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CHECK report for TypeInfo on machv2

This page was generated on 2020-10-17 11:59:51 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE TypeInfo PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1854/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
TypeInfo 1.54.0
Duncan Temple Lang
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/TypeInfo
Branch: RELEASE_3_11
Last Commit: e81f346
Last Changed Date: 2020-04-27 14:13:23 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  NA 
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: TypeInfo
Version: 1.54.0
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_1.54.0.tar.gz
StartedAt: 2020-10-17 06:09:29 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 06:10:05 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 36.3 seconds
RetCode: 0
Status:  OK 
CheckDir: TypeInfo.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### 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_1.54.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/TypeInfo.Rcheck’
* using R version 4.0.3 (2020-10-10)
* 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 ‘1.54.0’
* 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
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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.11-bioc/meat/TypeInfo.Rcheck/00check.log’
for details.



Installation output

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/4.0/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)

Tests output

TypeInfo.Rcheck/tests/copyEnv.Rout


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 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, 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 
  1.161   0.115   1.252 

TypeInfo.Rcheck/tests/copySubstitute.Rout


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 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, 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 
  1.355   0.120   1.452 

Example timings

TypeInfo.Rcheck/TypeInfo-Ex.timings

nameusersystemelapsed
DynamicTypeTest-class0.0310.0020.034
IndependentTypeSpecification-class0.0470.0020.048
IndependentTypeSpecification0.0250.0010.027
NamedTypeTest-class0.0050.0010.005
ReturnTypeSpecification0.0050.0010.006
SimultaneousTypeSpecification0.0130.0000.014
TypedSignature0.0020.0000.003
checkArgs0.0010.0010.002
hasParameterType0.0130.0010.014
rewriteTypeCheck0.0010.0000.001
showTypeInfo0.0060.0000.006