Back to Multiple platform build/check report for BioC 3.14 |
|
This page was generated on 2022-04-13 12:07:44 -0400 (Wed, 13 Apr 2022).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4324 |
tokay2 | Windows Server 2012 R2 Standard | x64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4077 |
machv2 | macOS 10.14.6 Mojave | x86_64 | 4.1.3 (2022-03-10) -- "One Push-Up" | 4137 |
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 |
To the developers/maintainers of the Category package: - Please 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 How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 250/2083 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
Category 2.60.0 (landing page) Bioconductor Package Maintainer
| nebbiolo2 | Linux (Ubuntu 20.04.4 LTS) / x86_64 | OK | OK | OK | |||||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |||||||||
machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |||||||||
Package: Category |
Version: 2.60.0 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:Category.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings Category_2.60.0.tar.gz |
StartedAt: 2022-04-12 11:12:16 -0400 (Tue, 12 Apr 2022) |
EndedAt: 2022-04-12 11:17:56 -0400 (Tue, 12 Apr 2022) |
EllapsedTime: 340.4 seconds |
RetCode: 0 |
Status: OK |
CheckDir: Category.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:Category.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings Category_2.60.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.14-bioc/meat/Category.Rcheck’ * using R version 4.1.3 (2022-03-10) * using platform: x86_64-apple-darwin17.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘Category/DESCRIPTION’ ... OK * this is package ‘Category’ version ‘2.60.0’ * 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 for sufficient/correct file permissions ... 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 R 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 ... 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 Examples with CPU (user + system) or elapsed time > 5s user system elapsed ChrBandTree-class 5.879 0.299 6.18 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘runTests.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 1 NOTE See ‘/Users/biocbuild/bbs-3.14-bioc/meat/Category.Rcheck/00check.log’ for details.
Category.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL Category ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/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 version 4.1.3 (2022-03-10) -- "One Push-Up" Copyright (C) 2022 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin17.0 (64-bit) 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 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, 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, sort, table, tapply, union, 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 objects are masked from 'package:base': I, expand.grid, unname 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 -- Tue Apr 12 11:17:45 2022 *********************************************** 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 81.746 16.379 98.789
Category.Rcheck/Category-Ex.timings
name | user | system | elapsed | |
ChrBandTree-class | 5.879 | 0.299 | 6.180 | |
ChrMapHyperGParams-class | 0.002 | 0.001 | 0.003 | |
ChrMapHyperGResult-class | 0.001 | 0.001 | 0.001 | |
ChrMapLinearMParams-class | 0.001 | 0.001 | 0.002 | |
ChrMapLinearMResult-class | 0.001 | 0.000 | 0.002 | |
DatPkg-class | 0.058 | 0.004 | 0.062 | |
HyperGResult-accessors | 1.252 | 0.057 | 1.376 | |
LinearMResult-class | 0.001 | 0.001 | 0.002 | |
MAPAmat | 4.090 | 0.308 | 4.407 | |
applyByCategory | 0.004 | 0.000 | 0.005 | |
cateGOryMatrix | 0.332 | 0.033 | 0.366 | |
cb_parse_band_Hs | 0.000 | 0.001 | 0.000 | |
cb_parse_band_Mm | 0.001 | 0.001 | 0.001 | |
findAMstats | 0.002 | 0.001 | 0.002 | |
getPathNames | 0.040 | 0.009 | 1.692 | |
gseattperm | 1.560 | 0.048 | 1.614 | |
hyperg | 0.911 | 0.064 | 0.976 | |
makeChrBandGraph | 3.043 | 0.101 | 3.145 | |
makeEBcontr | 0.228 | 0.014 | 0.243 | |
probes2MAP | 0.185 | 0.004 | 0.189 | |
probes2Path | 0.063 | 0.002 | 0.065 | |
ttperm | 0.020 | 0.004 | 0.024 | |