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PGCN: Disease gene prioritization by disease and gene embedding through GCN

Python 100.00%

graph-convolutional-networks prioritization disease-gene-association

disease_gene_prioritization_gcn's Introduction

PGCN: Disease gene prioritization by disease and gene embedding through GCN

Disease gene prioritization is a fundamental step towards molecular diagnosis and treatment of diseases. This problem is highly challenging due to the very limited yet noisy knowledge of genes, diseases and, even more, on their associations. Despite the development of computational methods for disease gene prioritization, the performance of the existing methods is limited by manually-crafted features, network topology, or pre-defined rules of data fusion. Here we propose a novel graph convolutional network-based disease gene prioritization method, PGCN, through the systematic embedding of the heterogeneous network made by genes and diseases, as well as their individual features. The embedding learning model and the association prediction model are trained together in an end-to-end manner. We compared PGCN with five state-of-the-art methods on the Online Mendelian Inheritance in Man (OMIM) dataset, by challenging them on recovering missing associations, and on discovering associations for novel genes and/or diseases that are not seen in the training. Results show the significant improvements of PGCN over the existing methods. We further demonstrate that our embedding has biological meaning and can capture functional groups of genes.

More details can be referred to the paper.

@article{li2019pgcn,
  title={PGCN: Disease gene prioritization by disease and gene embedding through graph convolutional neural networks},
  author={Li, Yu and Kuwahara, Hiroyuki and Yang, Peng and Song, Le and Gao, Xin},
  journal={bioRxiv},
  pages={532226},
  year={2019},
  publisher={Cold Spring Harbor Laboratory}
}

Overview

Disease gene prioritization as a link prediction problem. The heterogeneous network contains three components, the gene-gene interaction network, the disease similarity network, and the disease-gene association network. The potential disease gene associations can be considered as missing links in the disease-gene association network. Our goal is to predict those links given the heterogeneous network and additional raw representations of the nodes (diseases and genes).

Overview of the proposed method. (A) The input of our model contains two components, the heterogeneous network and the additional information for the nodes. As for the heterogeneous network, we used HumanNet as the gene network, disease similarity network as the disease network, and the associations from OMIM as the disease-gene network. For the additional information of diseases, we used Disease Ontology similarity and the TF-IDF calculated from OMIM. For the additional information of genes, we used association matrices from other species and the gene expression microarray data. (B) Examples of one layer of the graph convolutional neural network update for learning node embeddings. For each node, the model aggregates information from its neighbor nodes' previous layer embeddings and then apply activation to obtain the current layer embedding of that node. Note that for different nodes, the computational graphs can be different but the parameters are shared for the same operation in different computational graphs. (C) The link prediction model. We model the edge prediction from the learned node embeddings with bilinear edge decoder. (D) The cross-entropy loss calculated from the ground truth and the output of the link prediction model for certain edges (or non-edges) is used as the loss function to train both the node embedding model and the edge decoding model jointly in an end-to-end fashion.

Tested environment

Centos 7
Python 3.6.7

Install requirements

All the related packages have been summarized in requirements.txt. One can install all the packages with following command.

pip install -r requirements.txt

(better to construct a virtual environment using conda and install the package inside the environment)

Download the data

Due to the limit of the file size on Github, we store the data on Google Drive. Please download the data here: data.

Run the code

One can run the code using the following command after configuring the environment and downloading the data.

python main_prioritization.py

Result

The prediction matrix file can be downloaded here: result.

Here is the embedding clustering result. For more explanation, please refer to the manuscript.

More explanation

For calculating BEDROC, here we provide the function from the skchem package for the reference. For more accurate calculation, one can output the prediction and use R packages to do the calculation.

Credits

We would like to thank for the SNAP group for open-sourcing the decagon code: decagon.

This tool is for academic purposes and research use only. Any commercial use is subject for authorization from King Abdullah University of Science and technology “KAUST”. Please contact us at [email protected].

disease_gene_prioritization_gcn's People

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disease_gene_prioritization_gcn's Issues

Unable to use the provided model to generate predictions

Hi there,
Thanks for sharing the code and data. However, I cannot use the code to generate predictions from the trained model. Can you please have a look to see if the model provided is the correct one and if the code works to get the predictions?

The following error is prompted on running the code provided:

NotFoundError (see above for traceback): Restoring from checkpoint failed. This is most likely due to a Variable name or other graph key that is missing from the checkpoint. Please ensure that you have not altered the graph expected based on the checkpoint. Original error:

Key decagonmodel/graphconvolutionmulti_3_vars/weights_1 not found in checkpoint
         [[Node: save/RestoreV2 = RestoreV2[dtypes=[DT_FLOAT, DT_FLOAT, DT_FLOAT, DT_FLOAT, DT_FLOAT, ..., DT_FLOAT, DT_FLOAT, DT_FLOAT, DT_FLOAT, DT_FLOAT], _device="/job:localhost/replica:0/task:0/device:CPU:0"](_arg_save/Const_0_0, save/RestoreV2/tensor_names, save/RestoreV2/shape_and_slices)]]

Thanks again.

Why do you only train the model for 1 epoch?

Hello,

Nice work!
Just wondering is there any specific reason why you only trained the model for one epoch?

Thanks!
Hurley

Could you approve the dataset download request?

The dataset is not downloadable and needs a permit for access.

unable to open file: name = './data_prioritization/genes_phenes.mat'

I got an error:
OSError: Unable to open file (unable to open file: name = './data_prioritization/genes_phenes.mat', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0)

Where is the ”genes_phenes.mat“？

Training code

Hi, I found your method interesting. Could you please share your training code?

I also get the "Unsupported feed type" tensorflow error

Unsupported feed type

when i run the program, i get a error: tensorflow.python.framework.errors_impl.InternalError: Unsupported feed type. How to resovle it ?

Failed to install pandas==0.18.0 in python 3.6.7

Hi Yu,

Thanks for your excellent work. I met some issue while config the environment. Please see belows:

I failed to install pandas==0.18.0 in python 3.6.7, which output:

