fix check warnings/notes in assim.batch package

modules/assim.batch/R/get.da.data.R

@@ -41,7 +41,15 @@ calculate.nee.L <- function(yeardoytime, model.i.nee, observed.flux, be, bu) {
 
 
 get.da.data <- function(out.dir, ameriflux.dir, years, be, bu, ensemble.size = 199) {
-  load(paste(out.dir, "samples.Rdata", sep = ""))
+  samples.file <- paste(out.dir, "samples.Rdata" , sep = "")
+  if(file.exists(samples.file)) {
+    samples <- new.env()
+    load(samples.file, envir = samples)
+    ensemble.samples <- samples$ensemble.samples
+    sa.samples <- samples$sa.samples
+  } else {
+    PEcAn.logger::logger.error(samples.file, "not found, this file is required by the get.da.data function")
+  }
 
   pfts <- names(ensemble.samples)
   pfts <- pfts[pfts != "env"]

modules/assim.batch/R/get.da.data.growth.R

@@ -80,7 +80,16 @@ get.da.data.growth <- function() {
   growth <- cbind(buds[, c("plot", "individual", "pft")], growth)
 
   ensemble.size <- 500
-  load(paste(out.dir, "samples.Rdata", sep = ""))
+  samples.file <- paste(out.dir, "samples.Rdata" , sep = "")
+
+  if(file.exists(samples.file)) {
+    samples <- new.env()
+    load(samples.file, envir = samples)
+    ensemble.samples <- samples$ensemble.samples
+    sa.samples <- samples$sa.samples
+  } else {
+    PEcAn.logger::logger.error(samples.file, "not found, this file is required by the get.da.data function")
+  }
 
   pfts <- names(ensemble.samples)
   pfts <- pfts[pfts != "env"]

modules/assim.batch/R/pda.utils.R

@@ -297,6 +297,7 @@ pda.load.priors <- function(settings, con, extension.check = FALSE) {
 
     if (length(pid) == 0) {
       pid <- grep("prior.distns.Rdata", files$file_name)  ## is there a prior file?
+
     }
 
     if (length(pid) > 0) {
@@ -322,7 +323,11 @@ pda.load.priors <- function(settings, con, extension.check = FALSE) {
     # make sure there are no left over distributions in the environment
     suppressWarnings(rm(post.distns, prior.distns))
 
-    load(prior.paths[[i]])
+    distns <- new.env()
+    load(prior.paths[[i]], envir = "distns")
+    prior.distns <- distns$prior.distns
+    post.distns <- distns$post.distns
+
     if (!exists("post.distns")) {
       prior.out[[i]] <- prior.distns
     } else {

modules/assim.batch/R/plot.da.R

@@ -23,8 +23,27 @@ plot.da <- function(prior.dir, prior.file, in.dir, out.dir, next.run.dir) {
   num.run.ids <- 5  #commandArgs(trailingOnly = TRUE)
   print(num.run.ids)
 
-  load(paste(in.dir, "samples.Rdata", sep = ""))
-  load(paste(in.dir, "L.nee.Rdata", sep = ""))
+  samples.file <- paste(in.dir, "samples.Rdata", sep = "")
+  L.nee.file <- paste(in.dir, "L.nee.Rdata", sep = "")
+
+  if(file.exists(samples.file)) {
+    samples <- new.env()
+    load(samples.file, envir = "samples")
+    ensemble.samples <- samples$ensemble.samples
+    sa.samples <- samples$sa.samples
+  } else {
+    PEcAn.logger::logger.error(samples.file, "not found, this file is required by the plot.da function")
+  }
+
+  if(file.exists(L.nee.file)) {
+    L.nee <- new.env()
+    load(L.nee.file, envir = "L.nee")
+    x <- L.nee$x
+    y <- L.nee$y
+  } else {
+    PEcAn.logger::logger.error(L.nee.file, "not found, this file is required by the plot.da function")
+  }
+
   prior.x <- x
   prior.y <- y
 
@@ -90,7 +109,16 @@ plot.da <- function(prior.dir, prior.file, in.dir, out.dir, next.run.dir) {
 
   samp <- lapply(seq(num.run.ids), function(run.id) {
     print(paste0(in.dir, "./mcmc", run.id, ".Rdata"))
-    load(paste0(in.dir, "./mcmc", run.id, ".Rdata"))
+    run.id.file <- paste0(in.dir, "./mcmc", run.id, ".Rdata")
+
+    if(file.exists(run.id.file)) {
+      run.env <- new.env()
+      load(run.id.file, envir = "run.env")
+      m <- run.env$m
+    } else {
+      PEcAn.logger::logger.error(run.id.file, "not found, this file is required by the plot.da function")
+    }
+
     return(m)
   })
 

