From 5bdece1f9d61e5abb494649f53ad5fa0a7f89fcb Mon Sep 17 00:00:00 2001 From: "Matthijs S. Berends" Date: Thu, 30 Apr 2020 09:05:03 +0200 Subject: [PATCH] (v1.1.0.9000) CI fix --- DESCRIPTION | 2 +- NAMESPACE | 1 + NEWS.md | 2 +- R/data.R | 4 ++-- R/vctrs.R | 2 ++ appveyor.yml | 5 +++-- docs/news/index.html | 4 ++-- docs/pkgdown.yml | 2 +- docs/reference/microorganisms.html | 4 ++-- docs/reference/mo_property.html | 2 +- man/microorganisms.Rd | 4 ++-- tests/appveyor/travis_tool.sh | 12 ++++++++++++ 12 files changed, 30 insertions(+), 14 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 4dbc26f6..ab32382b 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: AMR Version: 1.1.0.9000 -Date: 2020-04-29 +Date: 2020-04-30 Title: Antimicrobial Resistance Analysis Authors@R: c( person(role = c("aut", "cre"), diff --git a/NAMESPACE b/NAMESPACE index 16f0244e..7d92f085 100755 --- a/NAMESPACE +++ b/NAMESPACE @@ -397,6 +397,7 @@ importFrom(utils,adist) importFrom(utils,browseURL) importFrom(utils,menu) importFrom(vctrs,vec_cast) +importFrom(vctrs,vec_default_cast) importFrom(vctrs,vec_ptype2.character) importFrom(vctrs,vec_ptype_abbr) importFrom(vctrs,vec_ptype_full) diff --git a/NEWS.md b/NEWS.md index 5d88146f..208fbcae 100755 --- a/NEWS.md +++ b/NEWS.md @@ -1,5 +1,5 @@ # AMR 1.1.0.9000 -## Last updated: 29-Apr-2020 +## Last updated: 30-Apr-2020 ### Changed * Small fix for some text input that could not be coerced as valid MIC values diff --git a/R/data.R b/R/data.R index ddd0f041..c108cbec 100755 --- a/R/data.R +++ b/R/data.R @@ -111,10 +111,10 @@ #' @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. #' -#' From: +#' From: #' @source Catalogue of Life: Annual Checklist (public online taxonomic database), (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, (check included version with [catalogue_of_life_version()]). +#' Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Germany, Prokaryotic Nomenclature Up-to-Date, (check included version with [catalogue_of_life_version()]). #' @inheritSection AMR Read more on our website! #' @seealso [as.mo()], [mo_property()], [microorganisms.codes] "microorganisms" diff --git a/R/vctrs.R b/R/vctrs.R index 607a98e5..a6d4132b 100644 --- a/R/vctrs.R +++ b/R/vctrs.R @@ -90,6 +90,7 @@ vec_cast.mo.character <- function(x, to, ...) { } #' @method vec_cast.mo default +#' @importFrom vctrs vec_default_cast #' @export vec_cast.mo.default <- function(x, to, ...) { vec_default_cast(x, to) @@ -166,6 +167,7 @@ vec_cast.ab.character <- function(x, to, ...) { } #' @method vec_cast.ab default +#' @importFrom vctrs vec_default_cast #' @export vec_cast.ab.default <- function(x, to, ...) { vec_default_cast(x, to) diff --git a/appveyor.yml b/appveyor.yml index 3e9570f2..f7100c88 100644 --- a/appveyor.yml +++ b/appveyor.yml @@ -48,9 +48,10 @@ environment: matrix: allow_failures: - - R_VERSION: "devel" # 9 nov 19: searches for R 4.0 and now fails... - + - R_VERSION: "devel" + build_script: + - travis_tool.sh clean_library # turn off for caching, turn on for release of new R versions - travis_tool.sh install_deps test_script: diff --git a/docs/news/index.html b/docs/news/index.html index 6c2f95cb..85060cb6 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -233,9 +233,9 @@

