Start RStudio project, some maintenance

8 files changed, 136 insertions, 11 deletions

diff --git a/.Rbuildignore b/.Rbuildignore
index 10e9266..4159cc9 100644
--- a/.Rbuildignore
+++ b/.Rbuildignore
@@ -10,3 +10,5 @@
 ^_pkgdown.yml$
 ^\.travis\.yml$
 ^docs$
+^.*\.Rproj$
+^\.Rproj\.user$
diff --git a/.Rhistory b/.Rhistory
new file mode 100644
index 0000000..cf5f28b
--- /dev/null
+++ b/.Rhistory
@@ -0,0 +1,21 @@
+install.packages("chents")
+library(chents)
+atrazine <- pai.new("atrazine")
+atra <- pai$new("atrazine")
+atra
+atra$mw
+library(units)
+as_unit("3 g/mol")
+as_units(3, g/mol)
+as_units(3, "g/mol")
+cym <- pai$new("cymoxanil")
+cym
+py_install("rdkit")
+reticulate::py_install("rdkit")
+cym <- pai$new("cymoxanil")
+library(reticulate)
+py_install("rdkit")
+rdkit <- py_import(rdkit)
+rdkit <- import("rdkit")
+rdkit
+chent$new("isopropanol")
diff --git a/.gitignore b/.gitignore
index 490c91a..d548326 100644
--- a/.gitignore
+++ b/.gitignore
@@ -4,3 +4,4 @@ pfm\.Rcheck
 test.R
 inst/extdata/Tabelle\ der\ Abdrifteckwerte.xls
 inst/extdata/FOCUS_Step_12_scenarios.txt
+.Rproj.user
diff --git a/ChangeLog b/ChangeLog
index ae0a684..0ad0374 100644
--- a/ChangeLog
+++ b/ChangeLog
@@ -1,3 +1,84 @@
+commit df4034c64aa3590c3911dca88b066332dc8e4df1
+Author: Johannes Ranke <jranke@uni-bremen.de>
+Date:   2022-11-11 14:35:37 +0100
+
+    Simplify travis config
+
+commit f4e22fc28fa0b05b05c8a1277333777635802e86
+Author: Johannes Ranke <jranke@uni-bremen.de>
+Date:   2022-11-11 13:46:24 +0100
+
+    Try to simplify drat configuration
+
+commit 6bc40dbd4e7c76179009a501ae168f0fa73f2be2
+Author: Johannes Ranke <jranke@uni-bremen.de>
+Date:   2022-11-11 12:12:09 +0100
+
+    Disable bspm to make install from drat work
+
+commit 96b6f8954d4eb9ec5b8ee9209074d21fdd67f966
+Author: Johannes Ranke <jranke@uni-bremen.de>
+Date:   2022-11-11 12:04:15 +0100
+
+    Fix last commit
+
+commit c9e9f1312e7b73c8596d2d01324fcb67c000f3e9
+Author: Johannes Ranke <jranke@uni-bremen.de>
+Date:   2022-11-11 12:00:39 +0100
+
+    Install drat to use it...
+
+commit b0a7a94ac0a7070e8612e443b4aa485beb07b85d
+Author: Johannes Ranke <jranke@uni-bremen.de>
+Date:   2022-11-11 11:57:20 +0100
+
+    Another attempt to make drat work on travis
+
+commit 854cc695a1f64a9b37957fdcd81c1ce23a6a2d69
+Author: Johannes Ranke <jranke@uni-bremen.de>
+Date:   2022-11-11 11:52:53 +0100
+
+    Try to make drat work
+
+commit c463f9fb197f70f97831b3648bc398be8ff9ae7d
+Author: Johannes Ranke <jranke@uni-bremen.de>
+Date:   2022-11-11 11:41:40 +0100
+
+    mkin was not pulled from the drat repo
+
+commit f3ba961b6be63d3995cccea2968d7b2fb907ca16
+Author: Johannes Ranke <jranke@uni-bremen.de>
+Date:   2022-11-11 11:35:27 +0100
+
+    Use drat instead of install_github
+
+commit 510416bc07eb7b3197c20d687f6c51a032cfbfec
+Author: Johannes Ranke <jranke@uni-bremen.de>
+Date:   2022-11-11 11:12:59 +0100
+
+    Forgot to commit .travis.yml ...
+
+commit f21a53421dc481604c681c2be8438c8a8b5db23d
+Author: Johannes Ranke <jranke@uni-bremen.de>
+Date:   2022-11-11 10:58:46 +0100
+
+    mkin and chents from github for check on travis
+
+commit e63dbdf1fdae0abc7246f721357504798309033d
+Author: Johannes Ranke <jranke@uni-bremen.de>
+Date:   2022-11-11 10:52:07 +0100
+
+    Don't force suggested packages
+
+commit 60a217ecc9a035ab956bd4229da6ad4c654e7d6e
+Author: Johannes Ranke <jranke@uni-bremen.de>
+Date:   2022-11-11 10:37:13 +0100
+
+    Remove Remotes: field from DESCRIPTION
+    
+    It causes trouble with remotes::install_deps() on travis, see the
+    various previous build logs.
+
 commit 3ef243d18b7972eb8cb4a561ac07d93b46df13a5
 Author: Johannes Ranke <jranke@uni-bremen.de>
 Date:   2022-11-11 10:06:39 +0100
diff --git a/DESCRIPTION b/DESCRIPTION
index 9543fdd..8d11e33 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,10 +1,10 @@
 Package: pfm
 Type: Package
 Title: Utilities for Pesticide Fate Modelling
-Version: 0.5.9
-Date: 2022-11-11
-Authors@R: person("Johannes Ranke", email = "jranke@uni-bremen.de",
-                  role = c("aut", "cre", "cph"),
+Version: 0.6.0
+Date: 2023-11-11
+Authors@R: person("Johannes Ranke", email = "johannes.ranke@agroscope.admin.ch",
+                  role = c("aut", "cre"),
                   comment = c(ORCID = "0000-0003-4371-6538"))
 Description: Utilities for simple calculations of predicted environmental
     concentrations ('PEC' values) and for dealing with data from some FOCUS
@@ -27,4 +27,4 @@ LazyLoad: yes
 LazyData: yes
 Encoding: UTF-8
 URL: https://pkgdown.jrwb.de/pfm
-RoxygenNote: 7.2.1
+RoxygenNote: 7.2.3
diff --git a/GNUmakefile b/GNUmakefile
index d993d27..fae80e3 100644
--- a/GNUmakefile
+++ b/GNUmakefile
@@ -7,8 +7,10 @@ DATE    := $(shell date +%Y-%m-%d)
 
 .PHONEY: usage check clean
 
-pkgfiles = DESCRIPTION \
+pkgfiles = \
 	.Rbuildignore \
+	ChangeLog \
+	DESCRIPTION \
 	data/* \
 	docs/* \
 	docs/reference/* \
@@ -23,7 +25,7 @@ clean:
 	rm -fR pfm.Rcheck
 	@echo "DONE."
 
-roxygen: 
+roxygen:
 	@echo "Roxygenizing package..."
 	"$(R_HOME)/bin/Rscript" -e 'devtools::document()'
 	@echo "DONE."
diff --git a/build.log b/build.log
index e909b56..b1447b2 100644
--- a/build.log
+++ b/build.log
@@ -3,14 +3,13 @@
 * checking DESCRIPTION meta-information ... OK
 * checking for LF line-endings in source and make files and shell scripts
 * checking for empty or unneeded directories
-Removed empty directory ‘pfm/inst/testdata/SwashProjects/Project_1/MACRO’
-Removed empty directory ‘pfm/inst/testdata/SwashProjects/Project_1’
-Removed empty directory ‘pfm/inst/testdata/SwashProjects’
   NB: this package now depends on R (>= 3.5.0)
   WARNING: Added dependency on R >= 3.5.0 because serialized objects in
   serialize/load version 3 cannot be read in older versions of R.
   File(s) containing such objects:
     ‘pfm/data/EFSA_GW_interception_2014.RData’
     ‘pfm/data/EFSA_washoff_2017.RData’
-* building ‘pfm_0.5.9.tar.gz’
+* building ‘pfm_0.6.0.tar.gz’
+Warning: invalid uid value replaced by that for user 'nobody'
+Warning: invalid gid value replaced by that for user 'nobody'
 
diff --git a/pfm.Rproj b/pfm.Rproj
new file mode 100644
index 0000000..8de5cfd
--- /dev/null
+++ b/pfm.Rproj
@@ -0,0 +1,19 @@
+Version: 1.0
+
+RestoreWorkspace: Default
+SaveWorkspace: Default
+AlwaysSaveHistory: Default
+
+EnableCodeIndexing: Yes
+UseSpacesForTab: Yes
+NumSpacesForTab: 2
+Encoding: UTF-8
+
+RnwWeave: Sweave
+LaTeX: pdfLaTeX
+
+AutoAppendNewline: Yes
+
+BuildType: Package
+PackageUseDevtools: Yes
+PackageInstallArgs: --no-multiarch --with-keep.source