Last updated: 05-Nov-2019
+Last updated: 06-Nov-2019
as.mo(..., allow_uncertain = 3)
Contents
In 2019, EUCAST has decided to change the definitions of susceptibility testing categories S, I and R as shown below (http://www.eucast.org/newsiandr/). Results of several consultations on the new definitions are available on the EUCAST website under "Consultations".
+In 2019, the European Committee on Antimicrobial Susceptibility Testing (EUCAST) has decided to change the definitions of susceptibility testing categories S, I and R as shown below (http://www.eucast.org/newsiandr/). Results of several consultations on the new definitions are available on the EUCAST website under "Consultations".
S - Susceptible, standard dosing regimen: A microorganism is categorised as "Susceptible, standard dosing regimen", when there is a high likelihood of therapeutic success using a standard dosing regimen of the agent.
I - Susceptible, increased exposure: A microorganism is categorised as "Susceptible, Increased exposure" when there is a high likelihood of therapeutic success because exposure to the agent is increased by adjusting the dosing regimen or by its concentration at the site of infection.
In 2019, EUCAST has decided to change the definitions of susceptibility testing categories S, I and R as shown below (http://www.eucast.org/newsiandr/). Results of several consultations on the new definitions are available on the EUCAST website under "Consultations".
+In 2019, the European Committee on Antimicrobial Susceptibility Testing (EUCAST) has decided to change the definitions of susceptibility testing categories S, I and R as shown below (http://www.eucast.org/newsiandr/). Results of several consultations on the new definitions are available on the EUCAST website under "Consultations".
S - Susceptible, standard dosing regimen: A microorganism is categorised as "Susceptible, standard dosing regimen", when there is a high likelihood of therapeutic success using a standard dosing regimen of the agent.
I - Susceptible, increased exposure: A microorganism is categorised as "Susceptible, Increased exposure" when there is a high likelihood of therapeutic success because exposure to the agent is increased by adjusting the dosing regimen or by its concentration at the site of infection.
mdro(x, guideline = NULL, col_mo = NULL, info = TRUE, - verbose = FALSE, pct_required_classes = 0.5, ...) + pct_required_classes = 0.5, combine_SI = TRUE, verbose = FALSE, + ...) brmo(x, guideline = "BRMO", ...) @@ -269,14 +270,18 @@info - print progress
- verbose -- a logical to turn Verbose mode on and off (default is off). In Verbose mode, the function does not return the MDRO results, but instead returns a data set in logbook form with extensive info about which isolates would be MDRO-positive, or why they are not.
+ pct_required_classes minimal required percentage of antimicrobial classes that must be available per isolate, rounded down. For example, with the default guideline, 17 antimicrobial classes must be available for S. aureus. Setting this
pct_required_classesargument to0.5(default) means that for every S. aureus isolate at least 8 different classes must be available. Any lower number of available classes will returnNAfor that isolate.+ +combine_SI ++ a logical to indicate whether all values of S and I must be merged into one, so resistance is only considered when isolates are R, not I. As this is the default behaviour of the
mdro()function, it follows the redefinition by EUCAST about the interpretion of I (increased exposure) in 2019, see section 'Interpretation of S, I and R' below. When usingcombine_SI = FALSE, resistance is considered when isolates are R or I.+ verbose ++ a logical to turn Verbose mode on and off (default is off). In Verbose mode, the function does not return the MDRO results, but instead returns a data set in logbook form with extensive info about which isolates would be MDRO-positive, or why they are not.
... @@ -394,6 +399,19 @@ TMP: trimethoprim (J01EA01), SXT: trimethoprim/sulfamethoxazole (J01EE01), VAN: vancomycin (J01XA01). + column name of an antibiotic, see section Antibiotics
Interpretation of S, I and R
+ + + +In 2019, the European Committee on Antimicrobial Susceptibility Testing (EUCAST) has decided to change the definitions of susceptibility testing categories S, I and R as shown below (http://www.eucast.org/newsiandr/). Results of several consultations on the new definitions are available on the EUCAST website under "Consultations".
++
+ +- +
S - Susceptible, standard dosing regimen: A microorganism is categorised as "Susceptible, standard dosing regimen", when there is a high likelihood of therapeutic success using a standard dosing regimen of the agent.
- +
I - Susceptible, increased exposure: A microorganism is categorised as "Susceptible, Increased exposure" when there is a high likelihood of therapeutic success because exposure to the agent is increased by adjusting the dosing regimen or by its concentration at the site of infection.
- +
R - Resistant: A microorganism is categorised as "Resistant" when there is a high likelihood of therapeutic failure even when there is increased exposure.
Exposure is a function of how the mode of administration, dose, dosing interval, infusion time, as well as distribution and excretion of the antimicrobial agent will influence the infecting organism at the site of infection.
+This AMR package honours this new insight. Use
portion_SIto determine antimicrobial susceptibility andcount_SIto count susceptible isolates.Read more on our website!
@@ -427,6 +445,7 @@Value Details Antibiotics +Interpretation of S, I and R Read more on our website! Examples diff --git a/docs/reference/portion.html b/docs/reference/portion.html index 2bbfd81a5..4cc9fdb4c 100644 --- a/docs/reference/portion.html +++ b/docs/reference/portion.html @@ -86,7 +86,7 @@ portion_R and portion_IR can be used to calculate resistance, portion_S and port @@ -353,7 +353,7 @@ portion_R and portion_IR can be used to calculate resistance, portion_S and port -In 2019, EUCAST has decided to change the definitions of susceptibility testing categories S, I and R as shown below (http://www.eucast.org/newsiandr/). Results of several consultations on the new definitions are available on the EUCAST website under "Consultations".