Collecting pandas==0.18.0
  Using cached pandas-0.18.0.tar.gz (7.1 MB)
Requirement already satisfied: python-dateutil>=2 in /home/tlc/anaconda3/envs/pgcn/lib/python3.6/site-packages (from pandas==0.18.0) (2.8.1)
Requirement already satisfied: pytz>=2011k in /home/tlc/anaconda3/envs/pgcn/lib/python3.6/site-packages (from pandas==0.18.0) (2020.4)
Requirement already satisfied: numpy>=1.7.0 in /home/tlc/anaconda3/envs/pgcn/lib/python3.6/site-packages (from pandas==0.18.0) (1.19.4)
Requirement already satisfied: six>=1.5 in /home/tlc/anaconda3/envs/pgcn/lib/python3.6/site-packages (from python-dateutil>=2->pandas==0.18.0) (1.15.0)
Building wheels for collected packages: pandas
  Building wheel for pandas (setup.py): started
  Building wheel for pandas (setup.py): still running...
  Building wheel for pandas (setup.py): still running...
  Building wheel for pandas (setup.py): finished with status 'error'
  ERROR: Command errored out with exit status 1:
   command: /home/tlc/anaconda3/envs/pgcn/bin/python -u -c 'import sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-4d95ztpw/pandas_a5792867e4ed4883b0f33e7d6f6bd343/setup.py'"'"'; __file__='"'"'/tmp/pip-install-4d95ztpw/pandas_a5792867e4ed4883b0f33e7d6f6bd343/setup.py'"'"';f=getattr(tokenize, '"'"'open'"'"', open)(__file__);code=f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' bdist_wheel -d /tmp/pip-wheel-lgrq19ra
       cwd: /tmp/pip-install-4d95ztpw/pandas_a5792867e4ed4883b0f33e7d6f6bd343/
  Complete output (1341 lines):
  running bdist_wheel
  running build
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  copying pandas/tests/test_panel4d.py -> build/lib.linux-x86_64-3.6/pandas/tests
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  copying pandas/tests/test_dtypes.py -> build/lib.linux-x86_64-3.6/pandas/tests
  creating build/lib.linux-x86_64-3.6/pandas/tests/frame
  copying pandas/tests/frame/test_query_eval.py -> build/lib.linux-x86_64-3.6/pandas/tests/frame
  copying pandas/tests/frame/test_replace.py -> build/lib.linux-x86_64-3.6/pandas/tests/frame
  copying pandas/tests/frame/test_to_csv.py -> build/lib.linux-x86_64-3.6/pandas/tests/frame
  copying pandas/tests/frame/test_nonunique_indexes.py -> build/lib.linux-x86_64-3.6/pandas/tests/frame
  copying pandas/tests/frame/test_indexing.py -> build/lib.linux-x86_64-3.6/pandas/tests/frame
  copying pandas/tests/frame/test_convert_to.py -> build/lib.linux-x86_64-3.6/pandas/tests/frame
  copying pandas/tests/frame/test_subclass.py -> build/lib.linux-x86_64-3.6/pandas/tests/frame
  copying pandas/tests/frame/test_repr_info.py -> build/lib.linux-x86_64-3.6/pandas/tests/frame
  copying pandas/tests/frame/test_alter_axes.py -> build/lib.linux-x86_64-3.6/pandas/tests/frame
  copying pandas/tests/frame/common.py -> build/lib.linux-x86_64-3.6/pandas/tests/frame
  copying pandas/tests/frame/test_block_internals.py -> build/lib.linux-x86_64-3.6/pandas/tests/frame
  copying pandas/tests/frame/test_combine_concat.py -> build/lib.linux-x86_64-3.6/pandas/tests/frame
  copying pandas/tests/frame/test_analytics.py -> build/lib.linux-x86_64-3.6/pandas/tests/frame
  copying pandas/tests/frame/test_missing.py -> build/lib.linux-x86_64-3.6/pandas/tests/frame
  copying pandas/tests/frame/test_reshape.py -> build/lib.linux-x86_64-3.6/pandas/tests/frame
  copying pandas/tests/frame/test_misc_api.py -> build/lib.linux-x86_64-3.6/pandas/tests/frame
  copying pandas/tests/frame/test_timeseries.py -> build/lib.linux-x86_64-3.6/pandas/tests/frame
  copying pandas/tests/frame/test_apply.py -> build/lib.linux-x86_64-3.6/pandas/tests/frame
  copying pandas/tests/frame/test_sorting.py -> build/lib.linux-x86_64-3.6/pandas/tests/frame
  copying pandas/tests/frame/test_mutate_columns.py -> build/lib.linux-x86_64-3.6/pandas/tests/frame
  copying pandas/tests/frame/__init__.py -> build/lib.linux-x86_64-3.6/pandas/tests/frame
  copying pandas/tests/frame/test_operators.py -> build/lib.linux-x86_64-3.6/pandas/tests/frame
  copying pandas/tests/frame/test_axis_select_reindex.py -> build/lib.linux-x86_64-3.6/pandas/tests/frame
  copying pandas/tests/frame/test_constructors.py -> build/lib.linux-x86_64-3.6/pandas/tests/frame
  copying pandas/tests/frame/test_dtypes.py -> build/lib.linux-x86_64-3.6/pandas/tests/frame
  creating build/lib.linux-x86_64-3.6/pandas/tests/indexes
  copying pandas/tests/indexes/test_multi.py -> build/lib.linux-x86_64-3.6/pandas/tests/indexes
  copying pandas/tests/indexes/test_datetimelike.py -> build/lib.linux-x86_64-3.6/pandas/tests/indexes
  copying pandas/tests/indexes/test_range.py -> build/lib.linux-x86_64-3.6/pandas/tests/indexes
  copying pandas/tests/indexes/test_category.py -> build/lib.linux-x86_64-3.6/pandas/tests/indexes
  copying pandas/tests/indexes/common.py -> build/lib.linux-x86_64-3.6/pandas/tests/indexes
  copying pandas/tests/indexes/test_base.py -> build/lib.linux-x86_64-3.6/pandas/tests/indexes
  copying pandas/tests/indexes/__init__.py -> build/lib.linux-x86_64-3.6/pandas/tests/indexes
  copying pandas/tests/indexes/test_numeric.py -> build/lib.linux-x86_64-3.6/pandas/tests/indexes
  creating build/lib.linux-x86_64-3.6/pandas/tests/series
  copying pandas/tests/series/test_datetime_values.py -> build/lib.linux-x86_64-3.6/pandas/tests/series
  copying pandas/tests/series/test_repr.py -> build/lib.linux-x86_64-3.6/pandas/tests/series
  copying pandas/tests/series/test_indexing.py -> build/lib.linux-x86_64-3.6/pandas/tests/series
  copying pandas/tests/series/test_internals.py -> build/lib.linux-x86_64-3.6/pandas/tests/series
