From 7394a6753feb6309e88e95ad7f361749c4019883 Mon Sep 17 00:00:00 2001 From: Andreas Gammelgaard Damsbo Date: Thu, 12 Mar 2026 13:49:57 +0100 Subject: [PATCH] rerender all --- CITATION.cff | 2 +- DESCRIPTION | 2 +- NEWS.md | 4 ++++ R/app_version.R | 2 +- R/hosted_version.R | 2 +- R/sysdata.rda | Bin 2671 -> 2645 bytes SESSION.md | 28 ++++++++++++++-------------- app_docker/app.R | 6 +++--- app_docker/renv.lock | 12 ++++++------ renv.lock | 12 ++++++------ 10 files changed, 37 insertions(+), 33 deletions(-) diff --git a/CITATION.cff b/CITATION.cff index 3baa4bf4..f7e2ec6a 100644 --- a/CITATION.cff +++ b/CITATION.cff @@ -8,7 +8,7 @@ message: 'To cite package "FreesearchR" in publications use:' type: software license: AGPL-3.0-or-later title: 'FreesearchR: Easy data analysis for clinicians' -version: 26.3.3 +version: 26.3.4 doi: 10.5281/zenodo.14527429 identifiers: - type: url diff --git a/DESCRIPTION b/DESCRIPTION index e47380cb..3e2cc6ab 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: FreesearchR Title: Easy data analysis for clinicians -Version: 26.3.3 +Version: 26.3.4 Authors@R: c( person("Andreas Gammelgaard", "Damsbo",email="agdamsbo@clin.au.dk", role = c("aut", "cre"), comment = c(ORCID = "0000-0002-7559-1154")), diff --git a/NEWS.md b/NEWS.md index b05d8909..f08ae0b2 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,3 +1,7 @@ +# FreesearchR 26.3.4 + + + # FreesearchR 26.3.3 *NEW* option to pass global settings when running as docker or launching from R. Support for INCLUDE_GLOBALENV, DATA_LIMIT_DEFAULT, DATA_LIMIT_UPPER and DATA_LIMIT_LOWER. Described in the README. diff --git a/R/app_version.R b/R/app_version.R index dccdf7c4..c6d7307c 100644 --- a/R/app_version.R +++ b/R/app_version.R @@ -1 +1 @@ -app_version <- function()'26.3.3' +app_version <- function()'26.3.4' diff --git a/R/hosted_version.R b/R/hosted_version.R index b15a5737..f0c656d1 100644 --- a/R/hosted_version.R +++ b/R/hosted_version.R @@ -1 +1 @@ -hosted_version <- function()'v26.3.3-260312' +hosted_version <- function()'v26.3.4-260312' diff --git a/R/sysdata.rda b/R/sysdata.rda index 7ab55e91eff8121f1805d27dc695bbd323b19233..f8b0df59c674b9d09f2de1dbfadcfb9a132325b6 100644 GIT binary patch delta 2644 zcmV-a3aj<+6x9?CLRx4!F+o`-Q(5#dim8zf9)A`h79InFQjG#Y7vB00pa1|b4NO1? z01-BXC#HzgNc5-aO&*9CLq>+wV@60dPtzcjQ%xpA)DO`^dV~N2AOH;pfHVe#Qz@tF zgFpZPG!IY>0Av~f0000a(nKXw^lD^-dZtYPJ*opikPS2dJwN~kgh{B=)HG-Tqd)^d z0Dlb{84UmpG#UURN+3l2O;1F?fN7?U02%-QF#(Xs440*jGGr*rLm71eZM1-;_yVS` zl_HD9_r6#n4VDnf@$YNom=MAkcy{=>Ok!qsAd=Xv$KCEZrljCVgMr|JRAGD 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zaktReA4%EON7ac*Hs4X1j1EL9dfTZgtv&BH7bZP?A=Yb!rXX{x9arfc0_pVO+m7DH z%!L$8ct<{7=O@VP;b~%3Npo4WW9L?