update revdep

rcannood · Sep 2, 2018 · 6aa3ff8 · 6aa3ff8
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diff --git a/cran-comments.md b/cran-comments.md
@@ -1,20 +1,11 @@
-There was a problem generating the vignettes because ffmpeg was not installed,
-resulting in warnings on fedora and solaris platforms.
-
-I rewrote the vignette to use `magick` instead of `animation`, which uses 
-imagemagick instead of ffmpeg as a back end. The updated vignette is based
-heavily on magick's vignettes, which all build 100% on CRAN 
-([link](https://cran.r-project.org/web/checks/check_results_magick.html))
-as to ensure the princurve vignettes also work fine.
+`analogue` and `aroma.light` both get warnings as a result of the deprecation of 
+`principal.curve()`. 
 
 ## Changelog
 
-  * DOCUMENTATION: Use the `magick` package to generate animated GIFs in 
-    the vignette, instead of the `animation` package, because
-    `animation` uses `ffmpeg` which is not installed on all CRAN systems.
-
-  * DEPRECATION: Added deprecation which will be triggered starting from 2018-08-01
-    upon calling `principal.curve()` or `get.lam()`.
+  * Removed extra dependencies in princurve by removing vignettes; fixes #28.
+
+  * Fully deprecated `principal.curve()` function.
 
 ## Test environments
 * local Fedora 28 install, R 3.5.0
@@ -33,19 +24,20 @@ as to ensure the princurve vignettes also work fine.
 
 ## Reverse dependencies
 
-R CMD check was run at 2018/07/24 13:40 using the following command:
+R CMD check was run at 2019/09/02 using the following command:
 
 ```r
 revdepcheck::revdep_check(timeout = as.difftime(60, units = "mins"), num_workers = 8)
 ```
 
 |package                                      |version |error |warning |note |
 |:--------------------------------------------|:-------|:-----|:-------|:----|
-|analogue                                     |0.17-0  |      |        |     |
-|[aroma.light](revdep/problems.md#aromalight) |3.10.0  |      |        |1    |
+|[analogue](revdep/problems.md#analogue)      |0.17-0  |      |__+1__  |     |
+|[aroma.light](revdep/problems.md#aromalight) |3.10.0  |      |__+1__  |1    |
 |ClusterSignificance                          |1.8.2   |      |        |     |
-|FateID                                       |0.1.2   |      |        |     |
-|MDSMap                                       |1.0     |      |        |     |
+|[FateID](revdep/problems.md#fateid)          |0.1.4   |      |1       |     |
+|[lilikoi](revdep/problems.md#lilikoi)        |0.1.0   |      |        |3    |
+|MDSMap                                       |1.1     |      |        |     |
 |[pathifier](revdep/problems.md#pathifier)    |1.20.0  |      |        |1    |
-|RSDA                                         |2.0.4   |      |        |     |
+|[RSDA](revdep/problems.md#rsda)              |2.0.5   |1     |        |     |
 |SCORPIUS                                     |1.0.2   |      |        |     |
diff --git a/revdep/README.md b/revdep/README.md
@@ -9,27 +9,34 @@
 |language |(EN)                            |
 |collate  |en_GB.UTF-8                     |
 |tz       |Europe/Brussels                 |
-|date     |2018-07-24                      |
+|date     |2018-09-02                      |
 
 # Dependencies
 
-|package   |old   |new        |Δ  |
-|:---------|:-----|:----------|:--|
-|princurve |2.1.1 |2.1.2.9001 |*  |
-|Rcpp      |NA    |0.12.18    |*  |
+|package   |old     |new        |Δ  |
+|:---------|:-------|:----------|:--|
+|princurve |2.1.2.1 |2.1.3.9001 |*  |
 
 # Revdeps
 
-## All (8)
+## Broken (2)
 