+In 2019, the European Committee on Antimicrobial Susceptibility Testing (EUCAST) has decided to change the definitions of susceptibility testing categories S, I and R as shown below (http://www.eucast.org/newsiandr/). Results of several consultations on the new definitions are available on the EUCAST website under "Consultations".
S - Susceptible, standard dosing regimen: A microorganism is categorised as "Susceptible, standard dosing regimen", when there is a high likelihood of therapeutic success using a standard dosing regimen of the agent.
- diff --git a/man/ab_property.Rd b/man/ab_property.Rd index 03e643d9c..af3bb84e9 100644 --- a/man/ab_property.Rd +++ b/man/ab_property.Rd @@ -4,6 +4,7 @@ \alias{ab_property} \alias{ab_name} \alias{ab_atc} +\alias{ATC} \alias{ab_cid} \alias{ab_synonyms} \alias{ab_tradenames} diff --git a/man/age_groups.Rd b/man/age_groups.Rd index ea760e197..8272e5780 100644 --- a/man/age_groups.Rd +++ b/man/age_groups.Rd @@ -74,5 +74,3 @@ example_isolates \%>\% \seealso{ To determine ages, based on one or more reference dates, use the \code{\link{age}} function. } -\keyword{age} -\keyword{age_group} diff --git a/man/as.ab.Rd b/man/as.ab.Rd index ab111a781..745b185c8 100644 --- a/man/as.ab.Rd +++ b/man/as.ab.Rd @@ -72,4 +72,3 @@ ab_name("eryt") # "Erythromycin" \seealso{ \code{\link{antibiotics}} for the dataframe that is being used to determine ATCs. } -\keyword{atc} diff --git a/man/as.disk.Rd b/man/as.disk.Rd index 463e13d7e..ccbc1d3a3 100644 --- a/man/as.disk.Rd +++ b/man/as.disk.Rd @@ -2,6 +2,7 @@ % Please edit documentation in R/disk.R \name{as.disk} \alias{as.disk} +\alias{disk} \alias{is.disk} \title{Class 'disk'} \usage{ @@ -42,4 +43,3 @@ as.rsi(x = 12, \seealso{ \code{\link{as.rsi}} } -\keyword{disk} diff --git a/man/as.mic.Rd b/man/as.mic.Rd index 25a09b472..34e7acf5f 100755 --- a/man/as.mic.Rd +++ b/man/as.mic.Rd @@ -2,6 +2,7 @@ % Please edit documentation in R/mic.R \name{as.mic} \alias{as.mic} +\alias{MIC} \alias{is.mic} \title{Class 'mic'} \usage{ @@ -52,4 +53,3 @@ freq(mic_data) \seealso{ \code{\link{as.rsi}} } -\keyword{mic} diff --git a/man/as.rsi.Rd b/man/as.rsi.Rd index 90faf7e49..ab14187f2 100755 --- a/man/as.rsi.Rd +++ b/man/as.rsi.Rd @@ -2,6 +2,7 @@ % Please edit documentation in R/rsi.R \name{as.rsi} \alias{as.rsi} +\alias{RSI} \alias{as.rsi.mic} \alias{as.rsi.disk} \alias{as.rsi.data.frame} @@ -52,7 +53,7 @@ The function \code{is.rsi.eligible} returns \code{TRUE} when a columns contains } \section{Interpretation of S, I and R}{ -In 2019, EUCAST has decided to change the definitions of susceptibility testing categories S, I and R as shown below (\url{http://www.eucast.org/newsiandr/}). Results of several consultations on the new definitions are available on the EUCAST website under "Consultations". +In 2019, the European Committee on Antimicrobial Susceptibility Testing (EUCAST) has decided to change the definitions of susceptibility testing categories S, I and R as shown below (\url{http://www.eucast.org/newsiandr/}). Results of several consultations on the new definitions are available on the EUCAST website under "Consultations". \itemize{ \item{\strong{S} - }{Susceptible, standard dosing regimen: A microorganism is categorised as "Susceptible, standard dosing regimen", when there is a high likelihood of therapeutic success using a standard dosing regimen of the agent.} @@ -110,4 +111,3 @@ is.rsi.eligible(WHONET$`First name`, threshold = 0.99) # succeeds \seealso{ \code{\link{as.mic}} } -\keyword{rsi} diff --git a/man/count.Rd b/man/count.Rd index bd483f27c..34d5fa4d0 100644 --- a/man/count.Rd +++ b/man/count.Rd @@ -66,7 +66,7 @@ The function \code{rsi_df} works exactly like \code{count_df}, but adds the perc } \section{Interpretation of S, I and R}{ -In 2019, EUCAST has decided to change the definitions of susceptibility testing categories S, I and R as shown below (\url{http://www.eucast.org/newsiandr/}). Results of several consultations on the new definitions are available on the EUCAST website under "Consultations". +In 2019, the European Committee on Antimicrobial Susceptibility Testing (EUCAST) has decided to change the definitions of susceptibility testing categories S, I and R as shown below (\url{http://www.eucast.org/newsiandr/}). Results of several consultations on the new definitions are available on the EUCAST website under "Consultations". \itemize{ \item{\strong{S} - }{Susceptible, standard dosing regimen: A microorganism is categorised as "Susceptible, standard dosing regimen", when there is a high likelihood of therapeutic success using a standard dosing regimen of the agent.} @@ -182,9 +182,3 @@ example_isolates \%>\% \seealso{ \code{\link{portion}_*} to calculate microbial resistance and susceptibility. } -\keyword{antibiotics} -\keyword{isolate} -\keyword{isolates} -\keyword{resistance} -\keyword{rsi} -\keyword{susceptibility} diff --git a/man/eucast_rules.Rd b/man/eucast_rules.Rd index f2085a292..97a982fdc 100644 --- a/man/eucast_rules.Rd +++ b/man/eucast_rules.Rd @@ -2,6 +2,7 @@ % Please edit documentation in R/eucast_rules.R \name{eucast_rules} \alias{eucast_rules} +\alias{EUCAST} \title{EUCAST rules} \source{ \itemize{ @@ -183,7 +184,3 @@ b c <- eucast_rules(a, verbose = TRUE) } } -\keyword{eucast} -\keyword{interpretive} -\keyword{reading} -\keyword{resistance} diff --git a/man/filter_ab_class.Rd b/man/filter_ab_class.Rd index 237f955d6..9bb77f0d4 100644 --- a/man/filter_ab_class.Rd +++ b/man/filter_ab_class.Rd @@ -89,5 +89,3 @@ example_isolates \%>\% filter_aminoglycosides("R", "all") \%>\% filter_fluoroquinolones("R", "all") } -\keyword{fillter_class} -\keyword{filter} diff --git a/man/first_isolate.Rd b/man/first_isolate.Rd index 3cad54fd6..8cf2639ba 100755 --- a/man/first_isolate.Rd +++ b/man/first_isolate.Rd @@ -160,6 +160,3 @@ x$first_blood_isolate <- first_isolate(x, specimen_group = "Blood") \seealso{ \code{\link{key_antibiotics}} } -\keyword{first} -\keyword{isolate} -\keyword{isolates} diff --git a/man/g.test.Rd b/man/g.test.Rd index 36a041193..a0f633dd0 100644 --- a/man/g.test.Rd +++ b/man/g.test.Rd @@ -145,4 +145,3 @@ g.test(x) \seealso{ \code{\link{chisq.test}} } -\keyword{chi} diff --git a/man/like.Rd b/man/like.Rd index 35e15b7e4..7ed6f949e 100755 --- a/man/like.Rd +++ b/man/like.Rd @@ -63,9 +63,8 @@ a \%like\% b # get frequencies of bacteria whose name start with 'Ent' or 'ent' library(dplyr) example_isolates \%>\% - left_join_microorganisms() \%>\% - filter(genus \%like\% '^ent') \%>\% - freq(genus, species) + filter(mo_genus(mo) \%like\% '^ent') \%>\% + freq(mo_fullname(mo)) } \seealso{ \code{\link[base]{grep}} diff --git a/man/mdro.Rd b/man/mdro.Rd index a714112af..3ec5afd02 100644 --- a/man/mdro.Rd +++ b/man/mdro.Rd @@ -2,6 +2,12 @@ % Please edit documentation in R/mdro.R \name{mdro} \alias{mdro} +\alias{MDR} +\alias{XDR} +\alias{PDR} +\alias{BRMO} +\alias{3MRGN} +\alias{4MRGN} \alias{brmo} \alias{mrgn} \alias{mdr_tb} @@ -13,7 +19,8 @@ Please see Details for the list of publications used for this function. } \usage{ mdro(x, guideline = NULL, col_mo = NULL, info = TRUE, - verbose = FALSE, pct_required_classes = 0.5, ...) + pct_required_classes = 0.5, combine_SI = TRUE, verbose = FALSE, + ...) brmo(x, guideline = "BRMO", ...) @@ -34,10 +41,12 @@ eucast_exceptional_phenotypes(x, guideline = "EUCAST", ...) \item{info}{print progress} -\item{verbose}{a logical to turn Verbose mode on and off (default is off). In Verbose mode, the function does not return the MDRO results, but instead returns a data set in logbook form with extensive info about which isolates would be MDRO-positive, or why they are not.} - \item{pct_required_classes}{minimal required percentage of antimicrobial classes that must be available per isolate, rounded down. For example, with the default guideline, 17 antimicrobial classes must be available for \emph{S. aureus}. Setting this \code{pct_required_classes} argument to \code{0.5} (default) means that for every \emph{S. aureus} isolate at least 8 different classes must be available. Any lower number of available classes will return \code{NA} for that isolate.} +\item{combine_SI}{a logical to indicate whether all values of S and I must be merged into one, so resistance is only considered when isolates are R, not I. As this is the default behaviour of the \code{mdro()} function, it follows the redefinition by EUCAST about the interpretion of I (increased exposure) in 2019, see section 'Interpretation of S, I and R' below. When using \code{combine_SI = FALSE}, resistance is considered when isolates are R or I.} + +\item{verbose}{a logical to turn Verbose mode on and off (default is off). In Verbose mode, the function does not return the MDRO results, but instead returns a data set in logbook form with extensive info about which isolates would be MDRO-positive, or why they are not.