Prepare CRAN release

R-Lum · Jun 29, 2017 · 0866fe5 · 0866fe5
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diff --git a/.Rbuildignore b/.Rbuildignore
@@ -10,6 +10,7 @@ NEWS\.html
 ^appveyor\.yml$
 ^codecov\.yml$
 ^cran-comments\.md$
+^cran-comments\.html$
 RLum.CHECK_AND_BUILD.sh
 RLum.CHECK_AND_BUILD_MacOSX.sh
 RLum.CHECK_AND_BUILD_Linux.sh

diff --git a/.gitignore b/.gitignore
@@ -21,4 +21,5 @@ src/*.dll
 src-i386/
 src-x64/
 NEWS_*
+cran-comments.html
 
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -75,7 +75,7 @@ Suggests:
     testthat (>= 1.0.2),
     devtools (>= 1.12.0)
 URL: https://CRAN.R-project.org/package=Luminescence
-Collate:
+Collate: 
     'Analyse_SAR.OSLdata.R'
     'CW2pHMi.R'
     'CW2pLM.R'

diff --git a/R/README.md b/R/README.md
diff --git a/RLum.BuildResults/Luminescence-Ex.pdf b/RLum.BuildResults/Luminescence-Ex.pdf
diff --git a/RLum.BuildResults/Luminescence-TimingExamples.0.7.5.pdf b/RLum.BuildResults/Luminescence-TimingExamples.0.7.5.pdf
diff --git a/RLum.BuildResults/Luminescence-manual.pdf b/RLum.BuildResults/Luminescence-manual.pdf
diff --git a/RLum.BuildResults/Luminescence_0.7.5-Functions.csv b/RLum.BuildResults/Luminescence_0.7.5-Functions.csv
diff --git a/RLum.BuildResults/Luminescence_0.7.5-Functions.html b/RLum.BuildResults/Luminescence_0.7.5-Functions.html
diff --git a/RLum.BuildResults/Luminescence_0.7.5-Functions.tex b/RLum.BuildResults/Luminescence_0.7.5-Functions.tex
diff --git a/RLum.BuildResults/Luminescence_0.7.5-Functions_Markdown.md b/RLum.BuildResults/Luminescence_0.7.5-Functions_Markdown.md
diff --git a/RLum.BuildResults/Outputs/check_Luminescence_stderr.txt b/RLum.BuildResults/Outputs/check_Luminescence_stderr.txt
@@ -0,0 +1,3 @@
+  Running ‘testthat.R’
+
+
diff --git a/RLum.BuildResults/Outputs/check_Luminescence_stdout.txt b/RLum.BuildResults/Outputs/check_Luminescence_stdout.txt
@@ -0,0 +1,58 @@
+* using log directory ‘/Users/kreutzer/GitHub/R_Luminescence/RLum.BuildResults/Luminescence.Rcheck’
+* using R version 3.4.1 RC (2017-06-22 r72859)
+* using platform: x86_64-apple-darwin15.6.0 (64-bit)
+* using session charset: UTF-8
+* checking for file ‘Luminescence/DESCRIPTION’ ... OK
+* checking extension type ... Package
+* this is package ‘Luminescence’ version ‘0.7.5’
+* checking package namespace information ... OK
+* checking package dependencies ... OK
+* checking if this is a source package ... OK
+* checking if there is a namespace ... OK
+* checking for executable files ... OK
+* checking for hidden files and directories ... OK
+* checking for portable file names ... OK
+* checking for sufficient/correct file permissions ... OK
+* checking whether package ‘Luminescence’ can be installed ... OK
+* checking installed package size ... OK
+* checking package directory ... OK
+* checking DESCRIPTION meta-information ... OK
+* checking top-level files ... OK
+* checking for left-over files ... OK
+* checking index information ... OK
+* checking package subdirectories ... OK
+* checking R files for non-ASCII characters ... OK
+* checking R files for syntax errors ... OK
+* checking whether the package can be loaded ... OK
+* checking whether the package can be loaded with stated dependencies ... OK
+* checking whether the package can be unloaded cleanly ... OK
+* 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 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 ... OK
+* checking Rd files ... OK
+* checking Rd metadata ... OK
+* checking Rd cross-references ... OK
+* checking for missing documentation entries ... OK
+* checking for code/documentation mismatches ... OK
+* checking Rd \usage sections ... OK
+* checking Rd contents ... OK
+* checking for unstated dependencies in examples ... OK
+* checking contents of ‘data’ directory ... OK
+* checking data for non-ASCII characters ... OK
+* checking data for ASCII and uncompressed saves ... OK
+* checking line endings in C/C++/Fortran sources/headers ... OK
+* checking compiled code ... OK
+* checking sizes of PDF files under ‘inst/doc’ ... OK
+* checking installed files from ‘inst/doc’ ... OK
+* checking examples ... OK
+* checking for unstated dependencies in ‘tests’ ... OK
+* checking tests ...
