From 92d1d382967397d670ec93a18e64cd41bcee947f Mon Sep 17 00:00:00 2001
From: meetagrawal09 <agrawalmeet91@gmail.com>
Date: Tue, 26 Sep 2023 22:41:09 +0530
Subject: [PATCH 01/28] moved test_that block

---
 .../test.download.AmerifluxLBL.R              | 32 ++++----
 .../integrationTests/test.download.ERA5.R     | 74 +++++++++----------
 2 files changed, 53 insertions(+), 53 deletions(-)

diff --git a/modules/data.atmosphere/inst/integrationTests/test.download.AmerifluxLBL.R b/modules/data.atmosphere/inst/integrationTests/test.download.AmerifluxLBL.R
index e46d1d4830f..659f016e5dd 100644
--- a/modules/data.atmosphere/inst/integrationTests/test.download.AmerifluxLBL.R
+++ b/modules/data.atmosphere/inst/integrationTests/test.download.AmerifluxLBL.R
@@ -31,23 +31,23 @@ test_download_AmerifluxLBL <- function(start_date, end_date, sitename, lat.in, l
       lon.in = lon.in,
       sitename = sitename
     )
-  })
-  
-  # checking if the file is downloaded
-  test_that("Downloaded files are present at the desired location", {
-    expect_true(file.exists(paste0(tmpdir, "/AMF_US-Akn_BASE_HH_6-5.csv")))
-  })
 
-  test_that("Downloaded data files have the right format", {
-    firstline <- system(paste0("head -4 ", paste0(tmpdir, "/AMF_US-Akn_BASE_HH_6-5.csv")), intern = TRUE)
-    lastline <- system(paste0("tail -1 ", paste0(tmpdir, "/AMF_US-Akn_BASE_HH_6-5.csv")), intern = TRUE)
-    
-    # checking if first line of CSV has the sitename
-    expect_true(grepl(sitename, firstline[1]))
-    
-    # fourth and last row checked to contain non-alphabetical data since these are used to verify start and end dates
-    expect_false(grepl("[A-Za-z]", firstline[4]))
-    expect_false(grepl("[A-Za-z]", lastline[1]))
+    # checking if the file is downloaded
+    test_that("Downloaded files are present at the desired location", {
+      expect_true(file.exists(paste0(tmpdir, "/AMF_US-Akn_BASE_HH_6-5.csv")))
+    })
+
+    test_that("Downloaded data files have the right format", {
+      firstline <- system(paste0("head -4 ", paste0(tmpdir, "/AMF_US-Akn_BASE_HH_6-5.csv")), intern = TRUE)
+      lastline <- system(paste0("tail -1 ", paste0(tmpdir, "/AMF_US-Akn_BASE_HH_6-5.csv")), intern = TRUE)
+      
+      # checking if first line of CSV has the sitename
+      expect_true(grepl(sitename, firstline[1]))
+      
+      # fourth and last row checked to contain non-alphabetical data since these are used to verify start and end dates
+      expect_false(grepl("[A-Za-z]", firstline[4]))
+      expect_false(grepl("[A-Za-z]", lastline[1]))
+    })
   })
 }
 
diff --git a/modules/data.atmosphere/inst/integrationTests/test.download.ERA5.R b/modules/data.atmosphere/inst/integrationTests/test.download.ERA5.R
index 90f37c8e0c0..fbcff615fd6 100644
--- a/modules/data.atmosphere/inst/integrationTests/test.download.ERA5.R
+++ b/modules/data.atmosphere/inst/integrationTests/test.download.ERA5.R
@@ -37,51 +37,51 @@ test_download_ERA5 <- function(start_date, end_date, lat.in, lon.in, product_typ
       product_types = product_types,
       reticulate_python = reticulate_python
     )
-  })
-
-  test_that("All the required files are downloaded and stored at desired location", { 
-    expect_true(file.exists(paste0(tmpdir, "/era5.2m_dewpoint_temperature.nc")))
-    expect_true(file.exists(paste0(tmpdir, "/era5.2m_temperature.nc")))
-    expect_true(file.exists(paste0(tmpdir, "/era5.10m_u_component_of_wind.nc")))
-    expect_true(file.exists(paste0(tmpdir, "/era5.10m_v_component_of_wind.nc")))
-    expect_true(file.exists(paste0(tmpdir, "/era5.surface_pressure.nc")))
-    expect_true(file.exists(paste0(tmpdir, "/era5.surface_solar_radiation_downwards.nc")))
-    expect_true(file.exists(paste0(tmpdir, "/era5.surface_thermal_radiation_downwards.nc")))
-    expect_true(file.exists(paste0(tmpdir, "/era5.total_precipitation.nc")))
-  })
+    
+    test_that("All the required files are downloaded and stored at desired location", { 
+      expect_true(file.exists(paste0(tmpdir, "/era5.2m_dewpoint_temperature.nc")))
+      expect_true(file.exists(paste0(tmpdir, "/era5.2m_temperature.nc")))
+      expect_true(file.exists(paste0(tmpdir, "/era5.10m_u_component_of_wind.nc")))
+      expect_true(file.exists(paste0(tmpdir, "/era5.10m_v_component_of_wind.nc")))
+      expect_true(file.exists(paste0(tmpdir, "/era5.surface_pressure.nc")))
+      expect_true(file.exists(paste0(tmpdir, "/era5.surface_solar_radiation_downwards.nc")))
+      expect_true(file.exists(paste0(tmpdir, "/era5.surface_thermal_radiation_downwards.nc")))
+      expect_true(file.exists(paste0(tmpdir, "/era5.total_precipitation.nc")))
+    })
 
-  test_that("All ERA5 data files have the correct variable units", {
-    nc <- nc_open(paste0(tmpdir, "/era5.2m_dewpoint_temperature.nc"))
-    expect_equal(nc$var$d2m$units, "K")
-    nc_close(nc)
+    test_that("All ERA5 data files have the correct variable units", {
+      nc <- nc_open(paste0(tmpdir, "/era5.2m_dewpoint_temperature.nc"))
+      expect_equal(nc$var$d2m$units, "K")
+      nc_close(nc)
 
-    nc <- nc_open(paste0(tmpdir, "/era5.2m_temperature.nc"))
-    expect_equal(nc$var$t2m$units, "K")
-    nc_close(nc)
+      nc <- nc_open(paste0(tmpdir, "/era5.2m_temperature.nc"))
+      expect_equal(nc$var$t2m$units, "K")
+      nc_close(nc)
 
-    nc <- nc_open(paste0(tmpdir, "/era5.10m_u_component_of_wind.nc"))
-    expect_equal(nc$var$u10$units, "m s**-1")
-    nc_close(nc)
+      nc <- nc_open(paste0(tmpdir, "/era5.10m_u_component_of_wind.nc"))
+      expect_equal(nc$var$u10$units, "m s**-1")
+      nc_close(nc)
 
-    nc <- nc_open(paste0(tmpdir, "/era5.10m_v_component_of_wind.nc"))
-    expect_equal(nc$var$v10$units, "m s**-1")
-    nc_close(nc)
+      nc <- nc_open(paste0(tmpdir, "/era5.10m_v_component_of_wind.nc"))
+      expect_equal(nc$var$v10$units, "m s**-1")
+      nc_close(nc)
 
-    nc <- nc_open(paste0(tmpdir, "/era5.surface_pressure.nc"))
-    expect_equal(nc$var$sp$units, "Pa")
-    nc_close(nc)
+      nc <- nc_open(paste0(tmpdir, "/era5.surface_pressure.nc"))
+      expect_equal(nc$var$sp$units, "Pa")
+      nc_close(nc)
 
-    nc <- nc_open(paste0(tmpdir, "/era5.surface_solar_radiation_downwards.nc"))
-    expect_equal(nc$var$ssrd$units, "J m**-2")
-    nc_close(nc)
+      nc <- nc_open(paste0(tmpdir, "/era5.surface_solar_radiation_downwards.nc"))
+      expect_equal(nc$var$ssrd$units, "J m**-2")
+      nc_close(nc)
 
-    nc <- nc_open(paste0(tmpdir, "/era5.surface_thermal_radiation_downwards.nc"))
-    expect_equal(nc$var$strd$units, "J m**-2")
-    nc_close(nc)
+      nc <- nc_open(paste0(tmpdir, "/era5.surface_thermal_radiation_downwards.nc"))
+      expect_equal(nc$var$strd$units, "J m**-2")
+      nc_close(nc)
 
-    nc <- nc_open(paste0(tmpdir, "/era5.total_precipitation.nc"))
-    expect_equal(nc$var$tp$units, "m")
-    nc_close(nc)
+      nc <- nc_open(paste0(tmpdir, "/era5.total_precipitation.nc"))
+      expect_equal(nc$var$tp$units, "m")
+      nc_close(nc)
+    })
   })
 }
 

From 0f19ee17c04da61248efb28828c9cd81de22fa5f Mon Sep 17 00:00:00 2001
From: meetagrawal09 <agrawalmeet91@gmail.com>
Date: Wed, 27 Sep 2023 01:10:58 +0530
Subject: [PATCH 02/28] updated function refs