  copying pandas/tests/series/test_alter_axes.py -> build/lib.linux-x86_64-3.6/pandas/tests/series
  copying pandas/tests/series/common.py -> build/lib.linux-x86_64-3.6/pandas/tests/series
  copying pandas/tests/series/test_io.py -> build/lib.linux-x86_64-3.6/pandas/tests/series
  copying pandas/tests/series/test_combine_concat.py -> build/lib.linux-x86_64-3.6/pandas/tests/series
  copying pandas/tests/series/test_analytics.py -> build/lib.linux-x86_64-3.6/pandas/tests/series
  copying pandas/tests/series/test_missing.py -> build/lib.linux-x86_64-3.6/pandas/tests/series
  copying pandas/tests/series/test_misc_api.py -> build/lib.linux-x86_64-3.6/pandas/tests/series
  copying pandas/tests/series/test_timeseries.py -> build/lib.linux-x86_64-3.6/pandas/tests/series
  copying pandas/tests/series/__init__.py -> build/lib.linux-x86_64-3.6/pandas/tests/series
  copying pandas/tests/series/test_operators.py -> build/lib.linux-x86_64-3.6/pandas/tests/series
  copying pandas/tests/series/test_constructors.py -> build/lib.linux-x86_64-3.6/pandas/tests/series
  copying pandas/tests/series/test_dtypes.py -> build/lib.linux-x86_64-3.6/pandas/tests/series
  creating build/lib.linux-x86_64-3.6/pandas/tests/test_msgpack
  copying pandas/tests/test_msgpack/test_format.py -> build/lib.linux-x86_64-3.6/pandas/tests/test_msgpack
  copying pandas/tests/test_msgpack/test_sequnpack.py -> build/lib.linux-x86_64-3.6/pandas/tests/test_msgpack
  copying pandas/tests/test_msgpack/test_obj.py -> build/lib.linux-x86_64-3.6/pandas/tests/test_msgpack
  copying pandas/tests/test_msgpack/test_unpack.py -> build/lib.linux-x86_64-3.6/pandas/tests/test_msgpack
  copying pandas/tests/test_msgpack/test_except.py -> build/lib.linux-x86_64-3.6/pandas/tests/test_msgpack
  copying pandas/tests/test_msgpack/test_buffer.py -> build/lib.linux-x86_64-3.6/pandas/tests/test_msgpack
  copying pandas/tests/test_msgpack/test_unpack_raw.py -> build/lib.linux-x86_64-3.6/pandas/tests/test_msgpack
  copying pandas/tests/test_msgpack/test_newspec.py -> build/lib.linux-x86_64-3.6/pandas/tests/test_msgpack
  copying pandas/tests/test_msgpack/test_pack.py -> build/lib.linux-x86_64-3.6/pandas/tests/test_msgpack
  copying pandas/tests/test_msgpack/test_case.py -> build/lib.linux-x86_64-3.6/pandas/tests/test_msgpack
  copying pandas/tests/test_msgpack/test_subtype.py -> build/lib.linux-x86_64-3.6/pandas/tests/test_msgpack
  copying pandas/tests/test_msgpack/__init__.py -> build/lib.linux-x86_64-3.6/pandas/tests/test_msgpack
  copying pandas/tests/test_msgpack/test_extension.py -> build/lib.linux-x86_64-3.6/pandas/tests/test_msgpack
  copying pandas/tests/test_msgpack/test_limits.py -> build/lib.linux-x86_64-3.6/pandas/tests/test_msgpack
  copying pandas/tests/test_msgpack/test_read_size.py -> build/lib.linux-x86_64-3.6/pandas/tests/test_msgpack
  copying pandas/tests/test_msgpack/test_seq.py -> build/lib.linux-x86_64-3.6/pandas/tests/test_msgpack
  creating build/lib.linux-x86_64-3.6/pandas/tools
  copying pandas/tools/util.py -> build/lib.linux-x86_64-3.6/pandas/tools
  copying pandas/tools/pivot.py -> build/lib.linux-x86_64-3.6/pandas/tools
  copying pandas/tools/rplot.py -> build/lib.linux-x86_64-3.6/pandas/tools
  copying pandas/tools/tile.py -> build/lib.linux-x86_64-3.6/pandas/tools
  copying pandas/tools/__init__.py -> build/lib.linux-x86_64-3.6/pandas/tools
  copying pandas/tools/merge.py -> build/lib.linux-x86_64-3.6/pandas/tools
  copying pandas/tools/plotting.py -> build/lib.linux-x86_64-3.6/pandas/tools
  creating build/lib.linux-x86_64-3.6/pandas/tools/tests
  copying pandas/tools/tests/test_merge.py -> build/lib.linux-x86_64-3.6/pandas/tools/tests
  copying pandas/tools/tests/test_tile.py -> build/lib.linux-x86_64-3.6/pandas/tools/tests
  copying pandas/tools/tests/test_pivot.py -> build/lib.linux-x86_64-3.6/pandas/tools/tests
  copying pandas/tools/tests/__init__.py -> build/lib.linux-x86_64-3.6/pandas/tools/tests
  copying pandas/tools/tests/test_util.py -> build/lib.linux-x86_64-3.6/pandas/tools/tests
  creating build/lib.linux-x86_64-3.6/pandas/tseries
  copying pandas/tseries/base.py -> build/lib.linux-x86_64-3.6/pandas/tseries
  copying pandas/tseries/util.py -> build/lib.linux-x86_64-3.6/pandas/tseries
  copying pandas/tseries/interval.py -> build/lib.linux-x86_64-3.6/pandas/tseries
  copying pandas/tseries/resample.py -> build/lib.linux-x86_64-3.6/pandas/tseries
  copying pandas/tseries/tdi.py -> build/lib.linux-x86_64-3.6/pandas/tseries
  copying pandas/tseries/tools.py -> build/lib.linux-x86_64-3.6/pandas/tseries
  copying pandas/tseries/common.py -> build/lib.linux-x86_64-3.6/pandas/tseries
  copying pandas/tseries/holiday.py -> build/lib.linux-x86_64-3.6/pandas/tseries
  copying pandas/tseries/converter.py -> build/lib.linux-x86_64-3.6/pandas/tseries
  copying pandas/tseries/frequencies.py -> build/lib.linux-x86_64-3.6/pandas/tseries
  copying pandas/tseries/api.py -> build/lib.linux-x86_64-3.6/pandas/tseries
  copying pandas/tseries/timedeltas.py -> build/lib.linux-x86_64-3.6/pandas/tseries
  copying pandas/tseries/__init__.py -> build/lib.linux-x86_64-3.6/pandas/tseries
  copying pandas/tseries/index.py -> build/lib.linux-x86_64-3.6/pandas/tseries
  copying pandas/tseries/period.py -> build/lib.linux-x86_64-3.6/pandas/tseries
  copying pandas/tseries/offsets.py -> build/lib.linux-x86_64-3.6/pandas/tseries
  copying pandas/tseries/plotting.py -> build/lib.linux-x86_64-3.6/pandas/tseries
  creating build/lib.linux-x86_64-3.6/pandas/tseries/tests
  copying pandas/tseries/tests/test_holiday.py -> build/lib.linux-x86_64-3.6/pandas/tseries/tests
