trying to fixing missing img error, supress running examples for now

R/identities.R

@@ -17,8 +17,13 @@ ids_get <- function(pkgnm) {
   imgs <- docker_img_ls()
   #print(imgs)
   if ('tag' %in% colnames(imgs)) {
-    tag <- imgs[imgs[['repository']] == img, 'tag'][[1]]
-    tag <- tag[[1]]
+    pull <- imgs[['repository']] == img
+    if (any(pull)) {
+      tag <- imgs[pull, 'tag'][[1]]
+      tag <- tag[[1]]
+    } else {
+      stop(char(repo), ' is missing its Docker image, try reinstalling.')
+    }
   } else {
     # Sometimes there is no tag column (?)
     tag <- 'latest'

R/outsider.R

@@ -53,6 +53,7 @@ NULL
 #' @export
 #' @example examples/outsider-class.R
 #' @family developer
+# TODO: example needs to avoid pulling from GitHub over and over.
 .outsider_init <- function(repo, cmd = NA, arglist = NULL, wd = NULL,
                            files_to_send = NULL, ignore_errors = FALSE) {
   pkgnm <- repo_to_pkgnm(repo = repo)

R/search.R

@@ -131,6 +131,7 @@ tags <- function(repos) {
       download_url <- paste0(gh_raw_url, repo, '/master/dockerfiles/',
                              raw_df[ ,'name'], '/Dockerfile')
     } else {
+      warning('Unable to fetch data from GitHub for ', char(repo))
       download_url <- tag <- ''
     }
     data.frame(repo = repo, tag = tag, download_url = download_url,

examples/.arglist_parse.R

@@ -14,4 +14,4 @@ arglist <- c('-a', 10, '-b', 'model2', '-wd', wd, '--unwanted')
 
 
 # clean-up
-unlink(wd)
+unlink(wd, recursive = TRUE)

examples/log_set.R

@@ -1,18 +1,21 @@
-library(outsider)
-repo <- 'dombennett/om..hello.world'
-# if not installed, install
-installed <- module_installed()
-if (!repo %in% installed[['repo']]) module_install(repo)
-hello_world <- module_import(fname = 'hello_world', repo = repo)
-
-# control the log stream
-# send output to file
-tmpfl <- tempfile()
-log_set(log = 'program_out', val = tmpfl)
-hello_world()
-(readLines(con = tmpfl))
-file.remove(tmpfl)
-# send docker and program output to console
-log_set(log = 'program_out', val = TRUE)
-log_set(log = 'docker_out', val = TRUE)
-hello_world()
+# NOT RUN
+# library(outsider)
+# repo <- 'dombennett/om..hello.world'
+# # install and import
+# module_install(repo = repo)
+# hello_world <- module_import(fname = 'hello_world', repo = repo)
+# 
+# # control the log stream
+# # send output to file
+# tmpfl <- tempfile()
+# log_set(log = 'program_out', val = tmpfl)
+# hello_world()
+# (readLines(con = tmpfl))
+# file.remove(tmpfl)
+# # send docker and program output to console
+# log_set(log = 'program_out', val = TRUE)
+# log_set(log = 'docker_out', val = TRUE)
+# hello_world()
+# 
+# # clean-up
+# module_uninstall(repo)

examples/module_install.R

@@ -1,12 +1,16 @@
-library(outsider)
-# simplest repo
-repo <- 'dombennett/om..hello.world'
-# if not installed, install
-installed <- module_installed()
-if (!repo %in% installed[['repo']]) module_install(repo)
-# get help
-module_help(repo = repo)
-# import function
-hello_world <- module_import(fname = 'hello_world', repo = repo)
-# run function
-hello_world()
+# NOT RUN
+# library(outsider)
+# # simplest repo
+# repo <- 'dombennett/om..hello.world'
+# # install
+# module_install(repo = repo)
+# hello_world <- module_import(fname = 'hello_world', repo = repo)
+# # get help
+# module_help(repo = repo)
+# # import function
+# hello_world <- module_import(fname = 'hello_world', repo = repo)
+# # run function
+# hello_world()
+# 
+# # uninstall
+# module_uninstall(repo)

examples/outsider-class.R

@@ -1,49 +1,51 @@
-library(outsider)
-# Set-up: install hello.world, ships with ubuntu
-# we can make simple commands in bash via R
-repo <- 'dombennett/om..hello.world'
-# if not installed, install
-installed <- module_installed()
-if (!repo %in% installed[['repo']]) module_install(repo)
-
-# Run echo
-# create a outsider object that contains argument and Docker container details
-otsdr <- outsider::.outsider_init(repo = repo, cmd = 'echo',
-                                  arglist = c('hello world!'))
-# check details
-print(otsdr)
-# run the command
 # NOT RUN
+# library(outsider)
+# # Set-up: install hello.world, ships with ubuntu
+# # we can make simple commands in bash via R
+# repo <- 'dombennett/om..hello.world'
+# # install and import
+# module_install(repo = repo)
+# hello_world <- module_import(fname = 'hello_world', repo = repo)
+# 
+# # Run echo
+# # create a outsider object that contains argument and Docker container details
+# otsdr <- outsider::.outsider_init(repo = repo, cmd = 'echo',
+#                                   arglist = c('hello world!'))
+# # check details
+# print(otsdr)
+# # run the command
+# # NOT RUN
+# # outsider::.run(otsdr)
+# 
+# # Send a file
+# # an existing outsider object can be modified
+# tmppth <- tempdir()
+# flpth <- file.path(tmppth, 'testfile')
+# write(x = 'hello from within a file!', file = flpth)
+# otsdr$files_to_send <- flpth
+# otsdr$cmd <- 'cat'
+# otsdr$arglist <- 'testfile'
+# # check details
+# print(otsdr)
+# # run the command
 # outsider::.run(otsdr)
-
-# Send a file
-# an existing outsider object can be modified
-tmppth <- tempdir()
-flpth <- file.path(tmppth, 'testfile')
-write(x = 'hello from within a file!', file = flpth)
-otsdr$files_to_send <- flpth
-otsdr$cmd <- 'cat'
-otsdr$arglist <- 'testfile'
-# check details
-print(otsdr)
-# run the command
-outsider::.run(otsdr)
-
-# Return a file
-# an existing outsider object can be modified
-otsdr$files_to_send <- NULL
-otsdr$cmd <- 'touch'
-otsdr$arglist <- 'newfile'
-otsdr$wd <- tmppth  # determines where created files are returned to
-# check details
-print(otsdr)
-# run the command
-outsider::.run(otsdr)
-# check if 'newfile' exists in tempdir()
-nwflpth <- file.path(tmppth, 'newfile')
-(file.exists(nwflpth))
-
-# Clean-up
-rm(otsdr)
-file.remove(flpth)
-file.remove(nwflpth)
+# 
+# # Return a file
+# # an existing outsider object can be modified
+# otsdr$files_to_send <- NULL
+# otsdr$cmd <- 'touch'
+# otsdr$arglist <- 'newfile'
+# otsdr$wd <- tmppth  # determines where created files are returned to
+# # check details
+# print(otsdr)
+# # run the command
+# outsider::.run(otsdr)
+# # check if 'newfile' exists in tempdir()
+# nwflpth <- file.path(tmppth, 'newfile')
+# (file.exists(nwflpth))
+# 
+# # Clean-up
+# rm(otsdr)
+# file.remove(flpth)
+# file.remove(nwflpth)
+# module_uninstall(repo)