modules/assim.batch/tests/Rcheck_reference.log

@@ -1,62 +1,13 @@
-* using log directory ‘/home/tanishq010/pecan/modules/PEcAn.assim.batch.Rcheck’
-* using R version 4.2.1 (2022-06-23)
+* using log directory ‘/tmp/Rtmp0m7lr6/PEcAn.assim.batch.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.assim.batch/DESCRIPTION’ ... OK
 * checking extension type ... Package
-* this is package ‘PEcAn.assim.batch’ version ‘1.7.2’
+* this is package ‘PEcAn.assim.batch’ version ‘1.7.2.9000’
 * package encoding: UTF-8
-* checking CRAN incoming feasibility ... WARNING
-Maintainer: ‘Istem Fer <[email protected]>’
-
-New submission
-
-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.benchmark, PEcAn.DB, PEcAn.emulator, PEcAn.logger, PEcAn.MA,
-    PEcAn.remote, PEcAn.settings, PEcAn.uncertainty, PEcAn.utils,
-    PEcAn.workflow
-
-The Date field is over a month old.
 * checking package namespace information ... OK
-* checking package dependencies ... WARNING
-Imports includes 27 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 27 non-default packages.
 Importing from so many packages makes the package vulnerable to any of
@@ -87,37 +38,17 @@ use conditionally.
 * 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 ... NOTE
-Namespace in Imports field not imported from: ‘dplyr’
-  All declared Imports should be used.
+* checking dependencies in R code ... OK
 * checking S3 generic/method consistency ... OK
 * checking replacement functions ... OK
 * checking foreign function calls ... OK
 * checking R code for possible problems ... NOTE
-get.da.data: no visible binding for global variable ‘ensemble.samples’
-get.da.data : <anonymous>: no visible binding for global variable
-  ‘sa.samples’
-get.da.data: no visible binding for global variable ‘sa.samples’
 get.da.data : <anonymous>: no visible global function definition for
   ‘read.output.type’
-get.da.data.growth: no visible binding for global variable
-  ‘ensemble.samples’
-get.da.data.growth: no visible binding for global variable ‘sa.samples’
 get.da.data.growth : <anonymous>: no visible global function definition
   for ‘read.output.type’
-pda.load.priors: no visible binding for global variable ‘post.distns’
-pda.load.priors: no visible binding for global variable ‘prior.distns’
-plot.da: no visible binding for global variable ‘y’
-plot.da: no visible binding for global variable ‘ensemble.samples’
-plot.da : <anonymous>: no visible binding for global variable
-  ‘ensemble.samples’
-plot.da : <anonymous>: no visible binding for global variable
-  ‘sa.samples’
-plot.da : <anonymous>: no visible binding for global variable ‘m’
 Undefined global functions or variables:
-  ensemble.samples m post.distns prior.distns read.output.type
-  sa.samples y
+  read.output.type
 
 Found the following assignments to the global environment:
 File ‘PEcAn.assim.batch/R/pda.get.model.output.R’:
@@ -140,9 +71,32 @@ File ‘PEcAn.assim.batch/R/pda.get.model.output.R’:
  OK
 * checking for unstated dependencies in vignettes ... OK
 * checking package vignettes in ‘inst/doc’ ... OK
-* checking re-building of vignette outputs ... OK
+* checking re-building of vignette outputs ... WARNING
+Error(s) in re-building vignettes:
+  ...
+--- re-building ‘AssimBatchVignette.Rmd’ using rmarkdown
+Error: processing vignette 'AssimBatchVignette.Rmd' failed with diagnostics:
+The function xfun::isFALSE() will be deprecated in the future. Please consider using base::isFALSE(x) or identical(x, FALSE) instead.
+--- failed re-building ‘AssimBatchVignette.Rmd’
+
+--- re-building ‘MultiSitePDAVignette.Rmd’ using rmarkdown
+Error: processing vignette 'MultiSitePDAVignette.Rmd' failed with diagnostics:
+The function xfun::isFALSE() will be deprecated in the future. Please consider using base::isFALSE(x) or identical(x, FALSE) instead.
+--- failed re-building ‘MultiSitePDAVignette.Rmd’
+
+SUMMARY: processing the following files failed:
+  ‘AssimBatchVignette.Rmd’ ‘MultiSitePDAVignette.Rmd’
+
+Error: Vignette re-building failed.
+Execution halted
+
 * checking for non-standard things in the check directory ... OK
 * checking for detritus in the temp directory ... OK
 * DONE
 
-Status: 2 WARNING, 3 NOTEs
+Status: 1 WARNING, 2 NOTEs
+See
+  ‘/tmp/Rtmp0m7lr6/PEcAn.assim.batch.Rcheck/00check.log’
+for details.
+
+