Merge pull request #346 from OuhscBbmc/dev

submit to CRAN; especially with changes of readr 2.0

Author: wibeasley

.Rbuildignore

@@ -24,3 +24,4 @@ utility/
 ^CRAN-RELEASE$
 ^codecov\.yml$
 ^pkgdown$
+^LICENSE\.md$

.github/workflows/check-release.yaml

@@ -19,6 +19,7 @@ jobs:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
     steps:
       - uses: actions/checkout@v2
+      
       - uses: r-lib/actions/setup-r@v1
 
       - uses: r-lib/actions/setup-pandoc@master
@@ -53,11 +54,22 @@ jobs:
           remotes::install_deps(dependencies = TRUE)
           remotes::install_cran("covr")
         shell: Rscript {0}
+
+      - name: Session info
+        run: |
+          options(width = 100)
+          pkgs <- installed.packages()[, "Package"]
+          sessioninfo::session_info(pkgs, include_base = TRUE)
+        shell: Rscript {0}
+
       - name: Check
+        env:
+          _R_CHECK_CRAN_INCOMING_: false
         run: |
           options(crayon.enabled = TRUE)
-          rcmdcheck::rcmdcheck(args = "--no-manual", error_on = "error")
+          rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "warning", check_dir = "check")
         shell: Rscript {0}
+
       - name: Test coverage
         run: covr::codecov()
         shell: Rscript {0}

CONDUCT.md

@@ -22,4 +22,4 @@ opening an issue or contacting one or more of the project maintainers.
 
 This Code of Conduct is adapted from the Contributor Covenant 
 (http:contributor-covenant.org), version 1.0.0, available at 
-http://contributor-covenant.org/version/1/0/0/
+https://contributor-covenant.org/version/1/0/0/

DESCRIPTION

@@ -6,7 +6,7 @@ Description: Encapsulates functions to streamline calls from R to the REDCap
     University.  The Application Programming Interface (API) offers an avenue
     to access and modify data programmatically, improving the capacity for
     literate and reproducible programming.
-Version: 0.11.1.9005
+Version: 1.0.0
 Authors@R: c(person("Will", "Beasley", role = c("aut", "cre"), email =
     "wibeasley@hotmail.com", comment = c(ORCID = "0000-0002-5613-5006")),
     person("David", "Bard", role = "ctb"),
@@ -20,7 +20,7 @@ Authors@R: c(person("Will", "Beasley", role = c("aut", "cre"), email =
     comment = c(ORCID = '0000-0002-3386-6076')), person("Felix", "Torres",
     role = "ctb", email = "fetorres@ucsd.edu"), person("Philip", "Chase",
     role = "ctb", email = "pbc@ufl.edu"))
-URL: https://ouhscbbmc.github.io/REDCapR, https://github.com/OuhscBbmc/REDCapR, http://ouhsc.edu/bbmc/, http://project-redcap.org
+URL: https://ouhscbbmc.github.io/REDCapR/, https://github.com/OuhscBbmc/REDCapR, https://www.ouhsc.edu/bbmc/, https://project-redcap.org
 BugReports: https://github.com/OuhscBbmc/REDCapR/issues
 Depends:
     R(>= 3.5.0)
@@ -43,8 +43,7 @@ Suggests:
     rmarkdown (>= 2.0),
     sessioninfo (>= 1.1.1),
     testthat (>= 3.0)
-License: GPL-2
-LazyData: TRUE
+License: MIT + file LICENSE
 VignetteBuilder: knitr
 Encoding: UTF-8
 RoxygenNote: 7.1.1

LICENSE

@@ -0,0 +1,2 @@
+YEAR: 2021
+COPYRIGHT HOLDER: REDCapR authors

LICENSE.md

@@ -0,0 +1,21 @@
+# MIT License
+
+Copyright (c) 2021 REDCapR authors
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

NEWS.md

@@ -4,9 +4,11 @@ Upcoming Versions
 In the future:
 ...
 
