mirror of https://github.com/msberends/AMR.git
(v1.1.0.9000) CI fix
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Package: AMR
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Version: 1.1.0.9000
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Date: 2020-04-29
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Date: 2020-04-30
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Title: Antimicrobial Resistance Analysis
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Authors@R: c(
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person(role = c("aut", "cre"),
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@ -397,6 +397,7 @@ importFrom(utils,adist)
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importFrom(utils,browseURL)
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importFrom(utils,menu)
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importFrom(vctrs,vec_cast)
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importFrom(vctrs,vec_default_cast)
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importFrom(vctrs,vec_ptype2.character)
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importFrom(vctrs,vec_ptype_abbr)
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importFrom(vctrs,vec_ptype_full)
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2
NEWS.md
2
NEWS.md
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@ -1,5 +1,5 @@
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# AMR 1.1.0.9000
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## <small>Last updated: 29-Apr-2020</small>
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## <small>Last updated: 30-Apr-2020</small>
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### Changed
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* Small fix for some text input that could not be coerced as valid MIC values
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4
R/data.R
4
R/data.R
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@ -111,10 +111,10 @@
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#' @section About the records from DSMZ (see source):
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#' Names of prokaryotes are defined as being validly published by the International Code of Nomenclature of Bacteria. Validly published are all names which are included in the Approved Lists of Bacterial Names and the names subsequently published in the International Journal of Systematic Bacteriology (IJSB) and, from January 2000, in the International Journal of Systematic and Evolutionary Microbiology (IJSEM) as original articles or in the validation lists.
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#'
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#' From: <https://www.dsmz.de/support/bacterial-nomenclature-up-to-date-downloads/readme.html>
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#' From: <https://www.dsmz.de/services/online-tools/prokaryotic-nomenclature-up-to-date/complete-list-readme>
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#' @source Catalogue of Life: Annual Checklist (public online taxonomic database), <http://www.catalogueoflife.org> (check included annual version with [catalogue_of_life_version()]).
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#'
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#' Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Germany, Prokaryotic Nomenclature Up-to-Date, <http://www.dsmz.de/bacterial-diversity/prokaryotic-nomenclature-up-to-date> (check included version with [catalogue_of_life_version()]).
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#' Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Germany, Prokaryotic Nomenclature Up-to-Date, <https://www.dsmz.de/services/online-tools/prokaryotic-nomenclature-up-to-date> (check included version with [catalogue_of_life_version()]).
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#' @inheritSection AMR Read more on our website!
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#' @seealso [as.mo()], [mo_property()], [microorganisms.codes]
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"microorganisms"
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@ -90,6 +90,7 @@ vec_cast.mo.character <- function(x, to, ...) {
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}
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#' @method vec_cast.mo default
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#' @importFrom vctrs vec_default_cast
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#' @export
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vec_cast.mo.default <- function(x, to, ...) {
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vec_default_cast(x, to)
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@ -166,6 +167,7 @@ vec_cast.ab.character <- function(x, to, ...) {
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}
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#' @method vec_cast.ab default
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#' @importFrom vctrs vec_default_cast
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#' @export
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vec_cast.ab.default <- function(x, to, ...) {
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vec_default_cast(x, to)
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@ -48,9 +48,10 @@ environment:
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matrix:
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allow_failures:
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- R_VERSION: "devel" # 9 nov 19: searches for R 4.0 and now fails...
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- R_VERSION: "devel"
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build_script:
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- travis_tool.sh clean_library # turn off for caching, turn on for release of new R versions
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- travis_tool.sh install_deps
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test_script:
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@ -233,9 +233,9 @@
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<h1 class="page-header" data-toc-text="1.1.0.9000">
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<a href="#amr-1-1-0-9000" class="anchor"></a>AMR 1.1.0.9000<small> Unreleased </small>
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</h1>
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<div id="last-updated-29-apr-2020" class="section level2">
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<div id="last-updated-30-apr-2020" class="section level2">
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<h2 class="hasAnchor">
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<a href="#last-updated-29-apr-2020" class="anchor"></a><small>Last updated: 29-Apr-2020</small>
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<a href="#last-updated-30-apr-2020" class="anchor"></a><small>Last updated: 30-Apr-2020</small>
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</h2>
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<div id="changed" class="section level3">
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<h3 class="hasAnchor">
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@ -10,7 +10,7 @@ articles:
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WHONET: WHONET.html
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benchmarks: benchmarks.html
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resistance_predict: resistance_predict.html
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last_built: 2020-04-29T11:27Z
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last_built: 2020-04-30T07:04Z
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urls:
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reference: https://msberends.gitlab.io/AMR/reference
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article: https://msberends.gitlab.io/AMR/articles
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@ -256,7 +256,7 @@
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<h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2>
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<p>Catalogue of Life: Annual Checklist (public online taxonomic database), <a href='http://www.catalogueoflife.org'>http://www.catalogueoflife.org</a> (check included annual version with <code><a href='catalogue_of_life_version.html'>catalogue_of_life_version()</a></code>).</p>
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<p>Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Germany, Prokaryotic Nomenclature Up-to-Date, <a href='http://www.dsmz.de/bacterial-diversity/prokaryotic-nomenclature-up-to-date'>http://www.dsmz.de/bacterial-diversity/prokaryotic-nomenclature-up-to-date</a> (check included version with <code><a href='catalogue_of_life_version.html'>catalogue_of_life_version()</a></code>).</p>
