fix winbuilder notes

sahirbhatnagar · Feb 1, 2024 · 7d788b4 · 7d788b4
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -2,7 +2,7 @@ Package: casebase
 Type: Package
 Title: Fitting Flexible Smooth-in-Time Hazards and Risk Functions via Logistic and Multinomial Regression
 Version: 0.10.4
-Date: 2022-11-09
+Date: 2024-02-01
 Authors@R: 
     c(person(given = "Sahir",
              family = "Bhatnagar",

diff --git a/README.Rmd b/README.Rmd
@@ -18,7 +18,7 @@ knitr::opts_chunk$set(
 # casebase
 
 <!-- badges: start -->
-[![Coverage Status](https://img.shields.io/codecov/c/github/sahirbhatnagar/casebase/master.svg)](https://codecov.io/github/sahirbhatnagar/casebase?branch=master) [![CRAN](https://www.r-pkg.org/badges/version/casebase?color=blue)](https://cran.r-project.org/package=casebase) [![Downloads](https://cranlogs.r-pkg.org/badges/grand-total/casebase?color=green)](https://www.r-pkg.org/pkg/casebase)
+[![Coverage Status](https://img.shields.io/codecov/c/github/sahirbhatnagar/casebase/master.svg)](https://app.codecov.io/github/sahirbhatnagar/casebase?branch=master) [![CRAN](https://www.r-pkg.org/badges/version/casebase?color=blue)](https://cran.r-project.org/package=casebase) [![Downloads](https://cranlogs.r-pkg.org/badges/grand-total/casebase?color=green)](https://www.r-pkg.org/pkg/casebase)
 [![Lifecycle: maturing](https://img.shields.io/badge/lifecycle-maturing-blue.svg)](https://lifecycle.r-lib.org/articles/stages.html)
 [![R-CMD-check](https://github.com/sahirbhatnagar/casebase/workflows/R-CMD-check/badge.svg)](https://github.com/sahirbhatnagar/casebase/actions)
 [![Codecov test coverage](https://codecov.io/gh/sahirbhatnagar/casebase/branch/master/graph/badge.svg)](https://app.codecov.io/gh/sahirbhatnagar/casebase?branch=master)
@@ -62,7 +62,7 @@ See the [package website](http://sahirbhatnagar.com/casebase/) for example usage
 
 ## Quickstart
 
-This is a basic example which shows you some of the main functionalities of the `casebase` package. We use data from the estrogen plus progestin trial from the [Women's Health Initiative](https://www.doi.org/10.1056/nejmoa030808) (included in the `casebase` package). This randomized clinical trial investigated the effect of estrogen plus progestin (`estPro`) on coronary heart disease (CHD) risk in 16,608 postmenopausal women who were 50 to 79 years of age at base line. Participants were randomly assigned to receive `estPro` or `placebo`. The primary efficacy outcome of the trial was CHD (nonfatal myocardial infarction or death due to CHD).  
+This is a basic example which shows you some of the main functionalities of the `casebase` package. We use data from the estrogen plus progestin trial from the [Women's Health Initiative](https://www.nejm.org/doi/full/10.1056/NEJMoa030808) (included in the `casebase` package). This randomized clinical trial investigated the effect of estrogen plus progestin (`estPro`) on coronary heart disease (CHD) risk in 16,608 postmenopausal women who were 50 to 79 years of age at base line. Participants were randomly assigned to receive `estPro` or `placebo`. The primary efficacy outcome of the trial was CHD (nonfatal myocardial infarction or death due to CHD).  
 
 ```{r example}
 library(casebase)

diff --git a/README.md b/README.md
@@ -6,7 +6,7 @@
 <!-- badges: start -->
 
 [![Coverage
-Status](https://img.shields.io/codecov/c/github/sahirbhatnagar/casebase/master.svg)](https://codecov.io/github/sahirbhatnagar/casebase?branch=master)
+Status](https://img.shields.io/codecov/c/github/sahirbhatnagar/casebase/master.svg)](https://app.codecov.io/github/sahirbhatnagar/casebase?branch=master)
 [![CRAN](https://www.r-pkg.org/badges/version/casebase?color=blue)](https://cran.r-project.org/package=casebase)
 [![Downloads](https://cranlogs.r-pkg.org/badges/grand-total/casebase?color=green)](https://www.r-pkg.org/pkg/casebase)
 [![Lifecycle:
@@ -72,13 +72,14 @@ useR](man/figures/jesse-user.png)](https://www.youtube.com/watch?v=DlppjRYVklQ)
 This is a basic example which shows you some of the main functionalities
 of the `casebase` package. We use data from the estrogen plus progestin
 trial from the [Women’s Health
-Initiative](https://www.doi.org/10.1056/nejmoa030808) (included in the
-`casebase` package). This randomized clinical trial investigated the
-effect of estrogen plus progestin (`estPro`) on coronary heart disease
-(CHD) risk in 16,608 postmenopausal women who were 50 to 79 years of age
-at base line. Participants were randomly assigned to receive `estPro` or
-`placebo`. The primary efficacy outcome of the trial was CHD (nonfatal
-myocardial infarction or death due to CHD).
+Initiative](https://www.nejm.org/doi/full/10.1056/NEJMoa030808)
+(included in the `casebase` package). This randomized clinical trial
+investigated the effect of estrogen plus progestin (`estPro`) on
+coronary heart disease (CHD) risk in 16,608 postmenopausal women who
+were 50 to 79 years of age at base line. Participants were randomly
+assigned to receive `estPro` or `placebo`. The primary efficacy outcome
+of the trial was CHD (nonfatal myocardial infarction or death due to
+CHD).
 