} + \item{...}{column name of an antibiotic, see section Antibiotics} } \value{ @@ -154,6 +163,21 @@ The following antibiotics are used for the functions \code{\link{eucast_rules}} \strong{VAN}: vancomycin (\href{https://www.whocc.no/atc_ddd_index/?code=J01XA01}{J01XA01}). } +\section{Interpretation of S, I and R}{ + +In 2019, the European Committee on Antimicrobial Susceptibility Testing (EUCAST) has decided to change the definitions of susceptibility testing categories S, I and R as shown below (\url{http://www.eucast.org/newsiandr/}). Results of several consultations on the new definitions are available on the EUCAST website under "Consultations". + +\itemize{ + \item{\strong{S} - }{Susceptible, standard dosing regimen: A microorganism is categorised as "Susceptible, standard dosing regimen", when there is a high likelihood of therapeutic success using a standard dosing regimen of the agent.} + \item{\strong{I} - }{Susceptible, increased exposure: A microorganism is categorised as "Susceptible, Increased exposure" when there is a high likelihood of therapeutic success because exposure to the agent is increased by adjusting the dosing regimen or by its concentration at the site of infection.} + \item{\strong{R} - }{Resistant: A microorganism is categorised as "Resistant" when there is a high likelihood of therapeutic failure even when there is increased exposure.} +} + +Exposure is a function of how the mode of administration, dose, dosing interval, infusion time, as well as distribution and excretion of the antimicrobial agent will influence the infecting organism at the site of infection. + +This AMR package honours this new insight. Use \code{\link{portion_SI}} to determine antimicrobial susceptibility and \code{\link{count_SI}} to count susceptible isolates. +} + \section{Read more on our website!}{ On our website \url{https://msberends.gitlab.io/AMR} you can find \href{https://msberends.gitlab.io/AMR/articles/AMR.html}{a tutorial} about how to conduct AMR analysis, the \href{https://msberends.gitlab.io/AMR/reference}{complete documentation of all functions} (which reads a lot easier than here in R) and \href{https://msberends.gitlab.io/AMR/articles/WHONET.html}{an example analysis using WHONET data}. diff --git a/man/portion.Rd b/man/portion.Rd index eedfb6545..722e12804 100644 --- a/man/portion.Rd +++ b/man/portion.Rd @@ -114,7 +114,7 @@ Using \code{only_all_tested} has no impact when only using one antibiotic as inp \section{Interpretation of S, I and R}{ -In 2019, EUCAST has decided to change the definitions of susceptibility testing categories S, I and R as shown below (\url{http://www.eucast.org/newsiandr/}). Results of several consultations on the new definitions are available on the EUCAST website under "Consultations". +In 2019, the European Committee on Antimicrobial Susceptibility Testing (EUCAST) has decided to change the definitions of susceptibility testing categories S, I and R as shown below (\url{http://www.eucast.org/newsiandr/}). Results of several consultations on the new definitions are available on the EUCAST website under "Consultations". \itemize{ \item{\strong{S} - }{Susceptible, standard dosing regimen: A microorganism is categorised as "Susceptible, standard dosing regimen", when there is a high likelihood of therapeutic success using a standard dosing regimen of the agent.} @@ -226,10 +226,3 @@ my_table \%>\% \seealso{ \code{\link[AMR]{count}_*} to count resistant and susceptible isolates. } -\keyword{antibiotics} -\keyword{isolate} -\keyword{isolates} -\keyword{resistance} -\keyword{rsi} -\keyword{rsi_df} -\keyword{susceptibility} diff --git a/tests/appveyor/appveyor_tool.ps1 b/tests/appveyor/appveyor_tool.ps1 new file mode 100644 index 000000000..8586f9edb --- /dev/null +++ b/tests/appveyor/appveyor_tool.ps1 @@ -0,0 +1,193 @@ +if ( -not(Test-Path Env:\CRAN) ) { + $CRAN = "https://cran.rstudio.com" +} +Else { + $CRAN = $env:CRAN +} + + +# Found at http://zduck.com/2012/powershell-batch-files-exit-codes/ +Function Exec +{ + [CmdletBinding()] + param ( + [Parameter(Position=0, Mandatory=1)] + [scriptblock]$Command, + [Parameter(Position=1, Mandatory=0)] + [string]$ErrorMessage = "Execution of command failed.