version 1.0.5

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: dynutils
 Type: Package
 Title: Common Functionality for the 'dynverse' Packages
-Version: 1.0.4
+Version: 1.0.5
 Authors@R: c(
     person(
       "Robrecht", 
@@ -22,11 +22,11 @@ Description:
   Provides common functionality for the 'dynverse' packages. 
   'dynverse' is created to support the development, execution, and benchmarking of trajectory inference methods.
   For more information, check out <https://dynverse.org>.
-License: GPL-3
-URL: http://github.com/dynverse/dynutils
+License: MIT + file LICENSE
+URL: https://github.com/dynverse/dynutils
 BugReports: https://github.com/dynverse/dynutils/issues
 LazyData: TRUE
-RoxygenNote: 6.1.1
+RoxygenNote: 7.0.2
 Depends: R (>= 3.0.0)
 Imports: assertthat, crayon, desc, dplyr, magrittr, Matrix, methods,
         proxyC, purrr, Rcpp, remotes, stringr, tibble
@@ -35,10 +35,10 @@ LinkingTo: Rcpp
 Encoding: UTF-8
 VignetteBuilder: knitr
 NeedsCompilation: yes
-Packaged: 2019-10-03 09:35:39 UTC; rcannood
+Packaged: 2020-02-21 10:46:37 UTC; rcannood
 Author: Robrecht Cannoodt [aut, cre] (<https://orcid.org/0000-0003-3641-729X>,
     rcannood),
   Wouter Saelens [aut] (<https://orcid.org/0000-0002-7114-6248>, zouter)
 Maintainer: Robrecht Cannoodt <rcannood@gmail.com>
 Repository: CRAN
-Date/Publication: 2019-10-03 11:40:05 UTC
+Date/Publication: 2020-02-21 12:30:02 UTC

LICENSE

@@ -0,0 +1,2 @@
+YEAR: 2014-2020
+COPYRIGHT HOLDER: Robrecht Cannoodt, Wouter Saelens