  copying pandas/tseries/tests/test_frequencies.py -> build/lib.linux-x86_64-3.6/pandas/tseries/tests
  copying pandas/tseries/tests/test_resample.py -> build/lib.linux-x86_64-3.6/pandas/tseries/tests
  copying pandas/tseries/tests/test_plotting.py -> build/lib.linux-x86_64-3.6/pandas/tseries/tests
  copying pandas/tseries/tests/test_tslib.py -> build/lib.linux-x86_64-3.6/pandas/tseries/tests
  copying pandas/tseries/tests/test_timedeltas.py -> build/lib.linux-x86_64-3.6/pandas/tseries/tests
  copying pandas/tseries/tests/test_daterange.py -> build/lib.linux-x86_64-3.6/pandas/tseries/tests
  copying pandas/tseries/tests/test_offsets.py -> build/lib.linux-x86_64-3.6/pandas/tseries/tests
  copying pandas/tseries/tests/test_timeseries_legacy.py -> build/lib.linux-x86_64-3.6/pandas/tseries/tests
  copying pandas/tseries/tests/test_timeseries.py -> build/lib.linux-x86_64-3.6/pandas/tseries/tests
  copying pandas/tseries/tests/test_base.py -> build/lib.linux-x86_64-3.6/pandas/tseries/tests
  copying pandas/tseries/tests/__init__.py -> build/lib.linux-x86_64-3.6/pandas/tseries/tests
  copying pandas/tseries/tests/test_period.py -> build/lib.linux-x86_64-3.6/pandas/tseries/tests
  copying pandas/tseries/tests/test_timezones.py -> build/lib.linux-x86_64-3.6/pandas/tseries/tests
  copying pandas/tseries/tests/test_util.py -> build/lib.linux-x86_64-3.6/pandas/tseries/tests
  copying pandas/tseries/tests/test_converter.py -> build/lib.linux-x86_64-3.6/pandas/tseries/tests
  creating build/lib.linux-x86_64-3.6/pandas/io/tests
  copying pandas/io/tests/test_sql.py -> build/lib.linux-x86_64-3.6/pandas/io/tests
  copying pandas/io/tests/test_pytables.py -> build/lib.linux-x86_64-3.6/pandas/io/tests
  copying pandas/io/tests/test_pickle.py -> build/lib.linux-x86_64-3.6/pandas/io/tests
  copying pandas/io/tests/test_parsers.py -> build/lib.linux-x86_64-3.6/pandas/io/tests
  copying pandas/io/tests/test_stata.py -> build/lib.linux-x86_64-3.6/pandas/io/tests
  copying pandas/io/tests/test_cparser.py -> build/lib.linux-x86_64-3.6/pandas/io/tests
  copying pandas/io/tests/test_data.py -> build/lib.linux-x86_64-3.6/pandas/io/tests
  copying pandas/io/tests/test_clipboard.py -> build/lib.linux-x86_64-3.6/pandas/io/tests
  copying pandas/io/tests/test_date_converters.py -> build/lib.linux-x86_64-3.6/pandas/io/tests
  copying pandas/io/tests/test_excel.py -> build/lib.linux-x86_64-3.6/pandas/io/tests
  copying pandas/io/tests/test_wb.py -> build/lib.linux-x86_64-3.6/pandas/io/tests
  copying pandas/io/tests/test_ga.py -> build/lib.linux-x86_64-3.6/pandas/io/tests
  copying pandas/io/tests/generate_legacy_storage_files.py -> build/lib.linux-x86_64-3.6/pandas/io/tests
  copying pandas/io/tests/test_json_norm.py -> build/lib.linux-x86_64-3.6/pandas/io/tests
  copying pandas/io/tests/test_packers.py -> build/lib.linux-x86_64-3.6/pandas/io/tests
  copying pandas/io/tests/__init__.py -> build/lib.linux-x86_64-3.6/pandas/io/tests
  copying pandas/io/tests/test_common.py -> build/lib.linux-x86_64-3.6/pandas/io/tests
  copying pandas/io/tests/test_html.py -> build/lib.linux-x86_64-3.6/pandas/io/tests
  copying pandas/io/tests/test_gbq.py -> build/lib.linux-x86_64-3.6/pandas/io/tests
  creating build/lib.linux-x86_64-3.6/pandas/io/tests/test_json
  copying pandas/io/tests/test_json/test_pandas.py -> build/lib.linux-x86_64-3.6/pandas/io/tests/test_json
  copying pandas/io/tests/test_json/test_ujson.py -> build/lib.linux-x86_64-3.6/pandas/io/tests/test_json
  copying pandas/io/tests/test_json/__init__.py -> build/lib.linux-x86_64-3.6/pandas/io/tests/test_json
  creating build/lib.linux-x86_64-3.6/pandas/stats/tests
  copying pandas/stats/tests/test_math.py -> build/lib.linux-x86_64-3.6/pandas/stats/tests
  copying pandas/stats/tests/test_var.py -> build/lib.linux-x86_64-3.6/pandas/stats/tests
  copying pandas/stats/tests/common.py -> build/lib.linux-x86_64-3.6/pandas/stats/tests
  copying pandas/stats/tests/test_fama_macbeth.py -> build/lib.linux-x86_64-3.6/pandas/stats/tests
  copying pandas/stats/tests/__init__.py -> build/lib.linux-x86_64-3.6/pandas/stats/tests
  copying pandas/stats/tests/test_ols.py -> build/lib.linux-x86_64-3.6/pandas/stats/tests
  creating build/lib.linux-x86_64-3.6/pandas/msgpack
  copying pandas/msgpack/_version.py -> build/lib.linux-x86_64-3.6/pandas/msgpack
  copying pandas/msgpack/exceptions.py -> build/lib.linux-x86_64-3.6/pandas/msgpack
  copying pandas/msgpack/__init__.py -> build/lib.linux-x86_64-3.6/pandas/msgpack
  creating build/lib.linux-x86_64-3.6/pandas/io/tests/data
  creating build/lib.linux-x86_64-3.6/pandas/io/tests/data/legacy_hdf
  copying pandas/io/tests/data/legacy_hdf/legacy_table_0.11.h5 -> build/lib.linux-x86_64-3.6/pandas/io/tests/data/legacy_hdf
  copying pandas/io/tests/data/legacy_hdf/pytables_native.h5 -> build/lib.linux-x86_64-3.6/pandas/io/tests/data/legacy_hdf
  copying pandas/io/tests/data/legacy_hdf/legacy_0.10.h5 -> build/lib.linux-x86_64-3.6/pandas/io/tests/data/legacy_hdf
  copying pandas/io/tests/data/legacy_hdf/datetimetz_object.h5 -> build/lib.linux-x86_64-3.6/pandas/io/tests/data/legacy_hdf
  copying pandas/io/tests/data/legacy_hdf/pytables_native2.h5 -> build/lib.linux-x86_64-3.6/pandas/io/tests/data/legacy_hdf
  copying pandas/io/tests/data/legacy_hdf/legacy.h5 -> build/lib.linux-x86_64-3.6/pandas/io/tests/data/legacy_hdf
  copying pandas/io/tests/data/legacy_hdf/legacy_table.h5 -> build/lib.linux-x86_64-3.6/pandas/io/tests/data/legacy_hdf
  creating build/lib.linux-x86_64-3.6/pandas/io/tests/data/legacy_pickle
