From 056eec01f53211eb7f7cdd7db35b9f069ad9b896 Mon Sep 17 00:00:00 2001 From: wojcieko Date: Wed, 3 Apr 2024 23:00:07 +0200 Subject: [PATCH] - pre CRAN submission commit --- CRAN-SUBMISSION | 4 ++-- DESCRIPTION | 6 +++--- NEWS.md | 7 ++++++ R/BMCPMod.R | 2 +- cran-comments.md | 55 ++++++++++++++++++++++++++++++++++++------------ 5 files changed, 54 insertions(+), 20 deletions(-) diff --git a/CRAN-SUBMISSION b/CRAN-SUBMISSION index c763b6b..e61c509 100644 --- a/CRAN-SUBMISSION +++ b/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 diff --git a/DESCRIPTION b/DESCRIPTION index dabb0f8..ba222ee 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,7 +1,7 @@ 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", , "stephan.wojciekowski@boehringer-ingelheim.com", role = c("aut", "cre")), @@ -9,7 +9,7 @@ Authors@R: c( person("Steven", "Brooks", , "steven.brooks@boehringer-ingelheim.com", role = "ctb"), person("Sebastian", "Bossert", , "sebastian.bossert@boehringer-ingelheim.com", role = "aut") ) -Description: Bayesian MCPMod (Fleischer et al. (2022) +Description: Bayesian MCPMod (Fleischer et al. (2022) ) 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 diff --git a/NEWS.md b/NEWS.md index 9ad6076..4aaf810 100644 --- a/NEWS.md +++ b/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 diff --git a/R/BMCPMod.R b/R/BMCPMod.R index 790b51e..3c86b1a 100644 --- a/R/BMCPMod.R +++ b/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. diff --git a/cran-comments.md b/cran-comments.md index f93c4d4..a366da9 100644 --- a/cran-comments.md +++ b/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 ' - 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 ' - 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 ' - 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 ' - 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