...
 
Commits (4)
......@@ -8,3 +8,19 @@ TODO.md
configure
tmp_.*
^\.gitlab-ci\.yml$
^.*\.tar\.gz$
^HandTill2001\.Rcheck$
^cran-comments\.md$
^\.Rprofile$
^TODO\.md$
^index\.html$
^Makefile$
^README\.Rmd$
^README-.*\.png$
^devel\.R$
^make\.R$
^\.log\.Rout$
^log$
^\.log\.log$
^doc$
^Meta$
......@@ -5,3 +5,8 @@ tmp_*
Makefile
*Rcheck
package_tools/
.Rprofile
*.tar.gz
HandTill2001.Rcheck
doc
Meta
Package: HandTill2001
Type: Package
Package: HandTill2001
Title: Multiple Class Area under ROC Curve
Version: 1.0.0.9000
[email protected]: c(person(given = c("Andreas", "Dominik"), family = "Cullmann",
email = "[email protected]", role = c("aut","cre")),
person(given = c("Edgar"), family=c("Kublin"), role = c("ctb"))
)
Description: An S4 implementation of Eq. (3) and Eq. (7) by David J. Hand and
Robert J. Till (2001) <DOI:10.1023/A:1010920819831>.
Version: 0.2-12.9000
[email protected]:
person(given = "Andreas Dominik",
family = "Cullmann",
role = c("aut", "cre"),
email = "[email protected]")
Description: An S4 implementation of Eq. (3) and Eq. (7) by
David J. Hand and Robert J. Till (2001) <DOI:10.1023/A:1010920819831>.
License: BSD_2_clause + file LICENSE
URL: https://gitlab.com/fvafrCU/HandTill2001
Depends:
R (>= 2.14)
......@@ -18,6 +20,14 @@ Suggests:
MASS,
rpart,
mda,
nnet
License: GPL (>= 2)
nnet,
knitr,
rmarkdown,
pkgload,
testthat,
RUnit,
devtools,
rprojroot
VignetteBuilder:
knitr
RoxygenNote: 7.0.2
YEAR: 2019
COPYRIGHT HOLDER: Andreas Dominik Cullmann
\ No newline at end of file
# HandTill2001 0.2-12.9000
* Added a `NEWS.md` file to track changes to the package.
#' What it Does (One Line, Title Case)
#'
#' A description is a paragraph consisting of one or more sentences.
#'
#' You will find the details in\cr
#' \code{vignette("An_Introduction_to_HandTill2001", package =
#' "HandTill2001")}.
#'
#' @name HandTill2001-package
#' @aliases HandTill2001-package
#' @docType package
#' @keywords package
NULL
#' Throw a Condition
#'
#' Throws a condition of class c("error", "HandTill2001", "condition").
#'
#' We use this condition as an error dedicated to \pkg{ HandTill2001.}
#'
#' @param message_string The message to be thrown.
#' @param system_call The call to be thrown.
#' @param ... Arguments to be passed to
#' \code{\link[base:structure]{base::structure}}.
#' @return The function does never return anything, it stops with a
#' condition of class c("error", "HandTill2001", "condition").
#' @keywords internal
#' @examples
#' tryCatch(HandTill2001:::throw("Hello error!"), HandTill2001 = function(e) return(e))
throw <- function(message_string, system_call = sys.call(-1), ...) {
condition <- structure(class = c("error", "HandTill2001", "condition"),
list(message = message_string, call = system_call),
...)
stop(condition)
}
[![pipeline status](https://gitlab.com/fvafrCU/HandTill2001/badges/master/pipeline.svg)](https://gitlab.com/fvafrCU/HandTill2001/commits/master)
[![coverage report](https://gitlab.com/fvafrCU/HandTill2001/badges/master/coverage.svg)](https://gitlab.com/fvafrCU/HandTill2001/commits/master)
<!--
[![Build Status](https://travis-ci.org/fvafrCU/HandTill2001.svg?branch=master)](https://travis-ci.org/fvafrCU/HandTill2001)
[![Coverage Status](https://codecov.io/github/fvafrCU/HandTill2001/coverage.svg?branch=master)](https://codecov.io/github/fvafrCU/HandTill2001?branch=master)
-->
[![CRAN_Status_Badge](https://www.r-pkg.org/badges/version/HandTill2001)](https://cran.r-project.org/package=HandTill2001)
[![RStudio_downloads_monthly](https://cranlogs.r-pkg.org/badges/HandTill2001)](https://cran.r-project.org/package=HandTill2001)
[![RStudio_downloads_total](https://cranlogs.r-pkg.org/badges/grand-total/HandTill2001)](https://cran.r-project.org/package=HandTill2001)
<!-- README.md is generated from README.Rmd. Please edit that file -->
```{r, echo = FALSE}
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>",
fig.path = "README-"
)
```
# HandTill2001
## Introduction
Please read the
[vignette](https://CRAN.R-project.org/package=HandTill2001/vignettes/consenus_auc.pdf).
Or, after installation, the help page:
```{r, eval = FALSE}
help("HandTill2001-package", package = "HandTill2001")
```
```{r, echo = FALSE}
# insert developement page
help_file <- file.path("man", "HandTill2001-package.Rd")
captured <- gsub('_\b', '', capture.output(tools:::Rd2txt(help_file) ))
cat(captured, sep = "\n")
```
## Installation
You can install HandTill2001 from gitlab via:
```{r gh-installation, eval = FALSE}
if (! require("remotes")) install.packages("remotes")
remotes::install_gitlab("fvafrCU/HandTill2001")
```
[![pipeline status](https://gitlab.com/fvafrCU/HandTill2001/badges/master/pipeline.svg)](https://gitlab.com/fvafrCU/HandTill2001/commits/master)
[![pipeline status](https://gitlab.com/fvafrCU/HandTill2001/badges/master/pipeline.svg)](https://gitlab.com/fvafrCU/HandTill2001/commits/master)
[![coverage report](https://gitlab.com/fvafrCU/HandTill2001/badges/master/coverage.svg)](https://gitlab.com/fvafrCU/HandTill2001/commits/master)
<!--
[![Build Status](https://travis-ci.org/fvafrCU/HandTill2001.svg?branch=master)](https://travis-ci.org/fvafrCU/HandTill2001)
[![Coverage Status](https://codecov.io/github/fvafrCU/HandTill2001/coverage.svg?branch=master)](https://codecov.io/github/fvafrCU/HandTill2001?branch=master)
-->
[![CRAN_Status_Badge](https://www.r-pkg.org/badges/version/HandTill2001)](https://cran.r-project.org/package=HandTill2001)
[![RStudio_downloads_monthly](https://cranlogs.r-pkg.org/badges/HandTill2001)](https://cran.r-project.org/package=HandTill2001)
[![RStudio_downloads_total](https://cranlogs.r-pkg.org/badges/grand-total/HandTill2001)](https://cran.r-project.org/package=HandTill2001)
<!-- README.md is generated from README.Rmd. Please edit that file -->
# HandTill2001
## Introduction
Please read the
[vignette](https://CRAN.R-project.org/package=HandTill2001/vignettes/consenus_auc.pdf).
