From eae04ffca8eda947f73a56b60936d203472baccf Mon Sep 17 00:00:00 2001 From: Wenjie Wang Date: Sun, 7 Jul 2024 21:54:30 -0400 Subject: [PATCH] Resolve some warnings from GCC for CRAN --- ChangeLog | 19 +++++++++++++------ DESCRIPTION | 4 ++-- R/bayesCox.R | 2 +- R/bayesCoxMcmc.R | 2 +- R/coef.R | 2 +- R/data.R | 2 +- R/dynsurv-package.R | 9 +++++---- R/jump.R | 2 +- R/misc.R | 2 +- R/plot.R | 2 +- R/print.R | 2 +- R/reexports.R | 2 +- R/splineCox.R | 2 +- R/survCurv.R | 2 +- R/tvTran.R | 2 +- inst/CITATION | 4 ++-- man/dynsurv.Rd | 20 ++++++++++++++++++++ misc/copyright.R | 2 +- src/CoxModel.h | 2 +- src/DynamicCoxModel.h | 2 +- src/DynamicCoxModel_v2.h | 2 +- src/DynamicModel.h | 2 +- src/IntRegModel.h | 2 +- src/IntRegPrior.h | 10 +++++----- src/TimeIndepCoxModel.h | 2 +- src/TimeIndepModel.h | 2 +- src/TimeVaryingCoxModel.h | 2 +- src/TimeVaryingModel.h | 2 +- 28 files changed, 69 insertions(+), 41 deletions(-) diff --git a/ChangeLog b/ChangeLog index 614f843..a7ec86a 100644 --- a/ChangeLog +++ b/ChangeLog @@ -1,34 +1,41 @@ +2024-07-07 Wenjie Wang + + * Fixed CRAN warning: "template-id not allowed for constructor in + C++20". + + * Changed package version to 0.4-7. + 2023-11-27 Wenjie Wang * Fixed CRAN warning: "GibbsSampler.h:91:27: warning: format ‘%d’ - expects argument of type ‘int’, but argument 2 has type ‘Size’" + expects argument of type ‘int’, but argument 2 has type ‘Size’". - * Changed package version to 0.4-6 + * Changed package version to 0.4-6. 2023-08-19 Wenjie Wang * Fixed broken roxygen2 documentation. - * Changed package version to 0.4-5 + * Changed package version to 0.4-5. 2023-04-28 Wenjie Wang * Fixed CRAN warning: "a function declaration without a prototype is deprecated in all versions of C [-Wstrict-prototypes]". - * Changed package version to 0.4-4 + * Changed package version to 0.4-4. 2022-02-15 Wenjie Wang * Fixed `coef` method for `splineCox` - * Changed package version to 0.4-3 + * Changed package version to 0.4-3. 2020-09-05 Wenjie Wang * Removed checks of examples to pass CRAN checks on Soloris. - * Changed package version to 0.4-2 + * Changed package version to 0.4-2. 2020-08-23 Wenjie Wang diff --git a/DESCRIPTION b/DESCRIPTION index 6fdbba7..373bf0b 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: dynsurv Title: Dynamic Models for Survival Data -Version: 0.4-6 +Version: 0.4-7 Authors@R: c( person(given = "Wenjie", family = "Wang", email = "wang@wwenjie.org", @@ -41,4 +41,4 @@ NeedsCompilation: yes Encoding: UTF-8 URL: https://github.com/wenjie2wang/dynsurv BugReports: https://github.com/wenjie2wang/dynsurv/issues -RoxygenNote: 7.2.3 +RoxygenNote: 7.3.2 diff --git a/R/bayesCox.R b/R/bayesCox.R index 35668bb..4a9ed4c 100644 --- a/R/bayesCox.R +++ b/R/bayesCox.R @@ -1,6 +1,6 @@ ## ## R package dynsurv by Wenjie Wang, Ming-Hui Chen, Xiaojing Wang, and Jun Yan -## Copyright (C) 2011-2023 +## Copyright (C) 2011-2024 ## ## This file is part of the R package dynsurv. ## diff --git a/R/bayesCoxMcmc.R b/R/bayesCoxMcmc.R index a2677d2..fb98fb2 100644 --- a/R/bayesCoxMcmc.R +++ b/R/bayesCoxMcmc.R @@ -1,6 +1,6 @@ ## ## R package dynsurv by Wenjie Wang, Ming-Hui Chen, Xiaojing Wang, and Jun Yan -## Copyright (C) 2011-2023 +## Copyright (C) 2011-2024 ## ## This file is part of the R package dynsurv. ## diff --git a/R/coef.R b/R/coef.R index ca7bc0d..9a84e69 100644 --- a/R/coef.R +++ b/R/coef.R @@ -1,6 +1,6 @@ ## ## R package dynsurv by Wenjie Wang, Ming-Hui Chen, Xiaojing Wang, and Jun Yan -## Copyright (C) 2011-2023 +## Copyright (C) 2011-2024 ## ## This file is part of the R package dynsurv. ## diff --git a/R/data.R b/R/data.R index 2bed015..1dbe6ec 100644 --- a/R/data.R +++ b/R/data.R @@ -1,6 +1,6 @@ ## ## R package dynsurv by Wenjie Wang, Ming-Hui Chen, Xiaojing Wang, and Jun Yan -## Copyright (C) 2011-2023 +## Copyright (C) 2011-2024 ## ## This file is part of the R package dynsurv. ## diff --git a/R/dynsurv-package.R b/R/dynsurv-package.R index e494db4..9dd9926 100644 --- a/R/dynsurv-package.R +++ b/R/dynsurv-package.R @@ -1,6 +1,6 @@ ## ## R package dynsurv by Wenjie Wang, Ming-Hui Chen, Xiaojing Wang, and Jun Yan -## Copyright (C) 2011-2023 +## Copyright (C) 2011-2024 ## ## This file is part of the R package dynsurv. ## @@ -29,8 +29,9 @@ ##' data using estimating equations. ##' } ##' -##' @docType package +##' @useDynLib dynsurv +##' ##' @name dynsurv ##' @aliases dynsurv-package -##' @useDynLib dynsurv -NULL +##' @keywords internal +"_PACKAGE" diff --git a/R/jump.R b/R/jump.R index a6107ed..eddda56 100644 --- a/R/jump.R +++ b/R/jump.R @@ -1,6 +1,6 @@ ## ## R package dynsurv by Wenjie Wang, Ming-Hui Chen, Xiaojing Wang, and Jun Yan -## Copyright (C) 2011-2023 +## Copyright (C) 2011-2024 ## ## This file is part of the R package dynsurv. ## diff --git a/R/misc.R b/R/misc.R index d771961..98acb59 100644 --- a/R/misc.R +++ b/R/misc.R @@ -1,6 +1,6 @@ ## ## R package dynsurv by Wenjie Wang, Ming-Hui Chen, Xiaojing Wang, and Jun Yan -## Copyright (C) 2011-2023 +## Copyright (C) 2011-2024 ## ## This file is part of the R package dynsurv. ## diff --git a/R/plot.R b/R/plot.R index 7f23efa..2eaa8fc 100644 --- a/R/plot.R +++ b/R/plot.R @@ -1,6 +1,6 @@ ## ## R package dynsurv by Wenjie Wang, Ming-Hui Chen, Xiaojing Wang, and Jun Yan -## Copyright (C) 2011-2023 +## Copyright (C) 2011-2024 ## ## This file is part of the R package dynsurv. ## diff --git a/R/print.R b/R/print.R index 35d10b7..72db0af 100644 --- a/R/print.R +++ b/R/print.R @@ -1,6 +1,6 @@ ## ## R package dynsurv by Wenjie Wang, Ming-Hui Chen, Xiaojing Wang, and Jun Yan -## Copyright (C) 2011-2023 +## Copyright (C) 2011-2024 ## ## This file is part of the R package dynsurv. ## diff --git a/R/reexports.R b/R/reexports.R index bb7f93b..0e74f35 100644 --- a/R/reexports.R +++ b/R/reexports.R @@ -1,6 +1,6 @@ ## ## R package dynsurv by Wenjie Wang, Ming-Hui Chen, Xiaojing Wang, and Jun Yan -## Copyright (C) 2011-2023 +## Copyright (C) 2011-2024 ## ## This file is part of the R package dynsurv. ## diff --git a/R/splineCox.R b/R/splineCox.R index 6e66e78..b619280 100644 --- a/R/splineCox.R +++ b/R/splineCox.R @@ -1,6 +1,6 @@ ## ## R package dynsurv by Wenjie Wang, Ming-Hui Chen, Xiaojing Wang, and Jun Yan -## Copyright (C) 2011-2023 +## Copyright (C) 2011-2024 ## ## This file is part of the R package dynsurv. ## diff --git a/R/survCurv.R b/R/survCurv.R index 8840987..c6076e7 100644 --- a/R/survCurv.R +++ b/R/survCurv.R @@ -1,6 +1,6 @@ ## ## R package dynsurv by Wenjie Wang, Ming-Hui Chen, Xiaojing Wang, and Jun Yan -## Copyright (C) 2011-2023 +## Copyright (C) 2011-2024 ## ## This file is part of the R package dynsurv. ## diff --git a/R/tvTran.R b/R/tvTran.R index 2fb6890..90a6124 100644 --- a/R/tvTran.R +++ b/R/tvTran.R @@ -1,6 +1,6 @@ ## ## R package dynsurv by Wenjie Wang, Ming-Hui Chen, Xiaojing Wang, and Jun Yan -## Copyright (C) 2011-2023 +## Copyright (C) 2011-2024 ## ## This file is part of the R package dynsurv. ## diff --git a/inst/CITATION b/inst/CITATION index 5c54435..a90dc4a 100644 --- a/inst/CITATION +++ b/inst/CITATION @@ -6,7 +6,7 @@ bibentry( as.person("Ming-Hui Chen"), as.person("Xiaojing Wang"), as.person("Jun Yan")), - year = "2023", + year = "2024", url = "https://CRAN.R-project.org/package=dynsurv", - note = "{R} package version 0.4-6" + note = "{R} package version 0.4-7" ) diff --git a/man/dynsurv.Rd b/man/dynsurv.Rd index db5730f..718cf9c 100644 --- a/man/dynsurv.Rd +++ b/man/dynsurv.Rd @@ -17,3 +17,23 @@ right censored survival data. Three major approaches are implemented: data using estimating equations. } } +\seealso{ +Useful links: +\itemize{ + \item \url{https://github.com/wenjie2wang/dynsurv} + \item Report bugs at \url{https://github.com/wenjie2wang/dynsurv/issues} +} + +} +\author{ +\strong{Maintainer}: Wenjie Wang \email{wang@wwenjie.org} (\href{https://orcid.org/0000-0003-0363-3180}{ORCID}) + +Authors: +\itemize{ + \item Ming-Hui Chen + \item Xiaojing Wang + \item Jun Yan (\href{https://orcid.org/0000-0003-4401-7296}{ORCID}) +} + +} +\keyword{internal} diff --git a/misc/copyright.R b/misc/copyright.R index 744135e..0337d49 100644 --- a/misc/copyright.R +++ b/misc/copyright.R @@ -1,6 +1,6 @@ ## ## R package dynsurv by Wenjie Wang, Ming-Hui Chen, Xiaojing Wang, and Jun Yan -## Copyright (C) 2011-2023 +## Copyright (C) 2011-2024 ## ## This file is part of the R package dynsurv. ## diff --git a/src/CoxModel.h b/src/CoxModel.h index 6d901e6..701fb31 100644 --- a/src/CoxModel.h +++ b/src/CoxModel.h @@ -23,7 +23,7 @@ namespace ir { class CoxModel: virtual public IntRegModel { public : - CoxModel(const boost::shared_ptr& pd) + CoxModel(const boost::shared_ptr& pd) : IntRegModel(pd) {} typedef typename Prior::BasePrior_type BasePrior_type; diff --git a/src/DynamicCoxModel.h b/src/DynamicCoxModel.h index b60f7e8..5a564ff 100644 --- a/src/DynamicCoxModel.h +++ b/src/DynamicCoxModel.h @@ -27,7 +27,7 @@ class DynamicCoxModel: public CoxModel { public : - DynamicCoxModel(const boost::shared_ptr& pd) + DynamicCoxModel(const boost::shared_ptr& pd) : IntRegModel(pd), DynamicModel(pd), CoxModel(pd) {} diff --git a/src/DynamicCoxModel_v2.h b/src/DynamicCoxModel_v2.h