- pre CRAN submission commit

CRAN-SUBMISSION

@@ -1,3 +1,3 @@
 Version: 1.0.0
-Date: 2023-12-31 09:37:06 UTC
-SHA: 0f4ef82319c944e10e364477896b82650825711c
+Date: 2024-01-07 23:15:59 UTC
+SHA: 61a20abc015f7794987d4af53aa35ba3a1c6bed7

DESCRIPTION

@@ -1,15 +1,15 @@
 Package: BayesianMCPMod
 Title: Simulate, Evaluate, and Analyze Dose Finding Trials with Bayesian
     MCPMod
-Version: 1.0.0
+Version: 1.0.1
 Authors@R: c(
     person("Boehringer Ingelheim Pharma GmbH & Co. KG", role = c("cph", "fnd")),
     person("Stephan", "Wojciekowski", , "[email protected]", role = c("aut", "cre")),
     person("Lars", "Andersen", , "[email protected]", role = "aut"),
     person("Steven", "Brooks", , "[email protected]", role = "ctb"),
     person("Sebastian", "Bossert", , "[email protected]", role = "aut")
   )
-Description: Bayesian MCPMod (Fleischer et al. (2022) 
+Description: Bayesian MCPMod (Fleischer et al. (2022)
     <doi:10.1002/pst.2193>) is an innovative method that improves the
     traditional MCPMod by systematically incorporating historical data,
     such as previous placebo group data. This R package offers functions
@@ -48,7 +48,7 @@ VignetteBuilder:
     knitr
 Config/testthat/edition: 3
 Encoding: UTF-8
+Language: en-US
 LazyData: true
 Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.2.3
-Language: en-US

NEWS.md

@@ -1,3 +1,10 @@
+## BayesianMCPMod 1.0.1 (03-Apr-2024)
+
+- Re-submission of the 'BayesianMCPMod' package
+- Removed a test that occasionally failed on the fedora CRAN test system
+- Fixed a bug that would return wrong bootstrapped quantiles in getBootstrappedQuantiles()
+- Added getBootstrapSamples(), a separate function for bootstrapping samples
+
 ## BayesianMCPMod 1.0.0 (31-Dec-2023)
 
 - Initial release of the 'BayesianMCPMod' package

R/BMCPMod.R

@@ -322,7 +322,7 @@ getCritProb <- function (
 
 #' @title performBayesianMCPMod
 #' 
-#' @description Performs Bayesian MCP Test step and modeling in a combined fashion. See performBayesianMCP() function for MCP Test step and getModelFits() for the modelling step
+#' @description Performs Bayesian MCP Test step and modeling in a combined fashion. See performBayesianMCP() function for MCP Test step and getModelFits() for the modeling step
 #' 
 #' @param posterior_list An object of class 'postList' as created by getPosterior() containing information about the (mixture) posterior distribution per dose group
 #' @param contr An object of class 'optContr' as created by the getContr() function. It contains the contrast matrix to be used for the testing step.

cran-comments.md

@@ -6,8 +6,8 @@
 
 ## Test environments
 - aarch64-apple-darwin20, R 4.2.1 (local)
-- x86_64-w64-mingw32, (unstable) (2023-12-29 r85751 ucrt)
-- r-release-macosx-arm64|4.3.0 (2023-05-18 r84451)
+- x86_64-w64-mingw32, (unstable) (R version 4.4.0 alpha, 2024-04-02 r86304 ucrt)
+- r-release-macosx-arm64 | R version 4.3.3 (2024-02-29)
 - R-hub Windows Server 2022, R-devel, 64 bit
 - R-hub Ubuntu Linux 20.04.1 LTS, R-release
 - R-hub Fedora Linux, R-devel
@@ -17,13 +17,14 @@
 ### aarch64-apple-darwin20, R 4.2.1 (local)
 0 errors √ | 0 warnings √ | 0 notes √
 
-### x86_64-w64-mingw32, (unstable) (2023-12-29 r85751 ucrt)
+### x86_64-w64-mingw32, (unstable) (R version 4.4.0 alpha, 2024-04-02 r86304 ucrt)
 
 0 errors | 0 warnings | 1 note
 
 - checking CRAN incoming feasibility
   - Maintainer: 'Stephan Wojciekowski <[email protected]>'
   - New submission
+  - Package was archived on CRAN
   - Possibly misspelled words in DESCRIPTION:
     - MCPMod (3:18, 12:23, 14:17, 16:56)
     - Pinheiro (25:25)
@@ -32,18 +33,23 @@
     - et (12:41, 21:24, 25:34)
 
     => marked spelling is correct
+
+  - CRAN repository db overrides:
+     X-CRAN-Comment: Archived on 2024-03-28 as issues were not corrected
+       in time.
 
