Merge pull request #3388 from infotroph/pecan-version-datafix

Small fixes in PEcAn.all

Makefile

@@ -132,12 +132,6 @@ $(subst .doc/models/template,,$(MODELS_D)): .install/models/template
 ### Order-only dependencies
 # (i.e. prerequisites must exist before building target, but
 # target need not be rebuilt when a prerequisite changes)
-
-.doc/base/all: | $(ALL_PKGS_D)
-.install/base/all: | $(ALL_PKGS_I)
-.check/base/all: | $(ALL_PKGS_C)
-.test/base/all: | $(ALL_PKGS_T)
-
 include Makefile.depends
 
 clean:

base/all/DESCRIPTION

@@ -1,7 +1,6 @@
 Package: PEcAn.all
 Type: Package
-Title: PEcAn functions used for ecological forecasts and
-    reanalysis
+Title: PEcAn Functions Used for Ecological Forecasts and Reanalysis
 Version: 1.8.0.9000
 Authors@R: c(person("Mike", "Dietze", role = c("aut"),
                      email = "[email protected]"),

base/all/R/pecan_version.R

@@ -55,23 +55,24 @@ pecan_version <- function(version = max(PEcAn.all::pecan_releases$version),
     all_pkgs <- sessioninfo::package_info(pkgs = "installed", dependencies = FALSE)
     our_pkgs <- all_pkgs[grepl("PEcAn", all_pkgs$package),]
 
+    # Why do we need this when `pkgs = "installed"` usually shows loaded too?
+    # Because there are times a package is loaded but not installed
+    # (e.g. notably during R CMD check)
     all_loaded <- sessioninfo::package_info(pkgs = "loaded", dependencies = FALSE)
     our_loaded <- all_loaded[grepl("PEcAn", all_loaded$package),]
 
-    unloaded <- our_pkgs[!our_pkgs$package %in% our_loaded$package,]
-    our_pkgs <- rbind(our_loaded, unloaded)
-    our_pkgs <- our_pkgs[order(our_pkgs$package),]
-
-
     # TODO: consider using package_info's callouts of packages where loaded and
     #   installed versions mismatch -- it's a more elegant version of what we
     #   were trying for with the "multiple rows for packages with multiple
     #   versions found" behavior.
-    our_pkgs$installed <- ifelse(
-      test = is.na(our_pkgs$loadedversion),
-      yes = our_pkgs$ondiskversion,
-      no = our_pkgs$loadedversion)
-    our_pkgs <- our_pkgs[, c("package", "installed", "source")]
+    our_pkgs <- merge(
+      x = our_pkgs[, c("package", "ondiskversion", "source")],
+      y = our_loaded[, c("package", "loadedversion", "source")],
+      by.x = c("package", "ondiskversion", "source"),
+      by.y = c("package", "loadedversion", "source"),
+      all = TRUE,
+      sort = TRUE)
+    colnames(our_pkgs) <- c("package", "installed", "source")
     our_pkgs$installed <- package_version(our_pkgs$installed)
 
   } else {
@@ -89,7 +90,8 @@ pecan_version <- function(version = max(PEcAn.all::pecan_releases$version),
       package = names(our_loaded),
       installed = sapply(our_loaded, `[[`, "Version"))
     our_loaded$installed <- package_version(our_loaded$installed)
-    our_pkgs <- merge(our_pkgs, our_loaded, all = TRUE)
+    our_pkgs <- merge(our_pkgs, our_loaded, all = TRUE, sort = TRUE)
+    our_pkgs <- our_pkgs[!duplicated(our_pkgs),]
   }
 
 

base/all/data/pecan_version_history.R

@@ -23,3 +23,8 @@ for (col in colnames(pecan_version_history)) {
       strict = strict)
   }
 }
+
+# Now remove local vars
+# Yes, this really is needed: _all_ objects left defined at end of script
+# will be added to the package data list!
+rm(strict, na_version, col)

base/all/tests/Rcheck_reference.log

@@ -14,38 +14,6 @@ New submission
 
 Version contains large components (1.7.2.9000)
 
-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.DB, PEcAn.settings, PEcAn.MA, PEcAn.logger, PEcAn.utils,
     PEcAn.uncertainty, PEcAn.data.atmosphere, PEcAn.data.land,
@@ -54,13 +22,6 @@ Strong dependencies not in mainstream repositories:
 Suggests or Enhances not in mainstream repositories:
   PEcAn.ED2, PEcAn.SIPNET, PEcAn.BIOCRO, PEcAn.DALEC, PEcAn.LINKAGES,
     PEcAn.allometry, PEcAn.photosynthesis
-
-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 ... NOTE
 Depends: includes the non-default packages: