Package: TypeInfo

Version: 1.46.0

Command: /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:TypeInfo.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings TypeInfo_1.46.0.tar.gz

StartedAt: 2018-10-16 04:22:13 -0400 (Tue, 16 Oct 2018)

EndedAt: 2018-10-16 04:22:34 -0400 (Tue, 16 Oct 2018)

EllapsedTime: 21.0 seconds

RetCode: 0

Status:  OK

CheckDir: TypeInfo.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:TypeInfo.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings TypeInfo_1.46.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.7-bioc/meat/TypeInfo.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘TypeInfo/DESCRIPTION’ ... OK
* this is package ‘TypeInfo’ version ‘1.46.0’
* 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 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
  ‘/home/biocbuild/bbs-3.7-bioc/meat/TypeInfo.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD INSTALL TypeInfo
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* installing to library ‘/home/biocbuild/bbs-3.7-bioc/R/library’
* installing *source* package ‘TypeInfo’ ...
** 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
* DONE (TypeInfo)

R version 3.5.1 Patched (2018-07-12 r74967) -- "Feather Spray"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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, colMeans, colSums, colnames,
    dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, lengths, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
    rowMeans, rowSums, 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 
  0.628   0.028   0.649 

R version 3.5.1 Patched (2018-07-12 r74967) -- "Feather Spray"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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, colMeans, colSums, colnames,
    dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, lengths, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, rank, rbind,
    rowMeans, rowSums, 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 
  0.700   0.056   0.746 

name	user	system	elapsed
DynamicTypeTest-class	0.016	0.000	0.017
IndependentTypeSpecification-class	0.028	0.004	0.030
IndependentTypeSpecification	0.020	0.000	0.018
NamedTypeTest-class	0.004	0.000	0.004
ReturnTypeSpecification	0.004	0.000	0.003
SimultaneousTypeSpecification	0.008	0.000	0.008
TypedSignature	0.004	0.000	0.002
checkArgs	0.000	0.000	0.001
hasParameterType	0.008	0.000	0.008
rewriteTypeCheck	0.000	0.000	0.001
showTypeInfo	0.004	0.000	0.003