Merge pull request #103 from ModelOriented/cran_sub

mayer79 · web-flow · commit 2a6fd0c45023 · 2023-09-24T16:57:53.000+02:00
CRAN submission
diff --git a/CRAN-SUBMISSION b/CRAN-SUBMISSION
@@ -1,3 +1,3 @@
-Version: 0.3.7
-Date: 2023-05-17 06:52:31 UTC
-SHA: b6e4ce87f93a54e5c451cd06315ab810bb29eb8a
+Version: 0.3.8
+Date: 2023-09-23 12:06:38 UTC
+SHA: 7ca4f7e46e925abd8cf0155227d126ebd9ea2364
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -7,10 +7,9 @@ Authors@R: c(
     person("Przemyslaw", "Biecek", , "przemyslaw.biecek@gmail.com", role = "ctb",
            comment = c(ORCID = "0000-0001-8423-1823"))
   )
-Description: Efficient implementation of Kernel SHAP, see Lundberg and Lee
-    (2017) <https://dl.acm.org/doi/10.5555/3295222.3295230>, and Covert
-    and Lee (2021) <http://proceedings.mlr.press/v130/covert21a>.  For
-    models with up to eight features, the results are exact regarding the
+Description: Efficient implementation of Kernel SHAP, see Lundberg and Lee (2017), 
+    and Covert and Lee (2021) <http://proceedings.mlr.press/v130/covert21a>.
+    For models with up to eight features, the results are exact regarding the
     selected background data.  Otherwise, an almost exact hybrid algorithm
     involving iterative sampling is used.  The package plays well together
     with meta-learning packages like 'tidymodels', 'caret' or 'mlr3'.
diff --git a/NEWS.md b/NEWS.md
@@ -7,11 +7,12 @@
 ## Bug fixes
 
 - {mlr3} probabilistic classification would not work out-of-the-box. This has been fixed (with corresponding example in the README) in https://github.com/ModelOriented/kernelshap/pull/100
+- The progress bar was initialized at 1 instead of 0. This is fixed.
 
 ## Maintenance
 
 - Added explanation of sampling Kernel SHAP to help file.
-- In internal calculations, use explicit `feature_names` as dimnames (https://github.com/ModelOriented/kernelshap/issues/96)
+- In internal calculations, use explicit `feature_names` as dimnames (https://github.com/ModelOriented/kernelshap/issues/96).
 
 # kernelshap 0.3.7
 
diff --git a/R/kernelshap.R b/R/kernelshap.R
@@ -290,7 +290,7 @@ kernelshap.default <- function(object, X, bg_X, pred_fun = stats::predict,
     )
   } else {
     if (verbose && n >= 2L) {
-      pb <- utils::txtProgressBar(1L, n, style = 3)  
+      pb <- utils::txtProgressBar(max = n, style = 3)  
     }
     res <- vector("list", n)
     for (i in seq_len(n)) {
diff --git a/cran-comments.md b/cran-comments.md
@@ -1,33 +1,75 @@
+# Resubmission II
+
+I have now removed the non-registered DOI from the description file.
+
+This was Uwe's comment:
+
+   Found the following (possibly) invalid DOIs:
+     DOI: 10.5555/3295222.3295230
+       From: DESCRIPTION
+       Status: 404
+       Message: Not Found
+
+and looking for the DOI shows it is not registered.
+Even when going to
+https://dl.acm.org/doi/10.5555/3295222.3295230
+and clicking on the "Publisher Site" link leads us into nirvana.
+
+So I guess the is ill registered and you have to revert the change. My 
+apologoies, I had not checked whether the DOI given is registreed or not.
+
+Best,
+
+
+# Resubmission I
+
+I stumbled over a DOI: Uwe gently pointed this out:
+
+"
+   The Description field contains
+     <https://dl.acm.org/doi/10.5555/3295222.3295230>, and Covert and Lee
+   Please use permanent DOI markup for linking to publications as in 
+<doi:prefix/suffix>.
+"
+
+This resubmission fixes this.
+
+# Original message
+
 Hello CRAN
 
-My recent change introduced Latex errors in help files on MacOS and "oldrel". The reason are "text" instead of "textrm" tags in eqn{} blocks. I will need to fix this in two additional packages, but I will test it with this one.
+This is a small maintenance release only.
 