+ OK
+* checking PDF version of manual ... OK
+* DONE
+Status: OK
diff --git a/RLum.BuildResults/Outputs/check_RLumModel_stderr.txt b/RLum.BuildResults/Outputs/check_RLumModel_stderr.txt
@@ -0,0 +1,3 @@
+  Running ‘testthat.R’
+
+
diff --git a/RLum.BuildResults/Outputs/check_RLumModel_stdout.txt b/RLum.BuildResults/Outputs/check_RLumModel_stdout.txt
@@ -0,0 +1,67 @@
+* using log directory ‘/Users/kreutzer/GitHub/R_Luminescence/RLum.BuildResults/RLumModel.Rcheck’
+* using R version 3.4.1 RC (2017-06-22 r72859)
+* using platform: x86_64-apple-darwin15.6.0 (64-bit)
+* using session charset: UTF-8
+* checking for file ‘RLumModel/DESCRIPTION’ ... OK
+* checking extension type ... Package
+* this is package ‘RLumModel’ version ‘0.2.1’
+* checking package namespace information ... OK
+* checking package dependencies ... OK
+* checking if this is a source package ... OK
+* checking if there is a namespace ... OK
+* checking for executable files ... OK
+* checking for hidden files and directories ... OK
+* checking for portable file names ... OK
+* checking for sufficient/correct file permissions ... OK
+* checking whether package ‘RLumModel’ can be installed ... OK
+* checking installed package size ... OK
+* checking package directory ... OK
+* checking ‘build’ directory ... OK
+* checking DESCRIPTION meta-information ... OK
+* checking top-level files ... OK
+* checking for left-over files ... OK
+* checking index information ... OK
+* checking package subdirectories ... OK
+* checking R files for non-ASCII characters ... OK
+* checking R files for syntax errors ... OK
+* checking whether the package can be loaded ... OK
+* checking whether the package can be loaded with stated dependencies ... OK
+* checking whether the package can be unloaded cleanly ... OK
+* 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 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 ... OK
+* checking Rd files ... OK
+* checking Rd metadata ... OK
+* checking Rd cross-references ... OK
+* checking for missing documentation entries ... OK
+* checking for code/documentation mismatches ... OK
+* checking Rd \usage sections ... OK
+* checking Rd contents ... OK
+* checking for unstated dependencies in examples ... OK
+* checking contents of ‘data’ directory ... OK
+* checking data for non-ASCII characters ... OK
+* checking data for ASCII and uncompressed saves ... OK
+* checking line endings in C/C++/Fortran sources/headers ... OK
+* checking compiled code ... OK
+* checking sizes of PDF files under ‘inst/doc’ ... OK
+* checking installed files from ‘inst/doc’ ... OK
+* checking files in ‘vignettes’ ... OK
+* checking examples ... OK
+* checking for unstated dependencies in ‘tests’ ... OK
+* checking tests ...
+ OK
+* checking for unstated dependencies in vignettes ... OK
+* checking package vignettes in ‘inst/doc’ ... OK
+* checking running R code from vignettes ...
