updating and adding new images

Author: tom-gu

bdverse_binder/Dockerfile

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+FROM rocker/binder:latest 
+
+MAINTAINER [email protected]
+USER root
+
+
+RUN apt-get update \
+  && apt-get install dialog apt-utils -y --no-install-recommends \
+	libpng-dev \
+	libv8-dev \
+	libgeos-dev \
+	libjq-dev \
+	texmaker \
+	libxml2-dev\
+	libgdal-dev \
+	xdg-utils
+
+
+RUN R -e "options(repos = list(CRAN = 'https://cran.microsoft.com/snapshot/2020-03-15/')); \
+  install.packages('remotes'); \
+  remotes::install_github('bd-R/bdverse'); \
+  remotes::install_github('bd-R/dashboard.demo'); \
+  tinytex::install_tinytex()"

bdverse_binder/bdverse_github_qa.R

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+remotes::install_github('bd-R/bdverse')
+library(bdverse)
+
+bdverse_app()
+
+remotes::install_github('bd-R/bdDwC')
+library(bdDwC)
+
+remotes::install_github('bd-R/bddwc.app')
+library(bddwc.app)
+bddwc_app()
+
+remotes::install_github('bd-R/bdchecks')
+library(bdchecks)
+bdchecks_app()
+
+
+remotes::install_github('bd-R/bdchecks.app')
+library(bdchecks.app)
+
+
+remotes::install_github('bd-R/bdclean')
+library(bdclean)
+bdclean_app()
+
+remotes::install_github('bd-R/bdutilities.app')

bdverse_binder/bdverse_github_script.R

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+
+remotes::install_github('bd-R/bdDwC')
+library(bdDwC)
+run_dwc()
+
+
+remotes::install_github('bd-R/bdchecks')
+library(bdchecks)
+runbdchecks()
+
+remotes::install_github('bd-R/bdclean@new_bdclean')
+library(bdclean)
+run_bdclean()
+
+

bdverse_binder/data/bdchecks_stuff.R

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+
+dc
+
+data.checks@dc_body$validation_taxon_empty@name
+
+data.checks@dc_body[1]@name
+
+t <- unlist(data.checks@dc_body[1])
+
+
+dc_names <- as.factor(names(data.checks@dc_body))
+
+result <- bdchecks::perform_dc(gbif_10k_latest, wanted_dc = dc_names[47])
+warnings()
+summary_dc(result)
+summary_dc(result, fancy = TRUE, filtering_dt = TRUE)
+
+FALSEdc_df <- get(parse(text = paste0("data.checks@dc_body$", dc_names[5], "@name" )))
+
+data.checks@dc_body$validation_taxon_empty@name
+is(result)
+
+install() # To have new check in `system.file("extdata/data_check.yaml")`
+data.checks <- bdchecks:::datacheck_info_export() # export documentation and combines new check with old ones
+use_data(data_taxonrank, data.checks, data_bats, overwrite = TRUE, internal = TRUE) # exports old (and new data checks)
+document() # document new check to `Rd`
+install() # install package with a new check
+
+perform_test_dc()
+
+data.checks@dc_body$dc_names[[1]]
+
+dc_names$
+for (slot in slotNames(data.checks@dc_body$validation_taxon_empty)) {
+  cat(slot, ":\n")
+  print(slot(data.checks@dc_body$validation_taxon_empty, slot))
+}
+
+getSlots(t)
+
+test <- list(str(data.checks))
+data.checks[1,]
+
+unique(data.checks@dc_body)
+
+bdchecks::data.checks@dc_body
+
+remotes::install_github("moodymudskipper/funflow")
+funflow::view_flow(bdchecks::perform_dc)

bdverse_binder/data/bdverse_github_qa-copy.R

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+remotes::install_github('bd-R/bdverse', force = TRUE)
+library(bdverse)
+bdverse_app()
+
+remotes::install_github('bd-R/bdDwC')
+library(bdDwC)
+
+remotes::install_github('bd-R/bddwc.app')
+library(bddwc.app)
+bddwc_app()
+
+remotes::install_github('bd-R/bdchecks')
+library(bdchecks)
+bdchecks_app()
+
+remotes::install_github('bd-R/bdchecks.app')
+library(bdchecks.app)
+
+
+remotes::install_github('bd-R/bdclean')
+library(bdclean)
+bdclean_app()
+
+remotes::install_github('bd-R/bdutilities.app')
+
+path_app <- system.file("app", package = "bddwc.app")
+shiny::runApp(path_app, launch.browser = TRUE, port = 1875)
+
+path_app <- system.file("app", package = "bdchecks.app")
+shiny::runApp(path_app, launch.browser = TRUE, port = 2875)
+
+Sys.time()
+
+library("spocc")
+
+out <- occ(query = 'Carcharodon carcharias', from = 'obis', limit = 1)
+
+
+bdverse::bd_packages()[[1]]
+
+
+utils::packageDescription("bdutilities"),
+utils::packageDescription("bdutilities.app"),
+utils::packageDescription("bdDwC"),
+utils::packageDescription("bddwc.app"),
+utils::packageDescription("bdchecks"),
+utils::packageDescription("bdchecks.app"),
+utils::packageDescription("bdclean")$Authors
+
+utils::packageDescription("bdverse")
+
+
+.libPaths()
+library(covr)
+covr::package_coverage("/usr/local/lib/R/site-library/bdchecks")
+
+
+remotes::install_github("moodymudskipper/funflow")
+funflow::view_flow(bdchecks::summary_dc)
+
+install.packages("githubinstall")