---
 .../test.download.AmerifluxLBL.R              | 18 +++++++++------
 .../integrationTests/test.download.CRUNCEP.R  | 22 +++++++++++--------
 .../integrationTests/test.download.ERA5.R     | 22 +++++++++++--------
 3 files changed, 37 insertions(+), 25 deletions(-)

diff --git a/modules/data.atmosphere/inst/integrationTests/test.download.AmerifluxLBL.R b/modules/data.atmosphere/inst/integrationTests/test.download.AmerifluxLBL.R
index 659f016e5dd..07412b4de31 100644
--- a/modules/data.atmosphere/inst/integrationTests/test.download.AmerifluxLBL.R
+++ b/modules/data.atmosphere/inst/integrationTests/test.download.AmerifluxLBL.R
@@ -1,19 +1,23 @@
 library(testthat)
+library(mockery)
+library(PEcAn.DB)
+library(PEcAn.logger)
+library(withr)
 
 test_download_AmerifluxLBL <- function(start_date, end_date, sitename, lat.in, lon.in) {
   # putting logger to debug mode
-  PEcAn.logger::logger.setUseConsole(TRUE, FALSE)
-  on.exit(PEcAn.logger::logger.setUseConsole(TRUE, TRUE), add = TRUE)
-  PEcAn.logger::logger.setLevel("DEBUG")
+  logger.setUseConsole(TRUE, FALSE)
+  on.exit(logger.setUseConsole(TRUE, TRUE), add = TRUE)
+  logger.setLevel("DEBUG")
 
   # mocking functions
-  mockery::stub(PEcAn.DB::convert_input, 'dbfile.input.check', data.frame())
-  mockery::stub(PEcAn.DB::convert_input, 'db.query', data.frame(id = 1))
+  stub(convert_input, 'dbfile.input.check', data.frame())
+  stub(convert_input, 'db.query', data.frame(id = 1))
 
-  withr::with_dir(tempdir(), {
+  with_dir(tempdir(), {
     tmpdir <- getwd()
     # calling download function
-    res <- PEcAn.DB::convert_input(
+    res <- convert_input(
       input.id = NA,
       outfolder = tmpdir,
       formatname = NULL,
diff --git a/modules/data.atmosphere/inst/integrationTests/test.download.CRUNCEP.R b/modules/data.atmosphere/inst/integrationTests/test.download.CRUNCEP.R
index 8512b49f34d..832667c101e 100644
--- a/modules/data.atmosphere/inst/integrationTests/test.download.CRUNCEP.R
+++ b/modules/data.atmosphere/inst/integrationTests/test.download.CRUNCEP.R
@@ -1,19 +1,23 @@
 library(testthat)
 library(ncdf4)
+library(mockery)
+library(PEcAn.DB)
+library(PEcAn.logger)
+library(withr)
 
 test_download_CRUNCEP <- function(start_date, end_date, lat.in, lon.in, method, maxErrors, sleep) {
   # putting logger to debug mode
-  PEcAn.logger::logger.setUseConsole(TRUE, FALSE)
-  on.exit(PEcAn.logger::logger.setUseConsole(TRUE, TRUE), add = TRUE)
-  PEcAn.logger::logger.setLevel("DEBUG")
+  logger.setUseConsole(TRUE, FALSE)
+  on.exit(logger.setUseConsole(TRUE, TRUE), add = TRUE)
+  logger.setLevel("DEBUG")
 
   # mocking functions
-  mockery::stub(PEcAn.DB::convert_input, 'dbfile.input.check', data.frame())
-  mockery::stub(PEcAn.DB::convert_input, 'db.query', data.frame(id = 1))
+  stub(convert_input, 'dbfile.input.check', data.frame())
+  stub(convert_input, 'db.query', data.frame(id = 1))
 
-  withr::with_dir(tempdir(), {
+  with_dir(tempdir(), {
     tmpdir <- getwd()
-    PEcAn.DB::convert_input(
+    convert_input(
       input.id = NA,
       outfolder = tmpdir,
       formatname = NULL,
@@ -44,8 +48,8 @@ test_download_CRUNCEP <- function(start_date, end_date, lat.in, lon.in, method,
 
     test_that("NetCDF file contains lat and lon variables", {
 
-      mask_nc <- ncdf4::nc_open(paste0(tmpdir, "/cruncep_landwater_mask.nc"))
-      on.exit(ncdf4::nc_close(mask_nc), add = TRUE)
+      mask_nc <- nc_open(paste0(tmpdir, "/cruncep_landwater_mask.nc"))
+      on.exit(nc_close(mask_nc), add = TRUE)
       expect_true("land_water_mask" %in% names(mask_nc$var))
       
       # Check the dimensions of "land_water_mask" variable
diff --git a/modules/data.atmosphere/inst/integrationTests/test.download.ERA5.R b/modules/data.atmosphere/inst/integrationTests/test.download.ERA5.R
index fbcff615fd6..30c6e7af027 100644
--- a/modules/data.atmosphere/inst/integrationTests/test.download.ERA5.R
+++ b/modules/data.atmosphere/inst/integrationTests/test.download.ERA5.R
@@ -1,24 +1,28 @@
 library(testthat)
 library(ncdf4)
+library(mockery)
+library(PEcAn.DB)
+library(PEcAn.logger)
+library(withr)
 
 test_download_ERA5 <- function(start_date, end_date, lat.in, lon.in, product_types, reticulate_python) {
   # putting logger to debug mode
-  PEcAn.logger::logger.setUseConsole(TRUE, FALSE)
-  on.exit(PEcAn.logger::logger.setUseConsole(TRUE, TRUE), add = TRUE)
-  PEcAn.logger::logger.setLevel("DEBUG")
+  logger.setUseConsole(TRUE, FALSE)
+  on.exit(logger.setUseConsole(TRUE, TRUE), add = TRUE)
+  logger.setLevel("DEBUG")
 
 
   # mocking functions
-  mockery::stub(PEcAn.DB::convert_input, 'dbfile.input.check', data.frame())
-  mockery::stub(PEcAn.DB::convert_input, 'db.query', data.frame(id = 1))
+  stub(convert_input, 'dbfile.input.check', data.frame())
+  stub(convert_input, 'db.query', data.frame(id = 1))
 
   # additional mocks needed since download.ERA5 does not return data as other download functions
-  mockery::stub(PEcAn.DB::convert_input, 'length', 2)
-  mockery::stub(PEcAn.DB::convert_input, 'purrr::map_dfr', data.frame(missing = c(FALSE), empty = c(FALSE)))
+  stub(convert_input, 'length', 2)
+  stub(convert_input, 'purrr::map_dfr', data.frame(missing = c(FALSE), empty = c(FALSE)))
 
-  withr::with_dir(tempdir(), {
+  with_dir(tempdir(), {
     tmpdir <- getwd()
-    PEcAn.DB::convert_input(
+    convert_input(
       input.id = NA,
       outfolder = tmpdir,
       formatname = NULL,

From 0baebb5aba368711d0d545d0f1a0820245a51bf6 Mon Sep 17 00:00:00 2001
From: meetagrawal09 <agrawalmeet91@gmail.com>
Date: Wed, 27 Sep 2023 09:46:28 +0530
Subject: [PATCH 03/28] added namespaces

---
 .../test.download.AmerifluxLBL.R              | 15 ++++++---------
 .../integrationTests/test.download.CRUNCEP.R  | 15 ++++++---------
 .../integrationTests/test.download.ERA5.R     | 19 ++++++++-----------
 3 files changed, 20 insertions(+), 29 deletions(-)

diff --git a/modules/data.atmosphere/inst/integrationTests/test.download.AmerifluxLBL.R b/modules/data.atmosphere/inst/integrationTests/test.download.AmerifluxLBL.R
index 07412b4de31..372f5bfb11d 100644
--- a/modules/data.atmosphere/inst/integrationTests/test.download.AmerifluxLBL.R
+++ b/modules/data.atmosphere/inst/integrationTests/test.download.AmerifluxLBL.R
@@ -1,20 +1,17 @@
 library(testthat)
-library(mockery)
 library(PEcAn.DB)
-library(PEcAn.logger)
-library(withr)
 
 test_download_AmerifluxLBL <- function(start_date, end_date, sitename, lat.in, lon.in) {
   # putting logger to debug mode
-  logger.setUseConsole(TRUE, FALSE)
-  on.exit(logger.setUseConsole(TRUE, TRUE), add = TRUE)
-  logger.setLevel("DEBUG")
+  PEcAn.logger::logger.setUseConsole(TRUE, FALSE)
+  on.exit(PEcAn.logger::logger.setUseConsole(TRUE, TRUE), add = TRUE)
+  PEcAn.logger::logger.setLevel("DEBUG")
 
   # mocking functions
-  stub(convert_input, 'dbfile.input.check', data.frame())
-  stub(convert_input, 'db.query', data.frame(id = 1))
+  mockery::stub(convert_input, 'dbfile.input.check', data.frame())
+  mockery::stub(convert_input, 'db.query', data.frame(id = 1))
 
-  with_dir(tempdir(), {
+  withr::with_dir(tempdir(), {
     tmpdir <- getwd()
     # calling download function
     res <- convert_input(
diff --git a/modules/data.atmosphere/inst/integrationTests/test.download.CRUNCEP.R b/modules/data.atmosphere/inst/integrationTests/test.download.CRUNCEP.R
index 832667c101e..396c7a0aae7 100644
--- a/modules/data.atmosphere/inst/integrationTests/test.download.CRUNCEP.R
+++ b/modules/data.atmosphere/inst/integrationTests/test.download.CRUNCEP.R
@@ -1,21 +1,18 @@
 library(testthat)
 library(ncdf4)
-library(mockery)
 library(PEcAn.DB)
-library(PEcAn.logger)
-library(withr)
 
 test_download_CRUNCEP <- function(start_date, end_date, lat.in, lon.in, method, maxErrors, sleep) {
   # putting logger to debug mode
-  logger.setUseConsole(TRUE, FALSE)
-  on.exit(logger.setUseConsole(TRUE, TRUE), add = TRUE)
-  logger.setLevel("DEBUG")
+  PEcAn.logger::logger.setUseConsole(TRUE, FALSE)
+  on.exit(PEcAn.logger::logger.setUseConsole(TRUE, TRUE), add = TRUE)
+  PEcAn.logger::logger.setLevel("DEBUG")
 