`n$Command" + ) + $ErrorActionPreference = "Continue" + & $Command 2>&1 | %{ "$_" } + if ($LastExitCode -ne 0) { + throw "Exec: $ErrorMessage`nExit code: $LastExitCode" + } +} + +Function Progress +{ + [CmdletBinding()] + param ( + [Parameter(Position=0, Mandatory=0)] + [string]$Message = "" + ) + + $ProgressMessage = '== ' + (Get-Date) + ': ' + $Message + + Write-Host $ProgressMessage -ForegroundColor Magenta +} + +Function TravisTool +{ + [CmdletBinding()] + param ( + [Parameter(Position=0, Mandatory=1)] + [string[]]$Params + ) + + Exec { bash.exe ../travis_tool.sh $Params } +} + +Function InstallR { + [CmdletBinding()] + Param() + + if ( -not(Test-Path Env:\R_VERSION) ) { + $version = "patched" + } + Else { + $version = $env:R_VERSION + } + + if ( -not(Test-Path Env:\R_ARCH) ) { + $arch = "x64" + } + Else { + $arch = $env:R_ARCH + } + + If ($arch -eq "i386") { + $mingw_path = "mingw_32" + } + Else { + $mingw_path = "mingw_64" + } + + Progress ("Version: " + $version) + + If ($version -eq "devel") { + $url_path = "" + $version = "devel" + } + ElseIf (($version -eq "stable") -or ($version -eq "release")) { + $url_path = "" + $version = $(ConvertFrom-JSON $(Invoke-WebRequest http://rversions.r-pkg.org/r-release-win).Content).version + If ($version -eq "3.2.4") { + $version = "3.2.4revised" + } + } + ElseIf ($version -eq "patched") { + $url_path = "" + $version = $(ConvertFrom-JSON $(Invoke-WebRequest http://rversions.r-pkg.org/r-release-win).Content).version + "patched" + } + ElseIf ($version -eq "oldrel") { + $version = $(ConvertFrom-JSON $(Invoke-WebRequest http://rversions.r-pkg.org/r-oldrel).Content).version + $url_path = ("old/" + $version + "/") + } + Else { + $url_path = ("old/" + $version + "/") + } + + Progress ("URL path: " + $url_path) + + $rurl = $CRAN + "/bin/windows/base/" + $url_path + "R-" + $version + "-win.exe" + + Progress ("Downloading R from: " + $rurl) + & "C:\Program Files\Git\mingw64\bin\curl.exe" -s -o ../R-win.exe -L $rurl + + Progress "Running R installer" + Start-Process -FilePath ..\R-win.exe -ArgumentList "/VERYSILENT /DIR=C:\R" -NoNewWindow -Wait + + $RDrive = "C:" + echo "R is now available on drive $RDrive" + + Progress "Setting PATH" + $env:PATH = $RDrive + '\R\bin\' + $arch + ';' + 'C:\Rtools\' + $mingw_path + '\bin;' + 'C:\MinGW\msys\1.0\bin;' + $env:PATH + + Progress "Testing R installation" + Rscript -e "sessionInfo()" +} + +Function InstallRtools { + if ( -not(Test-Path Env:\RTOOLS_VERSION) ) { + Progress "Determining Rtools version" + $rtoolsver = $(Invoke-WebRequest ($CRAN + "/bin/windows/Rtools/VERSION.txt")).Content.Split(' ')[2].Split('.')[0..1] -Join '' + } + Else { + $rtoolsver = $env:RTOOLS_VERSION + } + + $rtoolsurl = $CRAN + "/bin/windows/Rtools/Rtools$rtoolsver.exe" + + Progress ("Downloading Rtools from: " + $rtoolsurl) + & "C:\Program Files\Git\mingw64\bin\curl.exe" -s -o ../Rtools-current.exe -L $rtoolsurl + + Progress "Running Rtools installer" + Start-Process -FilePath ..\Rtools-current.exe -ArgumentList /VERYSILENT -NoNewWindow -Wait + + $RtoolsDrive = "C:" + echo "Rtools is now available on drive $RtoolsDrive" + + Progress "Setting PATH" + if ( -not(Test-Path Env:\GCC_PATH) ) { + $gcc_path = "gcc-4.6.3" + } + Else { + $gcc_path = $env:GCC_PATH + } + $env:PATH = $RtoolsDrive + '\Rtools\bin;' + $RtoolsDrive + '\Rtools\MinGW\bin;' + $RtoolsDrive + '\Rtools\' + $gcc_path + '\bin;' + $env:PATH + $env:BINPREF=$RtoolsDrive + '/Rtools/mingw_$(WIN)/bin/' +} + +Function Bootstrap { + [CmdletBinding()] + Param() + + Progress "Bootstrap: Start" + + Progress "Adding GnuWin32 tools to PATH" + $env:PATH = "C:\Program Files (x86)\Git\bin;" + $env:PATH + + Progress "Setting time zone" + tzutil /g + tzutil /s "GMT Standard Time" + tzutil /g + + InstallR + + if ((Test-Path "src") -or ($env:USE_RTOOLS -eq "true") -or ($env:USE_RTOOLS -eq "yes")) { + InstallRtools + } + Else { + Progress "Skipping download of Rtools because src/ directory is missing." + } + + Progress "Downloading and installing travis_tool.sh" + Invoke-WebRequest https://gitlab.com/msberends/AMR/raw/master/tests/appveyor/travis_tool.sh -OutFile "..\travis_tool.sh" + echo '@bash.exe ../travis_tool.sh %*' | Out-File -Encoding ASCII .\travis_tool.sh.cmd + cat .\travis_tool.sh.cmd + bash -c "( echo; echo '^travis_tool\.sh\.cmd$' ) >> .Rbuildignore" + cat .