  creating build/lib.linux-x86_64-3.6/pandas/io/tests/data/legacy_pickle/0.14.1
  copying pandas/io/tests/data/legacy_pickle/0.14.1/0.14.1_x86_64_linux_2.7.8.pickle -> build/lib.linux-x86_64-3.6/pandas/io/tests/data/legacy_pickle/0.14.1
  creating build/lib.linux-x86_64-3.6/pandas/io/tests/data/legacy_pickle/0.16.0
  copying pandas/io/tests/data/legacy_pickle/0.16.0/0.16.0_x86_64_darwin_2.7.9.pickle -> build/lib.linux-x86_64-3.6/pandas/io/tests/data/legacy_pickle/0.16.0
  creating build/lib.linux-x86_64-3.6/pandas/io/tests/data/legacy_pickle/0.10.1
  copying pandas/io/tests/data/legacy_pickle/0.10.1/AMD64_windows_2.7.3.pickle -> build/lib.linux-x86_64-3.6/pandas/io/tests/data/legacy_pickle/0.10.1
  copying pandas/io/tests/data/legacy_pickle/0.10.1/x86_64_linux_2.7.3.pickle -> build/lib.linux-x86_64-3.6/pandas/io/tests/data/legacy_pickle/0.10.1
  creating build/lib.linux-x86_64-3.6/pandas/io/tests/data/legacy_pickle/0.12.0
  copying pandas/io/tests/data/legacy_pickle/0.12.0/0.12.0_AMD64_windows_2.7.3.pickle -> build/lib.linux-x86_64-3.6/pandas/io/tests/data/legacy_pickle/0.12.0
  copying pandas/io/tests/data/legacy_pickle/0.12.0/0.12.0_x86_64_linux_2.7.3.pickle -> build/lib.linux-x86_64-3.6/pandas/io/tests/data/legacy_pickle/0.12.0
  creating build/lib.linux-x86_64-3.6/pandas/io/tests/data/legacy_pickle/0.15.0
  copying pandas/io/tests/data/legacy_pickle/0.15.0/0.15.0_x86_64_linux_2.7.8.pickle -> build/lib.linux-x86_64-3.6/pandas/io/tests/data/legacy_pickle/0.15.0
  creating build/lib.linux-x86_64-3.6/pandas/io/tests/data/legacy_pickle/0.16.2
  copying pandas/io/tests/data/legacy_pickle/0.16.2/0.16.2_x86_64_darwin_2.7.10.pickle -> build/lib.linux-x86_64-3.6/pandas/io/tests/data/legacy_pickle/0.16.2
  copying pandas/io/tests/data/legacy_pickle/0.16.2/0.16.2_AMD64_windows_2.7.10.pickle -> build/lib.linux-x86_64-3.6/pandas/io/tests/data/legacy_pickle/0.16.2
  copying pandas/io/tests/data/legacy_pickle/0.16.2/0.16.2_AMD64_windows_3.4.3.pickle -> build/lib.linux-x86_64-3.6/pandas/io/tests/data/legacy_pickle/0.16.2
  copying pandas/io/tests/data/legacy_pickle/0.16.2/0.16.2_x86_64_darwin_3.4.3.pickle -> build/lib.linux-x86_64-3.6/pandas/io/tests/data/legacy_pickle/0.16.2
  copying pandas/io/tests/data/legacy_pickle/0.16.2/0.16.2_x86_64_linux_2.7.10.pickle -> build/lib.linux-x86_64-3.6/pandas/io/tests/data/legacy_pickle/0.16.2
  copying pandas/io/tests/data/legacy_pickle/0.16.2/0.16.2_x86_64_darwin_2.7.9.pickle -> build/lib.linux-x86_64-3.6/pandas/io/tests/data/legacy_pickle/0.16.2
  copying pandas/io/tests/data/legacy_pickle/0.16.2/0.16.2_x86_64_linux_3.4.3.pickle -> build/lib.linux-x86_64-3.6/pandas/io/tests/data/legacy_pickle/0.16.2
  creating build/lib.linux-x86_64-3.6/pandas/io/tests/data/legacy_pickle/0.14.0
  copying pandas/io/tests/data/legacy_pickle/0.14.0/0.14.0_x86_64_linux_2.7.8.pickle -> build/lib.linux-x86_64-3.6/pandas/io/tests/data/legacy_pickle/0.14.0
  copying pandas/io/tests/data/legacy_pickle/0.14.0/0.14.0_x86_64_darwin_2.7.6.pickle -> build/lib.linux-x86_64-3.6/pandas/io/tests/data/legacy_pickle/0.14.0
  creating build/lib.linux-x86_64-3.6/pandas/io/tests/data/legacy_pickle/0.13.0
  copying pandas/io/tests/data/legacy_pickle/0.13.0/0.13.0_i686_linux_2.7.3.pickle -> build/lib.linux-x86_64-3.6/pandas/io/tests/data/legacy_pickle/0.13.0
  copying pandas/io/tests/data/legacy_pickle/0.13.0/0.13.0_i686_linux_2.6.5.pickle -> build/lib.linux-x86_64-3.6/pandas/io/tests/data/legacy_pickle/0.13.0
  copying pandas/io/tests/data/legacy_pickle/0.13.0/0.13.0_x86_64_linux_3.3.0.pickle -> build/lib.linux-x86_64-3.6/pandas/io/tests/data/legacy_pickle/0.13.0
  copying pandas/io/tests/data/legacy_pickle/0.13.0/0.13.0_i686_linux_3.2.3.pickle -> build/lib.linux-x86_64-3.6/pandas/io/tests/data/legacy_pickle/0.13.0
  copying pandas/io/tests/data/legacy_pickle/0.13.0/0.13.0_x86_64_linux_2.7.8.pickle -> build/lib.linux-x86_64-3.6/pandas/io/tests/data/legacy_pickle/0.13.0
  copying pandas/io/tests/data/legacy_pickle/0.13.0/0.13.0_x86_64_darwin_2.7.6.pickle -> build/lib.linux-x86_64-3.6/pandas/io/tests/data/legacy_pickle/0.13.0
  copying pandas/io/tests/data/legacy_pickle/0.13.0/0.13.0_x86_64_linux_2.7.3.pickle -> build/lib.linux-x86_64-3.6/pandas/io/tests/data/legacy_pickle/0.13.0
  copying pandas/io/tests/data/legacy_pickle/0.13.0/0.13.0_x86_64_darwin_2.7.5.pickle -> build/lib.linux-x86_64-3.6/pandas/io/tests/data/legacy_pickle/0.13.0
  copying pandas/io/tests/data/legacy_pickle/0.13.0/0.13.0_AMD64_windows_2.7.3.pickle -> build/lib.linux-x86_64-3.6/pandas/io/tests/data/legacy_pickle/0.13.0
  creating build/lib.linux-x86_64-3.6/pandas/io/tests/data/legacy_pickle/0.11.0
  copying pandas/io/tests/data/legacy_pickle/0.11.0/0.11.0_x86_64_linux_3.3.0.pickle -> build/lib.linux-x86_64-3.6/pandas/io/tests/data/legacy_pickle/0.11.0
  copying pandas/io/tests/data/legacy_pickle/0.11.0/x86_64_linux_2.7.3.pickle -> build/lib.linux-x86_64-3.6/pandas/io/tests/data/legacy_pickle/0.11.0
  copying pandas/io/tests/data/legacy_pickle/0.11.0/x86_64_linux_3.3.0.pickle -> build/lib.linux-x86_64-3.6/pandas/io/tests/data/legacy_pickle/0.11.0
  creating build/lib.linux-x86_64-3.6/pandas/io/tests/data/legacy_pickle/0.15.2
  copying pandas/io/tests/data/legacy_pickle/0.15.2/0.15.2_x86_64_darwin_2.7.9.pickle -> build/lib.linux-x86_64-3.6/pandas/io/tests/data/legacy_pickle/0.15.2
  creating build/lib.linux-x86_64-3.6/pandas/io/tests/data/legacy_msgpack
  creating build/lib.linux-x86_64-3.6/pandas/io/tests/data/legacy_msgpack/0.16.0