 ``` r
 library(casebase)
@@ -125,28 +126,24 @@ summary(fit)
 #> fitSmoothHazard(formula = status ~ treatment * ns(time, df = 3), 
 #>     data = eprchd, time = "time")
 #> 
-#> Deviance Residuals: 
-#>     Min       1Q   Median       3Q      Max  
-#> -0.2344  -0.1483  -0.1380  -0.1267   3.1466  
-#> 
 #> Coefficients:
 #>                                   Estimate Std. Error z value Pr(>|z|)    
-#> (Intercept)                       -5.80408    0.30090 -19.289  < 2e-16 ***
-#> treatmentestPro                    0.59882    0.37743   1.587 0.112608    
-#> ns(time, df = 3)1                 -0.36224    0.35878  -1.010 0.312654    
-#> ns(time, df = 3)2                  0.58913    0.73465   0.802 0.422601    
-#> ns(time, df = 3)3                  1.26391    0.34033   3.714 0.000204 ***
-#> treatmentestPro:ns(time, df = 3)1  0.05593    0.48546   0.115 0.908274    
-#> treatmentestPro:ns(time, df = 3)2 -1.19576    0.94034  -1.272 0.203506    
-#> treatmentestPro:ns(time, df = 3)3 -0.97627    0.48228  -2.024 0.042942 *  
+#> (Intercept)                       -5.86338    0.29756 -19.705  < 2e-16 ***
+#> treatmentestPro                    0.65749    0.37542   1.751   0.0799 .  
+#> ns(time, df = 3)1                 -0.41771    0.36175  -1.155   0.2482    
+#> ns(time, df = 3)2                  0.80356    0.72806   1.104   0.2697    
+#> ns(time, df = 3)3                  1.37487    0.34356   4.002 6.29e-05 ***
+#> treatmentestPro:ns(time, df = 3)1  0.06151    0.48825   0.126   0.8997    
+#> treatmentestPro:ns(time, df = 3)2 -1.40446    0.93844  -1.497   0.1345    
+#> treatmentestPro:ns(time, df = 3)3 -1.10495    0.48794  -2.265   0.0235 *  
 #> ---
 #> Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
 #> 
 #> (Dispersion parameter for binomial family taken to be 1)
 #> 
 #>     Null deviance: 3635.4  on 32723  degrees of freedom
-#> Residual deviance: 3615.2  on 32716  degrees of freedom
-#> AIC: 3631.2
+#> Residual deviance: 3614.1  on 32716  degrees of freedom
+#> AIC: 3630.1
 #> 
 #> Number of Fisher Scoring iterations: 7
 ```
@@ -250,13 +247,11 @@ Other packages with similar objectives but different parametric forms:
 