Or, after installation, the help page:
This is an R package to create area under ROC curve for multiple classes
following David J. Hand and Robert J. Till (2001)
[DOI:10.1023/A:1010920819831](https://dx.doi.org/DOI:10.1023/A:1010920819831
"David J. Hand and Robert J. Till (2001)").
```r
help("HandTill2001-package", package = "HandTill2001")
```
```
#> Multiple Class Area under ROC Curve
#>
#> Description:
#>
#> A very lean package implementing merely M given by Hand and Till
#> (2001), Eq. (7).
#>
#> Details:
#>
#> M given by Hand and Till (2001) defines a multiple class version
#> of the area under curve of the receiver operating characteristic.
#>
#> References:
#>
#> David J. Hand and Robert J. Till (2001). A Simple Generalisation
#> of the Area Under the ROC Curve for Multiple Class Classification
#> Problems. _Machine Learning_ *45*(2), p. 171-186. DOI:
#> 10.1023/A:1010920819831.
#>
#> See Also:
#>
#> 'help(package="HandTill2001")', especially '"methods?auc"';
#> various packages that calculate two class AUC ('"ROCR"') or
#> multiple class AUC (pROC, '"caTools"').
#>
#> Examples:
#>
#> library(HandTill2001)
#> data(ht01.multipleclass)
#> auc(
#> multcap(
#> response = ht01.multipleclass$observed
#> , predicted = as.matrix(ht01.multipleclass[, levels(ht01.multipleclass$observed)])
#> )
#> )
#>
```
## Installation
You can install HandTill2001 via:
You can install HandTill2001 from gitlab via:
```r
if (! require("remotes")) install.packages("remotes")
remotes::install_gitlab("fvafrCU/HandTill2001")
help("HandTill2001-package", package = "HandTill2001")
```
- make sure https://gitlab.com/fvafrCU/HandTill2001 exists!
- change documenation to roxygen2.
#!/bin/sh
# Well, this is quick and and dirty.
# And it's just a little helper script, it's not part of the package.
# I can't keep the R CMD stuff, and I'm used to 'make', so I wrap R CMDs into
# make.
R=~/svn/R/r-devel/build/bin/R
rpackage=$(basename $(pwd))
rpversion=$(grep 'Version:' DESCRIPTION |cut -f2 -d' ')
check_meta_info_script=tmp_check_meta_info.sh
cat > $check_meta_info_script <<EOF
## autogenerated by make.sh
find ./R -type f ! -name "*.swp" ! -name "*.tar.gz" -exec grep -i '~~' /dev/null {} \;
find . -type f ! -name "*.swp" -exec grep -i 'kludge' /dev/null {} \;
for target in Version Date
do
v=\$(
grep --exclude=*.pdf --exclude=.*.swp -R "\${target}:" . | sed -e"s/.*\${target}: //" -e's/\\tab //' \\
| tr '\\\\' ' ' | cut -f1 -d' ' | uniq
)
echo \$target \$v
[ \$(echo \$v | wc -w) -eq 1 ] || (printf "found different \${target}s \n"; exit 1)
done
EOF
chmod 700 $check_meta_info_script
package_tools=tmp_package_tools.r
cat > $package_tools <<EOF
#!/usr/bin/Rscript --vanilla
package <- "$rpackage"
EOF
chmod 700 $package_tools
cat >> $package_tools <<\EOF
library(package, character.only = TRUE)
output_directory <- "package_tools"
unlink(output_directory, recursive = TRUE)
dir.create(output_directory)
#% codetools
library("codetools")
# checkUsagePackage returns NULL, use sink
codetools_check <- capture.output(checkUsagePackage(package, all = TRUE))
outfile <- file.path(output_directory, "checkUsagePackage.out")
writeLines(codetools_check, outfile)
if(length(codetools_check) > 0) stop(paste("codetools failed, see ", outfile))
#% lintr
library("lintr")
linted <- lint_package(path = ".")
writeLines(unlist(lapply(linted, paste, collapse=" ")),
con = file.path(output_directory, "lint_package.out"))
#% formatR
library("formatR")
for (code_file in list.files(file.path(".", "R"), full.names = TRUE)) {
output_name <- file.path(output_directory, basename(code_file))
file.copy(code_file, output_name)
tidy_file <- paste(output_name, ".tidy", sep = "")
tidy_source(code_file, arrow = TRUE, width.cutoff = 70, file = tidy_file)
tidy_linted <- lint(tidy_file, linters = default_linters, cache = FALSE)
if (length(tidy_linted) > 0)
writeLines(unlist(lapply(tidy_linted, paste, collapse=" ")),
con = paste(tidy_file, ".linted", sep = ""))
code_linted <- lint(code_file, linters = default_linters, cache = FALSE)
if (length(code_linted) > 0)
writeLines(unlist(lapply(code_linted, paste, collapse=" ")),
con = paste(output_name, ".linted", sep = ""))
}
EOF
cat > Makefile <<EOF
R=${R}
rpackage=${rpackage}
rpversion=${rpversion}
check_meta_info_script=$check_meta_info_script
package_tools=${package_tools}
EOF
cat >> Makefile <<\EOF
all: craninstall clean
full: crancheck install clean
craninstall: crancheck
${R} --vanilla CMD INSTALL ${rpackage}_${rpversion}.tar.gz
crancheck: check
export _R_CHECK_FORCE_SUGGESTS_=FALSE && \
${R} CMD check --as-cran ${rpackage}_${rpversion}.tar.gz
install: check
${R} --vanilla CMD INSTALL ${rpackage}_${rpversion}.tar.gz && \
printf '===== have you run\n\tmake check_demo && ' && \
printf 'make package_tools && make runit && make coldr\n?!\n'
install_bare: build_bare
${R} --vanilla CMD INSTALL ${rpackage}_${rpversion}.tar.gz
check_bare: build_bare
export _R_CHECK_FORCE_SUGGESTS_=FALSE && \
${R} --vanilla CMD check --no-examples ${rpackage}_${rpversion}.tar.gz && \
printf '===== run\n\tmake install\n!!\n'
check: build
export _R_CHECK_FORCE_SUGGESTS_=FALSE && \
${R} --vanilla CMD check ${rpackage}_${rpversion}.tar.gz && \
printf '===== run\n\tmake install\n!!\n'
build_bare:
${R} --vanilla CMD build ../${rpackage}
build:
${R} --vanilla CMD build ../${rpackage}
check_meta_info:
./${check_meta_info_script}
direct_check:
${R} --vanilla CMD check ../${rpackage} ## check without build -- not recommended
check_demo:
