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mirror of https://github.com/msberends/AMR.git synced 2024-12-26 05:26:13 +01:00

(v1.1.0.9000) CI fix

This commit is contained in:
dr. M.S. (Matthijs) Berends 2020-04-30 09:05:03 +02:00
parent b040185269
commit 5bdece1f9d
12 changed files with 30 additions and 14 deletions

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@ -1,6 +1,6 @@
Package: AMR Package: AMR
Version: 1.1.0.9000 Version: 1.1.0.9000
Date: 2020-04-29 Date: 2020-04-30
Title: Antimicrobial Resistance Analysis Title: Antimicrobial Resistance Analysis
Authors@R: c( Authors@R: c(
person(role = c("aut", "cre"), person(role = c("aut", "cre"),

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@ -397,6 +397,7 @@ importFrom(utils,adist)
importFrom(utils,browseURL) importFrom(utils,browseURL)
importFrom(utils,menu) importFrom(utils,menu)
importFrom(vctrs,vec_cast) importFrom(vctrs,vec_cast)
importFrom(vctrs,vec_default_cast)
importFrom(vctrs,vec_ptype2.character) importFrom(vctrs,vec_ptype2.character)
importFrom(vctrs,vec_ptype_abbr) importFrom(vctrs,vec_ptype_abbr)
importFrom(vctrs,vec_ptype_full) importFrom(vctrs,vec_ptype_full)

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@ -1,5 +1,5 @@
# AMR 1.1.0.9000 # AMR 1.1.0.9000
## <small>Last updated: 29-Apr-2020</small> ## <small>Last updated: 30-Apr-2020</small>
### Changed ### Changed
* Small fix for some text input that could not be coerced as valid MIC values * Small fix for some text input that could not be coerced as valid MIC values

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@ -111,10 +111,10 @@
#' @section About the records from DSMZ (see source): #' @section About the records from DSMZ (see source):
#' 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. #' 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.
#' #'
#' From: <https://www.dsmz.de/support/bacterial-nomenclature-up-to-date-downloads/readme.html> #' From: <https://www.dsmz.de/services/online-tools/prokaryotic-nomenclature-up-to-date/complete-list-readme>
#' @source Catalogue of Life: Annual Checklist (public online taxonomic database), <http://www.catalogueoflife.org> (check included annual version with [catalogue_of_life_version()]). #' @source Catalogue of Life: Annual Checklist (public online taxonomic database), <http://www.catalogueoflife.org> (check included annual version with [catalogue_of_life_version()]).
#' #'
#' 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()]). #' 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()]).
#' @inheritSection AMR Read more on our website! #' @inheritSection AMR Read more on our website!
#' @seealso [as.mo()], [mo_property()], [microorganisms.codes] #' @seealso [as.mo()], [mo_property()], [microorganisms.codes]
"microorganisms" "microorganisms"

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@ -90,6 +90,7 @@ vec_cast.mo.character <- function(x, to, ...) {
} }
#' @method vec_cast.mo default #' @method vec_cast.mo default
#' @importFrom vctrs vec_default_cast
#' @export #' @export
vec_cast.mo.default <- function(x, to, ...) { vec_cast.mo.default <- function(x, to, ...) {
vec_default_cast(x, to) vec_default_cast(x, to)
@ -166,6 +167,7 @@ vec_cast.ab.character <- function(x, to, ...) {
} }
#' @method vec_cast.ab default #' @method vec_cast.ab default
#' @importFrom vctrs vec_default_cast
#' @export #' @export
vec_cast.ab.default <- function(x, to, ...) { vec_cast.ab.default <- function(x, to, ...) {
vec_default_cast(x, to) vec_default_cast(x, to)

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@ -48,9 +48,10 @@ environment:
matrix: matrix:
allow_failures: allow_failures:
- R_VERSION: "devel" # 9 nov 19: searches for R 4.0 and now fails... - R_VERSION: "devel"
build_script: build_script:
- travis_tool.sh clean_library # turn off for caching, turn on for release of new R versions
- travis_tool.sh install_deps - travis_tool.sh install_deps
test_script: test_script:

