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