-Version 0.12 (Unreleased on CRAN)
+Version 1.0 (released 2021-07-21)
 ==========================================================
 
+The package has been stable for years and should be reflected in the major version number.
+
 ### Minor Enhancements
 
 * When writing records to the server, the functions `redcap_write()` and `redcap_write_oneshot()` have a new parameter that converts R's `logical`/boolean columns to integers.  This meshes well with T/F and Y/N items that are coded as 1/0 underneath. The default will be FALSE (ie, the integers are not converted by default), so it doesn't break existing code. (#305)
@@ -20,7 +22,8 @@ Version 0.12 (Unreleased on CRAN)
 ### Stability Features
 
 * update for newer version of testthat -v3.0.0 (#312)
-* update for newer version of readr (#313)
+* update for newer version of readr 2.0.0 (#343)
+* update for newer version of readr 1.4.0 (#313)
 * update for newer version of REDCap on test server (#310)
 * save expected datasets as files -instead of included in the actual test code (#308)
 
@@ -127,7 +130,7 @@ Versions 0.9.7 (Released 2017-09-09)
 * Remove line breaks from token (Thanks @haozhu233 in issues #103 & #104)
 
 ### Minor Updates
-* When combining batches into a single data.frame, `data.table::rbindlist()` is used.  This should prevent errors with the first batch's data type (for a column) isn't compatible with a later batch.  For instance, this occurs when the first batch has only integers for `record_id`, but a subsequent batch has values like `aa-test-aa`.  The variable for the combined dataset should be a character. (Issue #128 & http://stackoverflow.com/questions/39377370/bind-rows-of-different-data-types; Thanks @arunsrinivasan)
+* When combining batches into a single data.frame, `data.table::rbindlist()` is used.  This should prevent errors with the first batch's data type (for a column) isn't compatible with a later batch.  For instance, this occurs when the first batch has only integers for `record_id`, but a subsequent batch has values like `aa-test-aa`.  The variable for the combined dataset should be a character. (Issue #128 & https://stackoverflow.com/questions/39377370/bind-rows-of-different-data-types; Thanks @arunsrinivasan)
 * Uses the `dplyr` package instead of `plyr`.  This shouldn't affect callers, because immediately before returning the data, `REDCapR::redcap_read()` coerces the `tibble::tibble` (which was formerly called `dplyr::tbl_df`) back to a vanilla `data.frame` with `as.data.frame()`.
 * A few more instances of validating input parameters to read functions. (Issue #8).
 
@@ -193,7 +196,7 @@ Version 0.4-28 (Released 2014-09-20)
 
 ### Updates
 * By default, the SSL certs come from the httr package.  However, REDCapR will continue to maintain a copy in case httr's version on CRAN gets out of date.
-* The tests are split into two collections: one that's run by the CRAN checks, and the other run manually.  [Thanks, Gabor Csardi](http://stackoverflow.com/questions/25595487/testthat-pattern-for-long-running-tests).  Any test with a dependency outside the package code (especially the REDCap test projects) is run manually so changes to the test databases won't affect the success of building the previous version on CRAN.
+* The tests are split into two collections: one that's run by the CRAN checks, and the other run manually.  [Thanks, Gabor Csardi](https://stackoverflow.com/questions/25595487/testthat-pattern-for-long-running-tests).  Any test with a dependency outside the package code (especially the REDCap test projects) is run manually so changes to the test databases won't affect the success of building the previous version on CRAN.
 * Corrected typo in `redcap_download_file_oneshot()` documentation, thanks to Andrew Peters (@ARPeters #45).
 
 
@@ -220,7 +223,7 @@ Version 0.2 (Released 2014-07-02)
 * The `redcap_project()` object reduces repeatedly passing parameters like the server URL, the user token, and the SSL cert location.
 
 ### Updates
-* New Mozilla SSL Certification Bundles released on cURL (released 2013-12-05; http://curl.haxx.se/ca/cacert.pem)
+* New Mozilla SSL Certification Bundles released on cURL (released 2013-12-05)
 * Renamed `redcap_read_batch()`  to `redcap_read()`. These changes reflect our suggestion that reads should typically be batched.
 * Renamed `redcap_read()` to `redcap_read_oneshot()`
 * Renamed `redcap_write()` to `redcap_write_oneshot()` (which is an internal function).