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@ -233,9 +233,9 @@
<h1 class="page-header" data-toc-text="1.1.0.9000"> <h1 class="page-header" data-toc-text="1.1.0.9000">
<a href="#amr-1-1-0-9000" class="anchor"></a>AMR 1.1.0.9000<small> Unreleased </small> <a href="#amr-1-1-0-9000" class="anchor"></a>AMR 1.1.0.9000<small> Unreleased </small>
</h1> </h1>
<div id="last-updated-29-apr-2020" class="section level2"> <div id="last-updated-30-apr-2020" class="section level2">
<h2 class="hasAnchor"> <h2 class="hasAnchor">
<a href="#last-updated-29-apr-2020" class="anchor"></a><small>Last updated: 29-Apr-2020</small> <a href="#last-updated-30-apr-2020" class="anchor"></a><small>Last updated: 30-Apr-2020</small>
</h2> </h2>
<div id="changed" class="section level3"> <div id="changed" class="section level3">
<h3 class="hasAnchor"> <h3 class="hasAnchor">

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@ -10,7 +10,7 @@ articles:
WHONET: WHONET.html WHONET: WHONET.html
benchmarks: benchmarks.html benchmarks: benchmarks.html
resistance_predict: resistance_predict.html resistance_predict: resistance_predict.html
last_built: 2020-04-29T11:27Z last_built: 2020-04-30T07:04Z
urls: urls:
reference: https://msberends.gitlab.io/AMR/reference reference: https://msberends.gitlab.io/AMR/reference
article: https://msberends.gitlab.io/AMR/articles article: https://msberends.gitlab.io/AMR/articles

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@ -256,7 +256,7 @@
<h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2> <h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2>
<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> <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>
<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> <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>
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2> <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
<p>Manually added were:</p><ul> <p>Manually added were:</p><ul>
@ -285,7 +285,7 @@
<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> <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>
<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> <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>
<h2 class="hasAnchor" id="catalogue-of-life"><a class="anchor" href="#catalogue-of-life"></a>Catalogue of Life</h2> <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 @@
<li><p><code>mo_ref("Chlamydophila psittaci")</code> will return <code>"Everett et al., 1999"</code> (without a warning)</p></li> <li><p><code>mo_ref("Chlamydophila psittaci")</code> will return <code>"Everett et al., 1999"</code> (without a warning)</p></li>
</ul> </ul>
<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> <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>
<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> <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>
<p>All output will be <a href='translate.html'>translate</a>d where possible.</p> <p>All output will be <a href='translate.html'>translate</a>d where possible.</p>
<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> <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:
\source{ \source{
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()}}). 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()}}).
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()}}). 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()}}).
} }
\usage{ \usage{
microorganisms microorganisms
@ -58,7 +58,7 @@ The file in R format (with preserved data structure) can be found here:
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. 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.
From: \url{https://www.dsmz.de/support/bacterial-nomenclature-up-to-date-downloads/readme.html} From: \url{https://www.dsmz.de/services/online-tools/prokaryotic-nomenclature-up-to-date/complete-list-readme}
} }
\section{Catalogue of Life}{ \section{Catalogue of Life}{

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@ -251,6 +251,11 @@ InstallGithub() {
Rscript -e 'options(repos = c(CRAN = "'"${CRAN}"'"), download.file.method = "'"${DOWNLOAD_FILE_METHOD}"'"); remotes::install_github(commandArgs(TRUE), type="'"${PKGTYPE}"'")' "$@" Rscript -e 'options(repos = c(CRAN = "'"${CRAN}"'"), download.file.method = "'"${DOWNLOAD_FILE_METHOD}"'"); remotes::install_github(commandArgs(TRUE), type="'"${PKGTYPE}"'")' "$@"
} }
CleanLibrary() {
# removes all installed package so ensures a clean library
Rscript -e 'remove.packages(installed.packages()[is.na(installed.packages()[,"Priority"]), "Package"])'
}
InstallDeps() { InstallDeps() {
EnsureRemotes EnsureRemotes
@ -294,6 +299,8 @@ DumpLogs() {
} }
RunTests() { RunTests() {
Rscript -e 'sessionInfo()'
echo "Building with: R CMD build ${R_BUILD_ARGS}" echo "Building with: R CMD build ${R_BUILD_ARGS}"
if [[ "${KEEP_VIGNETTES}" == "" ]]; then if [[ "${KEEP_VIGNETTES}" == "" ]]; then
if [[ "${OS:0:5}" == "MINGW" || "${OS:0:4}" == "MSYS" ]]; then if [[ "${OS:0:5}" == "MINGW" || "${OS:0:4}" == "MSYS" ]]; then
@ -360,6 +367,11 @@ case $COMMAND in
Bootstrap Bootstrap
;; ;;
## ##
## Clean library
"clean_library")
CleanLibrary
;;
##
## Ensure devtools is loaded (implicitly called) ## Ensure devtools is loaded (implicitly called)
"install_devtools"|"devtools_install") "install_devtools"|"devtools_install")
EnsureDevtools EnsureDevtools