From 56d4b4719fe2c9016d7bd02557073ccff4db36a2 Mon Sep 17 00:00:00 2001 From: "Matthijs S. Berends" Date: Fri, 29 Mar 2019 21:45:46 +0100 Subject: [PATCH] ci for devel and freq fix --- .gitlab-ci.yml | 10 +++++----- R/freq.R | 7 ++++--- 2 files changed, 9 insertions(+), 8 deletions(-) diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml index f0f3fba5..95459424 100644 --- a/.gitlab-ci.yml +++ b/.gitlab-ci.yml @@ -81,16 +81,16 @@ R-devel: image: rocker/r-devel allow_failure: true script: - - Rscript -e 'sessionInfo()' + - Rscriptdevel -e 'sessionInfo()' # install missing and outdated packages - - Rscript -e 'source(".gitlab-ci.R"); gl_update_pkg_all(repos = "https://cran.rstudio.com", quiet = TRUE, install_pkgdown = TRUE)' + - Rscriptdevel -e 'source(".gitlab-ci.R"); gl_update_pkg_all(repos = "https://cran.rstudio.com", quiet = TRUE, install_pkgdown = TRUE)' # remove vignettes folder and get VignetteBuilder field out of DESCRIPTION file - rm -rf vignettes - - Rscript -e 'd <- read.dcf("DESCRIPTION"); d[, colnames(d) == "VignetteBuilder"] <- NA; write.dcf(d, "DESCRIPTION")' + - Rscriptdevel -e 'd <- read.dcf("DESCRIPTION"); d[, colnames(d) == "VignetteBuilder"] <- NA; write.dcf(d, "DESCRIPTION")' # build package - - R CMD build . --no-build-vignettes --no-manual + - Rdevel CMD build . --no-build-vignettes --no-manual - PKG_FILE_NAME=$(ls -1t *.tar.gz | head -n 1) - - R CMD check "${PKG_FILE_NAME}" --no-build-vignettes --no-manual --as-cran + - Rdevel CMD check "${PKG_FILE_NAME}" --no-build-vignettes --no-manual --as-cran artifacts: paths: - '*.Rcheck/*' diff --git a/R/freq.R b/R/freq.R index cdb116eb..ac3e1655 100755 --- a/R/freq.R +++ b/R/freq.R @@ -391,9 +391,10 @@ frequency_tbl <- function(x, } if (NROW(x) > 0 & any(class(x) == "mo")) { - header_list$families <- x %>% mo_family() %>% n_distinct() - header_list$genera <- x %>% mo_genus() %>% n_distinct() - header_list$species <- x %>% mo_species() %>% n_distinct() + x_mo <- as.mo(x) # do it once for all three + header_list$families <- x_mo %>% mo_family() %>% n_distinct() + header_list$genera <- x_mo %>% mo_genus() %>% n_distinct() + header_list$species <- x_mo %>% mo_species() %>% n_distinct() } if (NROW(x) > 0 & any(class(x) == "difftime") & !is.hms(x)) {