 ``` r
 citation('casebase')
-#> 
 #> To cite casebase in publications use:
 #> 
-#>   Bhatnagar S, Turgeon M, Islam J, Saarela O, Hanley J (2020).
-#>   _casebase: Fitting Flexible Smooth-in-Time Hazards and Risk Functions
-#>   via Logistic and Multinomial Regression_. R package version 0.9.0,
-#>   <https://CRAN.R-project.org/package=casebase>.
+#>   Bhatnagar S, Turgeon M, Islam J, Saarela O, Hanley J (2022).
+#>   "casebase: An Alternative Framework for Survival Analysis and
+#>   Comparison of Event Rates." _The R Journal_, *14*(3).
 #> 
 #>   Hanley, James A., and Olli S. Miettinen. Fitting smooth-in-time
 #>   prognostic risk functions via logistic regression. International

diff --git a/cran-comments.md b/cran-comments.md
@@ -1,13 +1,14 @@
-## Resubmission
+## R CMD check results
 
-This is a resubmission. We corrected the maintainer email address, updated the data field in the DESCRIPTION file, and fixed a broken URL in our vignette.
+There were no ERRORs or WARNINGs
 
 ## Test environments
 
-* local macOS 13.0, R 4.2.1
-* ubuntu 20.04 (on GH-Actions), R-release, R-devel, R-oldrelease
+* local macOS 14.3, R 4.3.2
+* ubuntu 22.04 (on GH-Actions), R-release, R-devel, R-oldrelease
 * Windows Server 2022 x64 (on GH-Actions), R-release
-* macOS 11.7 (on GH-Actions), R-release
+* macOS 12.7 (on GH-Actions), R-release
+* Win-builder, R-devel
 
 ## R CMD check results
 

diff --git a/inst/CITATION b/inst/CITATION
@@ -21,52 +21,47 @@ bibentry(
      year = "2022",
    )
 
-citEntry(entry = "Article",
+bibentry(bibtype = "Article",
   title        = "Fitting smooth-in-time prognostic risk functions via logistic regression",
-  author       = personList(as.person("James A Hanley"),
-                    as.person("Olli S Miettinen")),
+  author       = c(as.person("James A Hanley"),
+                   as.person("Olli S Miettinen")),
   journal      = "International Journal of Biostatistics",
   volume       = "5",
   number       = "1",
   pages        = "1125--1125",
   year         = "2009",
   publisher    = "Berkeley Electronic Press",
-
   textVersion  =
   paste("Hanley, James A., and Olli S. Miettinen.",
         "Fitting smooth-in-time prognostic risk functions via logistic regression.",
         "International Journal of Biostatistics 5.1 (2009): 1125-1125.")
 )
 
-citEntry(entry = "Article",
+bibentry(bibtype = "Article",
   title        = "A case-base sampling method for estimating recurrent event intensities",
-  author       = personList(as.person("Olli Saarela")),
+  author       = c(as.person("Olli Saarela")),
   journal      = "Lifetime data analysis",
   volume       = "22",
   number       = "4",
   pages        = "589--605",
   year         = "2016",
   publisher    = "Springer",
-
   textVersion  =
   paste("Saarela, Olli.",
         "A case-base sampling method for estimating recurrent event intensities.",
         "Lifetime data analysis 22.4 (2016): 589-605.")
 )
 