\.Rbuildignore + + $env:PATH.Split(";") + + Progress "Setting R_LIBS_USER" + $env:R_LIBS_USER = 'c:\RLibrary' + if ( -not(Test-Path $env:R_LIBS_USER) ) { + mkdir $env:R_LIBS_USER + } + + Progress "Setting TAR to 'internal'" + $env:TAR = 'internal' + + Progress "Bootstrap: Done" +} diff --git a/tests/appveyor/travis_tool.sh b/tests/appveyor/travis_tool.sh new file mode 100644 index 000000000..5d9caf611 --- /dev/null +++ b/tests/appveyor/travis_tool.sh @@ -0,0 +1,428 @@ +#!/bin/bash +# -*- sh-basic-offset: 4; sh-indentation: 4 -*- +# Bootstrap an R/travis environment. + +set -e +# Comment out this line for quieter output: +set -x + +CRAN=${CRAN:-"https://cran.rstudio.com"} +BIOC=${BIOC:-"http://bioconductor.org/biocLite.R"} +PKGTYPE=${PKGTYPE:-"win.binary"} +BIOC_USE_DEVEL=${BIOC_USE_DEVEL:-"TRUE"} +OS=$(uname -s) +DOWNLOAD_FILE_METHOD=${DOWNLOAD_FILE_METHOD:-"auto"} + +PANDOC_VERSION='1.13.1' +PANDOC_DIR="${HOME}/opt/pandoc" +PANDOC_URL="https://s3.amazonaws.com/rstudio-buildtools/pandoc-${PANDOC_VERSION}.zip" + +# MacTeX installs in a new $PATH entry, and there's no way to force +# the *parent* shell to source it from here. So we just manually add +# all the entries to a location we already know to be on $PATH. +# +# TODO(craigcitro): Remove this once we can add `/usr/texbin` to the +# root path. +PATH="${PATH}:/usr/texbin" + +R_BUILD_ARGS=${R_BUILD_ARGS-"--no-manual"} +R_CHECK_ARGS=${R_CHECK_ARGS-"--no-manual --as-cran"} + +R_VERSION_TEST="getRversion() >= '3.5.0'" + +R_USE_BIOC_INST="source('${BIOC}');"\ +" tryCatch(useDevel(${BIOC_USE_DEVEL}),"\ +" error=function(e) {if (!grepl('already in use', e$message)) {e}});"\ +" options(repos=biocinstallRepos())" + +R_USE_BIOC_MNGR="if (!requireNamespace('BiocManager', quietly=TRUE))"\ +" install.packages('BiocManager', repos=c(CRAN='${CRAN}'));"\ +" if (${BIOC_USE_DEVEL})"\ +" BiocManager::install(version = 'devel', ask = FALSE);"\ +" options(repos=BiocManager::repositories())" + +R_USE_BIOC_CMDS="if (${R_VERSION_TEST}) {${R_USE_BIOC_MNGR}} else {${R_USE_BIOC_INST}};" + +BIOC_INSTALL="{if (${R_VERSION_TEST}) BiocManager::install else BiocInstaller::biocLite}" + +Bootstrap() { + if [[ "Darwin" == "${OS}" ]]; then + BootstrapMac + elif [[ "Linux" == "${OS}" ]]; then + BootstrapLinux + else + echo "Unknown OS: ${OS}" + exit 1 + fi + + if ! (test -e .Rbuildignore && grep -q 'travis-tool' .Rbuildignore); then + echo '^travis-tool\.sh$' >>.Rbuildignore + fi +} + +InstallPandoc() { + local os_path="$1" + mkdir -p "${PANDOC_DIR}" + curl -o /tmp/pandoc-${PANDOC_VERSION}.zip ${PANDOC_URL} + unzip -j /tmp/pandoc-${PANDOC_VERSION}.zip "pandoc-${PANDOC_VERSION}/${os_path}/pandoc" -d "${PANDOC_DIR}" + chmod +x "${PANDOC_DIR}/pandoc" + sudo ln -s "${PANDOC_DIR}/pandoc" /usr/local/bin + unzip -j /tmp/pandoc-${PANDOC_VERSION}.zip "pandoc-${PANDOC_VERSION}/${os_path}/pandoc-citeproc" -d "${PANDOC_DIR}" + chmod +x "${PANDOC_DIR}/pandoc-citeproc" + sudo ln -s "${PANDOC_DIR}/pandoc-citeproc" /usr/local/bin +} + +BootstrapLinux() { + # Set up our CRAN mirror. + sudo add-apt-repository "deb ${CRAN}/bin/linux/ubuntu $(lsb_release -cs)/" + sudo apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E084DAB9 + + # Add marutter's c2d4u repository. + sudo add-apt-repository -y "ppa:marutter/rrutter" + sudo add-apt-repository -y "ppa:marutter/c2d4u" + + # Update after adding all repositories. Retry several times to work around + # flaky connection to Launchpad PPAs. + Retry sudo apt-get update -qq + + # Install an R development environment. qpdf is also needed for + # --as-cran checks: + # https://stat.ethz.ch/pipermail/r-help//2012-September/335676.html + Retry sudo apt-get install -y --no-install-recommends r-base-dev r-recommended qpdf + + # Change permissions for /usr/local/lib/R/site-library + # This should really be via 'staff adduser travis staff' + # but that may affect only the next shell + sudo chmod 2777 /usr/local/lib/R /usr/local/lib/R/site-library + + # Process options + BootstrapLinuxOptions +} + +BootstrapLinuxOptions() { + if [[ -n "$BOOTSTRAP_LATEX" ]]; then + # We add a backports PPA for more recent TeX packages. + sudo add-apt-repository -y "ppa:texlive-backports/ppa" + + Retry sudo apt-get install -y --no-install-recommends \ + texlive-base texlive-latex-base texlive-generic-recommended \ + texlive-fonts-recommended texlive-fonts-extra \ + texlive-extra-utils texlive-latex-recommended texlive-latex-extra \ + texinfo lmodern + fi + if [[ -n "$BOOTSTRAP_PANDOC" ]]; then + InstallPandoc 