diff --git a/build/pkgs/cmake/spkg-configure.m4 b/build/pkgs/cmake/spkg-configure.m4
index ce36e8aa0cc..4210442c44c 100644
--- a/build/pkgs/cmake/spkg-configure.m4
+++ b/build/pkgs/cmake/spkg-configure.m4
@@ -1,13 +1,17 @@
-SAGE_SPKG_CONFIGURE(
-    [cmake], [
-        AC_CACHE_CHECK([for cmake >= 3.11], [ac_cv_path_CMAKE], [
-        AC_PATH_PROGS_FEATURE_CHECK([CMAKE], [cmake], [
-            cmake_version=`$ac_path_CMAKE --version 2>&1 \
-                | $SED -n -e 's/cmake version *\([[0-9]]*\.[[0-9]]*\.[[0-9]]*\)/\1/p'`
-            AS_IF([test -n "$cmake_version"], [
-                AX_COMPARE_VERSION([$cmake_version], [ge], [3.11], [
-                    ac_cv_path_CMAKE="$ac_path_CMAKE"
-                    ac_path_CMAKE_found=:
+SAGE_SPKG_CONFIGURE([cmake], [dnl
+        AC_CACHE_CHECK([for cmake >= 3.11], [ac_cv_path_CMAKE], [dnl
+        dnl Do not accept cmake installed via https://pypi.org/project/cmake/
+        dnl in the default user scheme; it will not work in our venv because
+        dnl we set PYTHONUSERBASE in sage-env.
+        WITH_SAGE_PYTHONUSERBASE([dnl
+            AC_PATH_PROGS_FEATURE_CHECK([CMAKE], [cmake], [dnl
+                cmake_version=`$ac_path_CMAKE --version 2>&1 \
+                    | $SED -n -e 's/cmake version *\([[0-9]]*\.[[0-9]]*\.[[0-9]]*\)/\1/p'`
+                AS_IF([test -n "$cmake_version"], [dnl
+                    AX_COMPARE_VERSION([$cmake_version], [ge], [3.11], [dnl
+                        ac_cv_path_CMAKE="$ac_path_CMAKE"
+                        ac_path_CMAKE_found=:
+                    ])
                 ])
             ])
         ])
diff --git a/build/pkgs/configure/checksums.ini b/build/pkgs/configure/checksums.ini
index 4448844093d..365d56084a3 100644
--- a/build/pkgs/configure/checksums.ini
+++ b/build/pkgs/configure/checksums.ini
@@ -1,4 +1,4 @@
 tarball=configure-VERSION.tar.gz
-sha1=b0dfc1d5886366b5c58354527810c1dbeffd78a3
-md5=c2f9837bcf2823d5b2f36063ebeedb38
-cksum=3535625335
+sha1=26e8d2b6804d9474bed32cba580e9edd9947723c
+md5=b6b9dbb57d17ba53f57f37f74c66a24c
+cksum=3731157415
diff --git a/build/pkgs/configure/package-version.txt b/build/pkgs/configure/package-version.txt
index cd15c46bb91..d7438585ccb 100644
--- a/build/pkgs/configure/package-version.txt
+++ b/build/pkgs/configure/package-version.txt
@@ -1 +1 @@
-686e933eb32ade977ed51836a33424e2095e5408
+4163e69cf94a4fbcf59e1297de0a4644d2e4291a
diff --git a/build/pkgs/ninja_build/spkg-configure.m4 b/build/pkgs/ninja_build/spkg-configure.m4
index 5b83d189801..01ee6a30f10 100644
--- a/build/pkgs/ninja_build/spkg-configure.m4
+++ b/build/pkgs/ninja_build/spkg-configure.m4
@@ -1,16 +1,20 @@
-SAGE_SPKG_CONFIGURE(
-    [ninja_build], [
-        dnl meson_python needs 1.8.2 or later
-        AC_CACHE_CHECK([for ninja >= 1.8.2], [ac_cv_path_NINJA], [
-        AC_PATH_PROGS_FEATURE_CHECK([NINJA], [ninja], [
-            dnl support both two- and three-component version schemes
-            dnl since samurai (a ninja alternative) uses two
-            ninja_version=`$ac_path_NINJA --version 2>&1 \
-                | $SED -n -e 's/\([[0-9]]*\(\.[[0-9]]*\)\{1,2\}\).*/\1/p'`
-            AS_IF([test -n "$ninja_version"], [
-                AX_COMPARE_VERSION([$ninja_version], [ge], [1.8.2], [
-                    ac_cv_path_NINJA="$ac_path_NINJA"
-                    ac_path_NINJA_found=:
+SAGE_SPKG_CONFIGURE([ninja_build], [dnl
+    dnl meson_python needs 1.8.2 or later
+    AC_CACHE_CHECK([for ninja >= 1.8.2], [ac_cv_path_NINJA], [dnl
+        dnl Do not accept ninja installed from https://pypi.org/project/ninja/
+        dnl in the default user scheme; it will not work in our venv because
+        dnl we set PYTHONUSERBASE in sage-env.
+        WITH_SAGE_PYTHONUSERBASE([dnl
+            AC_PATH_PROGS_FEATURE_CHECK([NINJA], [ninja], [dnl
+                dnl support both two- and three-component version schemes
+                dnl since samurai (a ninja alternative) uses two
+                ninja_version=`$ac_path_NINJA --version 2>&1 \
+                    | $SED -n -e 's/\([[0-9]]*\(\.[[0-9]]*\)\{1,2\}\).*/\1/p'`
+                AS_IF([test -n "$ninja_version"], [dnl
+                    AX_COMPARE_VERSION([$ninja_version], [ge], [1.8.2], [
+                        ac_cv_path_NINJA="$ac_path_NINJA"
+                        ac_path_NINJA_found=:
+                    ])
                 ])
             ])
         ])