Merge pull request #30 from HendrikSchultheis/master

cran submission 2.0.2
loosolab · Sep 19, 2018 · f4b57f5 · f4b57f5
2 parents 9547c57 + 6680b48
commit f4b57f5
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: wilson
 Type: Package
 Title: Web-Based Interactive Omics Visualization
-Version: 2.0.1.9000
+Version: 2.0.2
 Authors@R: c(
     person("Hendrik", "Schultheis", email = "hendrik.schultheis@mpi-bn.mpg.de", role = c("aut", "cre")),
     person("Jens", "Preussner", email = "jens.preussner@mpi-bn.mpg.de", role = "aut"),
@@ -46,7 +46,7 @@ Imports: shiny,
     openssl,
     methods,
     R6
-RoxygenNote: 6.0.1
+RoxygenNote: 6.1.0
 biocViews: 
 Suggests: knitr,
     rmarkdown,

diff --git a/NAMESPACE b/NAMESPACE
@@ -35,3 +35,4 @@ export(set_logger)
 export(transformation)
 export(transformationUI)
 import(data.table)
+importFrom(R6,R6Class)
diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,5 @@
+# wilson 2.0.2
+- fixed CRAN check Note/ Error
 # wilson 2.0.1
 - tests added
 # wilson 2.0.0 

diff --git a/R/clarion.R b/R/clarion.R
@@ -45,6 +45,7 @@
 #'
 #' @format NULL
 #' @usage NULL
+#' @importFrom R6 R6Class
 #' @export
 Clarion <- R6::R6Class("Clarion",
                        public = list(

diff --git a/cran-comments.md b/cran-comments.md
@@ -1,57 +1,24 @@
-# Submission 1
+# Submission
 ## Test environments
 * local windows 7 install, R 3.5.1
 * debian 9.4, R 3.4.1
 * win-builder (devel and release)
 
 ## R CMD check results
-There were no ERRORs or WARNINGs.
-
-There was 1 NOTE:
-
-* New submission
-
-* Possibly mis-spelled words in DESCRIPTION:
-  Omics (3:30)
-  omics (9:126)
-
-  Both are spelled correctly. First is capital because of title case.
+There were no NOTEs, ERRORs or WARNINGs.
 
 ## Downstream dependencies
 I have also run R CMD check on downstream dependencies of wilson 
 (https://github.molgen.mpg.de/loosolab/wilson/tree/master/revdep). 
 All packages that I could install passed.
 
-## Reviewer comments
-Thanks, we see you have lots of cuntions without examples (which may be reasonable given they are not intended t be called by users directly). 
-Nevertheless, it would be good to have them tested, so please create, if examples are not feasible, at least tests that execute the various functions in your package.
-
-Best,
-Uwe Ligges
+## CRAN Message
+Dear maintainer of package wilson,
 
-# Submission 2
-## Test environments
-* local windows 7 install, R 3.5.1
-* debian 9.4, R 3.4.1
-* win-builder (devel and release)
+please see <https://cran.r-project.org/web/checks/check_results_wilson.html>
+and find current problems with your package.
 
-## Submission comments
-Addressed reviewer comments by adding tests where possible.
+Please fix and resubmit before Sep 21 to safely retain the package on CRAN.
 
-## R CMD check results
-There were no ERRORs or WARNINGs.
-
-There was 1 NOTE:
-
-* New submission
-
-* Possibly mis-spelled words in DESCRIPTION:
-  Omics (3:30)
-  omics (9:126)
-
-  Both are spelled correctly. First is capital because of title case.
-
-## Downstream dependencies
-I have also run R CMD check on downstream dependencies of wilson 
-(https://github.molgen.mpg.de/loosolab/wilson/tree/master/revdep). 
-All packages that I could install passed.
+Best wishes,
+Uwe Ligges
diff --git a/man/colorPicker.Rd b/man/colorPicker.Rd
diff --git a/man/create_geneview.Rd b/man/create_geneview.Rd
diff --git a/man/create_heatmap.Rd b/man/create_heatmap.Rd
diff --git a/man/create_pca.Rd b/man/create_pca.Rd
diff --git a/man/create_scatterplot.Rd b/man/create_scatterplot.Rd
diff --git a/man/download.Rd b/man/download.Rd
diff --git a/man/global_cor_heatmap.Rd b/man/global_cor_heatmap.Rd
diff --git a/man/log_message.Rd b/man/log_message.Rd
diff --git a/man/orNumeric.Rd b/man/orNumeric.Rd
diff --git a/man/orTextual.Rd b/man/orTextual.Rd
diff --git a/man/parse_MaxQuant.Rd b/man/parse_MaxQuant.Rd
diff --git a/man/pca.Rd b/man/pca.Rd
diff --git a/man/scatterPlot.Rd b/man/scatterPlot.Rd
diff --git a/man/searchData.Rd b/man/searchData.Rd
diff --git a/revdep/README.md b/revdep/README.md
@@ -4,52 +4,52 @@
 