   # mocking functions
-  stub(convert_input, 'dbfile.input.check', data.frame())
-  stub(convert_input, 'db.query', data.frame(id = 1))
+  mockery::stub(convert_input, 'dbfile.input.check', data.frame())
+  mockery::stub(convert_input, 'db.query', data.frame(id = 1))
 
-  with_dir(tempdir(), {
+  withr::with_dir(tempdir(), {
     tmpdir <- getwd()
     convert_input(
       input.id = NA,
diff --git a/modules/data.atmosphere/inst/integrationTests/test.download.ERA5.R b/modules/data.atmosphere/inst/integrationTests/test.download.ERA5.R
index 30c6e7af027..bf84c31dd85 100644
--- a/modules/data.atmosphere/inst/integrationTests/test.download.ERA5.R
+++ b/modules/data.atmosphere/inst/integrationTests/test.download.ERA5.R
@@ -1,26 +1,23 @@
 library(testthat)
 library(ncdf4)
-library(mockery)
 library(PEcAn.DB)
-library(PEcAn.logger)
-library(withr)
 
 test_download_ERA5 <- function(start_date, end_date, lat.in, lon.in, product_types, reticulate_python) {
   # putting logger to debug mode
-  logger.setUseConsole(TRUE, FALSE)
-  on.exit(logger.setUseConsole(TRUE, TRUE), add = TRUE)
-  logger.setLevel("DEBUG")
+  PEcAn.logger::logger.setUseConsole(TRUE, FALSE)
+  on.exit(PEcAn.logger::logger.setUseConsole(TRUE, TRUE), add = TRUE)
+  PEcAn.logger::logger.setLevel("DEBUG")
 
 
   # mocking functions
-  stub(convert_input, 'dbfile.input.check', data.frame())
-  stub(convert_input, 'db.query', data.frame(id = 1))
+  mockery::stub(convert_input, 'dbfile.input.check', data.frame())
+  mockery::stub(convert_input, 'db.query', data.frame(id = 1))
 
   # additional mocks needed since download.ERA5 does not return data as other download functions
-  stub(convert_input, 'length', 2)
-  stub(convert_input, 'purrr::map_dfr', data.frame(missing = c(FALSE), empty = c(FALSE)))
+  mockery::stub(convert_input, 'length', 2)
+  mockery::stub(convert_input, 'purrr::map_dfr', data.frame(missing = c(FALSE), empty = c(FALSE)))
 
-  with_dir(tempdir(), {
+  withr::with_dir(tempdir(), {
     tmpdir <- getwd()
     convert_input(
       input.id = NA,

From dfb1dae78e82053af92d46560348c227e235ab42 Mon Sep 17 00:00:00 2001
From: meetagrawal09 <agrawalmeet91@gmail.com>
Date: Wed, 27 Sep 2023 09:48:25 +0530
Subject: [PATCH 04/28] added ns

---
 .../inst/integrationTests/test.download.CRUNCEP.R             | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/modules/data.atmosphere/inst/integrationTests/test.download.CRUNCEP.R b/modules/data.atmosphere/inst/integrationTests/test.download.CRUNCEP.R
index 396c7a0aae7..cfad888104b 100644
--- a/modules/data.atmosphere/inst/integrationTests/test.download.CRUNCEP.R
+++ b/modules/data.atmosphere/inst/integrationTests/test.download.CRUNCEP.R
@@ -45,8 +45,8 @@ test_download_CRUNCEP <- function(start_date, end_date, lat.in, lon.in, method,
 
     test_that("NetCDF file contains lat and lon variables", {
 
-      mask_nc <- nc_open(paste0(tmpdir, "/cruncep_landwater_mask.nc"))
-      on.exit(nc_close(mask_nc), add = TRUE)
+      mask_nc <- ncdf4::nc_open(paste0(tmpdir, "/cruncep_landwater_mask.nc"))
+      on.exit(ncdf4::nc_close(mask_nc), add = TRUE)
       expect_true("land_water_mask" %in% names(mask_nc$var))
       
       # Check the dimensions of "land_water_mask" variable

From 1aa068f07676a1a4b7822448ee61f78221584f9c Mon Sep 17 00:00:00 2001
From: meetagrawal09 <agrawalmeet91@gmail.com>
Date: Mon, 2 Oct 2023 19:27:54 +0530
Subject: [PATCH 05/28] updated edit url

---
 book_source/_bookdown.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/book_source/_bookdown.yml b/book_source/_bookdown.yml
index 45407cef0bc..fb22b3b1e6e 100644
--- a/book_source/_bookdown.yml
+++ b/book_source/_bookdown.yml
@@ -1,2 +1,2 @@
 rmd_subdir: true
-edit: https://github.com/tonygardella/pecan/edit/release/vtonydoc/book_source/%s
+edit: https://github.com/PecanProject/pecan/edit/develop/book_source/%s

From ac5caa7eb2762dfcfe223b2eae5a918fcf48efed Mon Sep 17 00:00:00 2001
From: Chris Black <chris@ckblack.org>
Date: Tue, 26 Sep 2023 23:48:38 -0700
Subject: [PATCH 06/28] wip

---
 scripts/check_with_errors.R | 24 +++++++++++++-----------
 1 file changed, 13 insertions(+), 11 deletions(-)

diff --git a/scripts/check_with_errors.R b/scripts/check_with_errors.R
index 4a4e8701658..f90a75532f4 100755
--- a/scripts/check_with_errors.R
+++ b/scripts/check_with_errors.R
@@ -7,6 +7,8 @@ log_level <- Sys.getenv("LOGLEVEL", unset = NA)
 die_level <- Sys.getenv("DIELEVEL", unset = NA)
 redocument <- as.logical(Sys.getenv("REBUILD_DOCS", unset = NA))
 runtests <- as.logical(Sys.getenv("RUN_TESTS", unset = TRUE))
+resave <- as.logical(Sys.getenv("RESAVE_CHECKS", unset = FALSE))
+if (resave) die_level <- "never"
 
 old_file <- file.path(pkg, "tests", "Rcheck_reference.log")
 if (file.exists(old_file)) {
@@ -71,7 +73,7 @@ if (log_notes && n_notes > 0) {
 # such that it's not yet practical to break the build on every warning.
 # Cleaning this up is a long-term goal, but will take time.
 # Meanwhile, we compare against a cached historic check output to enforce that
-# no *new* warnings are added. As historic warnings are removed, we will update
+# no *new* warnings are added. As historic warnings are removed, we update
 # the cached results to ensure they stay gone.
 #
 # To compare checks, we take a two-level approach:
@@ -83,16 +85,16 @@ if (log_notes && n_notes > 0) {
 ###
 # To update reference files after fixing an old warning:
 # * Run check_with_errors.R to be sure the check is currently passing
-# * Delete the file you want to update
-# * Uncomment this section
-# * run `DIELEVEL=never Rscript scripts/check_with_errors.R path/to/package`
-# * recomment this section
-# * Commit updated file
-# if (!file.exists(old_file)) {
-#     cat("No reference check file found. Saving current results as the new standard\n")
-#     cat(chk$stdout, file = old_file)
-#     quit("no")
-# }
+# * run `RESAVE_CHECKS=true Rscript scripts/check_with_errors.R path/to/package`
+# * Commit updated <pkgname>/tests/Rcheck_reference.log file
+if (resave) {
+    cat("Saving current check results as the new standard\n")
+    if (file.exists(old_file)) {
+        cat("**Overwriting** existing saved check output\n")
+    }
+    cat(chk$stdout, file = old_file)
+    quit("no")
+}
 ###
 
 # everything beyond this point is comparing to old version

From 38293ded78dd4fb176cc6a79eba6f55301f23d11 Mon Sep 17 00:00:00 2001
From: Shashank Singh <shashanksingh819@gmail.com>
Date: Mon, 18 Sep 2023 02:33:07 +0000
Subject: [PATCH 07/28] title in description to upper case

---
 modules/data.mining/DESCRIPTION | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/modules/data.mining/DESCRIPTION b/modules/data.mining/DESCRIPTION
index 74176560466..7ac5389be56 100644
--- a/modules/data.mining/DESCRIPTION
+++ b/modules/data.mining/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: PEcAn.data.mining
 Type: Package
-Title: PEcAn functions used for exploring model residuals and structures
+Title: PEcAn Functions Used for Exploring Model Residuals and Structures
 Description: (Temporary description) PEcAn functions used for exploring model residuals and structures
 Version: 1.7.2
 Date: 2021-10-04
@@ -21,4 +21,4 @@ LazyLoad: yes
 LazyData: FALSE
 Collate:
 Encoding: UTF-8
-RoxygenNote: 6.1.1
+RoxygenNote: 7.1.2