(3rRL3H0me~)kW^18RU%9MyaT3grH6` cW?XY0^fq8)w$jlpI!F9n$rRy2LE#Fm;L82umjD0& diff --git a/SESSION.md b/SESSION.md index 2f9f27b9..1bd978b0 100644 --- a/SESSION.md +++ b/SESSION.md @@ -15,7 +15,7 @@ |rstudio |2026.01.1+403 Apple Blossom (desktop) | |pandoc |3.6.4 @ /opt/homebrew/bin/ (via rmarkdown) | |quarto |1.7.30 @ /usr/local/bin/quarto | -|FreesearchR |26.3.3.260312 | +|FreesearchR |26.3.4.260312 | -------------------------------------------------------------------------------- @@ -32,7 +32,7 @@ |bit |4.6.0 |2025-03-06 |CRAN (R 4.5.0) | |bit64 |4.6.0-1 |2025-01-16 |CRAN (R 4.5.0) | |bitops |1.0-9 |2024-10-03 |CRAN (R 4.5.0) | -|boot |1.3-32 |2025-08-29 |CRAN (R 4.5.2) | +|boot |1.3-32 |2025-08-29 |CRAN (R 4.5.0) | |broom |1.0.12 |2026-01-27 |CRAN (R 4.5.2) | |broom.helpers |1.22.0 |2025-09-17 |CRAN (R 4.5.0) | |bsicons |0.1.2 |2023-11-04 |CRAN (R 4.5.0) | @@ -44,11 +44,11 @@ |caTools |1.18.3 |2024-09-04 |CRAN (R 4.5.0) | |cellranger |1.1.0 |2016-07-27 |CRAN (R 4.5.0) | |checkmate |2.3.4 |2026-02-03 |CRAN (R 4.5.2) | -|class |7.3-23 |2025-01-01 |CRAN (R 4.5.2) | +|class |7.3-23 |2025-01-01 |CRAN (R 4.5.0) | |classInt |0.4-11 |2025-01-08 |CRAN (R 4.5.0) | |cli |3.6.5 |2025-04-23 |CRAN (R 4.5.0) | |cluster |2.1.8.2 |2026-02-05 |CRAN (R 4.5.2) | -|codetools |0.2-20 |2024-03-31 |CRAN (R 4.5.2) | +|codetools |0.2-20 |2024-03-31 |CRAN (R 4.5.0) | |colorspace |2.1-2 |2025-09-22 |CRAN (R 4.5.0) | |commonmark |2.0.0 |2025-07-07 |CRAN (R 4.5.0) | |crayon |1.5.3 |2024-06-20 |CRAN (R 4.5.0) | @@ -79,9 +79,9 @@ |fontquiver |0.2.1 |2017-02-01 |CRAN (R 4.5.0) | |forcats |1.0.1 |2025-09-25 |CRAN (R 4.5.0) | |foreach |1.5.2 |2022-02-02 |CRAN (R 4.5.0) | -|foreign |0.8-90 |2025-03-31 |CRAN (R 4.5.2) | +|foreign |0.8-91 |2026-01-29 |CRAN (R 4.5.2) | |Formula |1.2-5 |2023-02-24 |CRAN (R 4.5.0) | -|FreesearchR |26.3.3 |NA |NA | +|FreesearchR |26.3.4 |NA |NA | |fs |1.6.7 |2026-03-06 |CRAN (R 4.5.2) | |gdtools |0.5.0 |2026-02-09 |CRAN (R 4.5.2) | |generics |0.1.4 |2025-05-09 |CRAN (R 4.5.0) | @@ -109,25 +109,25 @@ |iterators |1.0.14 |2022-02-05 |CRAN (R 4.5.0) | |jquerylib |0.1.4 |2021-04-26 |CRAN (R 4.5.0) | |jsonlite |2.0.0 |2025-03-27 |CRAN (R 4.5.0) | -|KernSmooth |2.23-26 |2025-01-01 |CRAN (R 4.5.2) | +|KernSmooth |2.23-26 |2025-01-01 |CRAN (R 4.5.0) | |keyring |1.4.1 |2025-06-15 |CRAN (R 4.5.0) | |knitr |1.51 |2025-12-20 |CRAN (R 4.5.2) | -|later |1.4.6 |2026-03-05 |CRAN (R 4.5.2) | +|later |1.4.8 |2026-03-05 |CRAN (R 4.5.2) | |lattice |0.22-7 |2025-04-02 |CRAN (R 4.5.2) | |lifecycle |1.0.5 |2026-01-08 |CRAN (R 4.5.2) | |lme4 |2.0-1 |2026-03-05 |CRAN (R 4.5.2) | |lubridate |1.9.5 |2026-02-04 |CRAN (R 4.5.2) | |magrittr |2.0.4 |2025-09-12 |CRAN (R 4.5.0) | |MASS |7.3-65 |2025-02-28 |CRAN (R 4.5.0) | -|Matrix |1.7-4 |2025-08-28 |CRAN (R 4.5.2) | +|Matrix |1.7-4 |2025-08-28 |CRAN (R 4.5.0) | |memoise |2.0.1 |2021-11-26 |CRAN (R 4.5.0) | |mime |0.13 |2025-03-17 |CRAN (R 4.5.0) | |minqa |1.2.8 |2024-08-17 |CRAN (R 4.5.0) | |mvtnorm |1.3-5 |2026-03-11 |CRAN (R 4.5.2) | |NHANES |2.1.0 |2015-07-02 |CRAN (R 4.5.0) | -|nlme |3.1-168 |2025-03-31 |CRAN (R 4.5.2) | +|nlme |3.1-168 |2025-03-31 |CRAN (R 4.5.0) | |nloptr |2.2.1 |2025-03-17 |CRAN (R 4.5.0) | -|nnet |7.3-20 |2025-01-01 |CRAN (R 4.5.2) | +|nnet |7.3-20 |2025-01-01 |CRAN (R 4.5.0) | |officer |0.7.3 |2026-01-16 |CRAN (R 4.5.2) | |opdisDownsampling |1.0.1 |2024-04-15 |CRAN (R 4.5.0) | |openssl |2.3.5 |2026-02-26 |CRAN (R 4.5.2) | @@ -170,14 +170,14 @@ |reformulas |0.4.4 |2026-02-02 |CRAN (R 4.5.2) | |remotes |2.5.0 |2024-03-17 |CRAN (R 4.5.0) | |rempsyc |0.2.0 |2025-09-15 |CRAN (R 4.5.0) | -|renv |1.1.7 |2026-03-05 |CRAN (R 4.5.2) | +|renv |1.1.8 |2026-03-05 |CRAN (R 4.5.2) | |reshape2 |1.4.5 |2025-11-12 |CRAN (R 4.5.0) | |rio |1.2.4 |2025-09-26 |CRAN (R 4.5.0) | |rlang |1.1.7 |2026-01-09 |CRAN (R 4.5.2) | |rmarkdown |2.30 |2025-09-28 |CRAN (R 4.5.0) | |robustbase |0.99-7 |2026-02-05 |CRAN (R 4.5.2) | |roxygen2 |7.3.3 |2025-09-03 |CRAN (R 4.5.0) | -|rpart |4.1.24 |2025-01-07 |CRAN (R 4.5.2) | +|rpart |4.1.24 |2025-01-07 |CRAN (R 4.5.0) | |rprojroot |2.1.1 |2025-08-26 |CRAN (R 4.5.0) | |rsconnect |1.7.0 |2025-12-06 |CRAN (R 4.5.2) | |rstudioapi |0.18.0 |2026-01-16 |CRAN (R 4.5.2) | @@ -217,6 +217,6 @@ |writexl |1.5.4 |2025-04-15 |CRAN (R 4.5.0) | |xfun |0.56 |2026-01-18 |CRAN (R 4.5.2) | |xml2 |1.5.2 |2026-01-17 |CRAN (R 4.5.2) | -|xtable |1.8-4 |2026-02-22 |CRAN (R 4.5.2) | +|xtable |1.8-8 |2026-02-22 |CRAN (R 4.5.2) | |yaml |2.3.12 |2025-12-10 |CRAN (R 4.5.2) | |zip |2.3.3 |2025-05-13 |CRAN (R 4.5.0) | diff --git a/app_docker/app.R b/app_docker/app.R index f50e462a..63a9e442 100644 --- a/app_docker/app.R +++ b/app_docker/app.R @@ -1,7 +1,7 @@ ######## -#### Current file: /var/folders/9l/xbc19wxx0g79jdd2sf_0v291mhwh7f/T//RtmpmhqokQ/file1a1412a8be28.R +#### Current file: /var/folders/9l/xbc19wxx0g79jdd2sf_0v291mhwh7f/T//Rtmp6ipYJe/file24f61644daa6.R ######## i18n_path <- here::here("translations") @@ -64,7 +64,7 @@ i18n$set_translation_language("en") #### Current file: /Users/au301842/FreesearchR/R//app_version.R ######## -app_version <- function()'26.3.3' +app_version <- function()'26.3.4' ######## @@ -4514,7 +4514,7 @@ data_types <- function() { #### Current file: /Users/au301842/FreesearchR/R//hosted_version.R ######## -hosted_version <- function()'v26.3.3-260312' +hosted_version <- function()'v26.3.4-260312' ######## diff --git a/app_docker/renv.lock b/app_docker/renv.lock index 11ae7b52..ca300008 100644 --- a/app_docker/renv.lock +++ b/app_docker/renv.lock @@ -3405,10 +3405,10 @@ }, "foreign": { "Package": "foreign", - "Version": "0.8-90", + "Version": "0.8-91", "Source": "Repository", "Priority": "recommended", - "Date": "2025-03-31", + "Date": "2026-01-29", "Title": "Read Data Stored by 'Minitab', 'S', 'SAS', 'SPSS', 'Stata', 'Systat', 'Weka', 'dBase', ...", "Depends": [ "R (>= 4.0.0)" @@ -3429,7 +3429,7 @@ "MailingList": "R-help@r-project.org", "URL": "https://svn.r-project.org/R-packages/trunk/foreign/", "NeedsCompilation": "yes", - "Author": "R Core Team [aut, cph, cre] (02zz1nj61), Roger Bivand [ctb, cph], Vincent J. Carey [ctb, cph], Saikat DebRoy [ctb, cph], Stephen Eglen [ctb, cph], Rajarshi Guha [ctb, cph], Swetlana Herbrandt [ctb], Nicholas Lewin-Koh [ctb, cph], Mark Myatt [ctb, cph], Michael Nelson [ctb], Ben Pfaff [ctb], Brian Quistorff [ctb], Frank Warmerdam [ctb, cph], Stephen Weigand [ctb, cph], Free Software Foundation, Inc. [cph]", + "Author": "R Core Team [aut, cph, cre] (ROR: ), Roger Bivand [ctb, cph], Vincent J. Carey [ctb, cph], Saikat DebRoy [ctb, cph], Stephen Eglen [ctb, cph], Rajarshi Guha [ctb, cph], Swetlana Herbrandt [ctb], Nicholas Lewin-Koh [ctb, cph], Mark Myatt [ctb, cph], Michael Nelson [ctb], Ben Pfaff [ctb], Brian Quistorff [ctb], Frank Warmerdam [ctb, cph], Stephen Weigand [ctb, cph], Free Software Foundation, Inc. [cph]", "Maintainer": "R Core Team ", "Repository": "CRAN" }, @@ -5462,14 +5462,14 @@ }, "mgcv": { "Package": "mgcv", - "Version": "1.9-3", + "Version": "1.9-4", "Source": "Repository", "Authors@R": "person(given = \"Simon\", family = \"Wood\", role = c(\"aut\", \"cre\"), email = \"simon.wood@r-project.org\")", "Title": "Mixed GAM Computation Vehicle with Automatic Smoothness Estimation", - "Description": "Generalized additive (mixed) models, some of their extensions and other generalized ridge regression with multiple smoothing parameter estimation by (Restricted) Marginal Likelihood, Generalized Cross Validation and similar, or using iterated nested Laplace approximation for fully Bayesian inference. See Wood (2017) for an overview. Includes a gam() function, a wide variety of smoothers, 'JAGS' support and distributions beyond the exponential family.", + "Description": "Generalized additive (mixed) models, some of their extensions and other generalized ridge regression with multiple smoothing parameter estimation by (Restricted) Marginal Likelihood, Cross Validation and similar, or using iterated nested Laplace approximation for fully Bayesian inference. See Wood (2025) for an overview. Includes a gam() function, a wide variety of smoothers, 'JAGS' support and distributions beyond the exponential family.", "Priority": "recommended", "Depends": [ - "R (>= 3.6.0)", + "R (>= 4.4.0)", "nlme (>= 3.1-64)" ], "Imports": [ diff --git a/renv.lock b/renv.lock index 11ae7b52..ca300008 100644 --- a/renv.lock +++ b/renv.lock @@ -3405,10 +3405,10 @@ }, "foreign": { "Package": "foreign", - "Version": "0.8-90", + "Version": "0.8-91", "Source": "Repository", "Priority": "recommended", - "Date": "2025-03-31", + "Date": "2026-01-29", "Title": "Read Data Stored by 'Minitab', 'S', 'SAS', 'SPSS', 'Stata', 'Systat', 'Weka', 'dBase', ...", "Depends": [ "R (>= 4.0.0)" @@ -3429,7 +3429,7 @@ "MailingList": "R-help@r-project.org", "URL": "https://svn.r-project.org/R-packages/trunk/foreign/", "NeedsCompilation": "yes", - "Author": "R Core Team [aut, cph, cre] (02zz1nj61), Roger Bivand [ctb, cph], Vincent J. Carey [ctb, cph], Saikat DebRoy [ctb, cph], Stephen Eglen [ctb, cph], Rajarshi Guha [ctb, cph], Swetlana Herbrandt [ctb], Nicholas Lewin-Koh [ctb, cph], Mark Myatt [ctb, cph], Michael Nelson [ctb], Ben Pfaff [ctb], Brian Quistorff [ctb], Frank Warmerdam [ctb, cph], Stephen Weigand [ctb, cph], Free Software Foundation, Inc. [cph]", + "Author": "R Core Team [aut, cph, cre] (ROR: ), Roger Bivand [ctb, cph], Vincent J. Carey [ctb, cph], Saikat DebRoy [ctb, cph], Stephen Eglen [ctb, cph], Rajarshi Guha [ctb, cph], Swetlana Herbrandt [ctb], Nicholas Lewin-Koh [ctb, cph], Mark Myatt [ctb, cph], Michael Nelson [ctb], Ben Pfaff [ctb], Brian Quistorff [ctb], Frank Warmerdam [ctb, cph], Stephen Weigand [ctb, cph], Free Software Foundation, Inc. [cph]", "Maintainer": "R Core Team ", "Repository": "CRAN" }, @@ -5462,14 +5462,14 @@ }, "mgcv": { "Package": "mgcv", - "Version": "1.9-3", + "Version": "1.9-4", "Source": "Repository", "Authors@R": "person(given = \"Simon\", family = \"Wood\", role = c(\"aut\", \"cre\"), email = \"simon.wood@r-project.org\")", "Title": "Mixed GAM Computation Vehicle with Automatic Smoothness Estimation", - "Description": "Generalized additive (mixed) models, some of their extensions and other generalized ridge regression with multiple smoothing parameter estimation by (Restricted) Marginal Likelihood, Generalized Cross Validation and similar, or using iterated nested Laplace approximation for fully Bayesian inference. See Wood (2017) for an overview. Includes a gam() function, a wide variety of smoothers, 'JAGS' support and distributions beyond the exponential family.", + "Description": "Generalized additive (mixed) models, some of their extensions and other generalized ridge regression with multiple smoothing parameter estimation by (Restricted) Marginal Likelihood, Cross Validation and similar, or using iterated nested Laplace approximation for fully Bayesian inference. See Wood (2025) for an overview. Includes a gam() function, a wide variety of smoothers, 'JAGS' support and distributions beyond the exponential family.", "Priority": "recommended", "Depends": [ - "R (>= 3.6.0)", + "R (>= 4.4.0)", "nlme (>= 3.1-64)" ], "Imports": [