ModelOriented · mayer79 · Jan 19, 2025 · Jan 19, 2025 · Jan 19, 2025
diff --git a/NEWS.md b/NEWS.md
@@ -7,6 +7,7 @@
 
 ### Compatibility
 
+- Adapt for upcoming {xgboost} version.
 - Adapt for upcoming {shapr} version, thanks @martinju for the fix [#162](https://github.com/ModelOriented/shapviz/pull/162).
 
 # shapviz 0.9.6

diff --git a/R/shapviz.R b/R/shapviz.R
@@ -116,7 +116,7 @@ shapviz.matrix = function(
 #' # XGBoost models
 #' X_pred <- data.matrix(iris[, -1])
 #' dtrain <- xgboost::xgb.DMatrix(X_pred, label = iris[, 1], nthread = 1)
-#' fit <- xgboost::xgb.train(data = dtrain, nrounds = 10, nthread = 1)
+#' fit <- xgboost::xgb.train(list(nthread = 1), data = dtrain, nrounds = 10)
 #'
 #' # Will use numeric matrix "X_pred" as feature matrix
 #' x <- shapviz(fit, X_pred = X_pred)
@@ -131,12 +131,12 @@ shapviz.matrix = function(
 #' x <- shapviz(fit, X_pred = dtrain, X = iris)
 #'
 #' # Multiclass setting
-#' params <- list(objective = "multi:softprob", num_class = 3)
+#' params <- list(objective = "multi:softprob", num_class = 3, nthread = 1)
 #' X_pred <- data.matrix(iris[, -5])
 #' dtrain <- xgboost::xgb.DMatrix(
 #'   X_pred, label = as.integer(iris[, 5]) - 1, nthread = 1
 #' )
-#' fit <- xgboost::xgb.train(params = params, data = dtrain, nrounds = 10, nthread = 1)
+#' fit <- xgboost::xgb.train(params = params, data = dtrain, nrounds = 10)
 #'
 #' # Select specific class
 #' x <- shapviz(fit, X_pred = X_pred, which_class = 3)
@@ -149,7 +149,7 @@ shapviz.matrix = function(
 #' # What if we would have one-hot-encoded values and want to explain the original column?
 #' X_pred <- stats::model.matrix(~ . -1, iris[, -1])
 #' dtrain <- xgboost::xgb.DMatrix(X_pred, label = as.integer(iris[, 1]), nthread = 1)
-#' fit <- xgboost::xgb.train(data = dtrain, nrounds = 10, nthread = 1)
+#' fit <- xgboost::xgb.train(list(nthread = 1), data = dtrain, nrounds = 10)
 #' x <- shapviz(
 #'   fit,
 #'   X_pred = X_pred,

diff --git a/cran-comments.md b/cran-comments.md
@@ -1,6 +1,6 @@
-# shapviz 0.9.6 (Fix CRAN errors)
+# shapviz 0.9.7
 
-One vignette points to a missing figure, leading errors or notes in different builds.
+Slight adaptions to comply with upcoming XGBoost version.
 
 ### Local checks
 
@@ -12,4 +12,5 @@ Status: OK
 
 ## Reverse dependencies (2)
 
-Not checked because the change affects only a vignette.
+OK: 2
+BROKEN: 0
diff --git a/man/shapviz.Rd b/man/shapviz.Rd
diff --git a/revdep/README.md b/revdep/README.md
@@ -1,53 +1,53 @@
 # Platform
 
-|field    |value                                    |
-|:--------|:----------------------------------------|
-|version  |R version 4.4.1 (2024-06-14 ucrt)        |
-|os       |Windows 11 x64 (build 22631)             |
-|system   |x86_64, mingw32                          |
-|ui       |RStudio                                  |
-|language |(EN)                                     |
-|collate  |English_Switzerland.utf8                 |
-|ctype    |English_Switzerland.utf8                 |
-|tz       |Europe/Zurich                            |
-|date     |2024-09-13                               |
-|rstudio  |2024.04.2+764 Chocolate Cosmos (desktop) |
-|pandoc   |NA                                       |
+|field    |value                                 |
+|:--------|:-------------------------------------|
+|version  |R version 4.4.1 (2024-06-14 ucrt)     |
+|os       |Windows 11 x64 (build 22631)          |
+|system   |x86_64, mingw32                       |
+|ui       |RStudio                               |
+|language |(EN)                                  |
+|collate  |English_Switzerland.utf8              |
+|ctype    |English_Switzerland.utf8              |
+|tz       |Europe/Zurich                         |
+|date     |2025-01-19                            |
+|rstudio  |2024.12.0+467 Kousa Dogwood (desktop) |
+|pandoc   |NA                                    |
 
 # Dependencies
 
 |package      |old     |new     |Δ  |
 |:------------|:-------|:-------|:--|
-|shapviz      |0.9.4   |0.9.5   |*  |
+|shapviz      |0.9.6   |0.9.7   |*  |
 |cli          |3.6.3   |3.6.3   |   |
 |colorspace   |2.1-1   |2.1-1   |   |
-|commonmark   |1.9.1   |1.9.1   |   |
-|curl         |5.2.2   |5.2.2   |   |
-|data.table   |1.16.0  |1.16.0  |   |
+|commonmark   |1.9.2   |1.9.2   |   |
+|curl         |6.1.0   |6.1.0   |   |
+|data.table   |1.16.4  |1.16.4  |   |
 |fansi        |1.0.6   |1.0.6   |   |
 |farver       |2.1.2   |2.1.2   |   |
 |ggfittext    |0.10.2  |0.10.2  |   |
 |gggenes      |0.5.1   |0.5.1   |   |
 |ggplot2      |3.5.1   |3.5.1   |   |
 |ggrepel      |0.9.6   |0.9.6   |   |
-|glue         |1.7.0   |1.7.0   |   |
+|glue         |1.8.0   |1.8.0   |   |
 |gridtext     |0.1.5   |0.1.5   |   |
-|gtable       |0.3.5   |0.3.5   |   |
+|gtable       |0.3.6   |0.3.6   |   |
 |isoband      |0.2.7   |0.2.7   |   |
 |jpeg         |0.1-10  |0.1-10  |   |
-|jsonlite     |1.8.8   |1.8.8   |   |
+|jsonlite     |1.8.9   |1.8.9   |   |
 |labeling     |0.4.3   |0.4.3   |   |
 |lifecycle    |1.0.4   |1.0.4   |   |
 |magrittr     |2.0.3   |2.0.3   |   |
 |markdown     |1.13    |1.13    |   |
 |munsell      |0.5.1   |0.5.1   |   |
-|patchwork    |1.2.0   |1.2.0   |   |
-|pillar       |1.9.0   |1.9.0   |   |
+|patchwork    |1.3.0   |1.3.0   |   |
+|pillar       |1.10.1  |1.10.1  |   |
 |pkgconfig    |2.0.3   |2.0.3   |   |
 |png          |0.1-8   |0.1-8   |   |
 |R6           |2.5.1   |2.5.1   |   |
 |RColorBrewer |1.1-3   |1.1-3   |   |
-|Rcpp         |1.0.13  |1.0.13  |   |
+|Rcpp         |1.0.14  |1.0.14  |   |
 |rlang        |1.1.4   |1.1.4   |   |
 |scales       |1.3.0   |1.3.0   |   |
 |shades       |1.4.0   |1.4.0   |   |
@@ -57,17 +57,10 @@
 |utf8         |1.2.4   |1.2.4   |   |
 |vctrs        |0.6.5   |0.6.5   |   |
 |viridisLite  |0.4.2   |0.4.2   |   |
-|withr        |3.0.1   |3.0.1   |   |
-|xfun         |0.47    |0.47    |   |
+|withr        |3.0.2   |3.0.2   |   |
+|xfun         |0.50    |0.50    |   |
 |xgboost      |1.7.8.1 |1.7.8.1 |   |
 |xml2         |1.3.6   |1.3.6   |   |
 
 # Revdeps
 
-## Failed to check (2)
-
-|package  |version |error |warning |note |
-|:--------|:-------|:-----|:-------|:----|
-|fastshap |0.1.1   |1     |        |2    |
-|flowml   |?       |      |        |     |
-
diff --git a/revdep/cran.md b/revdep/cran.md
@@ -1,12 +1,7 @@
 ## revdepcheck results
 
-We checked 2 reverse dependencies (1 from CRAN + 1 from Bioconductor), comparing R CMD check results across CRAN and dev versions of this package.
+We checked 2 reverse dependencies, comparing R CMD check results across CRAN and dev versions of this package.
 
