More missing PEcAn.remote references

benda1997 · Sep 13, 2017 · 0faa7ee · 0faa7ee
1 parent 91ce3de
commit 0faa7ee
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Showing 5 changed files with 7 additions and 7 deletions.
diff --git a/base/settings/R/check.all.settings.R b/base/settings/R/check.all.settings.R
@@ -389,7 +389,7 @@ check.settings <- function(settings, force=FALSE) {
   }
 
   # make sure remote folders are specified if need be
-  if (!is.localhost(settings$host)) {
+  if (!PEcAn.remote::is.localhost(settings$host)) {
     if (is.null(settings$host$folder)) {
       settings$host$folder <- paste0(remote.execute.cmd("pwd", host=settings$host), "/pecan_remote")
       PEcAn.logger::logger.info("Using ", settings$host$folder, "to store output on remote machine")      

diff --git a/base/utils/R/do_conversions.R b/base/utils/R/do_conversions.R
@@ -15,7 +15,7 @@ do_conversions <- function(settings, overwrite.met = FALSE, overwrite.fia = FALS
   }
 
   dbfiles.local <- settings$database$dbfiles
-  dbfiles <- ifelse(!PEcAn.utils::is.localhost(settings$host) & !is.null(settings$host$folder), settings$host$folder, dbfiles.local)
+  dbfiles <- ifelse(!PEcAn.remote::is.localhost(settings$host) & !is.null(settings$host$folder), settings$host$folder, dbfiles.local)
   PEcAn.logger::logger.debug("do.conversion outdir",dbfiles)
 
   for (i in seq_along(settings$run$inputs)) {

diff --git a/base/utils/inst/LBNL_remote_test.R b/base/utils/inst/LBNL_remote_test.R
@@ -53,4 +53,4 @@ d <- PEcAn.remote::remote.execute.R(script = "return(.libPaths())",host = host,R
 
 
 ## kill tunnels
-PEcAn.utils::kill.tunnel(settings)
+PEcAn.remote::kill.tunnel(settings)
diff --git a/modules/data.land/inst/LoadPalEONsites.R b/modules/data.land/inst/LoadPalEONsites.R
@@ -183,7 +183,7 @@ for(i in seq_along(paleon.sitegroups)){
 ## establish remote tunnel
 library(getPass)
 host <- list(name="geo.bu.edu",tunnel="~/.pecan/tunnel/")
-is.open <- open_tunnel(host$name,host$tunnel)
+is.open <- PEcAn.remote::open_tunnel(host$name,host$tunnel)
 if(!is.open){
   print("Could not open remote tunnel")
 } else {
@@ -262,7 +262,7 @@ for(i in c(1:5,7)){
 
 }
 
-PEcAn.utils::kill.tunnel(list(host=host))
+PEcAn.remote::kill.tunnel(list(host=host))
 
 ##################################
 ### merge in CO2 into met data

diff --git a/web/workflow.R b/web/workflow.R
@@ -19,7 +19,7 @@ library(RCurl)
 options(warn=1)
 options(error=quote({
   PEcAn.utils::status.end("ERROR")
-  PEcAn.utils::kill.tunnel(settings)
+  PEcAn.remote::kill.tunnel(settings)
   if (!interactive()) {
     q()
   }
@@ -161,7 +161,7 @@ if("benchmarking" %in% names(settings)){
 # Pecan workflow complete
 if (PEcAn.utils::status.check("FINISHED") == 0) {
   PEcAn.utils::status.start("FINISHED")
-  kill.tunnel(settings)
+  PEcAn.remote::kill.tunnel(settings)
   db.query(paste("UPDATE workflows SET finished_at=NOW() WHERE id=", settings$workflow$id, "AND finished_at IS NULL"), params=settings$database$bety)
 
   # Send email if configured
Original file line number	Diff line number	Diff line change
Expand Up		@@ -53,4 +53,4 @@ d <- PEcAn.remote::remote.execute.R(script = "return(.libPaths())",host = host,R


		## kill tunnels
		PEcAn.utils::kill.tunnel(settings)
		PEcAn.remote::kill.tunnel(settings)