In case this may help. If I run one script with the default definition of "base compile dir", the script works just fine.
In addtion to Theano 0.9.0, I also have these packages: pygpu 0.6.9 py36_0 mingw 4.7 1 libgpuarray 0.6.9 vc14_0 [vc14] m2w64-binutils 2.25.1 5 m2w64-bzip2 1.0.6 6 m2w64-crt-git 5.0.0.4636.2595836 2 m2w64-gcc 5.3.0 6 m2w64-gcc-ada 5.3.0 6 m2w64-gcc-fortran 5.3.0 6 m2w64-gcc-libgfortran 5.3.0 6 m2w64-gcc-libs 5.3.0 7 m2w64-gcc-libs-core 5.3.0 7 m2w64-gcc-objc 5.3.0 6 m2w64-gmp 6.1.0 2 m2w64-headers-git 5.0.0.4636.c0ad18a 2 m2w64-isl 0.16.1 2 m2w64-libiconv 1.14 6 m2w64-libmangle-git 5.0.0.4509.2e5a9a2 2 m2w64-libwinpthread-git 5.0.0.4634.697f757 2 m2w64-make 4.1.2351.a80a8b8 2 m2w64-mpc 1.0.3 3 m2w64-mpfr 3.1.4 4 m2w64-pkg-config 0.29.1 2 m2w64-toolchain 5.3.0 7 m2w64-tools-git 5.0.0.4592.90b8472 2 m2w64-windows-default-manifest 6.4 3 m2w64-winpthreads-git 5.0.0.4634.697f757 2 -- --- You received this message because you are subscribed to the Google Groups "theano-users" group. To unsubscribe from this group and stop receiving emails from it, send an email to theano-users+unsubscr...@googlegroups.com. For more options, visit https://groups.google.com/d/optout.