-
-
-citEntry(entry = "Article",
+bibentry(bibtype = "Article",
   title        = "Non-parametric Bayesian Hazard Regression for Chronic Disease Risk Assessment",
-  author       = personList(as.person("Olli Saarela"),
+  author       = c(as.person("Olli Saarela"),
                    as.person("Elja Arjas")),
   journal      = "Scandinavian Journal of Statistics",
   year         = "2015",
   volume       = "42",
   number       = "2",
   pages        = "609--626",
   publisher    = "Wiley Online Library",
-
   textVersion  =
   paste("Saarela, Olli, and Elja Arjas.",
         "Non-parametric Bayesian Hazard Regression for Chronic Disease Risk Assessment.",

diff --git a/man/figures/README-plot-mason-1.png b/man/figures/README-plot-mason-1.png
diff --git a/man/figures/README-unnamed-chunk-2-1.png b/man/figures/README-unnamed-chunk-2-1.png
diff --git a/man/figures/README-unnamed-chunk-3-1.png b/man/figures/README-unnamed-chunk-3-1.png
diff --git a/man/figures/README-unnamed-chunk-4-1.png b/man/figures/README-unnamed-chunk-4-1.png
diff --git a/revdep/README.md b/revdep/README.md
@@ -1,25 +1,31 @@
 # Platform
 
-|field    |value                                     |
-|:--------|:-----------------------------------------|
-|version  |R version 4.2.1 (2022-06-23)              |
-|os       |macOS Ventura 13.0                        |
-|system   |aarch64, darwin20                         |
-|ui       |RStudio                                   |
-|language |(EN)                                      |
-|collate  |en_CA.UTF-8                               |
-|ctype    |en_CA.UTF-8                               |
-|tz       |America/Edmonton                          |
-|date     |2022-11-08                                |
-|rstudio  |2022.07.1+554 Spotted Wakerobin (desktop) |
-|pandoc   |2.19 @ /opt/homebrew/bin/pandoc           |
+|field    |value                               |
+|:--------|:-----------------------------------|
+|version  |R version 4.3.2 (2023-10-31)        |
+|os       |macOS Sonoma 14.3                   |
+|system   |aarch64, darwin20                   |
+|ui       |RStudio                             |
+|language |(EN)                                |
+|collate  |en_US.UTF-8                         |
+|ctype    |en_US.UTF-8                         |
+|tz       |America/Toronto                     |
+|date     |2024-02-01                          |
+|rstudio  |2023.12.0+369 Ocean Storm (desktop) |
+|pandoc   |2.19 @ /opt/homebrew/bin/pandoc     |
 
 # Dependencies
 
-|package  |old    |new    |Δ  |
-|:--------|:------|:------|:--|
-|casebase |0.10.1 |0.10.2 |*  |
-|ggplot2  |NA     |3.4.0  |*  |
+|package    |old    |new    |Δ  |
+|:----------|:------|:------|:--|
+|casebase   |0.10.3 |0.10.4 |*  |
+|data.table |NA     |1.15.0 |*  |
 
 # Revdeps
 
+## Failed to check (1)
+
+|package        |version    |error |warning |note |
+|:--------------|:----------|:-----|:-------|:----|
+|riskRegression |2023.12.21 |1     |        |     |
+
diff --git a/revdep/cran.md b/revdep/cran.md
@@ -3,5 +3,10 @@
 We checked 1 reverse dependencies, comparing R CMD check results across CRAN and dev versions of this package.
 
  * We saw 0 new problems
- * We failed to check 0 packages
+ * We failed to check 1 packages
 
