[variables_helper.py:141]Variable [SecondStageBoxPredictor/BoxEncodingPredictor/biases] is available in checkpoint, but has an incompatible shape with model.

System information

What is the top-level directory of the model you are using: Object detection
Have I written custom code (as opposed to using a stock example script provided in TensorFlow): Yes, but I just edited the model_main.py at line 62:

config = tf.estimator.RunConfig(model_dir=FLAGS.model_dir,  
 save_checkpoints_steps=500,
 tf_random_seed=1230, 
 keep_checkpoint_max=100)

OS Platform and Distribution: Ubuntu "16.04.2 LTS (Xenial Xerus)"
TensorFlow installed from (source or binary): installed with Python's pip package
TensorFlow version (use command below): ('v1.9.0-0-g25c197e023', '1.9.0')
Bazel version: N/A
CUDA/cuDNN version: CUDA 8.0
GPU model and memory: Tesla P40 22919MiB
Exact command to reproduce:
export CUDA_VISIBLE_DEVICES=3
python object_detection/model_main_my.py
--pipeline_config_path=${train_path}/data/faster_rcnn_resnet101_t.config
--model_dir=${train_path}/model
--num_train_steps=50000
--sample_1_of_n_eval_examples=1
--alsologtostderr

Describe the problem

There always show warnings in the secondstage. I want to know if this in relation with the pretrain model and if it will influence the box detection precision.

Warnings:

W1209 21:57:14.465106 140428642035456 variables_helper.py:141] Variable [SecondStageBoxPredictor/BoxEncodingPredictor/biases] is available in checkpoint, but has an incompatible shape with model variable. Checkpoint shape: [[360]], model variable shape: [[4]]. This variable will not be initialized from the checkpoint.
W1209 21:57:14.465503 140428642035456 variables_helper.py:141] Variable [SecondStageBoxPredictor/BoxEncodingPredictor/weights] is available in checkpoint, but has an incompatible shape with model variable. Checkpoint shape: [[2048, 360]], model variable shape: [[2048, 4]]. This variable will not be initialized from the checkpoint.
W1209 21:57:14.465818 140428642035456 variables_helper.py:141] Variable [SecondStageBoxPredictor/ClassPredictor/biases] is available in checkpoint, but has an incompatible shape with model variable. Checkpoint shape: [[91]], model variable shape: [[2]]. This variable will not be initialized from the checkpoint.
W1209 21:57:14.466134 140428642035456 variables_helper.py:141] Variable [SecondStageBoxPredictor/ClassPredictor/weights] is available in checkpoint, but has an incompatible shape with model variable. Checkpoint shape: [[2048, 91]], model variable shape: [[2048, 2]]. This variable will not be initialized from the checkpoint.