Merge branch 'develop' into dev-fix-PecanProject#2758

meetagrawal09 · Feb 11, 2023 · ec736d3 · ec736d3
2 parents 33ddccd + a24e0c0
commit ec736d3
Show file tree

Hide file tree

Showing 5 changed files with 13 additions and 16 deletions.
diff --git a/models/ed/.Rbuildignore b/models/ed/.Rbuildignore
@@ -2,3 +2,5 @@
 ^model_info\.json$
 ^scripts$
 ^data-raw$
+^.*\.Rproj$
+^\.Rproj\.user$
diff --git a/models/ed/DESCRIPTION b/models/ed/DESCRIPTION
@@ -34,21 +34,22 @@ Description: The Predictive Ecosystem Carbon Analyzer (PEcAn) is a scientific
 Depends: 
     R (>= 2.10)
 Imports:
-    PEcAn.data.atmosphere,
-    PEcAn.data.land,
-    PEcAn.logger,
-    PEcAn.remote,
-    PEcAn.settings,
-    PEcAn.utils,
-    assertthat,
     abind (>= 1.4.5),
+    assertthat,
     dplyr,
     glue,
     hdf5r,
     lubridate,
     magrittr,
     ncdf4 (>= 1.15),
+    PEcAn.data.atmosphere,
+    PEcAn.data.land,
+    PEcAn.logger,
+    PEcAn.remote,
+    PEcAn.settings,
+    PEcAn.utils,
     purrr,
+    rlang,
     stringr(>= 1.1.0),
     tidyr,
     tibble,

diff --git a/models/ed/NAMESPACE b/models/ed/NAMESPACE
@@ -56,3 +56,4 @@ export(write_pss)
 export(write_restart.ED2)
 export(write_site)
 importFrom(magrittr,"%>%")
+importFrom(rlang,.data)
diff --git a/models/ed/R/read_ed_metheader.R b/models/ed/R/read_ed_metheader.R
@@ -45,6 +45,7 @@
 #' @param check_files Logical. If `TRUE`, perform basic diagnostics on met 
 #' files as well.
 #' @return List of ED met input parameters. See Details.
+#' @importFrom rlang .data
 #' @export
 read_ed_metheader <- function(filename, check = TRUE, check_files = TRUE) {
   if (!file.exists(filename)) {
@@ -88,7 +89,7 @@ read_ed_metheader <- function(filename, check = TRUE, check_files = TRUE) {
     variables_raw <- read.table(text = sub_file[4:6], header = TRUE)
     variables_raw$value_type <- c("update_frequency", "flag")
     variables_table <- variables_raw %>%
-      tidyr::gather("variable", "value", -value_type) %>%
+      tidyr::gather("variable", "value", -.data$value_type) %>%
       tidyr::spread("value_type", "value") %>%
       dplyr::left_join(met_variable_description, by = "variable") %>%
       dplyr::left_join(met_flag_description, by = "flag")

diff --git a/models/ed/tests/Rcheck_reference.log b/models/ed/tests/Rcheck_reference.log
@@ -101,32 +101,24 @@ download_edi: no visible global function definition for ‘unzip’
 modify_df: no visible global function definition for ‘modifyList’
 modify_ed2in: no visible global function definition for ‘modifyList’
 put_E_values: no visible global function definition for ‘data’
-put_E_values: no visible binding for global variable ‘pftmapping’
 put_T_values: no visible global function definition for ‘head’
 read_E_files: no visible global function definition for ‘data’
-read_E_files: no visible binding for global variable ‘pftmapping’
 read_S_files: no visible global function definition for ‘data’
-read_S_files: no visible binding for global variable ‘pftmapping’
 read_css: no visible global function definition for ‘read.table’
 read_ed_metheader: no visible global function definition for
   ‘read.table’
-read_ed_metheader: no visible binding for global variable ‘value_type’
 read_pss: no visible global function definition for ‘read.table’
 read_pss: ... may be used in an incorrect context: ‘check_pss(pss,
   ...)’
 read_site: no visible global function definition for ‘read.table’
 veg2model.ED2: no visible global function definition for ‘data’
-veg2model.ED2: no visible binding for global variable ‘pftmapping’
 veg2model.ED2: no visible global function definition for ‘median’
 veg2model.ED2: no visible global function definition for ‘write.table’
 write.config.ED2: no visible global function definition for ‘saveXML’
 write.config.ED2: no visible global function definition for ‘db.query’
 write.config.ED2: no visible global function definition for
   ‘modifyList’
 write.config.xml.ED2: no visible global function definition for ‘data’
-write.config.xml.ED2: no visible binding for global variable
-  ‘pftmapping’
-write.config.xml.ED2: no visible binding for global variable ‘soil’
 write.config.xml.ED2: no visible global function definition for
   ‘modifyList’
 write_css: no visible global function definition for ‘write.table’