 |setting  |value                        |
 |:--------|:----------------------------|
-|version  |R version 3.5.1 (2018-07-02) |
+|version  |R version 3.4.4 (2018-03-15) |
 |system   |x86_64, mingw32              |
 |ui       |RStudio (1.2.747)            |
 |language |(EN)                         |
 |collate  |German_Germany.1252          |
 |tz       |Europe/Berlin                |
-|date     |2018-07-16                   |
+|date     |2018-09-17                   |
 
 ## Packages
 
 |package         |*  |version |date       |source                              |
 |:---------------|:--|:-------|:----------|:-----------------------------------|
-|circlize        |   |0.4.4   |2018-06-10 |CRAN (R 3.5.1)                      |
-|colourpicker    |   |1.0     |2017-09-27 |CRAN (R 3.5.1)                      |
-|ComplexHeatmap  |   |1.18.1  |2018-06-19 |Bioconductor (R 3.5.0)              |
-|data.table      |   |1.11.4  |2018-05-27 |CRAN (R 3.5.1)                      |
-|DESeq2          |   |1.20.0  |2018-05-01 |Bioconductor                        |
-|DT              |   |0.4     |2018-01-30 |CRAN (R 3.5.1)                      |
-|factoextra      |   |1.0.5   |2017-08-22 |CRAN (R 3.5.1)                      |
-|FactoMineR      |   |1.41    |2018-05-04 |CRAN (R 3.5.1)                      |
-|ggplot2         |   |3.0.0   |2018-07-03 |CRAN (R 3.5.1)                      |
-|ggrepel         |   |0.8.0   |2018-05-09 |CRAN (R 3.5.1)                      |
-|gplots          |   |3.0.1   |2016-03-30 |CRAN (R 3.5.1)                      |
-|heatmaply       |   |0.15.2  |2018-07-06 |CRAN (R 3.5.1)                      |
-|knitr           |   |1.20    |2018-02-20 |CRAN (R 3.5.1)                      |
-|log4r           |   |0.2     |2014-09-29 |CRAN (R 3.5.1)                      |
-|openssl         |   |1.0.1   |2018-03-03 |CRAN (R 3.5.1)                      |
-|plotly          |   |4.7.1   |2017-07-29 |CRAN (R 3.5.1)                      |
-|plyr            |   |1.8.4   |2016-06-08 |CRAN (R 3.5.1)                      |
-|R6              |   |2.2.2   |2017-06-17 |CRAN (R 3.5.1)                      |
-|RColorBrewer    |   |1.1-2   |2014-12-07 |CRAN (R 3.5.0)                      |
-|reshape         |   |0.8.7   |2017-08-06 |CRAN (R 3.5.1)                      |
-|rintrojs        |   |0.2.0   |2017-07-04 |CRAN (R 3.5.1)                      |
-|rje             |   |1.9     |2014-08-06 |CRAN (R 3.5.0)                      |
-|rjson           |   |0.2.20  |2018-06-08 |CRAN (R 3.5.0)                      |
-|RJSONIO         |   |1.3-0   |2014-07-28 |CRAN (R 3.5.0)                      |
-|rmarkdown       |   |1.10    |2018-06-11 |CRAN (R 3.5.1)                      |
-|scales          |   |0.5.0   |2017-08-24 |CRAN (R 3.5.1)                      |
-|shiny           |   |1.1.0   |2018-05-17 |CRAN (R 3.5.1)                      |
-|shinycssloaders |   |0.2.0   |2017-05-12 |CRAN (R 3.5.1)                      |
-|shinydashboard  |   |0.7.0   |2018-03-21 |CRAN (R 3.5.1)                      |
-|shinyjs         |   |1.0     |2018-01-08 |CRAN (R 3.5.1)                      |