 |package                               |version |error |warning |note |
 |:-------------------------------------|:-------|:-----|:-------|:----|
-|analogue                              |0.17-0  |      |        |     |
-|[aroma.light](problems.md#aromalight) |3.10.0  |      |        |1    |
+|[analogue](problems.md#analogue)      |0.17-0  |      |__+1__  |     |
+|[aroma.light](problems.md#aromalight) |3.10.0  |      |__+1__  |1    |
+
+## All (9)
+
+|package                               |version |error |warning |note |
+|:-------------------------------------|:-------|:-----|:-------|:----|
+|[analogue](problems.md#analogue)      |0.17-0  |      |__+1__  |     |
+|[aroma.light](problems.md#aromalight) |3.10.0  |      |__+1__  |1    |
 |ClusterSignificance                   |1.8.2   |      |        |     |
-|FateID                                |0.1.2   |      |        |     |
-|MDSMap                                |1.0     |      |        |     |
+|[FateID](problems.md#fateid)          |0.1.4   |      |1       |     |
+|[lilikoi](problems.md#lilikoi)        |0.1.0   |      |        |3    |
+|MDSMap                                |1.1     |      |        |     |
 |[pathifier](problems.md#pathifier)    |1.20.0  |      |        |1    |
-|RSDA                                  |2.0.4   |      |        |     |
+|[RSDA](problems.md#rsda)              |2.0.5   |1     |        |     |
 |SCORPIUS                              |1.0.2   |      |        |     |
 
diff --git a/revdep/data.sqlite b/revdep/data.sqlite
diff --git a/revdep/problems.md b/revdep/problems.md
@@ -1,7 +1,52 @@
+# analogue
+
+Version: 0.17-0
+
+## Newly broken
+
+*   checking examples ... WARNING
+    ```
+    ...
+      Warning: 'get.lam' is deprecated.
+      Warning: 'get.lam' is deprecated.
+      Warning: 'get.lam' is deprecated.
+      Warning: 'get.lam' is deprecated.
+      Warning: 'get.lam' is deprecated.
+      Warning: 'get.lam' is deprecated.
+      Warning: 'get.lam' is deprecated.
+      Warning: 'get.lam' is deprecated.
+      Warning: 'get.lam' is deprecated.
+      Warning: 'get.lam' is deprecated.
+      Warning: 'get.lam' is deprecated.
+      Warning: 'get.lam' is deprecated.
+      Warning: 'get.lam' is deprecated.
+      Warning: 'get.lam' is deprecated.
+      Warning: 'get.lam' is deprecated.
+      Warning: 'get.lam' is deprecated.
+      Warning: 'get.lam' is deprecated.
+      Warning: 'get.lam' is deprecated.
+    Deprecated functions may be defunct as soon as of the next release of
+    R.
+    See ?Deprecated.
+    ```
+
 # aroma.light
 
 Version: 3.10.0
 
+## Newly broken
+
+*   checking examples ... WARNING
+    ```
+    Found the following significant warnings:
+    
+      Warning: 'principal.curve' is deprecated.
+      Warning: 'principal.curve' is deprecated.
+    Deprecated functions may be defunct as soon as of the next release of
+    R.
+    See ?Deprecated.
+    ```
+
 ## In both
 
 *   checking for hidden files and directories ... NOTE
@@ -12,6 +57,49 @@ Version: 3.10.0
     structure’ in the ‘Writing R Extensions’ manual.
     ```
 
+# FateID
+
+Version: 0.1.4
+
+## In both
+
+*   checking re-building of vignette outputs ... WARNING
+    ```
+    Error in re-building vignettes:
+      ...
+    Error running filter pandoc-citeproc:
+    Could not find executable pandoc-citeproc
+    Error: processing vignette 'FateID.Rmd' failed with diagnostics:
+    pandoc document conversion failed with error 83
+    Execution halted
+    ```
+
+# lilikoi
+
+Version: 0.1.0
+
+## In both
+
+*   checking installed package size ... NOTE
+    ```
+      installed size is  5.0Mb
+      sub-directories of 1Mb or more:
+        data      3.8Mb
+        extdata   1.1Mb
+    ```
+
+*   checking dependencies in R code ... NOTE
+    ```
+    Namespaces in Imports field not imported from:
+      ‘Matrix’ ‘devtools’ ‘e1071’ ‘glmnet’ ‘hash’ ‘pamr’ ‘randomForest’
+      All declared Imports should be used.
+    ```
+
+*   checking data for non-ASCII characters ... NOTE
+    ```
+      Note: found 3837 marked UTF-8 strings
+    ```
+
 # pathifier
 
 Version: 1.20.0
@@ -36,3 +124,17 @@ Version: 1.20.0
     to your NAMESPACE file.
     ```
 
+# RSDA
+
+Version: 2.0.5
+
+## In both
+
+*   checking package dependencies ... ERROR
+    ```
+    Package required but not available: ‘randomcoloR’
+    
+    See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
+    manual.
+    ```
+