update cpp exports and version number

Author: jhmigueles

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: GGIRread
 Type: Package
 Title: Wearable Accelerometer Data File Readers
-Version: 1.0.3
+Version: 1.0.4
 Date: 2025-03-07
 Authors@R: c(person("Vincent T","van Hees",role=c("aut","cre"),
                   email="v.vanhees@accelting.com"),

R/readParmayMatrix.R

@@ -279,7 +279,7 @@ readParmayMatrix = function(bin_file, output = c("all", "sf", "dynrange")[1],
   }
 
   # lists to data frames
-  acc_data = do.call(rbind, acc_readings)
+  if (any(acc_count > 0) & read_acc) acc_data = do.call(rbind, acc_readings)
   if (any(gyro_count > 0) & read_gyro) gyro_data = do.call(rbind, gyro_readings)
   if (any(temp_count > 0) & read_temp) temp_data = do.call(rbind, temp_readings)
   if (any(heart_count > 0) & read_heart) {
@@ -387,7 +387,7 @@ readParmayMatrix = function(bin_file, output = c("all", "sf", "dynrange")[1],
   data = data.frame(time = required_timepoints)
 
   # add sensors if available
-  if (any(gyro_count > 0) & read_acc) data[, c("acc_x", "acc_y", "acc_z")] = acc_resampled
+  if (any(acc_count > 0) & read_acc) data[, c("acc_x", "acc_y", "acc_z")] = acc_resampled
   if (any(gyro_count > 0) & read_gyro) data[, c("gyro_x", "gyro_y", "gyro_z")] = gyro_resampled
   if (any(temp_count > 0) & read_temp) data[, c("bodySurface_temp", "ambient_temp")] = temp_resampled
   if (any(heart_count > 0) & read_heart) data[, c("hr_raw", "hr")] = heart_resampled

src/find_matrix_packet_start.cpp

@@ -18,24 +18,27 @@ Rcpp::IntegerVector find_matrix_packet_start(std::string file_path, Rcpp::RawVec
     std::streamsize bytesRead = file.gcount();
     if (bytesRead == 0) break;  // Stop if no more bytes read
 
+    // Ensure we don't compare signed and unsigned types
+    size_t search_limit = static_cast<size_t>(std::max(static_cast<std::streamoff>(bytesRead) - pattern_len, static_cast<std::streamoff>(0)));
+    
     // Search for pattern in the current buffer
-    for (size_t i = 0; i <= bytesRead - pattern_len; ++i) {
+    for (size_t i = 0; i <= search_limit; ++i) {
       bool match = true;
-      for (size_t j = 0; j < pattern_len; ++j) {
+      for (size_t j = 0; j < static_cast<size_t>(pattern_len); ++j) {
         if (buffer[i + j] != pattern[j]) {
           match = false;
           break;
         }
       }
       if (match) {
-        indices.push_back(position + i + 1);  // Convert to 1-based index
+        indices.push_back(static_cast<int>(position + static_cast<std::streamoff>(i) + 1));  // Convert to 1-based index
       }
     }
 
     // Move back the last `pattern_len - 1` bytes for next chunk to prevent missed matches
     if (bytesRead >= pattern_len - 1) {
-      file.seekg(position + bytesRead - (pattern_len - 1));
-      position += bytesRead - (pattern_len - 1);
+      file.seekg(position + static_cast<std::streamoff>(bytesRead) - static_cast<std::streamoff>(pattern_len - 1));
+      position = file.tellg();
     } else {
       break; // If not enough bytes left, end
     }

tests/testthat/test_readParmayMatrix.R

@@ -19,9 +19,12 @@ test_that("File including accelerometer and heart rate data at 25Hz", {
   expect_equal(BIN$acc_dynrange, 8)
   expect_equal(as.numeric(BIN$starttime), BIN$data$time[1])
   expect_equal(nrow(BIN$data), 24525)
-  expect_equal(ncol(BIN$data), 7) # time, x, y, z, hr_raw, hr, remarks
+  expect_equal(ncol(BIN$data), 5) # time, x, y, z, remarks (no hr because deactivated by default)
   expect_equal(nrow(BIN$QClog), 4) # 4 packets in file
   expect_true(all(BIN$QClog$checksum_pass))
+  BIN = readParmayMatrix(bin_file = binfile, desiredtz = "Europe/Berlin", start = 1, end = NULL,
+                         read_heart = TRUE)
+  expect_equal(ncol(BIN$data), 7) # time, x, y, z, hr_raw, hr, remarks
 })
 
 test_that("File including accelerometer, heart rate, and temperature data at 100Hz", {
@@ -31,7 +34,10 @@ test_that("File including accelerometer, heart rate, and temperature data at 100
   expect_equal(BIN$acc_dynrange, 8)
   expect_equal(as.numeric(BIN$starttime), BIN$data$time[1])
   expect_equal(nrow(BIN$data), 39400)
-  expect_equal(ncol(BIN$data), 9) # time, x, y, z, boyd temp, ambient temp, hr_raw, hr, remarks
+  expect_equal(ncol(BIN$data), 7) # time, x, y, z, body temp, ambient temp,remarks
   expect_equal(nrow(BIN$QClog), 4) # 4 packets in file
   expect_true(all(BIN$QClog$checksum_pass))
+  BIN = readParmayMatrix(bin_file = binfile, desiredtz = "Europe/Berlin", start = 1, end = NULL,
+                         read_heart = TRUE)
+  expect_equal(ncol(BIN$data), 9) # time, x, y, z, body temp, ambient temp, hr_raw, hr, remarks
 })