MD5

@@ -1,18 +1,19 @@
-7cb192d75db723701f71178d68b024c8 *DESCRIPTION
+1dedbdd446a71fb6e0cd7acf0c4f8865 *DESCRIPTION
+ef3d9f056adaa322680184035912700f *LICENSE
 b6dec4db1cd993e42ffd95d92cba8d64 *NAMESPACE
-297d7883e7e41507719df466d52d1237 *NEWS.md
+3cd2614695426b6226bf22cc46ee6cc2 *NEWS.md
 dcdf2491b0e62a545623862a87d55529 *R/RcppExports.R
 6f7fc8ddd74f0326bf2b59a523681cf7 *R/add_class.R
 93ee58dfa8e9d0165a0aadbc62cfb01a *R/assertions.R
 0567136a0ea7179450e01daec3b56c88 *R/calculate_distance.R
 d6aa6f13af04adf14f579e08fc13d984 *R/calculate_mean.R
-d12293c4bf7b1a545afd8a8772ef9160 *R/check_packages.R
+e2b7b0caa56d6a39e5f74f05f1ba7546 *R/check_packages.R
 1a1b2bac9aa0637569d9de821ce01da4 *R/development.R
 ebced609202a59d493b476c3aac3fe8d *R/expand_matrix.R
 aa0987fdaaa50b3bf720eef589eb9cbe *R/extend_with.R
 a13cca47e183757563216d56990fc82c *R/h5.R
 56ddd7a01d957f768e214bf3ff7d1286 *R/inherit_default_params.R
-10578fb8a2f46f5ecb3b982175fa2b2f *R/install_packages.R
+54d7dba8e284ec639517ca1e31b66a83 *R/install_packages.R
 ad9da1318face1a62868506526ccb6b2 *R/mapdf.R
 1b5098c5f0d238d3fc738e27f0cae80e *R/news.R
 6af355edbc57f40b9a0c7d146f1d04fb *R/package.R
@@ -22,37 +23,37 @@ ad9da1318face1a62868506526ccb6b2 *R/mapdf.R
 3a163b578e254a622a259fb15598b87a *R/sparse_matrix.R
 ed5a6e94e1159f1aafdcfc1c82c27d49 *R/spearman_rank_sparse.R
 508280137e6c0eb4d37a5872de6ab486 *R/tibble.R
-48d895501ba6e7aee8abb5ab2798b933 *README.md
-17cf65be3e139c69126d46bd2eb705a4 *build/vignette.rds
-9b2832b80e7882c4d2ac183a85a9c734 *inst/doc/functionality.R
+397be7eff15f739c62736951d139e41b *README.md
+b2421696f8a91492d12c349d4277a765 *build/vignette.rds
+a60b55d68196751eae1016f1871240de *inst/doc/functionality.R
 fd437c3c797311ac07d31ffd0e74d86c *inst/doc/functionality.Rmd
-4c5894500d88dbf2fcae4edd14fb0cde *inst/doc/functionality.html
+7229fbbf14fc22687c8319a98cbb003b *inst/doc/functionality.html
 c3db2b03d9fad3aa6837b3f565dfdebd *man/add_class.Rd
 6bc340f4659bf12f836063f6dbdd2329 *man/all_in.Rd
 b5ac523861808607b014847cb3797765 *man/apply_minmax_scale.Rd
 64174b3e65b65ce84ce3293ae492f994 *man/apply_quantile_scale.Rd
 3bef0a231eef2816e0a263a1e4a2242c *man/apply_uniform_scale.Rd
-2a41ba64ac7e6974373c798d81c51322 *man/calculate_distance.Rd
+9e9d83fa65d3435bb9e808709fc6ccd6 *man/calculate_distance.Rd
 5b35a6f332946299b91d087180993a29 *man/calculate_mean.Rd
 3252699f0111548d1c5865b259fc6045 *man/check_packages.Rd
 8119f54576526e375c65967172a35730 *man/deprecated.Rd
-7af19552f7245eb474ebb2d702a532a4 *man/dynutils.Rd
+e2ceb10024be583a126677b4de494f0a *man/dynutils.Rd
 7709555d2461d3fdc0754ff9ed78c279 *man/expand_matrix.Rd
 3018e1eb12824f76075b195fe12a4916 *man/extend_with.Rd
 7613b5995b078d708cc26c1a5d2d9b88 *man/extract_row_to_list.Rd
 b13a5533db06c4565c8025ec07416d90 *man/figures/dependencies.png
 21c38d6edb23eb7766127edfb805d2cc *man/has_names.Rd
 e7578523a6fa518bfb8ed4c7def2a0ea *man/inherit_default_params.Rd
-7882b49fc121c84cc4ce635266e3392f *man/install_packages.Rd
-ffb5cc4ea8eb2cc74b8881ee03793acc *man/is_bounded.Rd
+a351ae26cd8158546f000ba27b14404a *man/install_packages.Rd
+b5e279e1ffba1a1a8a1ac1c0d43b58c6 *man/is_bounded.Rd
 b9518d93e55a498b29be70221d67e209 *man/is_single_numeric.Rd
 9c390e87ca76ed1d225baea185e4b038 *man/is_sparse.Rd
 c75c1e1f49dbefd8590f7424587ad69b *man/list_as_tibble.Rd
 accf4b9c8028a260b70a2e76e0c5cc04 *man/mapdf.Rd
 2b3a023bd618893c84f8145c2396ae97 *man/project_to_segments.Rd
 2cf7693dbaf3302c64209d7336c447d5 *man/random_time_string.Rd
 924b15280c2637b60a75a439b96da664 *man/read_h5.Rd
-b0cb95b27f4369b40ec09cdb98029c5d *man/recent_news.Rd
+ade76e3a41972c1df16527a5d29becb1 *man/recent_news.Rd
 4709d575d5fa06a874efac612a29ee78 *man/safe_tempdir.Rd
 3ebf0627b766e627129d9ea56bc4e725 *man/scale_minmax.Rd
 796b56abcd3919f503ddecb80735ea9a *man/scale_quantile.Rd
@@ -73,7 +74,6 @@ dbb99d66a04da64c942eeb3d2aad76a4 *tests/testthat/test-check_packages.R
 8faa7d5a28c69f65e45e8ff451fc705b *tests/testthat/test-extend_with.R
 6b476ee9c8230218a976b0abc9457fbf *tests/testthat/test-h5.R
 5ce31da95e0ab2cae64f31550e6957c1 *tests/testthat/test-inherit_default_params.R
-f665360485a47a68db1c5e78f4419139 *tests/testthat/test-install_packages.R
 eb500b1fea1726787b4e1cc25de6caa0 *tests/testthat/test-mapdf.R
 87086196556352c60f0e8a21d5e13e02 *tests/testthat/test-news.R
 12b22a50c13f031e04cafada2045e5eb *tests/testthat/test-project_to_segments.R

NEWS.md

@@ -1,4 +1,10 @@
-# dynutils 1.0.4
+# dynutils 1.0.5
+
+ * BUG FIX `install_packages()`: will not try to install packages when the session is not interactive.
+
+ * LICENSE: Change to MIT.
+
+# dynutils 1.0.4 (2019-10-03)
 
  * BUG FIX `recent_news()`: do not prepend subsections.
 