R/REDCapR-package.R

@@ -3,7 +3,7 @@
 #' @aliases REDCapR
 #'
 #' @title R utilities for interacting with a REDCap data system
-#' <http://www.project-redcap.org/>
+#' <https://www.project-redcap.org/>
 #'
 #' @description
 #'
@@ -14,28 +14,28 @@
 #' following projects.  We appreciate the support.
 #' * *OUHSC CCAN Independent Evaluation of the State of Oklahoma Competitive
 #' Maternal, Infant, and Early Childhood Home Visiting
-#' ([MIECHV](http://mchb.hrsa.gov/programs/homevisiting/)) Project*.
-#' [HRSA/ACF D89MC23154](https://grants6.hrsa.gov/MCHB/DGISReports/Abstract/AbstractDetails.aspx?cbAbstractSummary=D89MC23154_2012_NonResearch_4).
+#' ([MIECHV](https://mchb.hrsa.gov/maternal-child-health-initiatives/home-visiting-overview)) Project*.
+#' HRSA/ACF D89MC23154.
 #' David Bard, PI, OUHSC; 2011-2015.
 #' * *Independent Evaluation of the State of OK MIECHV Evidence Based Home
 #' Visitation Project*, [NIH](https://www.nih.gov/)-sponsored collaboration
-#' with [OSDH](https://ok.gov/health/).
+#' with [OSDH](https://oklahoma.gov/health.html).
 #' David Bard, PI, OUHSC; 2015-2017.
 #' * *OSDH ParentPRO Pilot Evaluation*, federally-sponsored collaboration
-#' with [OSDH](https://ok.gov/health/).
+#' with [OSDH](https://oklahoma.gov/health.html).
 #' David Bard, PI, OUHSC; 2015-2017.
-#' * *Title IV-E Waiver Project*, [HRSA/MCHB](http://mchb.hrsa.gov/)-sponsored
-#' collaboration with [OKDHS](http://www.okdhs.org/);
+#' * *Title IV-E Waiver Project*, [HRSA/MCHB](https://mchb.hrsa.gov/)-sponsored
+#' collaboration with [OKDHS](https://oklahoma.gov/okdhs.html);
 #' David Bard, PI, OUHSC; 2014-2017.
 #' * *Integrative Analysis of Longitudinal Studies of Aging (IALSA)*,
-#' sponsored by [NIH 5P01AG043362](http://grantome.com/grant/NIH/P01-AG043362).
+#' sponsored by [NIH 5P01AG043362](https://grantome.com/grant/NIH/P01-AG043362).
 #' Scott Hofer, PI, University of Victoria;
 #' Will Beasley, PI of site-award, OUHSC; 2013-2018.
 #' * *Oklahoma Shared Clinical and Translational Resources*, sponsored by
-#' [NIH NIGMS; U54 GM104938](http://grantome.com/grant/NIH/U54-GM104938).
+#' [NIH NIGMS; U54 GM104938](https://grantome.com/grant/NIH/U54-GM104938).
 #' Judith A. James, PI, OUHSC; 2013-2018.
 #' * Additional Institutional Support from OUHSC
-#' [Dept of Pediatrics](https://www.oumedicine.com/department-of-pediatrics);
+#' [Dept of Pediatrics](https://medicine.ouhsc.edu/Academic-Departments/Pediatrics);
 #' 2013-2017.
 #'
 #'

R/redcap-download-file-oneshot.R

@@ -34,7 +34,7 @@
 #' * `success`: A boolean value indicating if the operation was apparently
 #' successful.
 #' * `status_code`: The
-#' [http status code](http://en.wikipedia.org/wiki/List_of_HTTP_status_codes)
+#' [http status code](https://en.wikipedia.org/wiki/List_of_HTTP_status_codes)
 #' of the operation.
 #' * `outcome_message`: A human readable string indicating the operation's
 #' outcome.

R/redcap-download-instrument.R

@@ -29,7 +29,7 @@
 #' * `success`: A boolean value indicating if the operation was apparently
 #' successful.
 #' * `status_code`: The
-#' [http status code](http://en.wikipedia.org/wiki/List_of_HTTP_status_codes)
+#' [http status code](https://en.wikipedia.org/wiki/List_of_HTTP_status_codes)
 #' of the operation.
 #' * `outcome_message`: A human readable string indicating the operation's
 #' outcome.

