diff --git a/requirements-dev.txt b/requirements-dev.txt
index 89d713fc428b1271400fa50902a5b4161c80f8e1..50188f4deec66b2b89e719e2e5470856eafe5ddd 100644
--- a/requirements-dev.txt
+++ b/requirements-dev.txt
@@ -4,4 +4,4 @@ mock==2.*
 coverage==4.*
 pytest==3.*
 pytest-cov==2.*
-pytest-runner>=2,<=3
+pytest-runner>=2.*,<=4.*
diff --git a/requirements-extra.txt b/requirements-extra.txt
index 1c857ed164b8e2e6c93b44ca150a3cbee5199ea5..fa62f9919dfc96bbca30c655db0cb1ae8308641c 100644
--- a/requirements-extra.txt
+++ b/requirements-extra.txt
@@ -1,4 +1,4 @@
 indexed_gzip>=0.7.0,<1
 wxpython>=3.0.2.0,<4.1
 trimesh>=2.22.28,<3
-rtree==0.8
+rtree==0.8.3
diff --git a/requirements.txt b/requirements.txt
index 0ec1322f7bc0aa7bb5b9d25c6d3f8ba43a1cb221..51e205639f8e3e8cc298b82ee5116106b036e907 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -1,5 +1,5 @@
 six==1.*
-deprecation>=1,<=2
+deprecation>=1.*,<=2.*
 numpy==1.*
 scipy>=0.18,<2
 nibabel==2.*