From 9e9a9d30959ee7bed4f4b235b03db246a36e2dfd Mon Sep 17 00:00:00 2001
From: Shashank Singh <shashanksingh819@gmail.com>
Date: Sun, 8 Oct 2023 15:16:01 +0000
Subject: [PATCH 08/28] log file update

---
 .../data.mining/tests/Rcheck_reference.log    | 49 +++++++++++++++++++
 1 file changed, 49 insertions(+)
 create mode 100644 modules/data.mining/tests/Rcheck_reference.log

diff --git a/modules/data.mining/tests/Rcheck_reference.log b/modules/data.mining/tests/Rcheck_reference.log
new file mode 100644
index 00000000000..7746a8b418c
--- /dev/null
+++ b/modules/data.mining/tests/Rcheck_reference.log
@@ -0,0 +1,49 @@
+* using log directory ‘/tmp/Rtmpyv5R27/PEcAn.data.mining.Rcheck’
+* using R version 4.1.3 (2022-03-10)
+* using platform: x86_64-pc-linux-gnu (64-bit)
+* using session charset: UTF-8
+* using options ‘--no-manual --as-cran’
+* checking for file ‘PEcAn.data.mining/DESCRIPTION’ ... OK
+* checking extension type ... Package
+* this is package ‘PEcAn.data.mining’ version ‘1.7.2’
+* package encoding: UTF-8
+* checking package namespace information ... OK
+* checking package dependencies ... OK
+* checking if this is a source package ... OK
+* checking if there is a namespace ... OK
+* checking for executable files ... OK
+* checking for hidden files and directories ... OK
+* checking for portable file names ... OK
+* checking for sufficient/correct file permissions ... OK
+* checking serialization versions ... OK
+* checking whether package ‘PEcAn.data.mining’ can be installed ... OK
+* checking installed package size ... OK
+* checking package directory ... OK
+* checking for future file timestamps ... OK
+* checking DESCRIPTION meta-information ... NOTE
+Malformed Description field: should contain one or more complete sentences.
+* checking top-level files ... OK
+* checking for left-over files ... OK
+* checking index information ... OK
+* checking package subdirectories ... OK
+* checking whether the package can be loaded ... OK
+* checking whether the package can be loaded with stated dependencies ... OK
+* checking whether the package can be unloaded cleanly ... OK
+* checking whether the namespace can be loaded with stated dependencies ... OK
+* checking whether the namespace can be unloaded cleanly ... OK
+* checking loading without being on the library search path ... OK
+* checking examples ... NONE
+* checking for unstated dependencies in ‘tests’ ... OK
+* checking tests ...
+  Running ‘testthat.R’
+ OK
+* checking for non-standard things in the check directory ... OK
+* checking for detritus in the temp directory ... OK
+* DONE
+
+Status: 1 NOTE
+See
+  ‘/tmp/Rtmpyv5R27/PEcAn.data.mining.Rcheck/00check.log’
+for details.
+
+

From 11c4d454771fccb0e05b9b1df230261c113ce74f Mon Sep 17 00:00:00 2001
From: Shashank Singh <shashanksingh819@gmail.com>
Date: Sun, 15 Oct 2023 13:42:21 +0000
Subject: [PATCH 09/28] mend

---
 .../data.remote/tests/Rcheck_reference.log    | 93 +++----------------
 1 file changed, 13 insertions(+), 80 deletions(-)

diff --git a/modules/data.remote/tests/Rcheck_reference.log b/modules/data.remote/tests/Rcheck_reference.log
index 822a9411303..afd295d0b58 100644
--- a/modules/data.remote/tests/Rcheck_reference.log
+++ b/modules/data.remote/tests/Rcheck_reference.log
@@ -1,55 +1,12 @@
-* using log directory ‘/home/tanishq010/pecan/modules/PEcAn.data.remote.Rcheck’
-* using R version 4.2.1 (2022-06-23)
+* using log directory ‘/tmp/RtmpqErjWC/PEcAn.data.remote.Rcheck’
+* using R version 4.1.3 (2022-03-10)
 * using platform: x86_64-pc-linux-gnu (64-bit)
 * using session charset: UTF-8
-* using options ‘--no-tests --no-manual --as-cran’
+* using options ‘--no-manual --as-cran’
 * checking for file ‘PEcAn.data.remote/DESCRIPTION’ ... OK
 * checking extension type ... Package
 * this is package ‘PEcAn.data.remote’ version ‘1.7.2.9000’
 * package encoding: UTF-8
-* checking CRAN incoming feasibility ... WARNING
-Maintainer: ‘Bailey Morrison <bmorrison@bnl.gov>’
-
-New submission
-
-Version contains large components (1.7.2.9000)
-
-License components with restrictions and base license permitting such:
-  BSD_3_clause + file LICENSE
-File 'LICENSE':
-  University of Illinois/NCSA Open Source License
-
-  Copyright (c) 2012, University of Illinois, NCSA.  All rights reserved.
-
-  Permission is hereby granted, free of charge, to any person obtaining
-  a copy of this software and associated documentation files (the
-  "Software"), to deal with the Software without restriction, including
-  without limitation the rights to use, copy, modify, merge, publish,
-  distribute, sublicense, and/or sell copies of the Software, and to
-  permit persons to whom the Software is furnished to do so, subject to
-  the following conditions:
-
-  - Redistributions of source code must retain the above copyright
-    notice, this list of conditions and the following disclaimers.
-  - Redistributions in binary form must reproduce the above copyright
-    notice, this list of conditions and the following disclaimers in the
-    documentation and/or other materials provided with the distribution.
-  - Neither the names of University of Illinois, NCSA, nor the names
-    of its contributors may be used to endorse or promote products
-    derived from this Software without specific prior written permission.
-
-  THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
-  EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
-  MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.
-  IN NO EVENT SHALL THE CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR
-  ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF
-  CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
-  WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS WITH THE SOFTWARE.
-
-Strong dependencies not in mainstream repositories:
-  PEcAn.DB, PEcAn.utils, PEcAn.logger, PEcAn.remote
-
-The Date field is over a month old.
 * checking package namespace information ... OK
 * checking package dependencies ... OK
 * checking if this is a source package ... OK
@@ -63,11 +20,7 @@ The Date field is over a month old.
 * checking installed package size ... OK
 * checking package directory ... OK
 * checking for future file timestamps ... OK
-* checking DESCRIPTION meta-information ... NOTE
-Author field differs from that derived from Authors@R
-  Author:    ‘Mike Dietze, Bailey Morrison’
-  Authors@R: ‘Mike Dietze [aut], Bailey Morrison [aut, cre], University of Illinois, NCSA [cph]’
-
+* checking DESCRIPTION meta-information ... OK
 * checking top-level files ... OK
 * checking for left-over files ... OK
 * checking index information ... OK
@@ -80,7 +33,6 @@ Author field differs from that derived from Authors@R
 * checking whether the namespace can be loaded with stated dependencies ... OK
 * checking whether the namespace can be unloaded cleanly ... OK
 * checking loading without being on the library search path ... OK
-* checking use of S3 registration ... OK
 * checking dependencies in R code ... WARNING
 'library' or 'require' calls not declared from:
   ‘PEcAn.DB’ ‘doParallel’ ‘raster’
@@ -88,41 +40,17 @@ Author field differs from that derived from Authors@R
   ‘PEcAn.DB’ ‘doParallel’ ‘raster’ ‘rgdal’
   Please use :: or requireNamespace() instead.
   See section 'Suggested packages' in the 'Writing R Extensions' manual.
-Namespace in Imports field not imported from: ‘stringr’
-  All declared Imports should be used.
+Missing or unexported objects:
+  ‘PEcAn.utils::download_file’ ‘PEcAn.utils::need_packages’
 * checking S3 generic/method consistency ... OK
 * checking replacement functions ... OK
 * checking foreign function calls ... OK
 * checking R code for possible problems ... NOTE
-call_MODIS: no visible global function definition for ‘write.csv’
 download.LandTrendr.AGB: no visible binding for global variable ‘k’
-download.NLCD: no visible global function definition for ‘dbfile.check’
-download.NLCD: no visible global function definition for ‘db.query’
-download.NLCD: no visible global function definition for
-  ‘dbfile.insert’
-download.thredds.AGB : get_data: no visible global function definition
-  for ‘write.csv’
-download.thredds.AGB: no visible global function definition for
-  ‘foreach’
-download.thredds.AGB: no visible global function definition for
-  ‘stopCluster’
-extract_NLCD: no visible global function definition for ‘dbfile.check’
-extract_NLCD: no visible global function definition for ‘db.query’
-extract_NLCD: no visible global function definition for ‘raster’
-extract_NLCD: no visible global function definition for ‘SpatialPoints’
-extract_NLCD: no visible global function definition for ‘CRS’
-extract_NLCD: no visible global function definition for ‘spTransform’
-extract_NLCD: no visible global function definition for ‘crs’
-extract_NLCD: no visible global function definition for ‘extract’
 grid2netcdf: no visible binding for global variable ‘years’
 grid2netcdf: no visible binding for global variable ‘yieldarray’
 Undefined global functions or variables:
-  CRS SpatialPoints crs db.query dbfile.check dbfile.insert
-  download.file extract foreach k raster spTransform stopCluster
-  write.csv
-Consider adding
-  importFrom("utils", "download.file", "write.csv")
-to your NAMESPACE file.
+  k years yieldarray
 * checking Rd files ... OK
 * checking Rd metadata ... OK
 * checking Rd line widths ... OK
@@ -148,4 +76,9 @@ Extensions’ manual.
 * checking for detritus in the temp directory ... OK
 * DONE
 
