diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml index d6ec3501..e931eda2 100644 --- a/.gitlab-ci.yml +++ b/.gitlab-ci.yml @@ -117,7 +117,7 @@ coverage: script: - apt-get install --yes git # codecov token is set in https://gitlab.com/msberends/AMR/settings/ci_cd - - Rscript -e "cc <- covr::package_coverage(); covr::codecov(coverage = cc, token = '$codecov'); cat('Code coverage:', covr::percent_coverage(cc))" + - Rscript -e "Sys.setenv(NOT_CRAN = 'true'); cc <- covr::package_coverage(); covr::codecov(coverage = cc, token = '$codecov'); cat('Code coverage:', covr::percent_coverage(cc))" coverage: '/Code coverage: \d+\.\d+/' pages: diff --git a/DESCRIPTION b/DESCRIPTION index 7c7edde2..ef335c31 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,5 +1,5 @@ Package: AMR -Version: 0.8.0.9004 +Version: 0.8.0.9005 Date: 2019-10-26 Title: Antimicrobial Resistance Analysis Authors@R: c( diff --git a/NEWS.md b/NEWS.md index 66d7e65e..9627f8cd 100755 --- a/NEWS.md +++ b/NEWS.md @@ -1,4 +1,4 @@ -# AMR 0.8.0.9004 +# AMR 0.8.0.9005 Last updated: 26-Oct-2019 ### New diff --git a/R/globals.R b/R/globals.R index 5db2422b..8f0ac9d6 100755 --- a/R/globals.R +++ b/R/globals.R @@ -52,6 +52,7 @@ globalVariables(c(".", "Last name", "lookup", "mdr", + "MDRO", "median", "microorganisms", "microorganisms.codes", diff --git a/R/mdro.R b/R/mdro.R index 5ef60add..206de2b9 100755 --- a/R/mdro.R +++ b/R/mdro.R @@ -461,7 +461,7 @@ mdro <- function(x, left_join_microorganisms(by = col_mo) %>% # add unconfirmed to where genus is available mutate(MDRO = ifelse(!is.na(genus), 1, NA_integer_), - row_number = 1:nrow(x)) %>% + row_number = seq_len(nrow(x))) %>% # transform to data.frame so subsetting is possible with x[y, z] (might not be the case with tibble/data.table/...) as.data.frame(stringsAsFactors = FALSE) diff --git a/R/mo.R b/R/mo.R index 5ee429ce..d6eff413 100755 --- a/R/mo.R +++ b/R/mo.R @@ -241,7 +241,6 @@ as.mo <- function(x, Becker = FALSE, Lancefield = FALSE, allow_uncertain = TRUE, pull(mo) # don't save valid fullnames to history (i.e. values that are in microorganisms$fullname) - # set_mo_history(x, y, 0, force = isTRUE(list(...)$force_mo_history), disable = isTRUE(list(...)$disable_mo_history)) } else { # will be checked for mo class in validation and uses exec_as.mo internally if necessary @@ -636,7 +635,6 @@ exec_as.mo <- function(x, x[i] <- found[1L] if (initial_search == TRUE) { # don't save valid fullnames to history (i.e. values that are in microorganisms$fullname) - # set_mo_history(x_backup[i], get_mo_code(x[i], property), 0, force = force_mo_history, disable = disable_mo_history) } next } diff --git a/codecov.yml b/codecov.yml index fea6aac8..13bb0025 100644 --- a/codecov.yml +++ b/codecov.yml @@ -19,4 +19,3 @@ ignore: - "R/atc_online.R" - "R/mo_source.R" - "R/resistance_predict.R" - - "R/aa_test.R" diff --git a/docs/404.html b/docs/404.html index 7fd4293e..6c2205c5 100644 --- a/docs/404.html +++ b/docs/404.html @@ -84,7 +84,7 @@
diff --git a/docs/LICENSE-text.html b/docs/LICENSE-text.html index c1050c8f..896e346a 100644 --- a/docs/LICENSE-text.html +++ b/docs/LICENSE-text.html @@ -84,7 +84,7 @@ diff --git a/docs/articles/index.html b/docs/articles/index.html index 3136c996..aa9e1380 100644 --- a/docs/articles/index.html +++ b/docs/articles/index.html @@ -84,7 +84,7 @@ diff --git a/docs/authors.html b/docs/authors.html index 26436eaf..859e03c2 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -84,7 +84,7 @@ diff --git a/docs/index.html b/docs/index.html index 1cb0d83e..1749dd9b 100644 --- a/docs/index.html +++ b/docs/index.html @@ -45,7 +45,7 @@ diff --git a/docs/news/index.html b/docs/news/index.html index 35e7d21c..14ef92d4 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -84,7 +84,7 @@ @@ -231,9 +231,9 @@ -Last updated: 26-Oct-2019
as.mo(..., allow_uncertain = 3)
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