Hi, I've (apparently) managed to fix this bug although I'm not sure what the original code was trying to do.
Originally, d/rules: INCLUDE_PATHS = /usr/include/bamtools space= space+= override_dh_auto_configure: dh_auto_configure -- \ -DCMAKE_INCLUDE_PATH="$(subst $(space),:,$(strip $(INCLUDE_PATHS)))" When the build was attempted on bare metal with dpkg-buildpackage, DCMAKE_INCLUDE_PATH=/usr/include/bamtools which is right. However, everytime build was attempted inside a chroot with sbuild, DCMAKE_INCLUDE_PATH=/usr/include/bamtools: and the colon at the end is apparently what results in this error inside a chroot. After changing d/rules to INCLUDE_PATHS=/usr/include/bamtools override_dh_auto_configure: dh_auto_configure -- \ -DCMAKE_INCLUDE_PATH="${INCLUDE_PATHS}" the error goes away and the right files are included, outside as well as inside a chroot. I've committed this change but I'm not sure what the original code was trying to do so please take a look and sponsor if everything is right. Regards, Pranav ᐧ