| Back to Mac ARM64 build report for BioC 3.17 |
|
This page was generated on 2023-10-20 09:38:14 -0400 (Fri, 20 Oct 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kjohnson2 | macOS 12.6.1 Monterey | arm64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4347 |
| 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 2164/2230 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| TypeInfo 1.66.0 (landing page) Duncan Temple Lang
| kjohnson2 | macOS 12.6.1 Monterey / arm64 | OK | OK | OK | OK |  | |||||||
|
To the developers/maintainers of the TypeInfo package: - 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: 1.66.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:TypeInfo.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings TypeInfo_1.66.0.tar.gz |
| StartedAt: 2023-10-19 08:57:11 -0400 (Thu, 19 Oct 2023) |
| EndedAt: 2023-10-19 08:58:16 -0400 (Thu, 19 Oct 2023) |
| EllapsedTime: 64.9 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: TypeInfo.Rcheck |
| Warnings: 0 |
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###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:TypeInfo.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings TypeInfo_1.66.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/TypeInfo.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-apple-darwin20 (64-bit)
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘TypeInfo/DESCRIPTION’ ... OK
* this is package ‘TypeInfo’ version ‘1.66.0’
* 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 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-3.17-bioc-mac-arm64/meat/TypeInfo.Rcheck/00check.log’
for details.
TypeInfo.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL TypeInfo ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/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 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20 (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
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, 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
0.833 0.094 2.121
TypeInfo.Rcheck/tests/copySubstitute.Rout
R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20 (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
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, 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
0.928 0.105 2.511
TypeInfo.Rcheck/TypeInfo-Ex.timings
| name | user | system | elapsed | |
| DynamicTypeTest-class | 0.020 | 0.002 | 0.056 | |
| IndependentTypeSpecification-class | 0.037 | 0.002 | 0.103 | |
| IndependentTypeSpecification | 0.020 | 0.001 | 0.059 | |
| NamedTypeTest-class | 0.003 | 0.001 | 0.009 | |
| ReturnTypeSpecification | 0.003 | 0.001 | 0.010 | |
| SimultaneousTypeSpecification | 0.007 | 0.001 | 0.020 | |
| TypedSignature | 0.002 | 0.000 | 0.009 | |
| checkArgs | 0.001 | 0.000 | 0.001 | |
| hasParameterType | 0.009 | 0.001 | 0.024 | |
| rewriteTypeCheck | 0.001 | 0.000 | 0.000 | |
| showTypeInfo | 0.003 | 0.001 | 0.002 | |