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<p>Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Germany, Prokaryotic Nomenclature Up-to-Date, <a href='https://www.dsmz.de/services/online-tools/prokaryotic-nomenclature-up-to-date'>https://www.dsmz.de/services/online-tools/prokaryotic-nomenclature-up-to-date</a> (check included version with <code><a href='catalogue_of_life_version.html'>catalogue_of_life_version()</a></code>).</p>
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<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
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<p>Manually added were:</p><ul>
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@ -285,7 +285,7 @@
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<p>Names of prokaryotes are defined as being validly published by the International Code of Nomenclature of Bacteria. Validly published are all names which are included in the Approved Lists of Bacterial Names and the names subsequently published in the International Journal of Systematic Bacteriology (IJSB) and, from January 2000, in the International Journal of Systematic and Evolutionary Microbiology (IJSEM) as original articles or in the validation lists.</p>
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<p>From: <a href='https://www.dsmz.de/support/bacterial-nomenclature-up-to-date-downloads/readme.html'>https://www.dsmz.de/support/bacterial-nomenclature-up-to-date-downloads/readme.html</a></p>
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<p>From: <a href='https://www.dsmz.de/services/online-tools/prokaryotic-nomenclature-up-to-date/complete-list-readme'>https://www.dsmz.de/services/online-tools/prokaryotic-nomenclature-up-to-date/complete-list-readme</a></p>
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<h2 class="hasAnchor" id="catalogue-of-life"><a class="anchor" href="#catalogue-of-life"></a>Catalogue of Life</h2>
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@ -325,7 +325,7 @@
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<li><p><code>mo_ref("Chlamydophila psittaci")</code> will return <code>"Everett et al., 1999"</code> (without a warning)</p></li>
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</ul>
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<p>The short name - <code>mo_shortname()</code> - almost always returns the first character of the genus and the species, like <em>"E. coli"</em>. Exceptions are abbreviations of staphylococci and beta-haemolytic streptococci, like <em>"CoNS"</em> (Coagulase-Negative Staphylococci) and <em>"GBS"</em> (Group B Streptococci).</p>
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<p>The short name - <code>mo_shortname()</code> - almost always returns the first character of the genus and the full species, like <em>"E. coli"</em>. Exceptions are abbreviations of staphylococci and beta-haemolytic streptococci, like <em>"CoNS"</em> (Coagulase-Negative Staphylococci) and <em>"GBS"</em> (Group B Streptococci).</p>
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<p>The Gram stain - <code>mo_gramstain()</code> - will be determined on the taxonomic kingdom and phylum. According to Cavalier-Smith (2002) who defined subkingdoms Negibacteria and Posibacteria, only these phyla are Posibacteria: Actinobacteria, Chloroflexi, Firmicutes and Tenericutes. These bacteria are considered Gram-positive - all other bacteria are considered Gram-negative. Species outside the kingdom of Bacteria will return a value <code>NA</code>.</p>
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<p>All output will be <a href='translate.html'>translate</a>d where possible.</p>
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<p>The function <code>mo_url()</code> will return the direct URL to the online database entry, which also shows the scientific reference of the concerned species.</p>
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@ -22,7 +22,7 @@ A \code{\link{data.frame}} with 69,447 observations and 17 variables:
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\source{
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Catalogue of Life: Annual Checklist (public online taxonomic database), \url{http://www.catalogueoflife.org} (check included annual version with \code{\link[=catalogue_of_life_version]{catalogue_of_life_version()}}).
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Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Germany, Prokaryotic Nomenclature Up-to-Date, \url{http://www.dsmz.de/bacterial-diversity/prokaryotic-nomenclature-up-to-date} (check included version with \code{\link[=catalogue_of_life_version]{catalogue_of_life_version()}}).
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Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Germany, Prokaryotic Nomenclature Up-to-Date, \url{https://www.dsmz.de/services/online-tools/prokaryotic-nomenclature-up-to-date} (check included version with \code{\link[=catalogue_of_life_version]{catalogue_of_life_version()}}).
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}
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\usage{
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microorganisms
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@ -58,7 +58,7 @@ The file in R format (with preserved data structure) can be found here:
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Names of prokaryotes are defined as being validly published by the International Code of Nomenclature of Bacteria. Validly published are all names which are included in the Approved Lists of Bacterial Names and the names subsequently published in the International Journal of Systematic Bacteriology (IJSB) and, from January 2000, in the International Journal of Systematic and Evolutionary Microbiology (IJSEM) as original articles or in the validation lists.
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From: \url{https://www.dsmz.de/support/bacterial-nomenclature-up-to-date-downloads/readme.html}
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From: \url{https://www.dsmz.de/services/online-tools/prokaryotic-nomenclature-up-to-date/complete-list-readme}
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}
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\section{Catalogue of Life}{
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@ -251,6 +251,11 @@ InstallGithub() {
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Rscript -e 'options(repos = c(CRAN = "'"${CRAN}"'"), download.file.method = "'"${DOWNLOAD_FILE_METHOD}"'"); remotes::install_github(commandArgs(TRUE), type="'"${PKGTYPE}"'")' "$@"
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}
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CleanLibrary() {
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# removes all installed package so ensures a clean library
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Rscript -e 'remove.packages(installed.packages()[is.na(installed.packages()[,"Priority"]), "Package"])'
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}
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InstallDeps() {
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EnsureRemotes
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@ -294,6 +299,8 @@ DumpLogs() {
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}
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RunTests() {
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Rscript -e 'sessionInfo()'
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echo "Building with: R CMD build ${R_BUILD_ARGS}"
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if [[ "${KEEP_VIGNETTES}" == "" ]]; then
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if [[ "${OS:0:5}" == "MINGW" || "${OS:0:4}" == "MSYS" ]]; then
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Bootstrap
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;;
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##
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## Clean library
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"clean_library")
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CleanLibrary
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;;
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##
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## Ensure devtools is loaded (implicitly called)
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"install_devtools"|"devtools_install")
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EnsureDevtools
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