# ${R} CMD BATCH demo/${rpackage}.r ## Rscript doesn't load
# methods, but we fixed that.
demo/${rpackage}.r
runit:
./tests/runit.R
coldr:
Rscript --vanilla -e 'library("coldr"); check_directory("R/"); warnings()'
.PHONY: package_tools
package_tools:
./${package_tools} # codetools needs to load the package, so we need make
# install first
purge: clean clean_git remove
clean:
rm -rf *.Rcheck
clean_git:
git clean -x -f -d
remove:
${R} --vanilla CMD REMOVE ${rpackage}
EOF
Dear CRAN Team,
this is a resubmission of package 'HandTill2001'. I have added the following changes:
* Added a `NEWS.md` file to track changes to the package.
Please upload to CRAN.
Best, Andreas Dominik
# Package HandTill2001 0.2-12.9000
## Test environments
- R Under development (unstable) (2019-10-17 r77308)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Devuan GNU/Linux ascii
0 errors | 2 warnings | 1 note
- win-builder (devel)
if (FALSE) {
packager::set_package_info(path = ".", title = "YOUR TITLE HERE",
description = paste("Multiline",
"description here."),
details = paste("More",
"details here."),
force = packager:::is_force()
)
}
pkgload::load_all(".")
test_exception <- function() {
RUnit::checkException(HandTill2001:::throw("Hello, error!"))
}
checking for file ‘/home/qwer/git/cyclops/fvafrcu/HandTill2001/DESCRIPTION’ ... ✔ checking for file ‘/home/qwer/git/cyclops/fvafrcu/HandTill2001/DESCRIPTION’
─ preparing ‘HandTill2001’:
checking DESCRIPTION meta-information ... ✔ checking DESCRIPTION meta-information
─ excluding invalid files
Subdirectory 'R' contains invalid file names:
‘HandTill2001-package.R-packager’
─ checking for LF line-endings in source and make files and shell scripts
─ checking for empty or unneeded directories
─ looking to see if a ‘data/datalist’ file should be added
─ building ‘HandTill2001_0.2-12.9000.tar.gz’
[1] "./HandTill2001_0.2-12.9000.tar.gz"
* checking for file ‘/home/qwer/git/cyclops/fvafrcu/HandTill2001/DESCRIPTION’ ... OK
* preparing ‘HandTill2001’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... OK
* excluding invalid files
Subdirectory 'R' contains invalid file names:
‘HandTill2001-package.R-packager’
* checking for LF line-endings in source and make files
* checking for empty or unneeded directories
* looking to see if a ‘data/datalist’ file should be added
* re-saving tabular files
* building ‘HandTill2001_0.2-12.9000.tar.gz’
* using log directory ‘/home/qwer/git/cyclops/fvafrcu/HandTill2001/HandTill2001.Rcheck’
* using R Under development (unstable) (2019-10-17 r77308)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-manual’
* checking for file ‘HandTill2001/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘HandTill2001’ version ‘0.2-12.9000’
* 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 executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘HandTill2001’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... WARNING
Vignettes with missing or empty \VignetteIndexEntry:
consensus_auc.Rnw
See sections ‘The INDEX file’ and ‘Package subdirectories’ in the
‘Writing R Extensions’ manual.
* 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 line widths ... OK
* checking Rd cross-references ... NOTE
Packages unavailable to check Rd xrefs: ‘ROCR’, ‘caTools’
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘auc.R’
Running ‘constructors.R’
Running ‘runit.R’
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... WARNING
Failed to locate the ‘weave’ output file (by engine ‘knitr::rmarkdown’) for vignette with name ‘An_Introduction_to_HandTill2001’. The following files exist in directory ‘/home/qwer/git/cyclops/fvafrcu/HandTill2001/HandTill2001.Rcheck/00_pkg_src/HandTill2001/inst/doc’: ‘An_Introduction_to_HandTill2001.R’, ‘consensus_auc.Rnw’Failed to locate the ‘weave’ output file (by engine ‘utils::Sweave’) for vignette with name ‘consensus_auc’. The following files exist in directory ‘/home/qwer/git/cyclops/fvafrcu/HandTill2001/HandTill2001.Rcheck/00_pkg_src/HandTill2001/inst/doc’: ‘An_Introduction_to_HandTill2001.R’, ‘consensus_auc.Rnw’
Package vignettes without corresponding single PDF/HTML:
‘An_Introduction_to_HandTill2001.Rmd’
‘consensus_auc.Rnw’
* checking running R code from vignettes ...
‘An_Introduction_to_HandTill2001.Rmd’ using ‘UTF-8’... OK
‘consensus_auc.Rnw’ using ‘UTF-8’... OK
OK
* checking re-building of vignette outputs ... OK
* DONE
Status: 2 WARNINGs, 1 NOTE
See
‘/home/qwer/git/cyclops/fvafrcu/HandTill2001/HandTill2001.Rcheck/00check.log’
for details.
* using log directory ‘/home/qwer/git/cyclops/fvafrcu/HandTill2001/HandTill2001.Rcheck’
* using R Under development (unstable) (2019-10-17 r77308)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using options ‘--run-donttest --as-cran’
* checking for file ‘HandTill2001/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘HandTill2001’ version ‘0.2-12.9000’
* checking CRAN incoming feasibility ... NOTE
Maintainer: ‘Andreas Dominik Cullmann <[email protected]>’
Version contains large components (0.2-12.9000)
New maintainer:
Andreas Dominik Cullmann <[email protected]>
Old maintainer(s):
Andreas Dominik Cullmann <[email protected]>
Found the following (possibly) invalid URLs:
URL: DOI:10.1023/A:1010920819831
From: inst/doc/An_Introduction_to_HandTill2001.html
Message: Invalid URI scheme
Found the following \keyword or \concept entries
which likely give several index terms:
File ‘HandTill2001-package.Rd’:
\keyword{AUC,}
* 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 executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking serialization versions ... OK
* checking whether package ‘HandTill2001’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for future file timestamps ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... WARNING
Vignettes with missing or empty \VignetteIndexEntry:
consensus_auc.Rnw
See sections ‘The INDEX file’ and ‘Package subdirectories’ in the
‘Writing R Extensions’ manual.
