diff --git a/.ci/download-r-revdeps.R b/.ci/download-r-revdeps.R
index 8506afd0d0dd..f6e71def70ff 100644
--- a/.ci/download-r-revdeps.R
+++ b/.ci/download-r-revdeps.R
@@ -18,7 +18,11 @@ reverse_deps <- depDF[["to"]]
 # skip some dependencies with known issues:
 #
 #   * 'misspi' (https://github.com/microsoft/LightGBM/issues/6741)
-deps_to_skip <- "misspi"
+#   * 'qeML'   (checks take 45+ minutes to run)
+deps_to_skip <- c(
+    "misspi"
+    , "qeML"
+)
 .log(sprintf("excluding %i reverse deps: %s", length(deps_to_skip), toString(deps_to_skip)))
 reverse_deps <- reverse_deps[!reverse_deps %in% deps_to_skip]
 
diff --git a/.ci/run-revdep-checks.sh b/.ci/run-revdep-checks.sh
index 74027b87fafe..92cc0ab60f56 100755
--- a/.ci/run-revdep-checks.sh
+++ b/.ci/run-revdep-checks.sh
@@ -21,20 +21,20 @@ sh ./build-cran-package.sh --no-build-vignettes
 R CMD INSTALL --with-keep.source ./lightgbm_*.tar.gz
 
 # run 'R CMD check' on lightgbm's reverse dependencies
-#Rscript ./.ci/run-r-revdepchecks.R "${CHECKS_OUTPUT_DIR}"
+Rscript ./.ci/run-r-revdepchecks.R "${CHECKS_OUTPUT_DIR}"
 
-R CMD check --no-manual --run-dontrun --run-donttest ${CHECKS_OUTPUT_DIR}/EIX_*.tar.gz || true
-R CMD check --no-manual --run-dontrun --run-donttest ${CHECKS_OUTPUT_DIR}/SHAPforxgboost_*.tar.gz || true
-R CMD check --no-manual --run-dontrun --run-donttest ${CHECKS_OUTPUT_DIR}/cbl_*.tar.gz || true
-R CMD check --no-manual --run-dontrun --run-donttest ${CHECKS_OUTPUT_DIR}/bonsai_*.tar.gz || true
-R CMD check --no-manual --run-dontrun --run-donttest ${CHECKS_OUTPUT_DIR}/fastshap_*.tar.gz || true
-R CMD check --no-manual --run-dontrun --run-donttest ${CHECKS_OUTPUT_DIR}/fastml_*.tar.gz || true
-R CMD check --no-manual --run-dontrun --run-donttest ${CHECKS_OUTPUT_DIR}/fastshap_*.tar.gz || true
-R CMD check --no-manual --run-dontrun --run-donttest ${CHECKS_OUTPUT_DIR}/predhy.GUI_*.tar.gz || true
+# R CMD check --no-manual --run-dontrun --run-donttest ${CHECKS_OUTPUT_DIR}/EIX_*.tar.gz || true
+# R CMD check --no-manual --run-dontrun --run-donttest ${CHECKS_OUTPUT_DIR}/SHAPforxgboost_*.tar.gz || true
+# R CMD check --no-manual --run-dontrun --run-donttest ${CHECKS_OUTPUT_DIR}/cbl_*.tar.gz || true
+# R CMD check --no-manual --run-dontrun --run-donttest ${CHECKS_OUTPUT_DIR}/bonsai_*.tar.gz || true
+# R CMD check --no-manual --run-dontrun --run-donttest ${CHECKS_OUTPUT_DIR}/fastshap_*.tar.gz || true
+# R CMD check --no-manual --run-dontrun --run-donttest ${CHECKS_OUTPUT_DIR}/fastml_*.tar.gz || true
+# R CMD check --no-manual --run-dontrun --run-donttest ${CHECKS_OUTPUT_DIR}/fastshap_*.tar.gz || true
+# R CMD check --no-manual --run-dontrun --run-donttest ${CHECKS_OUTPUT_DIR}/predhy.GUI_*.tar.gz || true
 # qeML vignettes take a very very long time to run
 #R CMD check --no-manual --run-dontrun --run-donttest --ignore-vignettes ${CHECKS_OUTPUT_DIR}/qeML_*.tar.gz || true
-R CMD check --no-manual --run-dontrun --run-donttest ${CHECKS_OUTPUT_DIR}/mllrns_*.tar.gz || true
-R CMD check --no-manual --run-dontrun --run-donttest ${CHECKS_OUTPUT_DIR}/predhy_*.tar.gz || true
-R CMD check --no-manual --run-dontrun --run-donttest ${CHECKS_OUTPUT_DIR}/r2pmml_*.tar.gz || true
-R CMD check --no-manual --run-dontrun --run-donttest ${CHECKS_OUTPUT_DIR}/stackgbm_*.tar.gz || true
-R CMD check --no-manual --run-dontrun --run-donttest ${CHECKS_OUTPUT_DIR}/vip_*.tar.gz || true
+# R CMD check --no-manual --run-dontrun --run-donttest ${CHECKS_OUTPUT_DIR}/mllrns_*.tar.gz || true
+# R CMD check --no-manual --run-dontrun --run-donttest ${CHECKS_OUTPUT_DIR}/predhy_*.tar.gz || true
+# R CMD check --no-manual --run-dontrun --run-donttest ${CHECKS_OUTPUT_DIR}/r2pmml_*.tar.gz || true
+# R CMD check --no-manual --run-dontrun --run-donttest ${CHECKS_OUTPUT_DIR}/stackgbm_*.tar.gz || true
+# R CMD check --no-manual --run-dontrun --run-donttest ${CHECKS_OUTPUT_DIR}/vip_*.tar.gz || true