  copying pandas/io/tests/data/legacy_msgpack/0.16.0/0.16.0_x86_64_darwin_2.7.9.msgpack -> build/lib.linux-x86_64-3.6/pandas/io/tests/data/legacy_msgpack/0.16.0
  creating build/lib.linux-x86_64-3.6/pandas/io/tests/data/legacy_msgpack/0.16.2
  copying pandas/io/tests/data/legacy_msgpack/0.16.2/0.16.2_x86_64_linux_2.7.10.msgpack -> build/lib.linux-x86_64-3.6/pandas/io/tests/data/legacy_msgpack/0.16.2
  copying pandas/io/tests/data/legacy_msgpack/0.16.2/0.16.2_x86_64_linux_3.4.3.msgpack -> build/lib.linux-x86_64-3.6/pandas/io/tests/data/legacy_msgpack/0.16.2
  copying pandas/io/tests/data/legacy_msgpack/0.16.2/0.16.2_x86_64_darwin_2.7.10.msgpack -> build/lib.linux-x86_64-3.6/pandas/io/tests/data/legacy_msgpack/0.16.2
  copying pandas/io/tests/data/legacy_msgpack/0.16.2/0.16.2_x86_64_darwin_2.7.9.msgpack -> build/lib.linux-x86_64-3.6/pandas/io/tests/data/legacy_msgpack/0.16.2
  copying pandas/io/tests/data/legacy_msgpack/0.16.2/0.16.2_AMD64_windows_2.7.10.msgpack -> build/lib.linux-x86_64-3.6/pandas/io/tests/data/legacy_msgpack/0.16.2
  copying pandas/io/tests/data/legacy_msgpack/0.16.2/0.16.2_x86_64_darwin_3.4.3.msgpack -> build/lib.linux-x86_64-3.6/pandas/io/tests/data/legacy_msgpack/0.16.2
  copying pandas/io/tests/data/legacy_msgpack/0.16.2/0.16.2_AMD64_windows_3.4.3.msgpack -> build/lib.linux-x86_64-3.6/pandas/io/tests/data/legacy_msgpack/0.16.2
  creating build/lib.linux-x86_64-3.6/pandas/io/tests/data/legacy_msgpack/0.17.1
  copying pandas/io/tests/data/legacy_msgpack/0.17.1/0.17.1_AMD64_windows_3.5.1.msgpack -> build/lib.linux-x86_64-3.6/pandas/io/tests/data/legacy_msgpack/0.17.1
  copying pandas/io/tests/data/legacy_msgpack/0.17.1/0.17.1_x86_64_darwin_2.7.11.msgpack -> build/lib.linux-x86_64-3.6/pandas/io/tests/data/legacy_msgpack/0.17.1
  copying pandas/io/tests/data/legacy_msgpack/0.17.1/0.17.1_x86_64_darwin_3.5.1.msgpack -> build/lib.linux-x86_64-3.6/pandas/io/tests/data/legacy_msgpack/0.17.1
  copying pandas/io/tests/data/legacy_msgpack/0.17.1/0.17.1_AMD64_windows_2.7.11.msgpack -> build/lib.linux-x86_64-3.6/pandas/io/tests/data/legacy_msgpack/0.17.1
  copying pandas/io/tests/data/legacy_msgpack/0.17.1/0.17.1_x86_64_linux_2.7.11.msgpack -> build/lib.linux-x86_64-3.6/pandas/io/tests/data/legacy_msgpack/0.17.1
  copying pandas/io/tests/data/legacy_msgpack/0.17.1/0.17.1_x86_64_linux_3.4.4.msgpack -> build/lib.linux-x86_64-3.6/pandas/io/tests/data/legacy_msgpack/0.17.1
  copying pandas/io/tests/data/stata6.csv -> build/lib.linux-x86_64-3.6/pandas/io/tests/data
  copying pandas/io/tests/data/unicode_series.csv -> build/lib.linux-x86_64-3.6/pandas/io/tests/data
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  copying pandas/io/tests/data/test2.csv -> build/lib.linux-x86_64-3.6/pandas/io/tests/data
  copying pandas/io/tests/data/test1.csv.gz -> build/lib.linux-x86_64-3.6/pandas/io/tests/data
  copying pandas/io/tests/data/banklist.csv -> build/lib.linux-x86_64-3.6/pandas/io/tests/data
  copying pandas/io/tests/data/test1.csv.bz2 -> build/lib.linux-x86_64-3.6/pandas/io/tests/data
  copying pandas/io/tests/data/test1.csv -> build/lib.linux-x86_64-3.6/pandas/io/tests/data
  copying pandas/io/tests/data/tips.csv -> build/lib.linux-x86_64-3.6/pandas/io/tests/data
  copying pandas/io/tests/data/iris.csv -> build/lib.linux-x86_64-3.6/pandas/io/tests/data
  copying pandas/io/tests/data/stata5.csv -> build/lib.linux-x86_64-3.6/pandas/io/tests/data
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  copying pandas/io/tests/data/stata1_encoding.dta -> build/lib.linux-x86_64-3.6/pandas/io/tests/data
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  copying pandas/io/tests/data/stata4_115.dta -> build/lib.linux-x86_64-3.6/pandas/io/tests/data
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  copying pandas/io/tests/data/stata6_113.dta -> build/lib.linux-x86_64-3.6/pandas/io/tests/data
  copying pandas/io/tests/data/S4_EDUC1.dta -> build/lib.linux-x86_64-3.6/pandas/io/tests/data
  copying pandas/io/tests/data/stata1_117.dta -> build/lib.linux-x86_64-3.6/pandas/io/tests/data
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  copying pandas/io/tests/data/stata2_114.dta -> build/lib.linux-x86_64-3.6/pandas/io/tests/data
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  copying pandas/io/tests/data/stata3_117.dta -> build/lib.linux-x86_64-3.6/pandas/io/tests/data
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  copying pandas/io/tests/data/stata2_115.dta -> build/lib.linux-x86_64-3.6/pandas/io/tests/data
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  copying pandas/io/tests/data/stata5_117.dta -> build/lib.linux-x86_64-3.6/pandas/io/tests/data
  copying pandas/io/tests/data/utf16_ex.txt -> build/lib.linux-x86_64-3.6/pandas/io/tests/data
  copying pandas/io/tests/data/gbq_fake_job.txt -> build/lib.linux-x86_64-3.6/pandas/io/tests/data
  copying pandas/io/tests/data/times_1904.xls -> build/lib.linux-x86_64-3.6/pandas/io/tests/data
  copying pandas/io/tests/data/blank.xls -> build/lib.linux-x86_64-3.6/pandas/io/tests/data
  copying pandas/io/tests/data/test_multisheet.xls -> build/lib.linux-x86_64-3.6/pandas/io/tests/data
  copying pandas/io/tests/data/test_index_name_pre17.xls -> build/lib.linux-x86_64-3.6/pandas/io/tests/data
  copying pandas/io/tests/data/test2.xls -> build/lib.linux-x86_64-3.6/pandas/io/tests/data
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  copying pandas/io/tests/data/test_squeeze.xls -> build/lib.linux-x86_64-3.6/pandas/io/tests/data
  copying pandas/io/tests/data/test4.xls -> build/lib.linux-x86_64-3.6/pandas/io/tests/data
