Duncan Temple Lang
| Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019) |
| URL: https://git.bioconductor.org/packages/TypeInfo |
| Branch: master |
| Last Commit: 0404c98 |
| Last Changed Date: 2018-10-30 11:54:27 -0400 (Tue, 30 Oct 2018) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-04-09 11:55:05 -0400 (Tue, 09 Apr 2019).
| Package 1659/1703 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| TypeInfo 1.49.0 Duncan Temple Lang
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | OK | | ||||||
| celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | | ||||||
| merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK |
| Package: TypeInfo |
| Version: 1.49.0 |
| Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:TypeInfo.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings TypeInfo_1.49.0.tar.gz |
| StartedAt: 2019-04-09 06:32:44 -0400 (Tue, 09 Apr 2019) |
| EndedAt: 2019-04-09 06:33:23 -0400 (Tue, 09 Apr 2019) |
| EllapsedTime: 39.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: TypeInfo.Rcheck |
| Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:TypeInfo.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings TypeInfo_1.49.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/TypeInfo.Rcheck' * using R Under development (unstable) (2019-03-09 r76216) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * using option '--no-vignettes' * checking for file 'TypeInfo/DESCRIPTION' ... OK * this is package 'TypeInfo' version '1.49.0' * 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 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 * loading checks for arch 'i386' ** 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 * loading checks for arch 'x64' ** 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 ... ** running examples for arch 'i386' ... OK ** running examples for arch 'x64' ... OK * checking for unstated dependencies in 'tests' ... OK * checking tests ... ** running tests for arch 'i386' ... Running 'copyEnv.R' Running 'copySubstitute.R' OK ** running tests for arch 'x64' ... 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 'C:/Users/biocbuild/bbs-3.9-bioc/meat/TypeInfo.Rcheck/00check.log' for details.
TypeInfo.Rcheck/00install.out
##############################################################################
##############################################################################
###
### Running command:
###
### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/TypeInfo_1.49.0.tar.gz && rm -rf TypeInfo.buildbin-libdir && mkdir TypeInfo.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=TypeInfo.buildbin-libdir TypeInfo_1.49.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL TypeInfo_1.49.0.zip && rm TypeInfo_1.49.0.tar.gz TypeInfo_1.49.0.zip
###
##############################################################################
##############################################################################
% Total % Received % Xferd Average Speed Time Time Time Current
Dload Upload Total Spent Left Speed
0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0
100 33248 100 33248 0 0 524k 0 --:--:-- --:--:-- --:--:-- 590k
install for i386
* installing *source* package 'TypeInfo' ...
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'TypeInfo'
finding HTML links ... done
ClassNameOrExpression-class html
DynamicTypeTest-class html
IndependentTypeSpecification-class html
IndependentTypeSpecification html
NamedTypeTest-class html
ReturnTypeSpecification html
SimultaneousTypeSpecification html
TypedSignature-class html
TypedSignature html
checkArgs html
checkReturnValue html
hasParameterType html
paramNames html
rewriteTypeCheck html
showTypeInfo html
typeInfo html
** 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
install for x64
* installing *source* package 'TypeInfo' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'TypeInfo' as TypeInfo_1.49.0.zip
* DONE (TypeInfo)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'TypeInfo' successfully unpacked and MD5 sums checked
|
TypeInfo.Rcheck/tests_i386/copyEnv.Rout
R Under development (unstable) (2019-03-09 r76216) -- "Unsuffered Consequences"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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, 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
1.01 0.04 1.04
|
TypeInfo.Rcheck/tests_x64/copyEnv.Rout
R Under development (unstable) (2019-03-09 r76216) -- "Unsuffered Consequences"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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, 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
1.20 0.14 1.53
|
|
TypeInfo.Rcheck/tests_i386/copySubstitute.Rout
R Under development (unstable) (2019-03-09 r76216) -- "Unsuffered Consequences"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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, 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
1.20 0.09 1.26
|
TypeInfo.Rcheck/tests_x64/copySubstitute.Rout
R Under development (unstable) (2019-03-09 r76216) -- "Unsuffered Consequences"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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, 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
1.35 0.09 1.48
|
|
TypeInfo.Rcheck/examples_i386/TypeInfo-Ex.timings
|
TypeInfo.Rcheck/examples_x64/TypeInfo-Ex.timings
|