+Issues with CRAN packages are summarised below.
+
+### Failed to check
+
+* riskRegression (NA)
diff --git a/revdep/data.sqlite b/revdep/data.sqlite
diff --git a/revdep/failures.md b/revdep/failures.md
@@ -1 +1,78 @@
-*Wow, no problems at all. :)*
+# riskRegression
+
+<details>
+
+* Version: 2023.12.21
+* GitHub: https://github.com/tagteam/riskRegression
+* Source code: https://github.com/cran/riskRegression
+* Date/Publication: 2023-12-19 17:00:02 UTC
+* Number of recursive dependencies: 188
+
+Run `revdepcheck::revdep_details(, "riskRegression")` for more info
+
+</details>
+
+## In both
+
+*   checking whether package ‘riskRegression’ can be installed ... ERROR
+    ```
+    Installation failed.
+    See ‘/Users/maxturgeon/git_repos/casebase/revdep/checks.noindex/riskRegression/new/riskRegression.Rcheck/00install.out’ for details.
+    ```
+
+## Installation
+
+### Devel
+
+```
+* installing *source* package ‘riskRegression’ ...
+** package ‘riskRegression’ successfully unpacked and MD5 sums checked
+** using staged installation
+** libs
+using C++ compiler: ‘Homebrew clang version 14.0.6’
+using SDK: ‘MacOSX14.2.sdk’
+/opt/homebrew/opt/llvm/bin/clang++ -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Users/maxturgeon/git_repos/casebase/revdep/library.noindex/riskRegression/Rcpp/include' -I'/Users/maxturgeon/git_repos/casebase/revdep/library.noindex/riskRegression/RcppArmadillo/include' -I/opt/homebrew/opt/gettext/include -I/opt/homebrew/opt/llvm/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include    -fPIC  -g -O3 -Wall -pedantic -std=c++11 -mtune=native -pipe -c IC-Nelson-Aalen-cens-time.cpp -o IC-Nelson-Aalen-cens-time.o
+In file included from IC-Nelson-Aalen-cens-time.cpp:2:
+In file included from ./IC-Nelson-Aalen-cens-time.h:1:
+In file included from /Users/maxturgeon/git_repos/casebase/revdep/library.noindex/riskRegression/RcppArmadillo/include/RcppArmadillo.h:29:
+...
+        return complex<_Tp>(abs(__x.real()), __x.imag());
+                            ^
+/opt/homebrew/opt/llvm/bin/../include/c++/v1/cmath:338:1: note: using declaration annotated with 'using_if_exists' here
+using ::abs _LIBCPP_USING_IF_EXISTS;
+^
+fatal error: too many errors emitted, stopping now [-ferror-limit=]
+20 errors generated.
+make: *** [IC-Nelson-Aalen-cens-time.o] Error 1
+ERROR: compilation failed for package ‘riskRegression’
+* removing ‘/Users/maxturgeon/git_repos/casebase/revdep/checks.noindex/riskRegression/new/riskRegression.Rcheck/riskRegression’
+
+
+```
+### CRAN
+
+```
+* installing *source* package ‘riskRegression’ ...
+** package ‘riskRegression’ successfully unpacked and MD5 sums checked
+** using staged installation
+** libs
+using C++ compiler: ‘Homebrew clang version 14.0.6’
+using SDK: ‘MacOSX14.2.sdk’
+/opt/homebrew/opt/llvm/bin/clang++ -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Users/maxturgeon/git_repos/casebase/revdep/library.noindex/riskRegression/Rcpp/include' -I'/Users/maxturgeon/git_repos/casebase/revdep/library.noindex/riskRegression/RcppArmadillo/include' -I/opt/homebrew/opt/gettext/include -I/opt/homebrew/opt/llvm/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include    -fPIC  -g -O3 -Wall -pedantic -std=c++11 -mtune=native -pipe -c IC-Nelson-Aalen-cens-time.cpp -o IC-Nelson-Aalen-cens-time.o
+In file included from IC-Nelson-Aalen-cens-time.cpp:2:
+In file included from ./IC-Nelson-Aalen-cens-time.h:1:
+In file included from /Users/maxturgeon/git_repos/casebase/revdep/library.noindex/riskRegression/RcppArmadillo/include/RcppArmadillo.h:29:
+...
+        return complex<_Tp>(abs(__x.real()), __x.imag());
+                            ^
+/opt/homebrew/opt/llvm/bin/../include/c++/v1/cmath:338:1: note: using declaration annotated with 'using_if_exists' here
+using ::abs _LIBCPP_USING_IF_EXISTS;
+^
+fatal error: too many errors emitted, stopping now [-ferror-limit=]
+20 errors generated.
+make: *** [IC-Nelson-Aalen-cens-time.o] Error 1
+ERROR: compilation failed for package ‘riskRegression’
+* removing ‘/Users/maxturgeon/git_repos/casebase/revdep/checks.noindex/riskRegression/old/riskRegression.Rcheck/riskRegression’
+
+
+```