* 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 use of S3 registration ... 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 line widths ... OK
* checking Rd cross-references ... NOTE
Packages unavailable to check Rd xrefs: ‘ROCR’, ‘caTools’
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ... OK
Running ‘auc.R’
Running ‘constructors.R’
Running ‘runit.R’
Running ‘testthat.R’
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* checking for non-standard things in the check directory ... OK
* checking for detritus in the temp directory ... OK
* DONE
Status: 1 WARNING, 2 NOTEs
Warning in getPackageName(where) :
Created a package name, ‘2019-12-12 20:41:13’, when none found
Warning in getPackageName(where) :
Created a package name, ‘2019-12-12 20:41:13’, when none found
<simpleError in setMethod(f = "auc", signature(object = "bincap"), function(object) { n0 <- sum(([email protected] == [email protected]) * 1) n1 <- sum(([email protected] != [email protected]) * 1) s0 <- sum(rank([email protected], ties.method = "average", na.last = TRUE) * ([email protected] == [email protected])) return((s0 - n0 * (n0 + 1)/2)/(n0 * n1))}): no existing definition for function ‘auc’. Probably due to failed S4 method loading.>
Loading HandTill2001
<error in cleanr::check_package(".", check_return = FALSE): . /home/qwer/git/cyclops/fvafrcu/HandTill2001/R/AllClasses.R: line 62 counts 81 characters.
/home/qwer/git/cyclops/fvafrcu/HandTill2001/R/AllClasses.R: line 63 counts 90 characters.
/home/qwer/git/cyclops/fvafrcu/HandTill2001/R/AllClasses.R: line 129 counts 81 characters.
/home/qwer/git/cyclops/fvafrcu/HandTill2001/R/AllClasses.R: line 132 counts 81 characters.
. /home/qwer/git/cyclops/fvafrcu/HandTill2001/R/AllConstructors.R: line 20 counts 86 characters.
/home/qwer/git/cyclops/fvafrcu/HandTill2001/R/AllConstructors.R: line 56 counts 94 characters.
/home/qwer/git/cyclops/fvafrcu/HandTill2001/R/AllConstructors.R: line 59 counts 89 characters.
. /home/qwer/git/cyclops/fvafrcu/HandTill2001/R/auc-methods.R: line 54 counts 91 characters.
/home/qwer/git/cyclops/fvafrcu/HandTill2001/R/auc-methods.R: line 83 counts 102 characters.
/home/qwer/git/cyclops/fvafrcu/HandTill2001/R/auc-methods.R: line 88 counts 111 characters.
/home/qwer/git/cyclops/fvafrcu/HandTill2001/R/auc-methods.R: line 94 counts 112 characters.
. /home/qwer/git/cyclops/fvafrcu/HandTill2001/R/HandTill2001-package.R: line 29 counts 89 characters.
. /home/qwer/git/cyclops/fvafrcu/HandTill2001/R/throw.R: line 15 counts 87 characters.>
Warning messages:
1: In getPackageName(where) :
Created a package name, ‘2019-12-12 20:33:53’, when none found
2: In getPackageName(where) :
Created a package name, ‘2019-12-12 20:33:53’, when none found
[1] filename functions line value
<0 rows> (or 0-length row.names)
HandTill2001 Coverage: 100.00%
R/AllConstructors.R: 100.00%
R/AllGenerics.R: 100.00%
R/auc-methods.R: 100.00%
R/throw.R: 100.00%
[1] filename functions line value
<0 rows> (or 0-length row.names)
HandTill2001 Coverage: 100.00%
R/AllConstructors.R: 100.00%
R/AllGenerics.R: 100.00%
R/auc-methods.R: 100.00%
R/throw.R: 100.00%
checking index information ... WARNING
Vignettes with missing or empty \VignetteIndexEntry:
consensus_auc.Rnw
See sections ‘The INDEX file’ and ‘Package subdirectories’ in the
‘Writing R Extensions’ manual.
checking package vignettes in ‘inst/doc’ ... WARNING
Failed to locate the ‘weave’ output file (by engine ‘knitr::rmarkdown’) for vignette with name ‘An_Introduction_to_HandTill2001’. The following files exist in directory ‘/home/qwer/git/cyclops/fvafrcu/HandTill2001/HandTill2001.Rcheck/00_pkg_src/HandTill2001/inst/doc’: ‘An_Introduction_to_HandTill2001.R’, ‘consensus_auc.Rnw’Failed to locate the ‘weave’ output file (by engine ‘utils::Sweave’) for vignette with name ‘consensus_auc’. The following files exist in directory ‘/home/qwer/git/cyclops/fvafrcu/HandTill2001/HandTill2001.Rcheck/00_pkg_src/HandTill2001/inst/doc’: ‘An_Introduction_to_HandTill2001.R’, ‘consensus_auc.Rnw’
Package vignettes without corresponding single PDF/HTML:
‘An_Introduction_to_HandTill2001.Rmd’
‘consensus_auc.Rnw’
checking Rd cross-references ... NOTE
Packages unavailable to check Rd xrefs: ‘ROCR’, ‘caTools’
checking index information ... WARNING
Vignettes with missing or empty \VignetteIndexEntry:
consensus_auc.Rnw
See sections ‘The INDEX file’ and ‘Package subdirectories’ in the
‘Writing R Extensions’ manual.