-Status: 3 WARNINGs, 2 NOTEs
+Status: 2 WARNINGs, 1 NOTE
+See
+  ‘/tmp/RtmpqErjWC/PEcAn.data.remote.Rcheck/00check.log’
+for details.
+
+

From ab57f797185f4dbed15a4cee32ce325d622694df Mon Sep 17 00:00:00 2001
From: Shashank Singh <shashanksingh819@gmail.com>
Date: Mon, 18 Sep 2023 03:18:53 +0000
Subject: [PATCH 10/28] fix warnings/notes in data.remote package

---
 modules/data.remote/R/NLCD.R             | 18 +++++++++---------
 modules/data.remote/R/call_MODIS.R       |  2 +-
 modules/data.remote/R/download.thredds.R |  6 +++---
 3 files changed, 13 insertions(+), 13 deletions(-)

diff --git a/modules/data.remote/R/NLCD.R b/modules/data.remote/R/NLCD.R
index dfc712f2e09..f1a8a6b868a 100644
--- a/modules/data.remote/R/NLCD.R
+++ b/modules/data.remote/R/NLCD.R
@@ -24,9 +24,9 @@ download.NLCD <- function(outdir, year = 2011, con = NULL) {
     ## before downloading, check if the file already exists on this host
     if (!is.null(con)) {
         library(PEcAn.DB)
-        chk <- dbfile.check(type = "Input", id = input.id, con = con)
+        chk <- PEcAn.DB::dbfile.check(type = "Input", id = input.id, con = con)
         if (nrow(chk) > 0) {
-            machines <- db.query(paste("SELECT * from machines where id in (", 
+            machines <- PEcAn.DB::db.query(paste("SELECT * from machines where id in (", 
                                        paste(chk$machine_id, sep = ","), ")"), con)
             if (PEcAn.remote::fqdn() %in% machines$hostname) {
                 ## record already exists on this host
@@ -49,7 +49,7 @@ download.NLCD <- function(outdir, year = 2011, con = NULL) {
         prefix <- table(sapply(strsplit(dir(data_dir), ".", fixed = TRUE), function(x) { x[1] }))
         prefix <- names(which.max(prefix))
         site.id <- 1000000676
-        return(dbfile.insert(data_dir, in.prefix = prefix, type = "Input", input.id, con, 
+        return(PEcAn.DB::dbfile.insert(data_dir, in.prefix = prefix, type = "Input", input.id, con, 
             reuse = TRUE))
     }
     return(data_dir)
@@ -80,9 +80,9 @@ extract_NLCD <- function(buffer, coords, data_dir = NULL, con = NULL, year = 201
         } else {
             print(paste("Year not yet supported: ", year))
         }
-        chk <- dbfile.check(type = "Input", id = input.id, con = con)
+        chk <- PEcAn.DB::dbfile.check(type = "Input", id = input.id, con = con)
         if (nrow(chk) > 0) {
-            machines <- db.query(paste("SELECT * from machines where id in (",
+            machines <- PEcAn.DB::db.query(paste("SELECT * from machines where id in (",
                                        paste(chk$machine_id, sep = ","), ")"), con)
             if (PEcAn.remote::fqdn() %in% machines$hostname) {
                 ## record already exists on this host
@@ -104,14 +104,14 @@ extract_NLCD <- function(buffer, coords, data_dir = NULL, con = NULL, year = 201
         print(paste("File not found:", filename))
         return(NULL)
     }
-    nlcd <- raster(filename)
+    nlcd <- raster::raster(filename)
     
     # transform points
-    sites <- SpatialPoints(coords = coords, proj4string = CRS("+proj=longlat +datum=WGS84"))
-    sites <- spTransform(sites, crs(nlcd))
+    sites <- sp::SpatialPoints(coords = coords, proj4string = sp::CRS("+proj=longlat +datum=WGS84"))
+    sites <- sp::spTransform(sites, raster::crs(nlcd))
     
     # extract
-    sum.raw <- table(extract(nlcd, sites, buffer = buffer))
+    sum.raw <- table(raster::extract(nlcd, sites, buffer = buffer))
     summ <- prop.table(sum.raw)
     mydf <- data.frame(cover = names(summ), percent = as.vector(summ), count = as.vector(sum.raw))
     
diff --git a/modules/data.remote/R/call_MODIS.R b/modules/data.remote/R/call_MODIS.R
index 61e41a6f845..b4791cd004e 100755
--- a/modules/data.remote/R/call_MODIS.R
+++ b/modules/data.remote/R/call_MODIS.R
@@ -283,7 +283,7 @@ call_MODIS <- function(var, product,
         fname <- paste(site_info$site_id[i], "/", product, "_", band, "_", start_date, "-", end_date, "_unfiltered.csv", sep = "")
       }
       fname <- file.path(outdir, fname)
-      write.csv(site, fname, row.names = FALSE)
+      utils::write.csv(site, fname, row.names = FALSE)
     }
     
   }
diff --git a/modules/data.remote/R/download.thredds.R b/modules/data.remote/R/download.thredds.R
index 09d44ac1337..6e61e92ffa9 100755
--- a/modules/data.remote/R/download.thredds.R
+++ b/modules/data.remote/R/download.thredds.R
@@ -69,7 +69,7 @@ download.thredds.AGB <- function(outdir = NULL, site_ids, run_parallel = FALSE,
     # option to save output dataset to directory for user.
     if (!(is.null(outdir)))
     {
-      write.csv(output, file = paste0(outdir, "THREDDS_", sub("^([^.]*).*", "\\1",basename(files[1])), "_site_", site, ".csv"), row.names = FALSE)
+      utils::write.csv(output, file = paste0(outdir, "THREDDS_", sub("^([^.]*).*", "\\1",basename(files[1])), "_site_", site, ".csv"), row.names = FALSE)
     }
     
     return(output)
@@ -86,8 +86,8 @@ download.thredds.AGB <- function(outdir = NULL, site_ids, run_parallel = FALSE,
     PEcAn.logger::logger.info(paste0("Running in parallel with: ", ncores))
     cl = parallel::makeCluster(ncores)
     doParallel::registerDoParallel(cl)
-    data = foreach(i = seq_along(mylat), .combine = rbind) %dopar% get_data(i)
-    stopCluster(cl)
+    data = foreach::foreach(i = seq_along(mylat), .combine = rbind) %dopar% get_data(i)
+    parallel::stopCluster(cl)
     
   } else {
     # setup sequential run

From 248e78ccc872f5b084053a39f6a5813cb7c698e7 Mon Sep 17 00:00:00 2001
From: Shashank Singh <shashanksingh819@gmail.com>
Date: Wed, 25 Oct 2023 05:07:13 +0000
Subject: [PATCH 11/28] add log file

---
 modules/data.remote/tests/Rcheck_reference.log | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/modules/data.remote/tests/Rcheck_reference.log b/modules/data.remote/tests/Rcheck_reference.log
index afd295d0b58..e5c565fd010 100644
--- a/modules/data.remote/tests/Rcheck_reference.log
+++ b/modules/data.remote/tests/Rcheck_reference.log
@@ -1,4 +1,4 @@
-* using log directory ‘/tmp/RtmpqErjWC/PEcAn.data.remote.Rcheck’
+* using log directory ‘/tmp/Rtmpr2UgRH/PEcAn.data.remote.Rcheck’
 * using R version 4.1.3 (2022-03-10)
 * using platform: x86_64-pc-linux-gnu (64-bit)
 * using session charset: UTF-8
@@ -78,7 +78,7 @@ Extensions’ manual.
 
 Status: 2 WARNINGs, 1 NOTE
 See
-  ‘/tmp/RtmpqErjWC/PEcAn.data.remote.Rcheck/00check.log’
+  ‘/tmp/Rtmpr2UgRH/PEcAn.data.remote.Rcheck/00check.log’
 for details.
 
 

From 202f656a1e8d2a49ef0310f75f2e69322706437b Mon Sep 17 00:00:00 2001
From: istfer <fer.istem@gmail.com>
Date: Wed, 1 Nov 2023 11:34:12 +0200
Subject: [PATCH 12/28] changed rgdal function to terra in GEFS_helpers

---
 .../data.atmosphere/R/GEFS_helper_functions.R | 29 +++++++++++--------
 1 file changed, 17 insertions(+), 12 deletions(-)

diff --git a/modules/data.atmosphere/R/GEFS_helper_functions.R b/modules/data.atmosphere/R/GEFS_helper_functions.R
index 99b0a4db6e6..c63768daf11 100644
--- a/modules/data.atmosphere/R/GEFS_helper_functions.R
+++ b/modules/data.atmosphere/R/GEFS_helper_functions.R
@@ -243,25 +243,30 @@ process_gridded_noaa_download <- function(lat_list,
     
     for(hr in 1:length(curr_hours)){
       file_name <- paste0(base_filename2, curr_hours[hr])
+      grib_file_name <- paste0(working_directory,"/", file_name,".grib")
       
-      if(file.exists(paste0(working_directory,"/", file_name,".grib"))){
-        grib <- rgdal::readGDAL(paste0(working_directory,"/", file_name,".grib"), silent = TRUE)
-        lat_lon <- sp::coordinates(grib)
+      if(file.exists(grib_file_name)){
+        grib_data <- terra::rast(grib_file_name)
+        
+        ## Convert to data frame
+        grib_data_df <- terra::as.data.frame(grib_data, xy=TRUE)
+        lat_lon <- grib_data_df[, c("x", "y")]
+        
         for(s in 1:length(site_id)){
           
           index <- which(lat_lon[,2] == lats[s] & lat_lon[,1] == lons[s])
           
