add check.log file

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.
+
+