| Back to Multiple platform build/check report for BioC 3.13 |
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This page was generated on 2021-10-15 15:06:57 -0400 (Fri, 15 Oct 2021).
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To the developers/maintainers of the TypeInfo package: - Please 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 How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 1982/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| TypeInfo 1.58.0 (landing page) Duncan Temple Lang
| nebbiolo1 | Linux (Ubuntu 20.04.2 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: TypeInfo |
| Version: 1.58.0 |
| Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:TypeInfo.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings TypeInfo_1.58.0.tar.gz |
| StartedAt: 2021-10-15 01:02:59 -0400 (Fri, 15 Oct 2021) |
| EndedAt: 2021-10-15 01:03:39 -0400 (Fri, 15 Oct 2021) |
| EllapsedTime: 39.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: TypeInfo.Rcheck |
| Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:TypeInfo.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings TypeInfo_1.58.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/TypeInfo.Rcheck’ * using R version 4.1.1 (2021-08-10) * using platform: x86_64-apple-darwin17.0 (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘TypeInfo/DESCRIPTION’ ... OK * this is package ‘TypeInfo’ version ‘1.58.0’ * 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 ... NOTE Found the following hidden files and directories: .git_fetch_output.txt .git_merge_output.txt 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 ‘TypeInfo’ can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... NOTE Deprecated license: BSD * 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 ... 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 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 ‘copyEnv.R’ Running ‘copySubstitute.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: 2 NOTEs See ‘/Users/biocbuild/bbs-3.13-bioc/meat/TypeInfo.Rcheck/00check.log’ for details.
TypeInfo.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL TypeInfo ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/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 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 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.
> library(Biobase)
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
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
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
1.149 0.109 1.236
TypeInfo.Rcheck/tests/copySubstitute.Rout
R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 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.
> library(TypeInfo)
> require(Biobase)
Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
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
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
1.185 0.108 1.271
TypeInfo.Rcheck/TypeInfo-Ex.timings
| name | user | system | elapsed | |
| DynamicTypeTest-class | 0.024 | 0.002 | 0.025 | |
| IndependentTypeSpecification-class | 0.035 | 0.002 | 0.036 | |
| IndependentTypeSpecification | 0.019 | 0.001 | 0.020 | |
| NamedTypeTest-class | 0.003 | 0.001 | 0.003 | |
| ReturnTypeSpecification | 0.003 | 0.001 | 0.004 | |
| SimultaneousTypeSpecification | 0.008 | 0.000 | 0.008 | |
| TypedSignature | 0.005 | 0.000 | 0.005 | |
| checkArgs | 0.001 | 0.000 | 0.001 | |
| hasParameterType | 0.012 | 0.001 | 0.013 | |
| rewriteTypeCheck | 0.001 | 0.000 | 0.000 | |
| showTypeInfo | 0.003 | 0.000 | 0.003 | |