Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-08-27 11:40 -0400 (Tue, 27 Aug 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
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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" | 4421 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4415 |
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 2185/2255 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
TypeInfo 1.71.0 (landing page) Duncan Temple Lang
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | ![]() | ||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | ERROR | skipped | skipped | |||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | ![]() | ||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | ERROR | skipped | skipped | |||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
To the developers/maintainers of the TypeInfo package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/TypeInfo.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: TypeInfo |
Version: 1.71.0 |
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:TypeInfo.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings TypeInfo_1.71.0.tar.gz |
StartedAt: 2024-08-27 04:56:08 -0400 (Tue, 27 Aug 2024) |
EndedAt: 2024-08-27 04:56:29 -0400 (Tue, 27 Aug 2024) |
EllapsedTime: 21.0 seconds |
RetCode: 0 |
Status: OK |
CheckDir: TypeInfo.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:TypeInfo.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings TypeInfo_1.71.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/TypeInfo.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 * running under: Ubuntu 22.04.4 LTS * using session charset: UTF-8 * checking for file ‘TypeInfo/DESCRIPTION’ ... OK * this is package ‘TypeInfo’ version ‘1.71.0’ * 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 ‘TypeInfo’ can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... NOTE License components which are templates and need '+ file LICENSE': BSD_2_clause * checking top-level files ... NOTE File LICENSE is not mentioned in the DESCRIPTION file. * 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 loading without being on the library search path ... 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 ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking files in ‘vignettes’ ... OK * checking examples ... OK * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘copyEnv.R’ Running ‘copySubstitute.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 2 NOTEs See ‘/home/biocbuild/bbs-3.20-bioc/meat/TypeInfo.Rcheck/00check.log’ for details.
TypeInfo.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL TypeInfo ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’ * installing *source* package ‘TypeInfo’ ... ** using staged installation ** R ** 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 (TypeInfo)
TypeInfo.Rcheck/tests/copyEnv.Rout
R version 4.4.1 (2024-06-14) -- "Race for Your Life" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu 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(Biobase) 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 Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. > library(TypeInfo) > typeInfo( copyEnv ) <- + SimultaneousTypeSpecification( + TypedSignature( + oldEnv = "environment" , + newEnv = "environment" , + all.names = "logical" + ), + returnType = "vector") > > proc.time() user system elapsed 0.665 0.036 0.690
TypeInfo.Rcheck/tests/copySubstitute.Rout
R version 4.4.1 (2024-06-14) -- "Race for Your Life" Copyright (C) 2024 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu 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(TypeInfo) > require(Biobase) Loading required package: Biobase 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 Welcome to Bioconductor Vignettes contain introductory material; view with 'browseVignettes()'. To cite Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'. > copySubstitute <- Biobase::copySubstitute > > > typeInfo( copySubstitute ) <- + IndependentTypeSpecification( + src = c("character", "connection"), + dest = expression(is(dest, class(src))), + symbolValues = "list" , + symbolDelimiter = expression(is.character(symbolDelimiter) && + length(symbolDelimiter) == 1 && + all(nchar(symbolDelimiter) == 1)), + allowUnresolvedSymbols = "logical" , + recursive = "logical" , + removeExtension = "character", + returnType = "NULL") > > > infile = tempfile() > outfile = tempfile() > > writeLines(text=c("We will perform in @WHAT@:", + "So, thanks to @WHOM@ at once and to each one,", + "Whom we invite to see us crown'd at @WHERE@."), + con = infile) > > ## create the symbol table > z = list(WHAT="measure, time and place", WHOM="all", WHERE="Scone") > > ## run copySubstitute > copySubstitute(infile, outfile, z) NULL > > cat("Next call should be an error\n") Next call should be an error > ## should be caught, but is not > tryCatch({ + copySubstitute(123, outfile, z); + stop("should have caught that!") + }, error=function(err) {}) NULL > > proc.time() user system elapsed 0.728 0.052 0.769
TypeInfo.Rcheck/TypeInfo-Ex.timings
name | user | system | elapsed | |
DynamicTypeTest-class | 0.034 | 0.004 | 0.038 | |
IndependentTypeSpecification-class | 0.029 | 0.000 | 0.029 | |
IndependentTypeSpecification | 0.016 | 0.000 | 0.016 | |
NamedTypeTest-class | 0.003 | 0.000 | 0.002 | |
ReturnTypeSpecification | 0.003 | 0.000 | 0.002 | |
SimultaneousTypeSpecification | 0.007 | 0.000 | 0.006 | |
TypedSignature | 0.001 | 0.000 | 0.001 | |
checkArgs | 0.000 | 0.000 | 0.001 | |
hasParameterType | 0.006 | 0.000 | 0.007 | |
rewriteTypeCheck | 0 | 0 | 0 | |
showTypeInfo | 0.002 | 0.000 | 0.002 | |