+   ‘RLumModel_-_Getting_started_with_RLumModel.pdf.asis’ ... OK
+   ‘RLumModel_-_Using_own_parameter_sets.pdf.asis’ ... OK
+ NONE
+* checking re-building of vignette outputs ... OK
+* checking PDF version of manual ... OK
+* DONE
+Status: OK
diff --git a/RLum.BuildResults/Outputs/check_RLumShiny_stderr.txt b/RLum.BuildResults/Outputs/check_RLumShiny_stderr.txt
@@ -0,0 +1,2 @@
+
+
diff --git a/RLum.BuildResults/Outputs/check_RLumShiny_stdout.txt b/RLum.BuildResults/Outputs/check_RLumShiny_stdout.txt
@@ -0,0 +1,48 @@
+* using log directory ‘/Users/kreutzer/GitHub/R_Luminescence/RLum.BuildResults/RLumShiny.Rcheck’
+* using R version 3.4.1 RC (2017-06-22 r72859)
+* using platform: x86_64-apple-darwin15.6.0 (64-bit)
+* using session charset: UTF-8
+* checking for file ‘RLumShiny/DESCRIPTION’ ... OK
+* checking extension type ... Package
+* this is package ‘RLumShiny’ version ‘0.2.0’
+* checking package namespace information ... OK
+* checking package dependencies ... OK
+* checking if this is a source package ... OK
+* checking if there is a namespace ... OK
+* checking for executable files ... OK
+* checking for hidden files and directories ... OK
+* checking for portable file names ... OK
+* checking for sufficient/correct file permissions ... OK
+* checking whether package ‘RLumShiny’ can be installed ... OK
+* checking installed package size ... OK
+* checking package directory ... OK
+* checking DESCRIPTION meta-information ... OK
+* checking top-level files ... OK
+* checking for left-over files ... OK
+* checking index information ... OK
+* checking package subdirectories ... OK
+* checking R files for non-ASCII characters ... OK
+* checking R files for syntax errors ... OK
+* checking whether the package can be loaded ... OK
+* checking whether the package can be loaded with stated dependencies ... OK
+* checking whether the package can be unloaded cleanly ... OK
+* 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 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 ... OK
+* checking Rd files ... OK
+* checking Rd metadata ... OK
+* checking Rd cross-references ... OK
+* checking for missing documentation entries ... OK
+* checking for code/documentation mismatches ... OK
+* checking Rd \usage sections ... OK
+* checking Rd contents ... OK
+* checking for unstated dependencies in examples ... OK
+* checking examples ... OK
+* checking PDF version of manual ... OK
+* DONE
+Status: OK
diff --git a/RLum.BuildResults/Outputs/check_TLdating_stderr.txt b/RLum.BuildResults/Outputs/check_TLdating_stderr.txt
@@ -0,0 +1,2 @@
+
+
diff --git a/RLum.BuildResults/Outputs/check_TLdating_stdout.txt b/RLum.BuildResults/Outputs/check_TLdating_stdout.txt
@@ -0,0 +1,48 @@
+* using log directory ‘/Users/kreutzer/GitHub/R_Luminescence/RLum.BuildResults/TLdating.Rcheck’
+* using R version 3.4.1 RC (2017-06-22 r72859)
+* using platform: x86_64-apple-darwin15.6.0 (64-bit)
+* using session charset: UTF-8
+* checking for file ‘TLdating/DESCRIPTION’ ... OK
+* checking extension type ... Package
+* this is package ‘TLdating’ version ‘0.1.3’
+* package encoding: UTF-8
+* checking package namespace information ... OK
+* checking package dependencies ... OK
+* checking if this is a source package ... OK
+* checking if there is a namespace ... OK