-          pressfc[s, hr]  <- grib$band1[index]
-          tmp2m[s, hr] <- grib$band2[index]
-          rh2m[s, hr]  <- grib$band3[index]
-          ugrd10m[s, hr]  <- grib$band4[index]
-          vgrd10m[s, hr]  <- grib$band5[index]
+          pressfc[s, hr]  <- grib_data_df$`SFC=Ground or water surface; Pressure [Pa]`[index]
+          tmp2m[s, hr]    <- grib_data_df$`2[m] HTGL=Specified height level above ground; Temperature [C]`[index]
+          rh2m[s, hr]     <- grib_data_df$`2[m] HTGL=Specified height level above ground; Relative humidity [%]`[index]
+          ugrd10m[s, hr]  <- grib_data_df$`10[m] HTGL=Specified height level above ground; u-component of wind [m/s]`[index]
+          vgrd10m[s, hr]  <- grib_data_df$`10[m] HTGL=Specified height level above ground; v-component of wind [m/s]`[index]
           
           if(curr_hours[hr] != "000"){
-            apcpsfc[s, hr]  <- grib$band6[index]
-            tcdcclm[s, hr]  <-  grib$band7[index]
-            dswrfsfc[s, hr]  <- grib$band8[index]
-            dlwrfsfc[s, hr]  <- grib$band9[index]
+            apcpsfc[s, hr]  <- grib_data_df$`SFC=Ground or water surface; 03 hr Total precipitation [kg/(m^2)]`[index]
+            tcdcclm[s, hr]  <- grib_data_df$`RESERVED(10) (Reserved); Total cloud cover [%]`[index]
+            dswrfsfc[s, hr] <- grib_data_df$`SFC=Ground or water surface; Downward Short-Wave Rad. Flux [W/(m^2)]`[index]
+            dlwrfsfc[s, hr] <- grib_data_df$`SFC=Ground or water surface; Downward Long-Wave Rad. Flux [W/(m^2)]`[index]
           }
         }
       }

From a5c65a6a177eb9a9d480529f459448e5ba2ae8ef Mon Sep 17 00:00:00 2001
From: istfer <fer.istem@gmail.com>
Date: Wed, 1 Nov 2023 11:59:03 +0200
Subject: [PATCH 13/28] replace rgdal with sf

---
 modules/data.atmosphere/R/download.NARR_site.R | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/modules/data.atmosphere/R/download.NARR_site.R b/modules/data.atmosphere/R/download.NARR_site.R
index 7ecfbca6bae..703546874e2 100644
--- a/modules/data.atmosphere/R/download.NARR_site.R
+++ b/modules/data.atmosphere/R/download.NARR_site.R
@@ -465,9 +465,9 @@ latlon2narr <- function(nc, lat.in, lon.in) {
 #' @inheritParams get_NARR_thredds
 #' @return `sp::SpatialPoints` object containing transformed x and y
 #' coordinates, in km, which should match NARR coordinates
-#' @importFrom rgdal checkCRSArgs
+#' @importFrom sf st_crs
   # ^not used directly here, but needed by sp::CRS.
-  # sp lists rgdal in Suggests rather than Imports,
+  # sp lists sf in Suggests rather than Imports,
   # so importing it here to ensure it's available at run time
 #' @author Alexey Shiklomanov
 #' @export

From f5756af4e69d80f7c8f215b7644c1ece96386777 Mon Sep 17 00:00:00 2001
From: istfer <fer.istem@gmail.com>
Date: Wed, 1 Nov 2023 12:02:54 +0200
Subject: [PATCH 14/28] roxygenize

---
 modules/data.atmosphere/DESCRIPTION | 3 ++-
 modules/data.atmosphere/NAMESPACE   | 2 +-
 2 files changed, 3 insertions(+), 2 deletions(-)

diff --git a/modules/data.atmosphere/DESCRIPTION b/modules/data.atmosphere/DESCRIPTION
index a29287049c5..9b9d5706e3a 100644
--- a/modules/data.atmosphere/DESCRIPTION
+++ b/modules/data.atmosphere/DESCRIPTION
@@ -49,10 +49,11 @@ Imports:
     raster,
     REddyProc,
     reshape2,
-    rgdal,
     rlang (>= 0.2.0),
+    sf,
     sp,
     stringr (>= 1.1.0),
+    terra,
     testthat (>= 2.0.0),
     tibble,
     tidyr,
diff --git a/modules/data.atmosphere/NAMESPACE b/modules/data.atmosphere/NAMESPACE
index 7183782887f..9dd14faa440 100644
--- a/modules/data.atmosphere/NAMESPACE
+++ b/modules/data.atmosphere/NAMESPACE
@@ -113,5 +113,5 @@ export(write_noaa_gefs_netcdf)
 import(dplyr)
 import(tidyselect)
 importFrom(magrittr,"%>%")
-importFrom(rgdal,checkCRSArgs)
 importFrom(rlang,.data)
+importFrom(sf,st_crs)

From 9624d3d4946c775f5e5180c8ecb81647ce9cb95f Mon Sep 17 00:00:00 2001
From: istfer <fer.istem@gmail.com>
Date: Wed, 1 Nov 2023 12:20:06 +0200
Subject: [PATCH 15/28] change maptools to suntools

---
 modules/data.atmosphere/DESCRIPTION                         | 2 +-
 .../R/met_temporal_downscale.Gaussian_ensemble.R            | 6 +++---
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/modules/data.atmosphere/DESCRIPTION b/modules/data.atmosphere/DESCRIPTION
index 9b9d5706e3a..b07be4c42d9 100644
--- a/modules/data.atmosphere/DESCRIPTION
+++ b/modules/data.atmosphere/DESCRIPTION
@@ -36,7 +36,6 @@ Imports:
     jsonlite,
     lubridate (>= 1.6.0),
     magrittr,
-    maptools,
     MASS,
     mgcv,
     ncdf4 (>= 1.15),
@@ -53,6 +52,7 @@ Imports:
     sf,
     sp,
     stringr (>= 1.1.0),
+    suntools,
     terra,
     testthat (>= 2.0.0),
     tibble,
diff --git a/modules/data.atmosphere/R/met_temporal_downscale.Gaussian_ensemble.R b/modules/data.atmosphere/R/met_temporal_downscale.Gaussian_ensemble.R
index 1082ffb60e3..a241d1fbe5f 100644
--- a/modules/data.atmosphere/R/met_temporal_downscale.Gaussian_ensemble.R
+++ b/modules/data.atmosphere/R/met_temporal_downscale.Gaussian_ensemble.R
@@ -216,11 +216,11 @@ met_temporal_downscale.Gaussian_ensemble <- function(in.path, in.prefix, outfold
       day <- as.POSIXct(sprintf("%s 12:00:00", date), tz = tz)
       sequence <- seq(from = day, length.out = span, by = "days")
       
-      sunrise <- maptools::sunriset(lon.lat, sequence, direction = "sunrise", 
+      sunrise <- suntools::sunriset(lon.lat, sequence, direction = "sunrise", 
                                     POSIXct.out = TRUE)
-      sunset <- maptools::sunriset(lon.lat, sequence, direction = "sunset", 
+      sunset <- suntools::sunriset(lon.lat, sequence, direction = "sunset", 
                                    POSIXct.out = TRUE)
-      solar_noon <- maptools::solarnoon(lon.lat, sequence, POSIXct.out = TRUE)
+      solar_noon <- suntools::solarnoon(lon.lat, sequence, POSIXct.out = TRUE)
       
       data.frame(date = as.Date(sunrise$time), sunrise = as.numeric(format(sunrise$time, "%H%M")), 
                  solarnoon = as.numeric(format(solar_noon$time, "%H%M")), 

From c3221122c313f79b3ca41f9aa63ae1bfc9d7255b Mon Sep 17 00:00:00 2001
From: istfer <fer.istem@gmail.com>
Date: Wed, 1 Nov 2023 12:29:43 +0200
Subject: [PATCH 16/28] add suntools remove maptools

---
 docker/depends/pecan.depends.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docker/depends/pecan.depends.R b/docker/depends/pecan.depends.R
index c208e5e5525..69728e55fbc 100644
--- a/docker/depends/pecan.depends.R
+++ b/docker/depends/pecan.depends.R
@@ -76,7 +76,6 @@ wanted <- c(
 'magic',
 'magrittr',
 'maps',
-'maptools',
 'markdown',
 'MASS',
 'Matrix',
@@ -130,6 +129,7 @@ wanted <- c(
 'stats',
 'stringi',
 'stringr',
+'suntools',
 'swfscMisc',
 'terra',
 'testthat',

From b24df9751dbcfb57bb349cd65734a1be21ed9a09 Mon Sep 17 00:00:00 2001
From: istfer <fer.istem@gmail.com>
Date: Wed, 1 Nov 2023 14:05:05 +0200
Subject: [PATCH 17/28] rgdal to sf in gis.functions