  * We saw 0 new problems
- * We failed to check 1 packages
+ * We failed to check 0 packages
 
-Issues with CRAN packages are summarised below.
-
-### Failed to check
-
-* fastshap (NA)
diff --git a/revdep/failures.md b/revdep/failures.md
@@ -1,142 +1 @@
-# fastshap
-
-<details>
-
-* Version: 0.1.1
-* GitHub: https://github.com/bgreenwell/fastshap
-* Source code: https://github.com/cran/fastshap
-* Date/Publication: 2024-02-22 22:00:02 UTC
-* Number of recursive dependencies: 90
-
-Run `revdepcheck::revdep_details(, "fastshap")` for more info
-
-</details>
-
-## In both
-
-*   R CMD check timed out
-
-
-*   checking package dependencies ... NOTE
-    ```
-    Package which this enhances but not available for checking: 'lightgbm'
-    ```
-
-*   checking Rd cross-references ... NOTE
-    ```
-    Package unavailable to check Rd xrefs: 'lightgbm'
-    ```
-
-# flowml
-
-<details>
-
-* Version: 
-* GitHub: https://github.com/ModelOriented/shapviz
-* Source code: NA
-* Number of recursive dependencies: 0
-
-</details>
-
-## Error before installation
-
-### Devel
-
-```
-
-  There are binary versions available but the source versions are later:
-                binary   source needs_compilation
-abind            1.4-5    1.4-8             FALSE
-gam             1.22-4   1.22-5              TRUE
-ps               1.7.7    1.8.0              TRUE
-RcppArmadillo 14.0.0-1 14.0.2-1              TRUE
-
-  Binaries will be installed
-package 'ABCanalysis' successfully unpacked and MD5 sums checked
-...
-package 'pls' successfully unpacked and MD5 sums checked
-package 'plyr' successfully unpacked and MD5 sums checked
-package 'png' successfully unpacked and MD5 sums checked
-package 'prettyunits' successfully unpacked and MD5 sums checked
-package 'pROC' successfully unpacked and MD5 sums checked
-package 'processx' successfully unpacked and MD5 sums checked
-package 'prodlim' successfully unpacked and MD5 sums checked
-package 'progress' successfully unpacked and MD5 sums checked
-package 'progressr' successfully unpacked and MD5 sums checked
-package 'promises' successfully unpacked and MD5 sums checked
-
-
-Warning: unable to access index for repository https://bioconductor.org/packages/3.18/bioc/bin/windows/contrib/4.4:
-  cannot open URL 'https://bioconductor.org/packages/3.18/bioc/bin/windows/contrib/4.4/PACKAGES'
-Warning: unable to access index for repository https://bioconductor.org/packages/3.18/bioc/bin/windows/contrib/4.4:
-  cannot open URL 'https://bioconductor.org/packages/3.18/bioc/bin/windows/contrib/4.4/PACKAGES'
-Warning: unable to access index for repository https://bioconductor.org/packages/3.18/data/annotation/bin/windows/contrib/4.4:
-  cannot open URL 'https://bioconductor.org/packages/3.18/data/annotation/bin/windows/contrib/4.4/PACKAGES'
-Warning: unable to access index for repository https://bioconductor.org/packages/3.18/data/annotation/bin/windows/contrib/4.4:
-  cannot open URL 'https://bioconductor.org/packages/3.18/data/annotation/bin/windows/contrib/4.4/PACKAGES'
-Warning: unable to access index for repository https://bioconductor.org/packages/3.18/data/experiment/bin/windows/contrib/4.4:
-  cannot open URL 'https://bioconductor.org/packages/3.18/data/experiment/bin/windows/contrib/4.4/PACKAGES'
-...
-2: In download.file(url, destfile, method, mode = "wb", ...) :
-  downloaded length 247004746 != reported length 266665380
-3: In download.file(url, destfile, method, mode = "wb", ...) :
-  URL 'https://cran.rstudio.com/bin/windows/contrib/4.4/h2o_3.44.0.3.zip': Timeout of 60 seconds was reached
-4: In download.file(url, destfile, method, mode = "wb", ...) :
-  URL 'https://cran.rstudio.com/bin/windows/contrib/4.4/h2o_3.44.0.3.zip': Timeout of 60 seconds was reached
-Warning in download.packages(pkgs, destdir = tmpd, available = available,  :
-  download of package 'h2o' failed
