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 11:41 -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 272/2274 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
Category 2.73.0 (landing page) Bioconductor Package Maintainer
| 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 | OK | ||||||||||
To the developers/maintainers of the Category package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/Category.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: Category |
Version: 2.73.0 |
Command: E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:Category.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings Category_2.73.0.tar.gz |
StartedAt: 2024-12-23 22:54:50 -0500 (Mon, 23 Dec 2024) |
EndedAt: 2024-12-23 23:01:04 -0500 (Mon, 23 Dec 2024) |
EllapsedTime: 374.1 seconds |
RetCode: 0 |
Status: OK |
CheckDir: Category.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:Category.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings Category_2.73.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'E:/biocbuild/bbs-3.21-bioc/meat/Category.Rcheck' * using R Under development (unstable) (2024-10-26 r87273 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 'Category/DESCRIPTION' ... OK * this is package 'Category' version '2.73.0' * 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 'Category' 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 ... NOTE checkRd: (-1) HyperGParams-class.Rd:99: Lost braces 99 | \item{code{annotation(object)}}{Accessor for annotation. If you want | ^ checkRd: (-1) cb_parse_band_Hs.Rd:23: Escaped LaTeX specials: \_ \_ \_ checkRd: (-1) cb_parse_band_Mm.Rd:22: Escaped LaTeX specials: \& * checking Rd metadata ... OK * checking Rd cross-references ... NOTE Unknown package 'KEGG.db' in Rd xrefs * 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 sizes of PDF files under 'inst/doc' ... OK * checking files in 'vignettes' ... OK * checking examples ... OK * checking for unstated dependencies in 'tests' ... OK * checking tests ... Running 'runTests.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: 2 NOTEs See 'E:/biocbuild/bbs-3.21-bioc/meat/Category.Rcheck/00check.log' for details.
Category.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD INSTALL Category ### ############################################################################## ############################################################################## * installing to library 'E:/biocbuild/bbs-3.21-bioc/R/library' * installing *source* package 'Category' ... ** 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 (Category)
Category.Rcheck/tests/runTests.Rout
R Under development (unstable) (2024-10-26 r87273 ucrt) -- "Unsuffered Consequences" 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. > require("Category") || stop("unable to load Category") Loading required package: Category Loading required package: stats4 Loading required package: BiocGenerics Loading required package: generics Attaching package: 'generics' The following objects are masked from 'package:base': as.difftime, as.factor, as.ordered, intersect, is.element, setdiff, setequal, union 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, is.unsorted, lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply, saveRDS, table, tapply, unique, unsplit, which.max, which.min Loading required package: AnnotationDbi 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")'. Loading required package: IRanges 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 Attaching package: 'IRanges' The following object is masked from 'package:grDevices': windows Loading required package: Matrix Attaching package: 'Matrix' The following object is masked from 'package:S4Vectors': expand [1] TRUE > BiocGenerics:::testPackage("Category", "UnitTests", ".*_test\\.R$") Loading required package: org.Hs.eg.db 'select()' returned 1:many mapping between keys and columns 'select()' returned 1:many mapping between keys and columns 'select()' returned 1:many mapping between keys and columns Loading required package: graph Attaching package: 'GOstats' The following object is masked from 'package:AnnotationDbi': makeGOGraph RUNIT TEST PROTOCOL -- Mon Dec 23 23:00:50 2024 *********************************************** Number of test functions: 14 Number of errors: 0 Number of failures: 0 1 Test Suite : Category RUnit Tests - 14 test functions, 0 errors, 0 failures Number of test functions: 14 Number of errors: 0 Number of failures: 0 Warning messages: 1: In makeValidParams(.Object) : removing duplicate IDs in geneIds 2: In makeValidParams(.Object) : removing duplicate IDs in universeGeneIds 3: In makeValidParams(.Object) : removing geneIds not in universeGeneIds 4: In makeValidParams(.Object) : removing duplicate IDs in geneIds 5: In makeValidParams(.Object) : removing duplicate IDs in universeGeneIds 6: In makeValidParams(.Object) : removing geneIds not in universeGeneIds 7: In makeValidParams(.Object) : converting geneIds from list to atomic vector via unlist 8: In makeValidParams(.Object) : converting univ from list to atomic vector via unlist 9: In makeValidParams(.Object) : removing duplicate IDs in universeGeneIds > > proc.time() user system elapsed 52.65 18.20 185.92
Category.Rcheck/Category-Ex.timings
name | user | system | elapsed | |
ChrBandTree-class | 4.65 | 0.27 | 5.00 | |
ChrMapHyperGParams-class | 0 | 0 | 0 | |
ChrMapHyperGResult-class | 0 | 0 | 0 | |
ChrMapLinearMParams-class | 0 | 0 | 0 | |
ChrMapLinearMResult-class | 0 | 0 | 0 | |
DatPkg-class | 0.04 | 0.00 | 0.04 | |
HyperGResult-accessors | 1.03 | 0.02 | 1.12 | |
LinearMResult-class | 0 | 0 | 0 | |
MAPAmat | 3.56 | 0.11 | 3.67 | |
applyByCategory | 0 | 0 | 0 | |
cateGOryMatrix | 0.22 | 0.03 | 0.26 | |
cb_parse_band_Hs | 0 | 0 | 0 | |
cb_parse_band_Mm | 0 | 0 | 0 | |
findAMstats | 0 | 0 | 0 | |
getPathNames | 0.03 | 0.01 | 1.20 | |
gseattperm | 1.04 | 0.08 | 1.13 | |
hyperg | 0.62 | 0.02 | 0.64 | |
makeChrBandGraph | 2.28 | 0.07 | 2.36 | |
makeEBcontr | 0.16 | 0.03 | 0.18 | |
probes2MAP | 0.22 | 0.00 | 0.22 | |
probes2Path | 0.06 | 0.00 | 0.08 | |
ttperm | 0.02 | 0.00 | 0.02 | |