R/redcap-metadata-read.R

@@ -29,7 +29,7 @@
 #' * `success`: A boolean value indicating if the operation was apparently
 #' successful.
 #' * `status_codes`: A collection of
-#' [http status codes](http://en.wikipedia.org/wiki/List_of_HTTP_status_codes),
+#' [http status codes](https://en.wikipedia.org/wiki/List_of_HTTP_status_codes),
 #' separated by semicolons.  There is one code for each batch attempted.
 #' * `outcome_messages`: A collection of human readable strings indicating the
 #' operations' semicolons.  There is one code for each batch attempted.  In an

R/redcap-metadata-write.R

@@ -22,7 +22,7 @@
 #' * `success`: A boolean value indicating if the operation was apparently
 #' successful.
 #' * `status_code`: The
-#' [http status code](http://en.wikipedia.org/wiki/List_of_HTTP_status_codes)
+#' [http status code](https://en.wikipedia.org/wiki/List_of_HTTP_status_codes)
 #' of the operation.
 #' * `outcome_message`: A human readable string indicating the operation's
 #' outcome.
@@ -73,7 +73,7 @@ redcap_metadata_write <- function(
   verbose         = TRUE,
   config_options  = NULL
 ) {
-  csv_elements <- NULL #This prevents the R CHECK NOTE: 'No visible binding for global variable Note in R CMD check';  Also see  if( getRversion() >= "2.15.1" )    utils::globalVariables(names=c("csv_elements")) #http://stackoverflow.com/questions/8096313/no-visible-binding-for-global-variable-note-in-r-cmd-check; http://stackoverflow.com/questions/9439256/how-can-i-handle-r-cmd-check-no-visible-binding-for-global-variable-notes-when
+  csv_elements <- NULL #This prevents the R CHECK NOTE: 'No visible binding for global variable Note in R CMD check';  Also see  if( getRversion() >= "2.15.1" )    utils::globalVariables(names=c("csv_elements")) #https://stackoverflow.com/questions/8096313/no-visible-binding-for-global-variable-note-in-r-cmd-check; https://stackoverflow.com/questions/9439256/how-can-i-handle-r-cmd-check-no-visible-binding-for-global-variable-notes-when
 
   checkmate::assert_character(redcap_uri, any.missing = FALSE, len = 1, pattern = "^.{1,}$")
   checkmate::assert_character(token     , any.missing = FALSE, len = 1, pattern = "^.{1,}$")

R/redcap-project.R

@@ -131,5 +131,5 @@ redcap_project <- setRefClass(
   ) #End methods list
 ) #End class
 
-# http://adv-r.had.co.nz/OO-essentials.html # nolint
-# http://stackoverflow.com/questions/21875596/mapping-a-c-sharp-class-definition-to-an-r-reference-class-definition # nolint
+# https://adv-r.had.co.nz/OO-essentials.html # nolint
+# https://stackoverflow.com/questions/21875596/mapping-a-c-sharp-class-definition-to-an-r-reference-class-definition # nolint

R/redcap-read-oneshot-eav.R

@@ -65,7 +65,7 @@
 #' * `success`: A boolean value indicating if the operation was apparently
 #' successful.
 #' * `status_code`: The
-#' [http status code](http://en.wikipedia.org/wiki/List_of_HTTP_status_codes)
+#' [http status code](https://en.wikipedia.org/wiki/List_of_HTTP_status_codes)
 #' of the operation.
 #' * `outcome_message`: A human readable string indicating the operation's
 #' outcome.

R/redcap-read-oneshot.R

@@ -74,7 +74,7 @@
 #' * `success`: A boolean value indicating if the operation was apparently
 #' successful.
 #' * `status_code`: The
-#' [http status code](http://en.wikipedia.org/wiki/List_of_HTTP_status_codes)
+#' [http status code](https://en.wikipedia.org/wiki/List_of_HTTP_status_codes)
 #' of the operation.
 #' * `outcome_message`: A human readable string indicating the operation's
 #' outcome.

R/redcap-read.R

@@ -89,7 +89,7 @@
 #' * `success`: A boolean value indicating if the operation was apparently
 #' successful.
 #' * `status_codes`: A collection of
-#' [http status codes](http://en.wikipedia.org/wiki/List_of_HTTP_status_codes),
+#' [http status codes](https://en.wikipedia.org/wiki/List_of_HTTP_status_codes),
 #' separated by semicolons.  There is one code for each batch attempted.
 #' * `outcome_messages`: A collection of human readable strings indicating the
 #' operations' semicolons.  There is one code for each batch attempted.  In an

R/redcap-report.R

@@ -39,7 +39,7 @@
 #' * `success`: A boolean value indicating if the operation was apparently
 #' successful.
 #' * `status_code`: The
-#' [http status code](http://en.wikipedia.org/wiki/List_of_HTTP_status_codes)
+#' [http status code](https://en.wikipedia.org/wiki/List_of_HTTP_status_codes)
 #' of the operation.
 #' * `outcome_message`: A human readable string indicating the operation's
 #' outcome.

