.13 | 0.03 | 0.16 | |
getHlaFrequencies | 0.11 | 0.03 | 0.14 | |
getHlaKirInteractions | 3.12 | 0.25 | 3.48 | |
getKIRFrequencies | 0.02 | 0.00 | 0.02 | |
getKirCalls | 0.08 | 0.07 | 0.14 | |
getOmnibusGroups | 0.00 | 0.03 | 0.03 | |
getPlaceholder | 0 | 0 | 0 | |
getVariableAAPos | 0.02 | 0.01 | 0.03 | |
hlaCallsGranthamDistance | 1.19 | 0.13 | 1.31 | |
hlaToAAVariation | 3.72 | 0.37 | 4.10 | |
hlaToVariable | 0.34 | 0.04 | 0.39 | |
kableResults | 6.12 | 0.14 | 6.29 | |
omnibusTest | 5.49 | 0.18 | 5.67 | |
prepareMiDAS | 0.30 | 0.02 | 0.32 | |
readHlaAlignments | 1.20 | 0.05 | 1.25 | |
readHlaCalls | 0.15 | 0.00 | 0.15 | |
readKirCalls | 0.10 | 0.04 | 0.16 | |
reduceAlleleResolution | 0 | 0 | 0 | |
reduceHlaCalls | 0.33 | 0.08 | 0.41 | |
runMiDAS | 12.61 | 0.24 | 12.87 | |
summariseAAPosition | 0.51 | 0.01 | 0.53 | |