-Warning in download.packages(pkgs, destdir = tmpd, available = available,  :
-  download of package 'h2o' failed
-
-
-```
-### CRAN
-
-```
-
-  There are binary versions available but the source versions are later:
-                binary   source needs_compilation
-abind            1.4-5    1.4-8             FALSE
-gam             1.22-4   1.22-5              TRUE
-ps               1.7.7    1.8.0              TRUE
-RcppArmadillo 14.0.0-1 14.0.2-1              TRUE
-
-  Binaries will be installed
-package 'ABCanalysis' successfully unpacked and MD5 sums checked
-...
-package 'pls' successfully unpacked and MD5 sums checked
-package 'plyr' successfully unpacked and MD5 sums checked
-package 'png' successfully unpacked and MD5 sums checked
-package 'prettyunits' successfully unpacked and MD5 sums checked
-package 'pROC' successfully unpacked and MD5 sums checked
-package 'processx' successfully unpacked and MD5 sums checked
-package 'prodlim' successfully unpacked and MD5 sums checked
-package 'progress' successfully unpacked and MD5 sums checked
-package 'progressr' successfully unpacked and MD5 sums checked
-package 'promises' successfully unpacked and MD5 sums checked
-
-
-Warning: unable to access index for repository https://bioconductor.org/packages/3.18/bioc/bin/windows/contrib/4.4:
-  cannot open URL 'https://bioconductor.org/packages/3.18/bioc/bin/windows/contrib/4.4/PACKAGES'
-Warning: unable to access index for repository https://bioconductor.org/packages/3.18/bioc/bin/windows/contrib/4.4:
-  cannot open URL 'https://bioconductor.org/packages/3.18/bioc/bin/windows/contrib/4.4/PACKAGES'
-Warning: unable to access index for repository https://bioconductor.org/packages/3.18/data/annotation/bin/windows/contrib/4.4:
-  cannot open URL 'https://bioconductor.org/packages/3.18/data/annotation/bin/windows/contrib/4.4/PACKAGES'
-Warning: unable to access index for repository https://bioconductor.org/packages/3.18/data/annotation/bin/windows/contrib/4.4:
-  cannot open URL 'https://bioconductor.org/packages/3.18/data/annotation/bin/windows/contrib/4.4/PACKAGES'
-Warning: unable to access index for repository https://bioconductor.org/packages/3.18/data/experiment/bin/windows/contrib/4.4:
-  cannot open URL 'https://bioconductor.org/packages/3.18/data/experiment/bin/windows/contrib/4.4/PACKAGES'
-...
-2: In download.file(url, destfile, method, mode = "wb", ...) :
-  downloaded length 247004746 != reported length 266665380
-3: In download.file(url, destfile, method, mode = "wb", ...) :
-  URL 'https://cran.rstudio.com/bin/windows/contrib/4.4/h2o_3.44.0.3.zip': Timeout of 60 seconds was reached
-4: In download.file(url, destfile, method, mode = "wb", ...) :
-  URL 'https://cran.rstudio.com/bin/windows/contrib/4.4/h2o_3.44.0.3.zip': Timeout of 60 seconds was reached
-Warning in download.packages(pkgs, destdir = tmpd, available = available,  :
-  download of package 'h2o' failed
-Warning in download.packages(pkgs, destdir = tmpd, available = available,  :
-  download of package 'h2o' failed
-
-
-```
+*Wow, no problems at all. :)*
diff --git a/shapviz.Rproj b/shapviz.Rproj
@@ -1,4 +1,5 @@
 Version: 1.0
+ProjectId: 53532cda-0245-4018-9318-405db5e4b62a
 
 RestoreWorkspace: Default
 SaveWorkspace: Default

diff --git a/tests/testthat/test-interface.R b/tests/testthat/test-interface.R
@@ -261,11 +261,9 @@ test_that("combining incompatible shapviz objects fails", {
 X_pred <- data.matrix(iris[, -5L])
 dtrain <- xgboost::xgb.DMatrix(X_pred, label = as.integer(iris[, 5L]) - 1L, nthread = 1)
 fit <- xgboost::xgb.train(
-  params = list(nthread = 1L),
+  params = list(nthread = 1L, num_class = 3L, objective = "multi:softprob"),
   data = dtrain,
-  nrounds = 1L,
-  objective="multi:softprob",
-  num_class = 3L
+  nrounds = 1L
 )
 shp3 <- shapviz(fit, X_pred = X_pred, which_class = 3L, interactions = TRUE)
 mshp <- shapviz(fit, X_pred = X_pred, interactions = TRUE)