This was broken in #20692, the "cd src" should NOT have been removed:
diff --git a/build/pkgs/gap3/spkg-install b/build/pkgs/gap3/spkg-install
index a91ab6f..cf76e22 100755
--- a/build/pkgs/gap3/spkg-install
+++ b/build/pkgs/gap3/spkg-install
@@ -17,20 +17,6 @@ echo "GAP3_DIR = $GAP3_DIR"
echo "INSTALL_DIR = $INSTALL_DIR"
###########################################
-## MODIFY UPSTREAM
-###########################################
-
-cd src
-for patch in ../patches/*.patch; do
- [ -r "$patch" ] || continue # Skip non-existing or non-readable
patches
- patch -p1 <"$patch"
- if [ $? -ne 0 ]; then
- echo >&2 "Error applying '$patch'"
- exit 1
- fi
-done
-
-###########################################
## INSTALLATION
###########################################
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