AMR 1.1.0.9000 Unreleased

-
+

-Last updated: 29-Apr-2020 +Last updated: 30-Apr-2020

diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml index 9c0f82fc..6450ee97 100644 --- a/docs/pkgdown.yml +++ b/docs/pkgdown.yml @@ -10,7 +10,7 @@ articles: WHONET: WHONET.html benchmarks: benchmarks.html resistance_predict: resistance_predict.html -last_built: 2020-04-29T11:27Z +last_built: 2020-04-30T07:04Z urls: reference: https://msberends.gitlab.io/AMR/reference article: https://msberends.gitlab.io/AMR/articles diff --git a/docs/reference/microorganisms.html b/docs/reference/microorganisms.html index 140bbcfe..5f5ee736 100644 --- a/docs/reference/microorganisms.html +++ b/docs/reference/microorganisms.html @@ -256,7 +256,7 @@

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()).

Details

Manually added were:

    @@ -285,7 +285,7 @@

    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

    Catalogue of Life

    diff --git a/docs/reference/mo_property.html b/docs/reference/mo_property.html index 26fff214..34450164 100644 --- a/docs/reference/mo_property.html +++ b/docs/reference/mo_property.html @@ -325,7 +325,7 @@

  • mo_ref("Chlamydophila psittaci") will return "Everett et al., 1999" (without a warning)

-

The short name - mo_shortname() - almost always returns the first character of the genus and the species, like "E. coli". Exceptions are abbreviations of staphylococci and beta-haemolytic streptococci, like "CoNS" (Coagulase-Negative Staphylococci) and "GBS" (Group B Streptococci).

+

The short name - mo_shortname() - almost always returns the first character of the genus and the full species, like "E. coli". Exceptions are abbreviations of staphylococci and beta-haemolytic streptococci, like "CoNS" (Coagulase-Negative Staphylococci) and "GBS" (Group B Streptococci).

The Gram stain - mo_gramstain() - 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 NA.

All output will be translated where possible.

The function mo_url() will return the direct URL to the online database entry, which also shows the scientific reference of the concerned species.

diff --git a/man/microorganisms.Rd b/man/microorganisms.Rd index 800b7deb..083ee77a 100755 --- a/man/microorganisms.Rd +++ b/man/microorganisms.Rd @@ -22,7 +22,7 @@ A \code{\link{data.frame}} with 69,447 observations and 17 variables: \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()}}). -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{ 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. -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}{ diff --git a/tests/appveyor/travis_tool.sh b/tests/appveyor/travis_tool.sh index 54cc6a33..c0493277 100644 --- a/tests/appveyor/travis_tool.sh +++ b/tests/appveyor/travis_tool.sh @@ -251,6 +251,11 @@ InstallGithub() { Rscript -e 'options(repos = c(CRAN = "'"${CRAN}"'"), download.file.method = "'"${DOWNLOAD_FILE_METHOD}"'"); remotes::install_github(commandArgs(TRUE), type="'"${PKGTYPE}"'")' "$@" } +CleanLibrary() { + # removes all installed package so ensures a clean library + Rscript -e 'remove.packages(installed.packages()[is.na(installed.packages()[,"Priority"]), "Package"])' +} + InstallDeps() { EnsureRemotes @@ -294,6 +299,8 @@ DumpLogs() { } RunTests() { + Rscript -e 'sessionInfo()' + echo "Building with: R CMD build ${R_BUILD_ARGS}" if [[ "${KEEP_VIGNETTES}" == "" ]]; then if [[ "${OS:0:5}" == "MINGW" || "${OS:0:4}" == "MSYS" ]]; then @@ -360,6 +367,11 @@ case $COMMAND in Bootstrap ;; ## + ## Clean library + "clean_library") + CleanLibrary + ;; + ## ## Ensure devtools is loaded (implicitly called) "install_devtools"|"devtools_install") EnsureDevtools