index 10dd564..c6945df 100644 --- a/src/DynamicCoxModel_v2.h +++ b/src/DynamicCoxModel_v2.h @@ -23,7 +23,7 @@ class DynamicCoxModel_v2: public DynamicCoxModel { public : - DynamicCoxModel_v2(const boost::shared_ptr& pd) + DynamicCoxModel_v2(const boost::shared_ptr& pd) : IntRegModel(pd), DynamicCoxModel(pd) {} diff --git a/src/DynamicModel.h b/src/DynamicModel.h index 77dfd5d..0b296bb 100644 --- a/src/DynamicModel.h +++ b/src/DynamicModel.h @@ -25,7 +25,7 @@ namespace ir { { public : /* Class constructor */ - DynamicModel(const boost::shared_ptr& pd) + DynamicModel(const boost::shared_ptr& pd) : IntRegModel(pd), a0_ (100.0), prob_(2, 0.35), diff --git a/src/IntRegModel.h b/src/IntRegModel.h index 7160cf5..d15b850 100644 --- a/src/IntRegModel.h +++ b/src/IntRegModel.h @@ -25,7 +25,7 @@ template class IntRegModel { public: - IntRegModel(const boost::shared_ptr& pd); + IntRegModel(const boost::shared_ptr& pd); //~IntRegModel() {}; diff --git a/src/IntRegPrior.h b/src/IntRegPrior.h index e7493eb..f434bd0 100644 --- a/src/IntRegPrior.h +++ b/src/IntRegPrior.h @@ -143,8 +143,8 @@ namespace ir { template struct CoxPrior { - CoxPrior(const BasePrior& bp, - const CoefPrior& cp) + CoxPrior(const BasePrior& bp, + const CoefPrior& cp) : base_prior(bp), coef_prior(cp) {} @@ -158,9 +158,9 @@ struct CoxPrior template struct GORHPrior { - GORHPrior(const BasePrior& bp, - const CoefPrior& cp, - const ThetaPrior& tp) + GORHPrior(const BasePrior& bp, + const CoefPrior& cp, + const ThetaPrior& tp) : base_prior(bp), coef_prior(cp), theta_prior(tp) {} diff --git a/src/TimeIndepCoxModel.h b/src/TimeIndepCoxModel.h index 47880c8..2e28bff 100644 --- a/src/TimeIndepCoxModel.h +++ b/src/TimeIndepCoxModel.h @@ -27,7 +27,7 @@ class TimeIndepCoxModel: public CoxModel { public : - TimeIndepCoxModel(const boost::shared_ptr& pd) + TimeIndepCoxModel(const boost::shared_ptr& pd) : IntRegModel(pd), TimeIndepModel(pd), CoxModel(pd) {} diff --git a/src/TimeIndepModel.h b/src/TimeIndepModel.h index 48e42ee..616a7cc 100644 --- a/src/TimeIndepModel.h +++ b/src/TimeIndepModel.h @@ -23,7 +23,7 @@ template class TimeIndepModel: virtual public IntRegModel { public : - TimeIndepModel(const boost::shared_ptr& pd) + TimeIndepModel(const boost::shared_ptr& pd) : IntRegModel(pd) {} protected : diff --git a/src/TimeVaryingCoxModel.h b/src/TimeVaryingCoxModel.h index d90a6f2..8582204 100644 --- a/src/TimeVaryingCoxModel.h +++ b/src/TimeVaryingCoxModel.h @@ -27,7 +27,7 @@ class TimeVaryingCoxModel: public CoxModel { public : - TimeVaryingCoxModel(const boost::shared_ptr& pd) + TimeVaryingCoxModel(const boost::shared_ptr& pd) : IntRegModel(pd), TimeVaryingModel(pd), CoxModel(pd) {} diff --git a/src/TimeVaryingModel.h b/src/TimeVaryingModel.h index 02de046..5d15bf2 100644 --- a/src/TimeVaryingModel.h +++ b/src/TimeVaryingModel.h @@ -24,7 +24,7 @@ template class TimeVaryingModel: virtual public IntRegModel { public : - TimeVaryingModel(const boost::shared_ptr& pd) + TimeVaryingModel(const boost::shared_ptr& pd) : IntRegModel(pd), a0_(100.0) {}