R/check_packages.R

@@ -11,6 +11,6 @@
 #' check_packages(c("princurve", "mlr", "tidyverse"))
 check_packages <- function(...) {
   packages <- unlist(list(...))
-  installed_packages <- rownames(utils::installed.packages())
-  set_names(packages %in% installed_packages, packages)
+  installed_packages <- map_lgl(packages, requireNamespace, quietly = TRUE)
+  set_names(installed_packages, packages)
 }

R/install_packages.R

@@ -4,10 +4,12 @@ parse_remotes <- function(remotes) {
     set_names(remotes)
 }
 
-#' Install packages, but first ask if interactive
+#' Check package availability
 #'
-#' @param ... The names of the packages to be installed
-#' @param is_interactive Whether running interactivly, which will prompt the user before installation
+#' If the session is interactive, prompt the user whether to install the packages.
+#'
+#' @param ... The names of the packages to be checked
+#' @param try_install Whether running interactivly, which will prompt the user before installation
 #'
 #' @importFrom remotes install_cran
 #' @importFrom utils setRepositories
@@ -18,11 +20,11 @@ parse_remotes <- function(remotes) {
 #' \dontrun{
 #' install_packages("SCORPIUS")
 #' }
-install_packages <- function(..., is_interactive = interactive()) {
+install_packages <- function(..., try_install = interactive()) {
   dependencies <- unlist(list(...)) %>% discard(check_packages)
 
   if (length(dependencies) > 0) {
-    if (is_interactive) {
+    if (try_install) {
       message(paste0(
         "Following packages have to be installed: ",
         paste(crayon::bold(dependencies), collapse = ", "),
@@ -40,6 +42,11 @@ install_packages <- function(..., is_interactive = interactive()) {
       if (answer %in% c("no", "n", "2")) {
         stop("Installation was interrupted.")
       }
+    } else {
+      stop(
+        "Please install the following packages: \n",
+        "  ", paste0("\"", dependencies, "\"", collapse = ",")
+      )
     }
 
     # set repositories to include bioconductor
@@ -48,14 +55,14 @@ install_packages <- function(..., is_interactive = interactive()) {
     message("Installing ", paste0(dependencies, collapse = ", "))
 
     # install other depencies from cran
-    remotes::install_cran(dependencies, repos = "http://cran.rstudio.com")
+    remotes::install_cran(dependencies)
 
     # display message
     message("Installed ", paste0(dependencies, collapse = ", "))
 
     # return installed dependencies at the end
     dependencies
   } else {
-    NULL
+    invisible(NULL)
   }
 }

README.md

@@ -26,27 +26,22 @@ changes.
 
 <!-- This section gets automatically generated from inst/NEWS.md, and also generates inst/NEWS -->
 
-### Recent changes in dynutils 1.0.4
+### Recent changes in dynutils 1.0.5
 
-  - BUG FIX `recent_news()`: do not prepend subsections.
-
-  - BUG FIX `switch_cran()`: add missing version variable.
-
-  - REMOVAL `update_news()` remove this function as R 3.6 natively
-    supports markdown news format.
+  - BUG FIX `install_packages()`: will not try to install packages when
+    the session is not interactive.
 
-### Recent changes in dynutils 1.0.3 (2019-05-02)
+  - LICENSE: Change to MIT.
 
-  - FUNCTIONALITY: Added `test_h5_installation()`.
+### Recent changes in dynutils 1.0.4 (2019-10-03)
 
-  - BUG FIX: Added compatibility workaround for being able to read hdf5
-    1.10.4 files on a hdf5 1.8.14 Windows platform (hhoeflin/hdf5r\#60).
+  - BUG FIX `recent_news()`: do not prepend subsections.
 
-  - FUNCTIONALITY: `calculate_distance()` and `calculate_similarity()`
-    now support sparse matrix calculation thanks to proxyC\!
+  - BUG FIX `switch_cran()`: add missing version variable.
 
-  - SMALL CHANGES: Remove dependencies: glue, Hmisc, devtools, testthat,
-    tidyr.
+  - REMOVAL `update_news()` remove this function as R 3.6 natively
+    supports markdown news
+format.
 
 ## Dynverse dependencies