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First you can verify that all urls listed under /etc/ros/rosdep/sources.list.d/ are valid. For me the file 20-default.list looks like:

# os-specific listings first
yaml https://github.com/ros/rosdistro/raw/master/rosdep/osx-homebrew.yaml osx
yaml https://github.com/ros/rosdistro/raw/master/rosdep/gentoo.yaml gentoo
# generic
yaml https://github.com/ros/rosdistro/raw/master/rosdep/base.yaml
yaml https://github.com/ros/rosdistro/raw/master/rosdep/python.yaml
yaml https://github.com/ros/rosdistro/raw/master/rosdep/ruby.yaml
gbpdistro https://github.com/ros/rosdistro/raw/master/releases/fuerte.yaml fuerte
gbpdistro https://github.com/ros/rosdistro/raw/master/releases/groovy.yaml groovy

Second you might have ran "rosdep init" once with sudo and now the file in your home directory are owner my root and not writable by you anymore. You should remove the folder ~/.ros/rosdep and call "rosdep update" again.

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No.2 Revision

First you can verify that all urls listed under /etc/ros/rosdep/sources.list.d/ are valid. For me the file 20-default.list looks like:

# os-specific listings first
yaml https://github.com/ros/rosdistro/raw/master/rosdep/osx-homebrew.yaml osx
yaml https://github.com/ros/rosdistro/raw/master/rosdep/gentoo.yaml gentoo
# generic
yaml https://github.com/ros/rosdistro/raw/master/rosdep/base.yaml
yaml https://github.com/ros/rosdistro/raw/master/rosdep/python.yaml
yaml https://github.com/ros/rosdistro/raw/master/rosdep/ruby.yaml
gbpdistro https://github.com/ros/rosdistro/raw/master/releases/fuerte.yaml fuerte
gbpdistro https://github.com/ros/rosdistro/raw/master/releases/groovy.yaml groovy

Second you might have ran "rosdep init" update" once with sudo and now the file in your home directory are owner my root and not writable by you anymore. You should remove the folder ~/.ros/rosdep and call "rosdep update" again.