+* checking for executable files ... OK
+* checking for hidden files and directories ... OK
+* checking for portable file names ... OK
+* checking for sufficient/correct file permissions ... OK
+* checking whether package ‘TLdating’ can be installed ... OK
+* checking installed package size ... OK
+* checking package directory ... OK
+* checking DESCRIPTION meta-information ... OK
+* checking top-level files ... OK
+* checking for left-over files ... OK
+* checking index information ... OK
+* checking package subdirectories ... OK
+* checking R files for non-ASCII characters ... OK
+* checking R files for syntax errors ... OK
+* checking whether the package can be loaded ... OK
+* checking whether the package can be loaded with stated dependencies ... OK
+* checking whether the package can be unloaded cleanly ... OK
+* checking whether the namespace can be loaded with stated dependencies ... OK
+* checking whether the namespace can be unloaded cleanly ... OK
+* 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 ... OK
+* checking Rd files ... OK
+* checking Rd metadata ... OK
+* checking Rd cross-references ... OK
+* checking for missing documentation entries ... OK
+* checking for code/documentation mismatches ... OK
+* checking Rd \usage sections ... OK
+* checking Rd contents ... OK
+* checking for unstated dependencies in examples ... OK
+* checking examples ... OK
+* checking PDF version of manual ... OK
+* DONE
+Status: OK
diff --git a/RLum.BuildResults/PACKAGES b/RLum.BuildResults/PACKAGES
@@ -0,0 +1,11 @@
+Package: Luminescence
+Version: 0.7.5
+Depends: R (>= 3.3.2), utils, magrittr (>= 1.5)
+Imports: bbmle (>= 1.0.18), data.table (>= 1.10.0), httr (>= 1.2.1), matrixStats (>= 0.51.0), methods, minpack.lm (>= 1.2-1), raster (>= 2.5-8), readxl (>=
+                  0.1.1), shape (>= 1.4.2), parallel, XML (>= 3.98-1.5), zoo (>= 1.7-14)
+LinkingTo: Rcpp (>= 0.12.9), RcppArmadillo (>= 0.7.600.1.0)
+Suggests: RLumShiny (>= 0.1.1), RLumModel (>= 0.1.2), plotly (>= 4.5.6), rmarkdown (>= 1.3), rjags (>= 4-6), coda (>= 0.19-1), pander (>= 0.6.0), rstudioapi (>=
+                  0.6), testthat (>= 1.0.2), devtools (>= 1.12.0)
+License: GPL-3
+MD5sum: 6bbc8eff45f3ce53bb7df05f7c422e7b
+NeedsCompilation: yes
diff --git a/RLum.BuildResults/PACKAGES.gz b/RLum.BuildResults/PACKAGES.gz
diff --git a/RLum.BuildResults/PACKAGES.rds b/RLum.BuildResults/PACKAGES.rds
diff --git a/RLum.BuildResults/RLumModel.Rcheck/00_pkg_src/RLumModel/DESCRIPTION b/RLum.BuildResults/RLumModel.Rcheck/00_pkg_src/RLumModel/DESCRIPTION
@@ -0,0 +1,38 @@
+Package: RLumModel
+Type: Package
+Title: Solving Ordinary Differential Equations to Understand
+        Luminescence
+Version: 0.2.1
+Date: 2017-04-13
+Author: Johannes Friedrich [aut, trl, cre],
+    Sebastian Kreutzer [aut, ths],
+    Christoph Schmidt [aut, ths]
+Authors@R: c(
+    person("Johannes", "Friedrich", role = c("aut","trl","cre"), email = "[email protected]"),
+    person("Sebastian", "Kreutzer", role = c("aut", "ths")),
+    person("Christoph", "Schmidt", role = c("aut", "ths"))
+    )
+Maintainer: Johannes Friedrich <[email protected]>
+Description: A collection of functions to simulate luminescence signals in the
+    mineral quartz based on published models.