-|testthat        |   |2.0.0   |2017-12-13 |CRAN (R 3.5.1)                      |
-|vdiffr          |   |0.2.3   |2018-04-27 |CRAN (R 3.5.1)                      |
-|viridis         |   |0.5.1   |2018-03-29 |CRAN (R 3.5.1)                      |
-|wilson          |   |2.0.1   |2018-07-16 |local (HendrikSchultheis/wilson@NA) |
+|circlize        |   |0.4.4   |2018-06-10 |CRAN (R 3.4.4)                      |
+|colourpicker    |   |1.0     |2017-09-27 |CRAN (R 3.4.4)                      |
+|ComplexHeatmap  |   |1.17.1  |2017-10-25 |Bioconductor (R 3.4.2)              |
+|data.table      |   |1.11.4  |2018-05-27 |CRAN (R 3.4.4)                      |
+|DESeq2          |   |1.18.1  |2017-11-12 |Bioconductor                        |
+|DT              |   |0.4     |2018-01-30 |CRAN (R 3.4.4)                      |
+|factoextra      |   |1.0.5   |2017-08-22 |CRAN (R 3.4.4)                      |
+|FactoMineR      |   |1.41    |2018-05-04 |CRAN (R 3.4.4)                      |
+|ggplot2         |   |3.0.0   |2018-07-03 |CRAN (R 3.4.4)                      |
+|ggrepel         |   |0.8.0   |2018-05-09 |CRAN (R 3.4.4)                      |
+|gplots          |   |3.0.1   |2016-03-30 |CRAN (R 3.4.4)                      |
+|heatmaply       |   |0.15.2  |2018-07-06 |CRAN (R 3.4.4)                      |
+|knitr           |   |1.20    |2018-02-20 |CRAN (R 3.4.4)                      |
+|log4r           |   |0.2     |2014-09-29 |CRAN (R 3.4.4)                      |
+|openssl         |   |1.0.2   |2018-07-30 |CRAN (R 3.4.4)                      |
+|plotly          |   |4.8.0   |2018-07-20 |CRAN (R 3.4.4)                      |
+|plyr            |   |1.8.4   |2016-06-08 |CRAN (R 3.4.4)                      |
+|R6              |   |2.2.2   |2017-06-17 |CRAN (R 3.4.4)                      |
+|RColorBrewer    |   |1.1-2   |2014-12-07 |CRAN (R 3.4.1)                      |
+|reshape         |   |0.8.7   |2017-08-06 |CRAN (R 3.4.4)                      |
+|rintrojs        |   |0.2.0   |2017-07-04 |CRAN (R 3.4.4)                      |
+|rje             |   |1.9     |2014-08-06 |CRAN (R 3.4.1)                      |
+|rjson           |   |0.2.20  |2018-06-08 |CRAN (R 3.4.4)                      |
+|RJSONIO         |   |1.3-0   |2014-07-28 |CRAN (R 3.4.1)                      |
+|rmarkdown       |   |1.10    |2018-06-11 |CRAN (R 3.4.4)                      |
+|scales          |   |1.0.0   |2018-08-09 |CRAN (R 3.4.4)                      |
+|shiny           |   |1.1.0   |2018-05-17 |CRAN (R 3.4.4)                      |
+|shinycssloaders |   |0.2.0   |2017-05-12 |CRAN (R 3.4.4)                      |
+|shinydashboard  |   |0.7.0   |2018-03-21 |CRAN (R 3.4.4)                      |
+|shinyjs         |   |1.0     |2018-01-08 |CRAN (R 3.4.4)                      |
+|testthat        |   |2.0.0   |2017-12-13 |CRAN (R 3.4.4)                      |
+|vdiffr          |   |0.2.3   |2018-04-27 |CRAN (R 3.4.4)                      |
+|viridis         |   |0.5.1   |2018-03-29 |CRAN (R 3.4.4)                      |
+|wilson          |*  |2.0.2   |2018-09-17 |local (HendrikSchultheis/wilson@NA) |
 
 # Check results
 

diff --git a/revdep/checks.rds b/revdep/checks.rds