---
 modules/data.land/DESCRIPTION       | 1 -
 modules/data.land/R/gis.functions.R | 8 ++++----
 2 files changed, 4 insertions(+), 5 deletions(-)

diff --git a/modules/data.land/DESCRIPTION b/modules/data.land/DESCRIPTION
index 5ec23616b0f..eb187ac1667 100644
--- a/modules/data.land/DESCRIPTION
+++ b/modules/data.land/DESCRIPTION
@@ -61,7 +61,6 @@ Suggests:
     PEcAn.settings,
     redland,
     raster,
-    rgdal,
     RPostgreSQL,
     testthat (>= 1.0.2)
 License: BSD_3_clause + file LICENSE
diff --git a/modules/data.land/R/gis.functions.R b/modules/data.land/R/gis.functions.R
index 8f9434aea3f..0fa83941f88 100644
--- a/modules/data.land/R/gis.functions.R
+++ b/modules/data.land/R/gis.functions.R
@@ -68,14 +68,13 @@ shp2kml <- function(dir, ext, kmz = FALSE, proj4 = NULL, color = NULL, NameField
     # Read in shapefile(s) & get coordinates/projection info shp.file <-
     # readShapeSpatial(file.path(dir,i),verbose=TRUE) coordinates(test) <- ~X+Y
     
-    layers <- rgdal::ogrListLayers(file.path(dir, i))
-    info   <- rgdal::ogrInfo(file.path(dir, i), layers)
+    layers <- sf::st_layers(file.path(dir, i))
     # shp.file <- readOGR(file.path(dir,i),layer=layers) # no need to read in file
     
     # Display vector info to the console
     print("")
-    print(paste0("Input layers: ", layers))
-    print(paste0("Input projection info: ", info$p4s))
+    print(paste0("Input layers: ", layers$name))
+    print(paste0("Input projection info: ", layers$crs[[1]]$input))
     print("")
     
     # Write out kml/kmz using plotKML package if (is.null(color)){ color <- 'grey70' }
@@ -133,6 +132,7 @@ get.attributes <- function(file, coords) {
   
   #library(fields)
   #require(rgdal)
+  # note that OGR support is now provided by the sf and terra packages among others 
   
   # print('NOT IMPLEMENTED YET') subset_layer(file,coords)
 } # get.attributes

From 87559d7c6130b629ca45cfe8fe68db02126515f4 Mon Sep 17 00:00:00 2001
From: istfer <fer.istem@gmail.com>
Date: Wed, 1 Nov 2023 14:25:19 +0200
Subject: [PATCH 18/28] removed rgdal call from data.remote as well

---
 modules/data.remote/DESCRIPTION | 1 -
 modules/data.remote/R/NLCD.R    | 3 +--
 2 files changed, 1 insertion(+), 3 deletions(-)

diff --git a/modules/data.remote/DESCRIPTION b/modules/data.remote/DESCRIPTION
index 68e3ee22e89..c994d1cd476 100644
--- a/modules/data.remote/DESCRIPTION
+++ b/modules/data.remote/DESCRIPTION
@@ -36,7 +36,6 @@ Suggests:
     dplyr,
     ggplot2,
     lubridate,
-    rgdal,
     reshape,
     testthat (>= 1.0.2),
     tibble
diff --git a/modules/data.remote/R/NLCD.R b/modules/data.remote/R/NLCD.R
index dfc712f2e09..98fc995fa1a 100644
--- a/modules/data.remote/R/NLCD.R
+++ b/modules/data.remote/R/NLCD.R
@@ -69,8 +69,7 @@ download.NLCD <- function(outdir, year = 2011, con = NULL) {
 ##' @description Based on codes from Christy Rollinson and from Max Joseph (http://mbjoseph.github.io/2014/11/08/nlcd.html)
 extract_NLCD <- function(buffer, coords, data_dir = NULL, con = NULL, year = 2011) {
     library(raster)
-    require(rgdal)
-    
+
     if (!is.null(con)) {
         library(PEcAn.DB)
         if (year == 2001) {

From c97edb155c0465a2666afd0f95df9590b26427fd Mon Sep 17 00:00:00 2001
From: istfer <fer.istem@gmail.com>
Date: Wed, 1 Nov 2023 16:34:00 +0200
Subject: [PATCH 19/28] attempt to change raster with terra

---
 modules/data.remote/R/NLCD.R | 18 +++++++++---------
 1 file changed, 9 insertions(+), 9 deletions(-)

diff --git a/modules/data.remote/R/NLCD.R b/modules/data.remote/R/NLCD.R
index 98fc995fa1a..6c7e1ff71cb 100644
--- a/modules/data.remote/R/NLCD.R
+++ b/modules/data.remote/R/NLCD.R
@@ -103,21 +103,21 @@ extract_NLCD <- function(buffer, coords, data_dir = NULL, con = NULL, year = 201
         print(paste("File not found:", filename))
         return(NULL)
     }
-    nlcd <- raster(filename)
+    nlcd <- terra::rast(filename)
     
     # transform points
-    sites <- SpatialPoints(coords = coords, proj4string = CRS("+proj=longlat +datum=WGS84"))
-    sites <- spTransform(sites, crs(nlcd))
+    sites <- terra::vect(coords, geom=c("long", "lat"), crs="+proj=longlat +datum=WGS84")
+    sites <- terra::buffer(x, width=buffer)
     
     # extract
-    sum.raw <- table(extract(nlcd, sites, buffer = buffer))
+    sum.raw <- table(terra::extract(nlcd, sites))
     summ <- prop.table(sum.raw)
-    mydf <- data.frame(cover = names(summ), percent = as.vector(summ), count = as.vector(sum.raw))
+    mydf <- data.frame(cover.name = colnames(summ), percent = as.vector(summ), count = as.vector(sum.raw))
+    mydf <- mydf[mydf$count!=0,]
     
-    # land cover number to name conversions
-    cover.table <- nlcd@data@attributes[[1]]
-    cover.names <- cover.table[as.numeric(as.character(mydf$cover)) + 1, grep("Land", names(cover.table))]
-    mydf$cover.name <- cover.names
+    # land cover name to number conversions
+    nlcd_levels <- terra::levels(nlcd)[[1]]
+    mydf$cover  <- nlcd_levels$value[nlcd_levels$`Land Cover Class` %in% mydf$cover.name]
     
     return(mydf)
 } # extract_NLCD

From 1114f56796a157b55a12d4cfa4b5afb31fa5e9fb Mon Sep 17 00:00:00 2001
From: istfer <fer.istem@gmail.com>
Date: Wed, 1 Nov 2023 16:39:38 +0200
Subject: [PATCH 20/28] add warning

---
 modules/data.remote/R/NLCD.R | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/modules/data.remote/R/NLCD.R b/modules/data.remote/R/NLCD.R
index 6c7e1ff71cb..01005ddc479 100644
--- a/modules/data.remote/R/NLCD.R
+++ b/modules/data.remote/R/NLCD.R
@@ -103,6 +103,9 @@ extract_NLCD <- function(buffer, coords, data_dir = NULL, con = NULL, year = 201
         print(paste("File not found:", filename))
         return(NULL)
     }
+    
+    # WARNING: the following extraction previously used raster and sp package functions
+    # this new implementation with terra functions has not been thoroughly tested
     nlcd <- terra::rast(filename)
     
     # transform points

From bfb03a83141bf131b23bc490c416f6e9962f838e Mon Sep 17 00:00:00 2001
From: istfer <fer.istem@gmail.com>
Date: Wed, 1 Nov 2023 16:50:46 +0200
Subject: [PATCH 21/28] remove library call to raster

---
 modules/data.remote/R/NLCD.R | 1 -
 1 file changed, 1 deletion(-)

diff --git a/modules/data.remote/R/NLCD.R b/modules/data.remote/R/NLCD.R
index 01005ddc479..a0416cdebbb 100644
--- a/modules/data.remote/R/NLCD.R
+++ b/modules/data.remote/R/NLCD.R
@@ -68,7 +68,6 @@ download.NLCD <- function(outdir, year = 2011, con = NULL) {
 ##' 
 ##' @description Based on codes from Christy Rollinson and from Max Joseph (http://mbjoseph.github.io/2014/11/08/nlcd.html)
 extract_NLCD <- function(buffer, coords, data_dir = NULL, con = NULL, year = 2011) {
-    library(raster)
 
     if (!is.null(con)) {
         library(PEcAn.DB)

From 20315900ada53664babefe13f957899f45fd7cc8 Mon Sep 17 00:00:00 2001
From: istfer <fer.istem@gmail.com>
Date: Wed, 1 Nov 2023 16:51:45 +0200
Subject: [PATCH 22/28] fix typo

---
 modules/data.remote/R/NLCD.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/data.remote/R/NLCD.R b/modules/data.remote/R/NLCD.R
index a0416cdebbb..0e891aec2eb 100644
--- a/modules/data.remote/R/NLCD.R
+++ b/modules/data.remote/R/NLCD.R
@@ -109,7 +109,7 @@ extract_NLCD <- function(buffer, coords, data_dir = NULL, con = NULL, year = 201
     
     # transform points
     sites <- terra::vect(coords, geom=c("long", "lat"), crs="+proj=longlat +datum=WGS84")
-    sites <- terra::buffer(x, width=buffer)
+    sites <- terra::buffer(sites, width=buffer)
     
     # extract
     sum.raw <- table(terra::extract(nlcd, sites))

From 8263c71e923cac88e92431b4be36c72d96d0a898 Mon Sep 17 00:00:00 2001
From: istfer <fer.istem@gmail.com>
Date: Thu, 2 Nov 2023 17:09:10 +0200
Subject: [PATCH 23/28] remove library and require calls from data.remote

