prepare for new release to fix CRAN errors

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: Cyclops
 Type: Package
 Title: Cyclic Coordinate Descent for Logistic, Poisson and Survival Analysis
-Version: 3.3.1.99
+Version: 3.3.1.999
 Authors@R: c(
     person("Marc A.", "Suchard", email = "[email protected]", role = c("aut","cre")),
     person("Martijn J.", "Schuemie", role = "aut"),
@@ -30,7 +30,7 @@ Biarch: true
 URL: https://github.com/ohdsi/cyclops
 BugReports: https://github.com/ohdsi/cyclops/issues
 Depends:
-    R (>= 3.1.0)
+    R (>= 3.5.0)
 Imports:
     rlang,
     Matrix,

NEWS.md

@@ -1,19 +1,22 @@
-develop
+Cyclops v3.4.0
 ==============
 
 Changes:
 
-1. improvements on adaptive likelihood profiling
-2. add `auto` option to `cvRepetitions`
-3. bumped explicit C++11 requirement up to R v4.1
+1. remove dependence on `BH`
+2. improvements on adaptive likelihood profiling
+3. add `auto` option to `cvRepetitions`
+4. bumped explicit C++11 requirement up to R v4.1
+5. removed deprecated use of `dbplyr:::$.tbl_lazy`
+   a. breaking change in `dbplyr v2.4.0`
 
 Cyclops v3.3.1
 ==============
 
 Changes:
 
-1. fix uninitialized value in detected in computeAsymptoticPrecisionMatrix(); value was priorType
-2. fix memory leak caused by call to ::Rf_error()
+1. fix uninitialized value in detected in `computeAsymptoticPrecisionMatrix()`; value was priorType
+2. fix memory leak caused by call to `::Rf_error()`
 3. fix line-endings on Makevar on windows
 
 Cyclops v3.3.0

R/DataManagement.R

@@ -634,8 +634,8 @@ reduce <- function(object, covariates, groupBy, power = 1) {
 #' \code{appendSqlCyclopsData} appends data to an OHDSI data object.
 #'
 #' @details Append data using two tables.  The outcomes table is dense and contains ...  The covariates table is sparse and contains ...
-#' All entries in the outcome table must be sorted in increasing order by {oStratumId, oRowId}.  All entries in the covariate table
-#' must be sorted in increasing order by {cRowId}. Each cRowId value must match exactly one oRowId value.
+#' All entries in the outcome table must be sorted in increasing order by (oStratumId, oRowId).  All entries in the covariate table
+#' must be sorted in increasing order by (cRowId). Each cRowId value must match exactly one oRowId value.
 #'
 #' @param object    OHDSI Cyclops data object to append entries
 #' @param oStratumId    Integer vector (optional): non-unique stratum identifier for each row in outcomes table

R/NewDataConversion.R

@@ -253,7 +253,7 @@ convertToCyclopsData.tbl_dbi <- function(outcomes,
     }
 
     if (modelType == "pr" | modelType == "cpr") {
-        if (any(outcomes$time <= 0)) {
+        if (any(pull(outcomes, .data$time) <= 0)) {
             stop("time cannot be non-positive", call. = FALSE)
         }
     }

R/TimeEffects.R

@@ -22,8 +22,8 @@ splitTime <- function(shortOut, cut) {
     if (!"y" %in% colnames(shortOut)) stop("Must provide observed event status.")
     if ("rowId" %in% colnames(shortOut)) {
         shortOut <- shortOut %>%
-            rename(subjectId = rowId) %>%
-            arrange(subjectId)
+            rename(subjectId = .data$rowId) %>%
+            arrange(.data$subjectId)
     } else {
         shortOut <- shortOut %>%
             mutate(subjectId = row_number())
@@ -36,10 +36,10 @@ splitTime <- function(shortOut, cut) {
                                          episode = "stratumId",
                                          id = "newSubjectId"))
     longOut <- longOut %>%
-        rename(y = event) %>%
-        mutate(time = tstop - tstart) %>%
-        select(-c(newSubjectId, tstart, tstop)) %>%
-        arrange(stratumId, subjectId)
+        rename(y = .data$event) %>%
+        mutate(time = .data$tstop - .data$tstart) %>%
+        select(-c(.data$newSubjectId, .data$tstart, .data$tstop)) %>%
+        arrange(.data$stratumId, .data$subjectId)
 
     # Restore rowIds
     SubjectIds <- shortOut$subjectId
@@ -49,9 +49,10 @@ splitTime <- function(shortOut, cut) {
 
     # Reorder columns
     longOut <- longOut %>%
-        select(rowId, everything()) %>%
-        select(subjectId, everything()) %>%
-        select(stratumId, everything())
+        select(.data$stratumId, .data$subjectId, .data$rowId, everything())
+        # select(.data$rowId, everything()) %>%
+        # select(.data$subjectId, everything()) %>%
+        # select(.data$stratumId, everything())
 
     return(longOut)
 }

src/cyclops/Iterators.h

@@ -16,8 +16,15 @@ namespace bsccs {
  */
 
 template <typename T>
-class IncrementableIterator : public std::iterator<std::input_iterator_tag, T> {
+class IncrementableIterator {
 public:
+
+    using iterator_category = std::forward_iterator_tag;
+    using value_type = T;
+    using difference_type = T;
+    using pointer = T*;
+    using reference = T&;
+
     IncrementableIterator(T value) : value(value) { }
 
     IncrementableIterator& operator++() {

src/cyclops/drivers/AbstractCrossValidationDriver.cpp

@@ -7,6 +7,7 @@
 
 #include <numeric>
 #include <cmath>
+#include <iterator>
 
 // #include "boost/iterator/counting_iterator.hpp"