'linux/debian/x86_64' + fi +} + +BootstrapMac() { + # Install from latest CRAN binary build for OS X + wget ${CRAN}/bin/macosx/R-latest.pkg -O /tmp/R-latest.pkg + + echo "Installing OS X binary package for R" + sudo installer -pkg "/tmp/R-latest.pkg" -target / + rm "/tmp/R-latest.pkg" + + # Process options + BootstrapMacOptions +} + +BootstrapMacOptions() { + if [[ -n "$BOOTSTRAP_LATEX" ]]; then + # TODO: Install MacTeX.pkg once there's enough disk space + MACTEX=BasicTeX.pkg + wget http://ctan.math.utah.edu/ctan/tex-archive/systems/mac/mactex/$MACTEX -O "/tmp/$MACTEX" + + echo "Installing OS X binary package for MacTeX" + sudo installer -pkg "/tmp/$MACTEX" -target / + rm "/tmp/$MACTEX" + # We need a few more packages than the basic package provides; this + # post saved me so much pain: + # https://stat.ethz.ch/pipermail/r-sig-mac/2010-May/007399.html + sudo tlmgr update --self + sudo tlmgr install inconsolata upquote courier courier-scaled helvetic + fi + if [[ -n "$BOOTSTRAP_PANDOC" ]]; then + InstallPandoc 'mac' + fi +} + +EnsureDevtools() { + if ! Rscript -e 'if (!("devtools" %in% rownames(installed.packages()))) q(status=1)' ; then + # Install devtools and testthat. + RBinaryInstall devtools testthat + fi +} + +EnsureRemotes() { + if ! Rscript -e 'if (!("remotes" %in% rownames(installed.packages()))) q(status=1)' ; then + # Install remotes. + RBinaryInstall remotes + fi + if ! Rscript -e 'if (!("remotes" %in% rownames(installed.packages()))) q(status=1)' ; then + # Fallback: Install remotes from URL. + Rscript -e 'path <- file.path(tempdir(), "remotes_1.0.0.tar.gz"); download.file("https://cran.rstudio.com/src/contrib/Archive/remotes/remotes_1.0.0.tar.gz", path); install.packages(path, repos = NULL, type = "source")' + fi +} + +AptGetInstall() { + if [[ "Linux" != "${OS}" ]]; then + echo "Wrong OS: ${OS}" + exit 1 + fi + + if [[ "" == "$*" ]]; then + echo "No arguments to aptget_install" + exit 1 + fi + + echo "Installing apt package(s) $@" + Retry sudo apt-get -y install "$@" +} + +DpkgCurlInstall() { + if [[ "Linux" != "${OS}" ]]; then + echo "Wrong OS: ${OS}" + exit 1 + fi + + if [[ "" == "$*" ]]; then + echo "No arguments to dpkgcurl_install" + exit 1 + fi + + echo "Installing remote package(s) $@" + for rf in "$@"; do + curl -OL ${rf} + f=$(basename ${rf}) + sudo dpkg -i ${f} + rm -v ${f} + done +} + +RInstall() { + if [[ "" == "$*" ]]; then + echo "No arguments to r_install" + exit 1 + fi + + echo "Installing R package(s): $@" + Rscript -e 'install.packages(commandArgs(TRUE), repos="'"${CRAN}"'", INSTALL_opts="", type="'"${PKGTYPE}"'")' "$@" +} + +BiocInstall() { + if [[ "" == "$*" ]]; then + echo "No arguments to bioc_install" + exit 1 + fi + + echo "Installing R Bioconductor package(s): $@" + Rscript -e "${R_USE_BIOC_CMDS}"" ${BIOC_INSTALL}(commandArgs(TRUE))" "$@" +} + +RBinaryInstall() { + if [[ -z "$#" ]]; then + echo "No arguments to r_binary_install" + exit 1 + fi + + if [[ "Linux" != "${OS}" ]] || [[ -n "${FORCE_SOURCE_INSTALL}" ]]; then + echo "Fallback: Installing from source" + RInstall "$@" + return + fi + + echo "Installing *binary* R packages: $*" + r_packages=$(echo $* | tr '[:upper:]' '[:lower:]') + r_debs=$(for r_package in ${r_packages}; do echo -n "r-cran-${r_package} "; done) + + AptGetInstall ${r_debs} +} + +InstallGithub() { + EnsureRemotes + + echo "Installing GitHub packages: $@" + # Install the package. + Rscript -e 'options(repos = c(CRAN = "'"${CRAN}"'"), download.file.method = "'"${DOWNLOAD_FILE_METHOD}"'"); remotes::install_github(commandArgs(TRUE), type="'"${PKGTYPE}"'")' "$@" +} + +InstallDeps() { + EnsureRemotes + + echo "Installing dependencies" + Rscript -e 'options(repos = c(CRAN = "'"${CRAN}"'"), download.file.method = "'"${DOWNLOAD_FILE_METHOD}"'"); remotes::install_deps(dependencies = TRUE, type="'"${PKGTYPE}"'")' +} + +InstallBiocDeps() { + EnsureDevtools + Rscript -e "${R_USE_BIOC_CMDS}"' library(devtools); install_deps(dependencies = TRUE, type="'"${PKGTYPE}"'")' +} + +DumpSysinfo() { + echo "Dumping system information." + R -e '.libPaths(); sessionInfo(); installed.packages()' +} + +DumpLogsByExtension() { + if [[ -z "$1" ]]; then + echo "dump_logs_by_extension requires exactly one argument, got: $@" + exit 1 + fi + extension=$1 + shift + package=$(find . -maxdepth 1 -name "*.Rcheck" -type d) + if [[ ${#package[@]} -ne 1 ]]; then + echo "Could