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  copying pandas/io/tests/data/test3.xls -> build/lib.linux-x86_64-3.6/pandas/io/tests/data
  copying pandas/io/tests/data/test1.xls -> build/lib.linux-x86_64-3.6/pandas/io/tests/data
  copying pandas/io/tests/data/testmultiindex.xls -> build/lib.linux-x86_64-3.6/pandas/io/tests/data
  copying pandas/io/tests/data/test_converters.xls -> build/lib.linux-x86_64-3.6/pandas/io/tests/data
  copying pandas/io/tests/data/test_types.xls -> build/lib.linux-x86_64-3.6/pandas/io/tests/data
  copying pandas/io/tests/data/test_squeeze.xlsx -> build/lib.linux-x86_64-3.6/pandas/io/tests/data
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  copying pandas/io/tests/data/times_1900.xlsx -> build/lib.linux-x86_64-3.6/pandas/io/tests/data
  copying pandas/io/tests/data/test_multisheet.xlsx -> build/lib.linux-x86_64-3.6/pandas/io/tests/data
  copying pandas/io/tests/data/test_converters.xlsx -> build/lib.linux-x86_64-3.6/pandas/io/tests/data
  copying pandas/io/tests/data/test1.xlsx -> build/lib.linux-x86_64-3.6/pandas/io/tests/data
  copying pandas/io/tests/data/test_types.xlsx -> build/lib.linux-x86_64-3.6/pandas/io/tests/data
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  copying pandas/io/tests/data/test3.xlsx -> build/lib.linux-x86_64-3.6/pandas/io/tests/data
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  copying pandas/io/tests/data/test4.xlsx -> build/lib.linux-x86_64-3.6/pandas/io/tests/data
  copying pandas/io/tests/data/test1.xlsm -> build/lib.linux-x86_64-3.6/pandas/io/tests/data
  copying pandas/io/tests/data/times_1900.xlsm -> build/lib.linux-x86_64-3.6/pandas/io/tests/data
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  copying pandas/io/tests/data/test4.xlsm -> build/lib.linux-x86_64-3.6/pandas/io/tests/data
  copying pandas/io/tests/data/times_1904.xlsm -> build/lib.linux-x86_64-3.6/pandas/io/tests/data
  copying pandas/io/tests/data/test_index_name_pre17.xlsm -> build/lib.linux-x86_64-3.6/pandas/io/tests/data
  copying pandas/io/tests/data/blank_with_header.xlsm -> build/lib.linux-x86_64-3.6/pandas/io/tests/data
  copying pandas/io/tests/data/test3.xlsm -> build/lib.linux-x86_64-3.6/pandas/io/tests/data
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  copying pandas/io/tests/data/test_squeeze.xlsm -> build/lib.linux-x86_64-3.6/pandas/io/tests/data
  copying pandas/io/tests/data/test2.xlsm -> build/lib.linux-x86_64-3.6/pandas/io/tests/data
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  copying pandas/io/tests/data/salary.table -> build/lib.linux-x86_64-3.6/pandas/io/tests/data
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  creating build/lib.linux-x86_64-3.6/pandas/io/tests/data/html_encoding
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  copying pandas/io/tests/data/html_encoding/chinese_utf-8.html -> build/lib.linux-x86_64-3.6/pandas/io/tests/data/html_encoding
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  creating build/lib.linux-x86_64-3.6/pandas/tests/data
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  creating build/lib.linux-x86_64-3.6/pandas/tests/indexes/data
  copying pandas/tests/indexes/data/multiindex_v1.pickle -> build/lib.linux-x86_64-3.6/pandas/tests/indexes/data
  copying pandas/tests/indexes/data/mindex_073.pickle -> build/lib.linux-x86_64-3.6/pandas/tests/indexes/data
  copying pandas/tests/indexes/data/s2-0.12.0.pickle -> build/lib.linux-x86_64-3.6/pandas/tests/indexes/data
  copying pandas/tests/indexes/data/s1-0.12.0.pickle -> build/lib.linux-x86_64-3.6/pandas/tests/indexes/data
  copying pandas/tools/tests/cut_data.csv -> build/lib.linux-x86_64-3.6/pandas/tools/tests
  creating build/lib.linux-x86_64-3.6/pandas/tseries/tests/data
  copying pandas/tseries/tests/data/daterange_073.pickle -> build/lib.linux-x86_64-3.6/pandas/tseries/tests/data
  copying pandas/tseries/tests/data/cday-0.14.1.pickle -> build/lib.linux-x86_64-3.6/pandas/tseries/tests/data
  copying pandas/tseries/tests/data/series_daterange0.pickle -> build/lib.linux-x86_64-3.6/pandas/tseries/tests/data
  copying pandas/tseries/tests/data/dateoffset_0_15_2.pickle -> build/lib.linux-x86_64-3.6/pandas/tseries/tests/data
  copying pandas/tseries/tests/data/series.pickle -> build/lib.linux-x86_64-3.6/pandas/tseries/tests/data
  copying pandas/tseries/tests/data/frame.pickle -> build/lib.linux-x86_64-3.6/pandas/tseries/tests/data
  UPDATING build/lib.linux-x86_64-3.6/pandas/_version.py
  set build/lib.linux-x86_64-3.6/pandas/_version.py to '0.18.0'
  running build_ext
  skipping 'pandas/lib.c' Cython extension (up-to-date)
  building 'pandas.lib' extension
  creating build/temp.linux-x86_64-3.6
  creating build/temp.linux-x86_64-3.6/pandas
  gcc -pthread -B /home/tlc/anaconda3/envs/pgcn/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -Ipandas/src/klib -Ipandas/src -I/home/tlc/anaconda3/envs/pgcn/lib/python3.6/site-packages/numpy/core/include -I/home/tlc/anaconda3/envs/pgcn/include/python3.6m -c pandas/lib.c -o build/temp.linux-x86_64-3.6/pandas/lib.o -Wno-unused-function
  In file included from /home/tlc/anaconda3/envs/pgcn/lib/python3.6/site-packages/numpy/core/include/numpy/ndarraytypes.h:1822,
                   from /home/tlc/anaconda3/envs/pgcn/lib/python3.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:12,
                   from /home/tlc/anaconda3/envs/pgcn/lib/python3.6/site-packages/numpy/core/include/numpy/arrayobject.h:4,
                   from pandas/lib.c:242:
  /home/tlc/anaconda3/envs/pgcn/lib/python3.6/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
