Unity will flag your humanoid rig configuration if it does not meet the Mecanim requirements for a humanoid. Please read and be familiar with this part of the Unity Manual when setting up your avatar: https://docs.unity3d.com/Manual/ConfiguringtheAvatar.html
Humanoid avatar must have head, hands and feet bones mapped.
You will see this message from the VRChat Build Control Panel if your avatar rig is humanoid but does not have the essential bones mapped.
If your avatar diverges greatly from a human (ie. quadruped, hunching monster, etc), you should consider using a Generic rig and your own Animation Controller. See the SimpleAvatarController for an example. This is more advanced than making a humanoid, so you should be very familiar with Unity's Animation Controller system.
Thumb, Index, and Middle finger bones are not mapped, Full-Body IK will be disabled.
In order to have full IK (allowing crouching and automatic foot placement) you need to have these three finger bones mapped. If you ignore this warning, your avatar will not be able to crouch, and it's feet will not automatically step (unless you use controller locomotion).
It will also prevent custom animation overrides on hand gestures from being played back. (This is not currently mentioned by the warning in the SDK.)
Your rig has the UPPERCHEST mapped in the Humanoid Rig. This will cause problems with IK.
Leave the upper chest bone blank when configuring your humanoid.
Spine hierarchy missing elements, make sure that Pelvis, Spine, Chest, Neck and Shoulders are mapped.
These bones must all be mapped. If you get this message make sure none of these slots are empty. Note that the Neck and Chest slots are optional for Mecanim, but required for VRChat.
Spine hierarchy incorrect. Make sure that the parent of both Shoulders and the Neck is the Chest.
For the IK to work properly, you must have a specific hierarchy of bones around the chest. In your rig, your shoulder bones (mapped into Left Arm > Shoulder, Right Arm > Shoulder slots) must be direct children of your chest bone (mapped into Body > Chest slot). Also, the neck bone (mapped into Head > Neck slot) must also be a direct child of the Chest.
LowerArm is not first child of UpperArm or Hand is not first child of LowerArm: you may have problems with Forearm rotations.
VRChat's IK system looks at the first child of the hierarchy when determining the bone layout. If you have other child bones, like prop-placement bones, or twist-bones in your rig, they can confuse the IK. To avoid this warning, move the child bone to the first position in the list of children of the parent bone. Note that this message is naming the slot, not the actual bone name in your rig, so you'll have to look to see what bone is in that slot.
LowerLeg is not first child of UpperLeg or Foot is not first child of LowerLeg: you may have problems with Shin rotations.
This avatar has a split heirarchy (Hips bone is not the ancestor of all humanoid bones). IK may not work correctly.
Some rigs split the hierarchy into two sections, upper and lower body. In this case the bone you put into the Body > Hips slot must be the ancestor (parent or higher) of the rest of the human bones you are mapping. Be very careful with these kinds of rigs! Often, the ancestor of these bones is a root bone on the ground or another placement which is a bad placement for a hip bone. Many of these rigs are unsuitable for use with VRChat and need to be re-rigged to work properly.
There are special considerations if you are using Full-Body tracking, ie. you have 3 Vive Pucks (or emulation) connected. Full-Body Tracking works best if the avatar you create has very similar dimensions to your own body.
The angle between pelvis and thigh bones should be close to 180 degrees (this avatar's angle is ___). Your avatar may not work well with full-body IK and Tracking.
Full-body tracking is sensitive to the angle between the hip and upper leg bones. It's best to measure this angle when the AvatarTPoseController is applied to your avatar. Ideally, the hip bone is pointing straight up and the upper leg bones point straight down in the TPose, but slight divergence is okay. You can ignore this message if you are not going to use Full-Body Tracking.
It is not required to map the Toe bones in a humanoid avatar. However, if you DO map them, your avatar is able to move up and down on their tiptoes. Mapping the toes also makes the automatic foot-stepping look more natural.