Merge branch 'develop' into check-on-newer-R

base/remote/R/qsub_parallel.R

@@ -103,7 +103,6 @@ qsub_parallel <- function(settings, files = NULL, prefix = "sipnet.out", sleep =
   folders <- file.path(settings$host$outdir, run_list)
   L_folder <- length(folders)
   pb <- utils::txtProgressBar(min = 0, max = L_folder, style = 3)
-  pbi <- 0
   #here we not only detect if the target files are generated.
   #we also detect if the jobs are still existed on the server.
   if (is_rabbitmq) {
@@ -121,7 +120,6 @@ qsub_parallel <- function(settings, files = NULL, prefix = "sipnet.out", sleep =
   } else {
     L_jobid <- length(jobids)
     pb1 <- utils::txtProgressBar(min = 0, max = L_jobid, style = 3)
-    pb1 <- 0
     if (hybrid) {
       while ((L_folder - length(folders)) < L_folder & 
              (L_jobid - length(jobids)) < L_jobid) {

base/workflow/DESCRIPTION

@@ -1,7 +1,7 @@
 Package: PEcAn.workflow
 Type: Package
-Title: PEcAn functions used for ecological forecasts and
-    reanalysis
+Title: PEcAn Functions Used for Ecological Forecasts and
+    Reanalysis
 Version: 1.7.2
 Date: 2021-10-04
 Authors@R: c(person("Mike", "Dietze", role = c("aut"),

base/workflow/R/run.write.configs.R

@@ -91,7 +91,7 @@ run.write.configs <- function(settings, write = TRUE, ens.sample.method = "unifo
     ensemble.samples <- samples$ensemble.samples
     sa.samples <- samples$sa.samples
     runs.samples <- samples$runs.samples
-    env.samples <- samples$env.samples
+    ## env.samples <- samples$env.samples
   } else {
     PEcAn.logger::logger.error(samples.file, "not found, this file is required by the run.write.configs function")
   }

base/workflow/tests/Rcheck_reference.log

@@ -48,11 +48,6 @@ Strong dependencies not in mainstream repositories:
   PEcAn.data.atmosphere, PEcAn.data.land, PEcAn.DB, PEcAn.logger,
     PEcAn.remote, PEcAn.settings, PEcAn.uncertainty, PEcAn.utils
 
-The Title field should be in title case. Current version is:
-‘PEcAn functions used for ecological forecasts and reanalysis’
-In title case that is:
-‘PEcAn Functions Used for Ecological Forecasts and Reanalysis’
-
 The Date field is over a month old.
 * checking package namespace information ... OK
 * checking package dependencies ... OK
@@ -93,14 +88,7 @@ Maintainer field differs from that derived from Authors@R
 * checking S3 generic/method consistency ... OK
 * checking replacement functions ... OK
 * checking foreign function calls ... OK
-* checking R code for possible problems ... NOTE
-run.write.configs: no visible binding for global variable
-  ‘trait.samples’
-run.write.configs: no visible binding for global variable ‘sa.samples’
-run.write.configs: no visible binding for global variable
-  ‘ensemble.samples’
-Undefined global functions or variables:
-  ensemble.samples sa.samples trait.samples
+* checking R code for possible problems ... OK
 * checking Rd files ... OK
 * checking Rd metadata ... OK
 * checking Rd line widths ... OK
@@ -119,4 +107,4 @@ Undefined global functions or variables:
 * checking for detritus in the temp directory ... OK
 * DONE
 
-Status: 1 WARNING, 2 NOTEs
+Status: 1 WARNING, 1 NOTEs

modules/assim.sequential/R/Analysis_sda_block.R

@@ -339,11 +339,11 @@ MCMC_Init <- function (block.list, X) {
     }
     #initialize q.
     #if we want the vector q.
-    if (block.list[[i]]$constant$q.type == 1) {
+    if (block.list[[i]]$constant$q.type == 3) {
       for (j in seq_along(block.list[[i]]$data$y.censored)) {
         block.list[[i]]$Inits$q <- c(block.list[[i]]$Inits$q, stats::rgamma(1, shape = block.list[[i]]$data$aq[j], rate = block.list[[i]]$data$bq[j]))
       }
-    } else if (block.list[[i]]$constant$q.type == 2) {
+    } else if (block.list[[i]]$constant$q.type == 4) {
       #if we want the wishart Q.
       if ("try-error" %in% class(try(block.list[[i]]$Inits$q <- 
                                      stats::rWishart(1, df = block.list[[i]]$data$bq, Sigma = block.list[[i]]$data$aq)[,,1], silent = T))) {