-https://cran.r-project.org/web/checks/check_results_kernelshap.html
+Thanks a lot
+
+Michael
 
 ## Checks
 
 ### Revdep
 
-survex:
-
+survex 1.1.3                                                                             
 - OK: 1
 - BROKEN: 0
 
-### `check(manual = TRUE, cran = TRUE)`
-
-❯ checking for future file timestamps ... NOTE
-  unable to verify current time
+### Local check with innocent NOTE
 
 ❯ checking HTML version of manual ... NOTE
   Skipping checking HTML validation: no command 'tidy' found
   
-### `check_win_devel()`
-
-OK
+### `check_win_devel()` NOTE
 
-### `check_rhub()` Notes
+- R Under development (unstable) (2023-09-11 r85126 ucrt)
 
-- kipping checking HTML validation: no command 'tidy' found
-- Skipping checking math rendering: package 'V8' unavailable
+### `check_rhub()` NOTES
 
+-> Note sure where the 403 problem comes from. Is it relevant?
 
+Found the following (possibly) invalid URLs:
+  URL: https://dl.acm.org/doi/10.5555/3295222.3295230
+    From: DESCRIPTION
+    Status: 403
+    Message: Forbidden
+* checking HTML version of manual ... NOTE
+Skipping checking HTML validation: no command 'tidy' found
+Skipping checking math rendering: package 'V8' unavailable
diff --git a/packaging.R b/packaging.R
@@ -17,7 +17,7 @@ use_description(
     Title = "Kernel SHAP",
     Version = "0.3.8",
     Description = "Efficient implementation of Kernel SHAP, 
-    see Lundberg and Lee (2017) <https://dl.acm.org/doi/10.5555/3295222.3295230>,
+    see Lundberg and Lee (2017),
     and Covert and Lee (2021) <http://proceedings.mlr.press/v130/covert21a>.
     For models with up to eight features, the results are exact regarding the selected background data.
     Otherwise, an almost exact hybrid algorithm involving iterative sampling is used.
diff --git a/revdep/README.md b/revdep/README.md
@@ -1,24 +1,24 @@
 # Platform
 
-|field    |value                                                |
-|:--------|:----------------------------------------------------|
-|version  |R version 4.3.0 (2023-04-21 ucrt)                    |
-|os       |Windows 11 x64 (build 22621)                         |
-|system   |x86_64, mingw32                                      |
-|ui       |RStudio                                              |
-|language |(EN)                                                 |
-|collate  |German_Switzerland.utf8                              |
-|ctype    |German_Switzerland.utf8                              |
-|tz       |Europe/Zurich                                        |
-|date     |2023-05-15                                           |
-|rstudio  |2023.03.0+386 Cherry Blossom (desktop)               |
-|pandoc   |2.12 @ C:\Users\Michael\anaconda3\Scripts\pandoc.exe |
+|field    |value                                                    |
+|:--------|:--------------------------------------------------------|
+|version  |R version 4.3.0 (2023-04-21 ucrt)                        |
+|os       |Windows 11 x64 (build 22621)                             |
+|system   |x86_64, mingw32                                          |
+|ui       |RStudio                                                  |
+|language |(EN)                                                     |
+|collate  |German_Switzerland.utf8                                  |
+|ctype    |German_Switzerland.utf8                                  |
+|tz       |Europe/Zurich                                            |
+|date     |2023-09-12                                               |
+|rstudio  |2023.06.1+524 Mountain Hydrangea (desktop)               |
+|pandoc   |3.1.6 @ C:\Users\Michael\AppData\Local\Pandoc\pandoc.exe |
 
 # Dependencies
 
 |package    |old    |new    |Δ  |
 |:----------|:------|:------|:--|
-|kernelshap |0.3.6  |0.3.7  |*  |
+|kernelshap |0.3.7  |0.3.8  |*  |
 |foreach    |1.5.2  |1.5.2  |   |
 |iterators  |1.0.14 |1.0.14 |   |
 

Original file line number	Diff line number	Diff line change
`@@ -290,7 +290,7 @@ kernelshap.default <- function(object, X, bg_X, pred_fun = stats::predict,`
`290`	`290`	`)`
`291`	`291`	`} else {`
`292`	`292`	`if (verbose && n >= 2L) {`
`293`		`- pb <- utils::txtProgressBar(1L, n, style = 3)`
	`293`	`+ pb <- utils::txtProgressBar(max = n, style = 3)`
`294`	`294`	`}`
`295`	`295`	`res <- vector("list", n)`
`296`	`296`	`for (i in seq_len(n)) {`