-### r-release-macosx-arm64|4.3.0 (2023-05-18 r84451)
+### r-release-macosx-arm64 | R version 4.3.3 (2024-02-29)
 
 0 errors | 0 warnings | 0 notes
 
 ### R-hub Windows Server 2022, R-devel, 64 bit
 
-0 errors | 0 warnings | 4 notes
+0 errors | 0 warnings | 5 notes
 
 - checking CRAN incoming feasibility
   - Maintainer: 'Stephan Wojciekowski <[email protected]>'
   - New submission
+  - Package was archived on CRAN
   - Possibly misspelled words in DESCRIPTION:
     - MCPMod (3:18, 12:23, 14:17, 16:56)
     - Pinheiro (25:25)
@@ -52,39 +58,48 @@
     - et (12:41, 21:24, 25:34)
 
     => marked spelling is correct
+
+  - CRAN repository db overrides:
+     X-CRAN-Comment: Archived on 2024-03-28 as issues were not corrected
+       in time.
 
 - checking HTML version of manual ... NOTE
   - Skipping checking math rendering: package 'V8' unavailable
 
-  => R-hub indueced note
+  => R-hub induced note
 
 - checking for non-standard things in the check directory ... NOTE
   - Found the following files/directories:
     - ''NULL''
 
-    => R-hub indueced note
+    => R-hub induced note
 
 - checking for detritus in the temp directory ... NOTE
   - Found the following files/directories:
     - 'lastMiKTeXException'
 
-    => R-hub indueced note
+    => R-hub induced note
 
 ### R-hub Ubuntu Linux 20.04.1 LTS, R-release
 
-0 errors | 0 warnings | 3 notes
+0 errors | 0 warnings | 5 notes
 
 - checking CRAN incoming feasibility
   - Maintainer: 'Stephan Wojciekowski <[email protected]>'
   - New submission
+  - Package was archived on CRAN
   - Possibly misspelled words in DESCRIPTION:
-    - al (12:44, 21:27, 25:37)
-    - et (12:41, 21:24, 25:34)
     - MCPMod (3:18, 12:23, 14:17, 16:56)
     - Pinheiro (25:25)
     - Schmidli (21:15)
+    - al (12:44, 21:27, 25:37)
+    - et (12:41, 21:24, 25:34)
 
     => marked spelling is correct
+
+  - CRAN repository db overrides:
+     X-CRAN-Comment: Archived on 2024-03-28 as issues were not corrected
+       in time.
 
 - checking examples ... [11s/25s] NOTE
   - Examples with CPU (user + system) or elapsed time > 5s
@@ -100,15 +115,16 @@
   - Skipping checking HTML validation: no command 'tidy' found
   - Skipping checking math rendering: package 'V8' unavailable
 
-  => R-hub indueced note
+  => R-hub induced note
 
 ### R-hub Fedora Linux, R-devel
 
-0 errors | 0 warnings | 3 notes
+0 errors | 0 warnings | 5 notes
 
 - checking CRAN incoming feasibility
   - Maintainer: 'Stephan Wojciekowski <[email protected]>'
   - New submission
+  - Package was archived on CRAN
   - Possibly misspelled words in DESCRIPTION:
     - MCPMod (3:18, 12:23, 14:17, 16:56)
     - Pinheiro (25:25)
@@ -117,6 +133,10 @@
     - et (12:41, 21:24, 25:34)
 
     => marked spelling is correct
+
+  - CRAN repository db overrides:
+     X-CRAN-Comment: Archived on 2024-03-28 as issues were not corrected
+       in time.
 
 - checking examples ... [11s/25s] NOTE
   - Examples with CPU (user + system) or elapsed time > 5s
@@ -132,10 +152,17 @@
   - Skipping checking HTML validation: no command 'tidy' found
   - Skipping checking math rendering: package 'V8' unavailable
 
-  => R-hub indueced note
+  => R-hub induced note
 
 ## From NEWS.md
 
+### BayesianMCPMod 1.0.1 (03-Apr-2024)
+
+- Re-submission of the 'BayesianMCPMod' package
+- Removed a test that occasionally failed on the fedora CRAN test system
+- Fixed a bug that would return wrong bootstrapped quantiles in getBootstrappedQuantiles()
+- Added getBootstrapSamples(), a separate function for bootstrapping samples
+
 ### BayesianMCPMod 1.0.0 (31-Dec-2023)
 
 - Initial release of the 'BayesianMCPMod' package