checking CRAN incoming feasibility ... NOTE
Maintainer: ‘Andreas Dominik Cullmann <[email protected]>’
Version contains large components (0.2-12.9000)
New maintainer:
Andreas Dominik Cullmann <[email protected]>
Old maintainer(s):
Andreas Dominik Cullmann <[email protected]>
Found the following (possibly) invalid URLs:
URL: DOI:10.1023/A:1010920819831
From: inst/doc/An_Introduction_to_HandTill2001.html
Message: Invalid URI scheme
Found the following \keyword or \concept entries
which likely give several index terms:
File ‘HandTill2001-package.Rd’:
\keyword{AUC,}
checking Rd cross-references ... NOTE
Packages unavailable to check Rd xrefs: ‘ROCR’, ‘caTools’
Warning: ‘HandTill2001’ namespace cannot be unloaded:
trying to get slot "defined" from an object of a basic class ("environment") with no slots
checking for file ‘/tmp/RtmpYZn5ft/remotes79335259d117/HandTill2001/DESCRIPTION’ ... ✔ checking for file ‘/tmp/RtmpYZn5ft/remotes79335259d117/HandTill2001/DESCRIPTION’
─ preparing ‘HandTill2001’:
checking DESCRIPTION meta-information ... ✔ checking DESCRIPTION meta-information
checking vignette meta-information ... ✔ checking vignette meta-information
─ checking for LF line-endings in source and make files and shell scripts
─ checking for empty or unneeded directories
─ looking to see if a ‘data/datalist’ file should be added
─ building ‘HandTill2001_0.2-12.9000.tar.gz’
[1] TRUE
checking for file ‘/tmp/RtmponEqfQ/remotes67c25376efd1/HandTill2001/DESCRIPTION’ ... ✔ checking for file ‘/tmp/RtmponEqfQ/remotes67c25376efd1/HandTill2001/DESCRIPTION’
─ preparing ‘HandTill2001’:
checking DESCRIPTION meta-information ... ✔ checking DESCRIPTION meta-information
checking vignette meta-information ... ✔ checking vignette meta-information
─ checking for LF line-endings in source and make files and shell scripts
─ checking for empty or unneeded directories
─ looking to see if a ‘data/datalist’ file should be added
─ building ‘HandTill2001_0.2-12.9000.tar.gz’
=========================
= Bitte haben Sie Spass. =
=========================
* installing *source* package ‘HandTill2001’ ...
** using staged installation
** R
** data
** demo
** inst
** byte-compile and prepare package for lazy loading
=========================
= Bitte haben Sie Spass. =
=========================
** help
*** installing help indices
** building package indices
=========================
= Bitte haben Sie Spass. =
=========================
** installing vignettes
** testing if installed package can be loaded from temporary location
=========================
= Bitte haben Sie Spass. =
=========================
** testing if installed package can be loaded from final location
=========================
= Bitte haben Sie Spass. =
=========================
** testing if installed package keeps a record of temporary installation path
* DONE (HandTill2001)
[1] TRUE
Loading required package: cleanr
Loading required package: covr
Loading required package: devtools
Loading required package: usethis
Loading required package: knitr
Loading required package: lintr
Attaching package: ‘lintr’
The following object is masked from ‘package:devtools’:
lint
Loading required package: packager
Attaching package: ‘packager’
The following objects are masked from ‘package:devtools’:
create, install_deps, release
The following objects are masked from ‘package:usethis’:
use_build_ignore, use_dev_version, use_directory
Loading required package: rhub
Attaching package: ‘rhub’
The following object is masked from ‘package:devtools’:
check
Loading required package: roxygen2
checking for file ‘/home/qwer/git/cyclops/fvafrcu/HandTill2001/DESCRIPTION’ ... ✔ checking for file ‘/home/qwer/git/cyclops/fvafrcu/HandTill2001/DESCRIPTION’
─ preparing ‘HandTill2001’:
checking DESCRIPTION meta-information ... ✔ checking DESCRIPTION meta-information
─ excluding invalid files
Subdirectory 'R' contains invalid file names:
‘HandTill2001-package.R-packager’
─ checking for LF line-endings in source and make files and shell scripts
─ checking for empty or unneeded directories
─ looking to see if a ‘data/datalist’ file should be added
─ building ‘HandTill2001_0.2-12.9000.tar.gz’
Running /home/qwer/svn/R/r-devel/build/bin/R CMD INSTALL \
/tmp/RtmpVGtZ8S/HandTill2001_0.2-12.9000.tar.gz --install-tests
* installing to library ‘/home/qwer/svn/R/r-devel/build/library’
* installing *source* package ‘HandTill2001’ ...
** using staged installation
** R
** data
** demo
** inst
** tests
** 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 (HandTill2001)
checking for file ‘/home/qwer/git/cyclops/fvafrcu/HandTill2001/DESCRIPTION’ ... ✔ checking for file ‘/home/qwer/git/cyclops/fvafrcu/HandTill2001/DESCRIPTION’
─ preparing ‘HandTill2001’:
✔ checking DESCRIPTION meta-information
─ excluding invalid files
Subdirectory 'R' contains invalid file names:
‘HandTill2001-package.R-packager’
─ checking for LF line-endings in source and make files
─ checking for empty or unneeded directories
─ looking to see if a ‘data/datalist’ file should be added
─ building ‘HandTill2001_0.2-12.9000.tar.gz’
Running /usr/lib/R/bin/R CMD INSTALL \
/tmp/RtmpZ448nq/HandTill2001_0.2-12.9000.tar.gz --install-tests
* installing to library ‘/home/qwer/R/x86_64-pc-linux-gnu-library/3.3’
* installing *source* package ‘HandTill2001’ ...
** R
** data
** demo
** inst
** tests
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (HandTill2001)
* installing to library ‘/home/qwer/svn/R/r-devel/build/library’
* installing *source* package ‘HandTill2001’ ...
** using staged installation
** R
** data
** demo
** inst
** 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 (HandTill2001)
This diff is collapsed.
This diff is collapsed.
Warning: roxygen2 requires Encoding: UTF-8
Writing NAMESPACE
Loading HandTill2001
Writing NAMESPACE
[[1]]
[1] "/home/qwer/git/cyclops/fvafrcu/HandTill2001/NAMESPACE"
[[2]]
[1] "/home/qwer/git/cyclops/fvafrcu/HandTill2001/man/cap-class.Rd"
[2] "/home/qwer/git/cyclops/fvafrcu/HandTill2001/man/bincap-class.Rd"
[3] "/home/qwer/git/cyclops/fvafrcu/HandTill2001/man/multcap-class.Rd"
[4] "/home/qwer/git/cyclops/fvafrcu/HandTill2001/man/bincap.Rd"
[5] "/home/qwer/git/cyclops/fvafrcu/HandTill2001/man/multcap.Rd"
[6] "/home/qwer/git/cyclops/fvafrcu/HandTill2001/man/HandTill2001-package.Rd"
[7] "/home/qwer/git/cyclops/fvafrcu/HandTill2001/man/auc-methods.Rd"
[8] "/home/qwer/git/cyclops/fvafrcu/HandTill2001/man/ht01.multipleclass.Rd"
[9] "/home/qwer/git/cyclops/fvafrcu/HandTill2001/man/ht01.twoclass.Rd"
[10] "/home/qwer/git/cyclops/fvafrcu/HandTill2001/man/throw.Rd"
R Under development (unstable) (2019-10-17 r77308) -- "Unsuffered Consequences"
Copyright (C) 2019 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.