not find package Rcheck directory, skipping log dump." + exit 0 + fi + for name in $(find "${package}" -type f -name "*${extension}"); do + echo ">>> Filename: ${name} <<<" + cat ${name} + done +} + +DumpLogs() { + echo "Dumping test execution logs." + DumpLogsByExtension "out" + DumpLogsByExtension "log" + DumpLogsByExtension "fail" +} + +RunTests() { + echo "Building with: R CMD build ${R_BUILD_ARGS}" + if [[ "${KEEP_VIGNETTES}" == "" ]]; then + if [[ "${OS:0:5}" == "MINGW" || "${OS:0:4}" == "MSYS" ]]; then + if [[ -d vignettes ]]; then + rm -rf vignettes + Rscript -e "d <- read.dcf('DESCRIPTION'); d[, colnames(d) == 'VignetteBuilder'] <- NA; write.dcf(d, 'DESCRIPTION')" + fi + fi + fi + R CMD build ${R_BUILD_ARGS} . + # We want to grab the version we just built. + FILE=$(ls -1t *.tar.gz | head -n 1) + + # Create binary package (currently Windows only) + if [[ "${OS:0:5}" == "MINGW" || "${OS:0:4}" == "MSYS" ]]; then + R_CHECK_INSTALL_ARGS="--install-args=--build" + fi + + echo "Testing with: R CMD check \"${FILE}\" ${R_CHECK_ARGS} ${R_CHECK_INSTALL_ARGS}" + _R_CHECK_CRAN_INCOMING_=${_R_CHECK_CRAN_INCOMING_:-FALSE} + if [[ "$_R_CHECK_CRAN_INCOMING_" == "FALSE" ]]; then + echo "(CRAN incoming checks are off)" + fi + _R_CHECK_CRAN_INCOMING_=${_R_CHECK_CRAN_INCOMING_} R_QPDF=true R CMD check "${FILE}" ${R_CHECK_ARGS} ${R_CHECK_INSTALL_ARGS} + + # Check reverse dependencies + if [[ -n "$R_CHECK_REVDEP" ]]; then + echo "Checking reverse dependencies" + EnsureDevtools + Rscript -e 'library(devtools); checkOutput <- unlist(revdep_check(as.package(".")$package));if (!is.null(checkOutput)) {print(data.frame(pkg = names(checkOutput), error = checkOutput));for(i in seq_along(checkOutput)){;cat("\n", names(checkOutput)[i], " Check Output:\n ", paste(readLines(regmatches(checkOutput[i], regexec("/.*\\.out", checkOutput[i]))[[1]]), collapse = "\n ", sep = ""), "\n", sep = "")};q(status = 1, save = "no")}' + fi + + if [[ -n "${WARNINGS_ARE_ERRORS}" ]]; then + if DumpLogsByExtension "00check.log" | grep -q WARNING; then + echo "Found warnings, treated as errors." + echo "Clear or unset the WARNINGS_ARE_ERRORS environment variable to ignore warnings." + exit 1 + fi + fi +} + +Retry() { + if "$@"; then + return 0 + fi + for wait_time in 5 20 30 60; do + echo "Command failed, retrying in ${wait_time} ..." + sleep ${wait_time} + if "$@"; then + return 0 + fi + done + echo "Failed all retries!" + exit 1 +} + +COMMAND=$1 +echo "Running command: ${COMMAND}" +shift +case $COMMAND in + ## + ## Bootstrap a new core system + "bootstrap") + Bootstrap + ;; + ## + ## Ensure devtools is loaded (implicitly called) + "install_devtools"|"devtools_install") + EnsureDevtools + ;; + ## + ## Ensure remotes is loaded (implicitly called) + "install_remotes"|"remotes_install") + EnsureRemotes + ;; + ## + ## Install a binary deb package via apt-get + "install_aptget"|"aptget_install") + AptGetInstall "$@" + ;; + ## + ## Install a binary deb package via a curl call and local dpkg -i + "install_dpkgcurl"|"dpkgcurl_install") + DpkgCurlInstall "$@" + ;; + ## + ## Install an R dependency from CRAN + "install_r"|"r_install") + RInstall "$@" + ;; + ## + ## Install an R dependency from Bioconductor + "install_bioc"|"bioc_install") + BiocInstall "$@" + ;; + ## + ## Install an R dependency as a binary (via c2d4u PPA) + "install_r_binary"|"r_binary_install") + RBinaryInstall "$@" + ;; + ## + ## Install a package from github sources (needs remotes) + "install_github"|"github_package") + InstallGithub "$@" + ;; + ## + ## Install package dependencies from CRAN (needs remotes) + "install_deps") + InstallDeps + ;; + ## + ## Install package dependencies from Bioconductor and CRAN (needs devtools) + "install_bioc_deps") + InstallBiocDeps + ;; + ## + ## Run the actual tests, ie R CMD check + "run_tests") + RunTests + ;; + ## + ## Dump information about installed packages + "dump_sysinfo") + DumpSysinfo + ;; + ## + ## Dump build or check logs + "dump_logs") + DumpLogs + ;; + ## + ## Dump selected build or check logs + "dump_logs_by_extension") + DumpLogsByExtension "$@" + ;; +esac
I - Susceptible, increased exposure: A microorganism is categorised as "Susceptible, Increased exposure" when there is a high likelihood of therapeutic success because exposure to the agent is increased by adjusting the dosing regimen or by its concentration at the site of infection.