R/redcap-survey-link-export-oneshot.R

@@ -20,7 +20,7 @@
 #' * `success`: A boolean value indicating if the operation was apparently
 #' successful.
 #' * `status_code`: The
-#' [http status code](http://en.wikipedia.org/wiki/List_of_HTTP_status_codes)
+#' [http status code](https://en.wikipedia.org/wiki/List_of_HTTP_status_codes)
 #' of the operation.
 #' * `outcome_message`: A human readable string indicating the operation's
 #' outcome.

R/redcap-upload-file-oneshot.R

@@ -22,7 +22,7 @@
 #' * `success`: A boolean value indicating if the operation was apparently
 #' successful.
 #' * `status_code`: The
-#' [http status code](http://en.wikipedia.org/wiki/List_of_HTTP_status_codes)
+#' [http status code](https://en.wikipedia.org/wiki/List_of_HTTP_status_codes)
 #' of the operation.
 #' * `outcome_message`: A human readable string indicating the operation's
 #' outcome.

R/redcap-variables.R

@@ -20,7 +20,7 @@
 #' * `success`: A boolean value indicating if the operation was apparently
 #' successful.
 #' * `status_code`: The
-#' [http status code](http://en.wikipedia.org/wiki/List_of_HTTP_status_codes)
+#' [http status code](https://en.wikipedia.org/wiki/List_of_HTTP_status_codes)
 #' of the operation.
 #' * `outcome_message`: A human readable string indicating the operation's
 #' outcome.

R/redcap-write-oneshot.R

@@ -30,7 +30,7 @@
 #' * `success`: A boolean value indicating if the operation was apparently
 #' successful.
 #' * `status_code`: The
-#' [http status code](http://en.wikipedia.org/wiki/List_of_HTTP_status_codes)
+#' [http status code](https://en.wikipedia.org/wiki/List_of_HTTP_status_codes)
 #' of the operation.
 #' * `outcome_message`: A human readable string indicating the operation's
 #' outcome.
@@ -97,7 +97,7 @@ redcap_write_oneshot <- function(
   config_options  = NULL
 ) {
 
-  csv_elements <- NULL #This prevents the R CHECK NOTE: 'No visible binding for global variable Note in R CMD check';  Also see  if( getRversion() >= "2.15.1" )    utils::globalVariables(names=c("csv_elements")) #http://stackoverflow.com/questions/8096313/no-visible-binding-for-global-variable-note-in-r-cmd-check; http://stackoverflow.com/questions/9439256/how-can-i-handle-r-cmd-check-no-visible-binding-for-global-variable-notes-when
+  csv_elements <- NULL #This prevents the R CHECK NOTE: 'No visible binding for global variable Note in R CMD check';  Also see  if( getRversion() >= "2.15.1" )    utils::globalVariables(names=c("csv_elements")) #https://stackoverflow.com/questions/8096313/no-visible-binding-for-global-variable-note-in-r-cmd-check; https://stackoverflow.com/questions/9439256/how-can-i-handle-r-cmd-check-no-visible-binding-for-global-variable-notes-when
 
   checkmate::assert_character(redcap_uri, any.missing=FALSE, len=1, pattern="^.{1,}$")
   checkmate::assert_character(token     , any.missing=FALSE, len=1, pattern="^.{1,}$")

R/redcap-write.R

@@ -37,7 +37,7 @@
 #' * `success`: A boolean value indicating if the operation was apparently
 #' successful.
 #' * `status_code`: The
-#' [http status code](http://en.wikipedia.org/wiki/List_of_HTTP_status_codes)
+#' [http status code](https://en.wikipedia.org/wiki/List_of_HTTP_status_codes)
 #' of the operation.
 #' * `outcome_message`: A human readable string indicating the operation's
 #' outcome.

R/retrieve-credential.R

@@ -42,7 +42,7 @@
 #' Defaults to FALSE.
 #' @param check_token_pattern A `logical` value indicates if the token in the
 #' credential file is a 32-character hexadecimal string.  Defaults to FALSE.
-#' @param dsn A [DSN](http://en.wikipedia.org/wiki/Data_source_name) on the
+#' @param dsn A [DSN](https://en.wikipedia.org/wiki/Data_source_name) on the
 #' local machine that points to the desired MSSQL database. Required.
 #' @param channel An *optional* connection handle as returned by
 #' [DBI::dbConnect()].  See Details below. Optional.