+Contact: Package Developer Team <[email protected]>
+License: GPL-3
+Depends: R (>= 3.3.0), utils, Luminescence (>= 0.7.0)
+Imports: deSolve (>= 1.12), methods, Rcpp
+URL: https://CRAN.R-project.org/package=RLumModel
+Collate: RLumModel-package.R RcppExports.R calc_signal.R
+        calc_concentrations.R create_DRT.sequence.R
+        create_SAR.sequence.R extract_pars.R
+        model_LuminescenceSignals.R read_SEQ2R.R set_pars.R
+        simulate_CW_OSL.R simulate_heating.R simulate_illumination.R
+        simulate_irradiation.R simulate_LM_OSL.R simulate_pause.R
+        simulate_RF.R simulate_RF_and_heating.R simulate_TL.R
+        translate_sequence.R
+RoxygenNote: 6.0.1
+Suggests: R.rsp, testthat
+VignetteBuilder: R.rsp
+LinkingTo: Rcpp, RcppArmadillo
+NeedsCompilation: yes
+Packaged: 2017-04-11 20:34:51 UTC; johannes
+Repository: CRAN
+Date/Publication: 2017-04-13 17:17:44 UTC
diff --git a/RLum.BuildResults/RLumModel.Rcheck/00_pkg_src/RLumModel/MD5 b/RLum.BuildResults/RLumModel.Rcheck/00_pkg_src/RLumModel/MD5
@@ -0,0 +1,60 @@
+b092f6b744da385536c2af6ec45b7793 *DESCRIPTION
+d038dce9c50f012aaadef5015b925d41 *NAMESPACE
+4dbe2b6344c7830bf14551c1c3cc0ba7 *NEWS
+76732e1ad017203d1867449370797f88 *R/RLumModel-package.R
+4447d3bfa7ee22570beb63af57808b22 *R/RcppExports.R
+cc539acd103dc0e565e3b89a93663ac7 *R/calc_concentrations.R
+3278d9b84010c24e9d054d1b2819ae03 *R/calc_signal.R
+f6f57f43450f27e0aa8bb866c8755b4d *R/create_DRT.sequence.R
+248d62f92c98f1eb5fa91e32fd9eae44 *R/create_SAR.sequence.R
+27f77306fd1f50c78d478aed4efd9625 *R/extract_pars.R
+45587b7738b4d509f69987a1eb07280c *R/model_LuminescenceSignals.R
+13efa05b3dd35955c79149a62fac6fee *R/read_SEQ2R.R
+d2f9b862a86a3b20a4bd7798b2c75c01 *R/set_pars.R
+37747800fe310a67e916e8cc83b06a60 *R/simulate_CW_OSL.R
+74d80f196961bddea529468df59550c0 *R/simulate_LM_OSL.R
+1ee3545bd18fbf385ada413e022a4dc1 *R/simulate_RF.R
+30cf19313b753e78755ecb6d50ee346e *R/simulate_RF_and_heating.R
+0bcf7212ff6b7243e6976989ca64f788 *R/simulate_TL.R
+76ccfa67c3ed6da7d41a9861f2153f31 *R/simulate_heating.R
+f82369fb275d64e6996f2e313e2e7db6 *R/simulate_illumination.R
+76fc9e95b519495cf1bb839fab88c6b7 *R/simulate_irradiation.R
+ebdc2368f29bea43d3052d0bf47fe902 *R/simulate_pause.R
+5e3ef8bc52e578e33daf7cc269a6f3eb *R/translate_sequence.R
+3955b4364cdd7465b6df9686c7858bb1 *build/vignette.rds
+5470aa077bd5056760184e930c992648 *data/ExampleData.ModelOutput.RData
+b78e6fd8b4dbd77bb5a3f25f5153d432 *inst/NEWS.Rd
+87bf0a572bd1a34c81e9738102d07351 *inst/doc/RLumModel_-_Getting_started_with_RLumModel.pdf
+a37192623e2bd1285fc04b895fc96bba *inst/doc/RLumModel_-_Getting_started_with_RLumModel.pdf.asis