Natural language support but running in an English locale
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.
> roxygen2::roxygenize(".")
Writing NAMESPACE
Loading HandTill2001
Writing NAMESPACE
Warning message:
roxygen2 requires Encoding: UTF-8
>
>
<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN"
"http://www.w3.org/TR/html4/transitional.dtd">
<html><head><title>RUNIT TEST PROTOCOL--Thu Dec 12 20:42:24 2019</title>
</head>
<body><h1 TRUE>RUNIT TEST PROTOCOL--Thu Dec 12 20:42:24 2019</h1>
<p>Number of test functions: 1</p>
<p>Number of errors: 0</p>
<p>Number of failures: 0</p>
<hr>
<h3 TRUE>1 Test suite</h3>
<table border="1" width="60%" >
<tr><th width="30%">Name</th>
<th width="30%">Test functions</th>
<th width="20%">Errors</th>
<th width="20%">Failures</th>
</tr>
<tr><td><a href="#HandTill2001_unit_test">HandTill2001_unit_test</a></td>
<td>1</td>
<td>0</td>
<td>0</td>
</tr>
</table>
<hr>
<h3 TRUE>Details</h3>
<p><a name="HandTill2001_unit_test"><h5 TRUE>Test Suite: HandTill2001_unit_test</h5>
</a>Test function regexp: ^test_+<br/>Test file regexp: ^.*\.[rR]<br/>Involved directory:<br/>/home/qwer/git/cyclops/fvafrcu/HandTill2001/HandTill2001.Rcheck/HandTill2001/runit_tests<br/><ul><li><a href="/home/qwer/git/cyclops/fvafrcu/HandTill2001/HandTill2001.Rcheck/HandTill2001/runit_tests/runit-throw.R">Test file: runit-throw.R</a><ul><li><a name="HandTill2001_unit_test__home_qwer_git_cyclops_fvafrcu_HandTill2001_HandTill2001.Rcheck_HandTill2001_runit_tests_runit-throw.R_test_exception">test_exception: (1 checks) ... OK (0 seconds)<br/></a></li></ul></li></ul><hr>
<table border="0" width="80%" >
<tr><th>Name</th>
<th>Value</th>
</tr>
<tr><td>platform</td>
<td>x86_64-pc-linux-gnu</td>
</tr>
<tr><td>arch</td>
<td>x86_64</td>
</tr>
<tr><td>os</td>
<td>linux-gnu</td>
</tr>
<tr><td>system</td>
<td>x86_64, linux-gnu</td>
</tr>
<tr><td>status</td>
<td>Under development (unstable)</td>
</tr>
<tr><td>major</td>
<td>4</td>
</tr>
<tr><td>minor</td>
<td>0.0</td>
</tr>
<tr><td>year</td>
<td>2019</td>
</tr>
<tr><td>month</td>
<td>10</td>
</tr>
<tr><td>day</td>
<td>17</td>
</tr>
<tr><td>svn rev</td>
<td>77308</td>
</tr>
<tr><td>language</td>
<td>R</td>
</tr>
<tr><td>version.string</td>
<td>R Under development (unstable) (2019-10-17 r77308)</td>
</tr>
<tr><td>nickname</td>
<td>Unsuffered Consequences</td>
</tr>
<tr><td>host</td>
<td>h6</td>
</tr>
<tr><td>compiler</td>
<td>g++ -std=gnu++11</td>
</tr>
</table>
</body>
</html>
RUNIT TEST PROTOCOL -- Thu Dec 12 20:42:24 2019
***********************************************
Number of test functions: 1
Number of errors: 0
Number of failures: 0
1 Test Suite :
HandTill2001_unit_test - 1 test function, 0 errors, 0 failures
Details
***************************
Test Suite: HandTill2001_unit_test
Test function regexp: ^test_+
Test file regexp: ^.*\.[rR]
Involved directory:
/home/qwer/git/cyclops/fvafrcu/HandTill2001/HandTill2001.Rcheck/HandTill2001/runit_tests
---------------------------
Test file: /home/qwer/git/cyclops/fvafrcu/HandTill2001/HandTill2001.Rcheck/HandTill2001/runit_tests/runit-throw.R
test_exception: (1 checks) ... OK (0 seconds)
DESCRIPTION does not contain 'Language' field. Defaulting to 'en-US'.
WORD FOUND IN
Andreas bincap-class.Rd:37
bincap.Rd:44
cap-class.Rd:20
multcap-class.Rd:28
multcap.Rd:41
bincap auc-methods.Rd:14
consenus consensus_auc.Rnw:75
DOI auc-methods.Rd:69
HandTill2001-package.Rd:32
description:2
An_Introduction_to_HandTill2001.Rmd:14
Dominik bincap-class.Rd:37
bincap.Rd:44
cap-class.Rd:20
multcap-class.Rd:28
multcap.Rd:41
Eq auc-methods.Rd:31,34
HandTill2001-package.Rd:10
description:1
An_Introduction_to_HandTill2001.Rmd:13
eval consensus_auc.Rnw:24
fgl consensus_auc.Rnw:18,24,33
Generalisation auc-methods.Rd:67
HandTill2001-package.Rd:30
gitlab README.md:71
README.Rmd:43
HandTill throw.Rd:19,22
NEWS.md:1
README.md:15,71
README.Rmd:21,43
An_Introduction_to_HandTill2001.Rmd:2
modelling consensus_auc.Rnw:19
multcap auc-methods.Rd:14
multinom consensus_auc.Rnw:47
multipleclass ht01.multipleclass.Rd:6
nnet consensus_auc.Rnw:19,47
pre consensus_auc.Rnw:76,99
pROC HandTill2001-package.Rd:39
rpart consensus_auc.Rnw:19,33
RStudio README.md:8,9
README.Rmd:8,9
Springer ht01.multipleclass.Rd:44
ht01.twoclass.Rd:41
th ht01.multipleclass.Rd:44
ht01.twoclass.Rd:41
twoclass ht01.twoclass.Rd:6
ui bincap.Rd:5
multcap.Rd:5
Venables ht01.multipleclass.Rd:32,43
ht01.twoclass.Rd:29,40
Warning in eval(parse(text = make_list[[index]][["code"]])) :
Spell check failed, see /home/qwer/git/cyclops/fvafrcu/HandTill2001/log/spell.Rout for details.
DESCRIPTION does not contain 'Language' field. Defaulting to 'en-US'.
WORD FOUND IN
Andreas bincap-class.Rd:37
bincap.Rd:44
cap-class.Rd:20
multcap-class.Rd:28
multcap.Rd:41
bincap auc-methods.Rd:14
consenus consensus_auc.Rnw:75
DOI auc-methods.Rd:69
HandTill2001-package.Rd:32
description:2
An_Introduction_to_HandTill2001.Rmd:14
Dominik bincap-class.Rd:37
bincap.Rd:44
cap-class.Rd:20
multcap-class.Rd:28
multcap.Rd:41
Eq auc-methods.Rd:31,34
HandTill2001-package.Rd:10
description:1
An_Introduction_to_HandTill2001.Rmd:13
eval consensus_auc.Rnw:24
fgl consensus_auc.Rnw:18,24,33
Generalisation auc-methods.Rd:67
HandTill2001-package.Rd:30
gitlab README.md:71
README.Rmd:43
HandTill throw.Rd:19,22
NEWS.md:1
README.md:15,71
README.Rmd:21,43
An_Introduction_to_HandTill2001.Rmd:2
modelling consensus_auc.Rnw:19
multcap auc-methods.Rd:14
multinom consensus_auc.Rnw:47
multipleclass ht01.multipleclass.Rd:6
nnet consensus_auc.Rnw:19,47
pre consensus_auc.Rnw:76,99
pROC HandTill2001-package.Rd:39
rpart consensus_auc.Rnw:19,33
RStudio README.md:8,9
README.Rmd:8,9
Springer ht01.multipleclass.Rd:44
ht01.twoclass.Rd:41
th ht01.multipleclass.Rd:44
ht01.twoclass.Rd:41
twoclass ht01.twoclass.Rd:6
ui bincap.Rd:5
multcap.Rd:5
Venables ht01.multipleclass.Rd:32,43
ht01.twoclass.Rd:29,40
Warning message:
spell check failed
Loading HandTill2001
Testing HandTill2001
✔ | OK F W S | Context
⠏ | 0 | Testing HandTill2001:::throw() ✔ | 1 1 | Testing HandTill2001:::throw()
────────────────────────────────────────────────────────────────────────────────
test-throw.R:5: warning: throw the HandTill2001 exception
`HandTill2001:::throw(string)` generated an S3 error and you are testing the error message.
* The error has class = c("error", "HandTill2001", "condition")
* Testing with `class` is more robust than testing with `regexp`.
* Do you want `expect_error(..., class = "error")`?
────────────────────────────────────────────────────────────────────────────────
══ Results ═════════════════════════════════════════════════════════════════════
OK: 1
Failed: 0
Warnings: 1
Skipped: 0
You are a coding rockstar!
Loading HandTill2001
Testing HandTill2001
✔ | OK F W S | Context
⠏ | 0 | Testing HandTill2001:::throw() ✔ | 1 1 | Testing HandTill2001:::throw()
────────────────────────────────────────────────────────────────────────────────
test-throw.R:5: warning: throw the HandTill2001 exception
`HandTill2001:::throw(string)` generated an S3 error and you are testing the error message.
* The error has class = c("error", "HandTill2001", "condition")
* Testing with `class` is more robust than testing with `regexp`.
* Do you want `expect_error(..., class = "error")`?
────────────────────────────────────────────────────────────────────────────────
══ Results ═════════════════════════════════════════════════════════════════════
OK: 1
Failed: 0
Warnings: 1
Skipped: 0
Warning: ‘HandTill2001’ namespace cannot be unloaded:
trying to get slot "defined" from an object of a basic class ("environment") with no slots
Loading HandTill2001
[1] "auc: parameter ‘object’ may not be used"
Loading HandTill2001
[1] "auc: parameter ‘object’ may not be used"
Warning: ‘HandTill2001’ namespace cannot be unloaded:
trying to get slot "defined" from an object of a basic class ("environment") with no slots
Building HandTill2001 vignettes
--- re-building ‘An_Introduction_to_HandTill2001.Rmd’ using rmarkdown
--- finished re-building ‘An_Introduction_to_HandTill2001.Rmd’
--- re-building ‘consensus_auc.Rnw’ using Sweave
Loading required package: class
Loaded mda 0.4-10
--- finished re-building ‘consensus_auc.Rnw’
Moving An_Introduction_to_HandTill2001.html, consensus_auc.pdf, An_Introduction_to_HandTill2001.R, consensus_auc.R to doc/
Copying An_Introduction_to_HandTill2001.Rmd, consensus_auc.Rnw to doc/
Building vignette index
processing file: /home/qwer/git/cyclops/fvafrcu/HandTill2001/vignettes/An_Introduction_to_HandTill2001.Rmd
| | | 0% | |....................... | 33% | |............................................... | 67% | |......................................................................| 100%
output file: ./inst/doc/An_Introduction_to_HandTill2001.R
Warning in remind_sweave(if (in.file) input, sweave_lines) :
It seems you are using the Sweave-specific syntax in line(s) 8, 9, 10, 21, 25, 34, 48, 54, 64, 78, 86, 100, 114, 122, 128, 133; you may need Sweave2knitr("/home/qwer/git/cyclops/fvafrcu/HandTill2001/vignettes/consensus_auc.Rnw") to convert it to knitr
processing file: /home/qwer/git/cyclops/fvafrcu/HandTill2001/vignettes/consensus_auc.Rnw
| | | 0% | |... | 4% | |..... | 7% | |........ | 11% | |.......... | 15% | |............. | 19% | |................ | 22% | |.................. | 26% | |..................... | 30% | |....................... | 33% | |.......................... | 37% | |............................. | 41% | |............................... | 44% | |.................................. | 48% | |.................................... | 52% | |....................................... | 56% | |......................................... | 59% | |............................................ | 63% | |............................................... | 67% | |................................................. | 70% | |.................................................... | 74% | |...................................................... | 78% | |......................................................... | 81% | |............................................................ | 85% | |.............................................................. | 89% | |................................................................. | 93% | |................................................................... | 96% | |......................................................................| 100%
output file: ./inst/doc/consensus_auc.Rnw
Building HandTill2001 vignettes
--- re-building ‘An_Introduction_to_HandTill2001.Rmd’ using rmarkdown
--- finished re-building ‘An_Introduction_to_HandTill2001.Rmd’
--- re-building ‘consensus_auc.Rnw’ using Sweave
Loading required package: class
Loaded mda 0.4-10
--- finished re-building ‘consensus_auc.Rnw’
