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Actually, you are right, the issue may not be that the box is not well placed indeed.
When I measure with a ruler on the robot the height of the small step where the arm is placed when off, I get something between 45 and 50mm. If I do the same in rviz, with collision enabled, along the black line below, I get about 33mm.
It seems that the origin of the first collision box of the torso is not correct. I expect it to be
tiago_robot/tiago_description/urdf/torso/torso.urdf.xacro
Line 46 in 31790ca
This is related to pal-robotics/pmb2_robot#6
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