+9b280d7389c497a61381c95bd7052a56 *inst/doc/RLumModel_-_Using_own_parameter_sets.pdf
+629e1b2db66725fdfafc105c555e00bc *inst/doc/RLumModel_-_Using_own_parameter_sets.pdf.asis
+e28aa6935c9dfcf084ed11223ce38a04 *inst/extdata/example_SAR_cycle.SEQ
+07f6bf0fadb18d44015656642f224fe3 *man/ExampleData.ModelOutput.Rd
+46c2ab1eddd5f542fbfe5021f6a7f1be *man/RLumModel-package.Rd
+84ad6aee332bf806b1ab92fb8397c99d *man/model_LuminescenceSignals.Rd
+013e70a99dfcf8d2a2b3b73ef2806e20 *man/read_SEQ2R.Rd
+2a6f9e9e044a78154d3cfda5936d6f48 *src/Makevars.win
+f40cd35ddefda53b7fb1b3ea58bfde07 *src/RLumModel_init.c
+5d6a885550790e1b5b22856800cd1246 *src/RcppExports.cpp
+d6f98597133853c37f9ad3033e4e1272 *src/set_ODE_Rcpp.cpp
+0a2e5aa23c882045ecf8590ee7b96898 *src/set_ODE_Rcpp_LM_OSL.cpp
+995c0038e6507194faa8f0abc4d259df *tests/testthat.R
+3f4d93a69b874ed9a9fcd20a4b84704c *tests/testthat/test-create_DRT.sequence.R
+ca3256885792e30dc5bdf85db2fab5c2 *tests/testthat/test-create_SAR.sequence.R
+8027361a4ade257667cfc9dc83f75a0b *tests/testthat/test-model_LuminescenceSignals.R
+2a475694d441bf4d8799affe9213e12d *tests/testthat/test-read_SEQ2R.R
+b7af5e8586139774d1f979deade13f71 *tests/testthat/test-set_pars.R
+ed5d4f221a19898d5e33ca97064f9361 *tests/testthat/test-simulate_CW_OSL.R
+f1893afd77ffd65edf9eead8eb14acfe *tests/testthat/test-simulate_LM_OSL.R
+dec70039a87e62ebed52f4c7b6bf6bdc *tests/testthat/test-simulate_RF.R
+a7858f35b0ccee3ff7e677380800e2de *tests/testthat/test-simulate_RF_and_heating.R
+98604177cdd4c119865dac2747da3bc7 *tests/testthat/test-simulate_TL.R
+45c439daaedcfdceccef5086cfddcb11 *tests/testthat/test-simulate_heating.R
+055f637431bb2c0c6a288303aef02eb5 *tests/testthat/test-simulate_illumination.R
+87659a27e09e49d5f9b0cf52f09827eb *tests/testthat/test-simulate_irradiation.R
+280d8e0fd0a95382188d3d746cc8445a *tests/testthat/test-simulate_pause.R
+f062a23fc25d87defd9b3c9abee83de3 *tests/testthat/test-translate_sequence.R
+457af5ebfd916a3463377ea04f190424 *vignettes/RLumModel_-_Getting_started_with_RLumModel.Rmd
+a37192623e2bd1285fc04b895fc96bba *vignettes/RLumModel_-_Getting_started_with_RLumModel.pdf.asis
+5404ddd1e9fe478376f68b0649975502 *vignettes/RLumModel_-_Using_own_parameter_sets.Rmd
+629e1b2db66725fdfafc105c555e00bc *vignettes/RLumModel_-_Using_own_parameter_sets.pdf.asis
diff --git a/RLum.BuildResults/RLumModel.Rcheck/00_pkg_src/RLumModel/NAMESPACE b/RLum.BuildResults/RLumModel.Rcheck/00_pkg_src/RLumModel/NAMESPACE
@@ -0,0 +1,11 @@
+# Generated by roxygen2: do not edit by hand
+
+export(model_LuminescenceSignals)
+export(read_SEQ2R)
+import(Luminescence)
+import(deSolve)
+import(methods)
+import(utils)
+importFrom(Rcpp,evalCpp)
+importFrom(stats,setNames)
+useDynLib(RLumModel)