Moving An_Introduction_to_HandTill2001.html, consensus_auc.pdf, An_Introduction_to_HandTill2001.R, consensus_auc.R to doc/
Copying An_Introduction_to_HandTill2001.Rmd, consensus_auc.Rnw to doc/
Building vignette index
processing file: /home/qwer/git/cyclops/fvafrcu/HandTill2001/vignettes/An_Introduction_to_HandTill2001.Rmd
| | | 0% | |....................... | 33% | |............................................... | 67% | |......................................................................| 100%
output file: ./inst/doc/An_Introduction_to_HandTill2001.R
processing file: /home/qwer/git/cyclops/fvafrcu/HandTill2001/vignettes/consensus_auc.Rnw
| | | 0% | |... | 4% | |..... | 7% | |........ | 11% | |.......... | 15% | |............. | 19% | |................ | 22% | |.................. | 26% | |..................... | 30% | |....................... | 33% | |.......................... | 37% | |............................. | 41% | |............................... | 44% | |.................................. | 48% | |.................................... | 52% | |....................................... | 56% | |......................................... | 59% | |............................................ | 63% | |............................................... | 67% | |................................................. | 70% | |.................................................... | 74% | |...................................................... | 78% | |......................................................... | 81% | |............................................................ | 85% | |.............................................................. | 89% | |................................................................. | 93% | |................................................................... | 96% | |......................................................................| 100%
output file: ./inst/doc/consensus_auc.Rnw
[[1]]
[1] "./inst/doc/An_Introduction_to_HandTill2001.R"
[[2]]
[1] "./inst/doc/consensus_auc.Rnw"
Warning message:
In remind_sweave(if (in.file) input, sweave_lines) :
It seems you are using the Sweave-specific syntax in line(s) 8, 9, 10, 21, 25, 34, 48, 54, 64, 78, 86, 100, 114, 122, 128, 133; you may need Sweave2knitr("/home/qwer/git/cyclops/fvafrcu/HandTill2001/vignettes/consensus_auc.Rnw") to convert it to knitr
#!/home/qwer/bin/Rscript-devel
arguments <- commandArgs(trailingOnly = TRUE)
target_arguments <- c("-t", "--target")
if (all(target_arguments %in% arguments)) stop(paste("got both",
paste(target_arguments,
collapse = " and ")))
for (target_argument in target_arguments) {
if (target_argument %in% arguments) {
target_name <- arguments[which(target_argument == arguments) + 1]
}
}
missing_target_name <- ! exists("target_name")
missing_target_options <- ! any(target_arguments %in% arguments)
if (missing_target_name && missing_target_options) {
# get target_name as last argument not starting with "-"
left_over <- grep("^-", arguments, invert = TRUE, value = TRUE)
num_left_over <- length(left_over)
if (num_left_over > 0) {
target_name <- left_over[num_left_over]
}
}
if (! exists("target_name")) {
target_name <- "cran_comments"
warning("Setting missing target to `", target_name,"`!")
}
if (devtools::as.package(".")[["package"]] == "packager") pkgload::load_all()
makelist <- packager::get_package_makelist()
print(fakemake::make(target_name, makelist, verbose = TRUE))
% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/throw.R
\name{throw}
\alias{throw}
\title{Throw a Condition}
\usage{
throw(message_string, system_call = sys.call(-1), ...)
}
\arguments{
\item{message_string}{The message to be thrown.}
\item{system_call}{The call to be thrown.}
\item{...}{Arguments to be passed to
\code{\link[base:structure]{base::structure}}.}
}
\value{
The function does never return anything, it stops with a
condition of class c("error", "HandTill2001", "condition").
}
\description{
Throws a condition of class c("error", "HandTill2001", "condition").
}
\details{
We use this condition as an error dedicated to \pkg{ HandTill2001.}
}
\examples{
tryCatch(HandTill2001:::throw("Hello error!"), HandTill2001 = function(e) return(e))
}
\keyword{internal}
#!/usr/bin/Rscript --vanilla
is_failure <- function(result) {
res <- RUnit::getErrors(result)
names(res) <- tolower(names(res)) # soothe lintr
sum_of_exceptions <- res[["nerr"]] + res[["nfail"]]
fail <- as.logical(sum_of_exceptions)
return(fail)
}
if (interactive()) {
pkgload::load_all(path = ".") # needed to use pkgload's shim version of
# base's system.file
unit_dir <- system.file("inst", "runit_tests", package = "HandTill2001")
} else {
require("HandTill2001", quietly = TRUE, character.only = TRUE) ||
pkgload::load_all(path = ".") # needed to use pkgload's shim version of
r_call <- commandArgs(trailingOnly = FALSE)
if (any(grepl("--file", r_call))) {
unit_dir <- file.path("inst", "runit_tests")
} else {
unit_dir <- system.file("runit_tests", package = "HandTill2001")
}
}
if (! dir.exists(unit_dir)) {
stop("Can not find RUnit test directory ", unit_dir,
". Try to (re)install the package first.")
}
package_suite <- RUnit::defineTestSuite("HandTill2001_unit_test",
dirs = unit_dir,
testFileRegexp = "^.*\\.[rR]",
testFuncRegexp = "^test_+")
test_result <- RUnit::runTestSuite(package_suite)
root <- tryCatch(rprojroot::find_root(rprojroot::is_r_package),
error = function(e) return(NULL))
if (! is.null(root)) {
log_dir <- file.path(root, "log")
dir.create(log_dir, showWarnings = FALSE)
file_name <- file.path(log_dir, "runit.log")
html_file <- file.path(log_dir, "runit.html")
RUnit::printHTMLProtocol(test_result, fileName = html_file)
if (interactive()) {
browseURL(paste0("file:", html_file))
}
} else {
file_name <- ""
}
RUnit::printTextProtocol(test_result, showDetails = TRUE, fileName = file_name)
if (is_failure(test_result)) {
RUnit::printTextProtocol(test_result, showDetails = TRUE)
stop("RUnit failed.")
}
library(testthat)
library(HandTill2001)
test_check("HandTill2001")
testthat::context("Testing HandTill2001:::throw()")
testthat::test_that("throw the HandTill2001 exception", {
error_message <- "hello, testthat"
string <- "hello, testthat"
testthat::expect_error(HandTill2001:::throw(string),
error_message)
}
)