---
 modules/data.remote/R/NLCD.R             | 4 ++--
 modules/data.remote/R/download.thredds.R | 2 +-
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/modules/data.remote/R/NLCD.R b/modules/data.remote/R/NLCD.R
index 0e891aec2eb..32517eff2ae 100644
--- a/modules/data.remote/R/NLCD.R
+++ b/modules/data.remote/R/NLCD.R
@@ -23,7 +23,7 @@ download.NLCD <- function(outdir, year = 2011, con = NULL) {
     
     ## before downloading, check if the file already exists on this host
     if (!is.null(con)) {
-        library(PEcAn.DB)
+
         chk <- dbfile.check(type = "Input", id = input.id, con = con)
         if (nrow(chk) > 0) {
             machines <- db.query(paste("SELECT * from machines where id in (", 
@@ -70,7 +70,7 @@ download.NLCD <- function(outdir, year = 2011, con = NULL) {
 extract_NLCD <- function(buffer, coords, data_dir = NULL, con = NULL, year = 2011) {
 
     if (!is.null(con)) {
-        library(PEcAn.DB)
+
         if (year == 2001) {
             input.id <- 1000000482
         } else if (year == 2011) {
diff --git a/modules/data.remote/R/download.thredds.R b/modules/data.remote/R/download.thredds.R
index 09d44ac1337..04fc4b99923 100755
--- a/modules/data.remote/R/download.thredds.R
+++ b/modules/data.remote/R/download.thredds.R
@@ -82,7 +82,7 @@ download.thredds.AGB <- function(outdir = NULL, site_ids, run_parallel = FALSE,
     } else {
       ncores <- parallel::detectCores() -1
     }
-    require(doParallel)
+  
     PEcAn.logger::logger.info(paste0("Running in parallel with: ", ncores))
     cl = parallel::makeCluster(ncores)
     doParallel::registerDoParallel(cl)

From 9137628fa99dd82ab1d1e98b059092d879fbdbcb Mon Sep 17 00:00:00 2001
From: istfer <fer.istem@gmail.com>
Date: Thu, 2 Nov 2023 18:56:38 +0200
Subject: [PATCH 24/28] CI updates

---
 modules/data.remote/DESCRIPTION                | 3 ++-
 modules/data.remote/tests/Rcheck_reference.log | 2 --
 2 files changed, 2 insertions(+), 3 deletions(-)

diff --git a/modules/data.remote/DESCRIPTION b/modules/data.remote/DESCRIPTION
index c994d1cd476..617f49b1338 100644
--- a/modules/data.remote/DESCRIPTION
+++ b/modules/data.remote/DESCRIPTION
@@ -20,7 +20,6 @@ Imports:
     PEcAn.utils,
     purrr,
     XML,
-    raster,
     sp,
     MODISTools (>= 1.1.0),
     reticulate,
@@ -28,6 +27,7 @@ Imports:
     magrittr,
     PEcAn.remote,
     stringr (>= 1.1.0),
+    terra,
     doParallel,
     parallel,
     foreach
@@ -36,6 +36,7 @@ Suggests:
     dplyr,
     ggplot2,
     lubridate,
+    raster,
     reshape,
     testthat (>= 1.0.2),
     tibble
diff --git a/modules/data.remote/tests/Rcheck_reference.log b/modules/data.remote/tests/Rcheck_reference.log
index 822a9411303..182f76f6d12 100644
--- a/modules/data.remote/tests/Rcheck_reference.log
+++ b/modules/data.remote/tests/Rcheck_reference.log
@@ -82,8 +82,6 @@ Author field differs from that derived from Authors@R
 * checking loading without being on the library search path ... OK
 * checking use of S3 registration ... OK
 * checking dependencies in R code ... WARNING
-'library' or 'require' calls not declared from:
-  ‘PEcAn.DB’ ‘doParallel’ ‘raster’
 'library' or 'require' calls in package code:
   ‘PEcAn.DB’ ‘doParallel’ ‘raster’ ‘rgdal’
   Please use :: or requireNamespace() instead.

From 00a12222c8e5a6eab8ad7ebfb3e4ab7a73065de9 Mon Sep 17 00:00:00 2001
From: istfer <fer.istem@gmail.com>
Date: Fri, 3 Nov 2023 09:07:22 +0200
Subject: [PATCH 25/28] generate dependencies

---
 docker/depends/pecan.depends.R | 1 -
 1 file changed, 1 deletion(-)

diff --git a/docker/depends/pecan.depends.R b/docker/depends/pecan.depends.R
index 69728e55fbc..5b03d7297e5 100644
--- a/docker/depends/pecan.depends.R
+++ b/docker/depends/pecan.depends.R
@@ -112,7 +112,6 @@ wanted <- c(
 'reshape',
 'reshape2',
 'reticulate',
-'rgdal',
 'rjags',
 'rjson',
 'rlang',

From a4c7e14697afc172710a235b31a25e9e4c663c11 Mon Sep 17 00:00:00 2001
From: istfer <fer.istem@gmail.com>
Date: Sun, 5 Nov 2023 09:32:13 +0200
Subject: [PATCH 26/28] remote install suntools

---
 docker/depends/pecan.depends.R      | 2 +-
 modules/data.atmosphere/DESCRIPTION | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/docker/depends/pecan.depends.R b/docker/depends/pecan.depends.R
index 5b03d7297e5..3e292529a6b 100644
--- a/docker/depends/pecan.depends.R
+++ b/docker/depends/pecan.depends.R
@@ -9,6 +9,7 @@ Sys.setenv(RLIB = rlib)
 
 # install remotes first in case packages are references in dependencies
 remotes::install_github(c(
+'adokter/suntools',
 'araiho/linkages_package',
 'chuhousen/amerifluxr',
 'ebimodeling/biocro@0.951',
@@ -128,7 +129,6 @@ wanted <- c(
 'stats',
 'stringi',
 'stringr',
-'suntools',
 'swfscMisc',
 'terra',
 'testthat',
diff --git a/modules/data.atmosphere/DESCRIPTION b/modules/data.atmosphere/DESCRIPTION
index b07be4c42d9..8f0482e9e41 100644
--- a/modules/data.atmosphere/DESCRIPTION
+++ b/modules/data.atmosphere/DESCRIPTION
@@ -52,7 +52,6 @@ Imports:
     sf,
     sp,
     stringr (>= 1.1.0),
-    suntools,
     terra,
     testthat (>= 2.0.0),
     tibble,
@@ -70,6 +69,7 @@ Suggests:
     progress,
     reticulate
 Remotes:
+    github::adokter/suntools,
     github::chuhousen/amerifluxr,
     github::ropensci/geonames,
     github::ropensci/nneo

From ad8adce78cccd7b5b457f96f475eb5d488972920 Mon Sep 17 00:00:00 2001
From: istfer <fer.istem@gmail.com>
Date: Sun, 5 Nov 2023 09:52:49 +0200
Subject: [PATCH 27/28] working with CI

---
 docker/depends/pecan.depends.R      | 1 +
 modules/data.atmosphere/DESCRIPTION | 1 +
 2 files changed, 2 insertions(+)

diff --git a/docker/depends/pecan.depends.R b/docker/depends/pecan.depends.R
index 3e292529a6b..e49b8fb72fb 100644
--- a/docker/depends/pecan.depends.R
+++ b/docker/depends/pecan.depends.R
@@ -129,6 +129,7 @@ wanted <- c(
 'stats',
 'stringi',
 'stringr',
+'suntools',
 'swfscMisc',
 'terra',
 'testthat',
diff --git a/modules/data.atmosphere/DESCRIPTION b/modules/data.atmosphere/DESCRIPTION
index 8f0482e9e41..097a134349e 100644
--- a/modules/data.atmosphere/DESCRIPTION
+++ b/modules/data.atmosphere/DESCRIPTION
@@ -52,6 +52,7 @@ Imports:
     sf,
     sp,
     stringr (>= 1.1.0),
+    suntools,
     terra,
     testthat (>= 2.0.0),
     tibble,

From 6900a0f40410792c6aa11a1579e480691a15e2b6 Mon Sep 17 00:00:00 2001
From: istfer <fer.istem@gmail.com>
Date: Sun, 5 Nov 2023 10:09:52 +0200
Subject: [PATCH 28/28] rcheck ref

---
 modules/data.atmosphere/tests/Rcheck_reference.log | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/modules/data.atmosphere/tests/Rcheck_reference.log b/modules/data.atmosphere/tests/Rcheck_reference.log
index 1f7a42f6634..be30baa7ac2 100644
--- a/modules/data.atmosphere/tests/Rcheck_reference.log
+++ b/modules/data.atmosphere/tests/Rcheck_reference.log
@@ -76,13 +76,13 @@ Found the following (possibly) invalid URLs:
 The Date field is over a month old.
 * checking package namespace information ... OK
 * checking package dependencies ... WARNING
-Imports includes 39 non-default packages.
+Imports includes 40 non-default packages.
 Importing from so many packages makes the package vulnerable to any of
 them becoming unavailable.  Move as many as possible to Suggests and
 use conditionally.
 
 * checking package dependencies ... NOTE
-Imports includes 39 non-default packages.
+Imports includes 40 non-default packages.
 Importing from so many packages makes the package vulnerable to any of
 them becoming unavailable.  Move as many as possible to Suggests and
 use conditionally.