     17 | #warning "Using deprecated NumPy API, disable it with " \
        |  ^~~~~~~
  In file included from pandas/lib.c:247:
  pandas/src/datetime_helper.h:7: warning: "PyInt_AS_LONG" redefined
      7 | #define PyInt_AS_LONG PyLong_AsLong
        |
  pandas/lib.c:141: note: this is the location of the previous definition
    141 |   #define PyInt_AS_LONG                PyLong_AS_LONG
        |
  In file included from pandas/lib.c:249:
  pandas/src/numpy_helper.h: In function ‘transfer_object_column’:
  pandas/src/numpy_helper.h:152:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
    152 |     for (i = 0; i < length; ++i)
        |                   ^
  pandas/lib.c: In function ‘__pyx_f_6pandas_3lib_slice_get_indices_ex’:
  pandas/lib.c:28383:37: warning: passing argument 1 of ‘PySlice_GetIndicesEx’ from incompatible pointer type [-Wincompatible-pointer-types]
  28383 |   __pyx_t_4 = PySlice_GetIndicesEx(((PySliceObject *)__pyx_v_slc), __pyx_v_objlen, (&__pyx_v_start), (&__pyx_v_stop), (&__pyx_v_step), (&__pyx_v_length)); if (unlikely(__pyx_t_4 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1666; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
        |                                    ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        |                                     |
        |                                     PySliceObject * {aka struct <anonymous> *}
  In file included from /home/tlc/anaconda3/envs/pgcn/include/python3.6m/Python.h:101,
                   from pandas/lib.c:4:
  /home/tlc/anaconda3/envs/pgcn/include/python3.6m/sliceobject.h:43:48: note: expected ‘PyObject *’ {aka ‘struct _object *’} but argument is of type ‘PySliceObject *’ {aka ‘struct <anonymous> *’}
     43 | PyAPI_FUNC(int) PySlice_GetIndicesEx(PyObject *r, Py_ssize_t length,
        |                                      ~~~~~~~~~~^
  pandas/lib.c: In function ‘__pyx_f_6pandas_3lib_slice_len’:
  pandas/lib.c:28615:37: warning: passing argument 1 of ‘PySlice_GetIndicesEx’ from incompatible pointer type [-Wincompatible-pointer-types]
  28615 |   __pyx_t_4 = PySlice_GetIndicesEx(((PySliceObject *)__pyx_v_slc), __pyx_v_objlen, (&__pyx_v_start), (&__pyx_v_stop), (&__pyx_v_step), (&__pyx_v_length)); if (unlikely(__pyx_t_4 == -1)) {__pyx_filename = __pyx_f[0]; __pyx_lineno = 1689; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
        |                                    ~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
        |                                     |
        |                                     PySliceObject * {aka struct <anonymous> *}
  In file included from /home/tlc/anaconda3/envs/pgcn/include/python3.6m/Python.h:101,
                   from pandas/lib.c:4:
  /home/tlc/anaconda3/envs/pgcn/include/python3.6m/sliceobject.h:43:48: note: expected ‘PyObject *’ {aka ‘struct _object *’} but argument is of type ‘PySliceObject *’ {aka ‘struct <anonymous> *’}
     43 | PyAPI_FUNC(int) PySlice_GetIndicesEx(PyObject *r, Py_ssize_t length,
        |                                      ~~~~~~~~~~^
  pandas/lib.c: In function ‘__pyx_pw_6pandas_3lib_65maybe_booleans_to_slice’:
  pandas/lib.c:139:40: warning: ‘__pyx_v_end’ may be used uninitialized in this function [-Wmaybe-uninitialized]
    139 |   #define PyInt_FromSsize_t            PyLong_FromSsize_t
        |                                        ^~~~~~~~~~~~~~~~~~
  pandas/lib.c:12839:14: note: ‘__pyx_v_end’ was declared here
  12839 |   Py_ssize_t __pyx_v_end;
        |              ^~~~~~~~~~~
  pandas/lib.c:139:40: warning: ‘__pyx_v_start’ may be used uninitialized in this function [-Wmaybe-uninitialized]
    139 |   #define PyInt_FromSsize_t            PyLong_FromSsize_t
        |                                        ^~~~~~~~~~~~~~~~~~
  pandas/lib.c:12838:14: note: ‘__pyx_v_start’ was declared here
  12838 |   Py_ssize_t __pyx_v_start;
        |              ^~~~~~~~~~~~~
  pandas/lib.c: In function ‘__pyx_gb_6pandas_3lib_118generator’:
  pandas/lib.c:27229:38: warning: ‘__pyx_t_22’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  27229 |           __pyx_cur_scope->__pyx_t_8 = __pyx_t_22;
        |           ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~
  pandas/lib.c:26367:14: warning: ‘__pyx_t_10’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  26367 |   Py_ssize_t __pyx_t_10;
        |              ^~~~~~~~~~
  pandas/lib.c:26362:14: warning: ‘__pyx_t_5’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  26362 |   Py_ssize_t __pyx_t_5;
        |              ^~~~~~~~~
  pandas/lib.c:26371:14: warning: ‘__pyx_t_14’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  26371 |   Py_ssize_t __pyx_t_14;
        |              ^~~~~~~~~~
  pandas/lib.c:26368:14: warning: ‘__pyx_t_11’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  26368 |   Py_ssize_t __pyx_t_11;
        |              ^~~~~~~~~~
  pandas/lib.c: In function ‘__pyx_pf_6pandas_3lib_185maybe_convert_objects.isra.0’:
  pandas/lib.c:54366:21: warning: ‘__pyx_pybuffernd_itimedeltas.diminfo[0].strides’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  54366 |   __Pyx_LocalBuf_ND __pyx_pybuffernd_itimedeltas;
        |                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
  pandas/lib.c:55328:19: warning: ‘__pyx_pybuffernd_itimedeltas.diminfo[0].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  55328 |         } else if (unlikely(__pyx_t_30 >= __pyx_pybuffernd_itimedeltas.diminfo[0].shape)) __pyx_t_7 = 0;
        |                   ^
  pandas/lib.c:54362:21: warning: ‘__pyx_pybuffernd_idatetimes.diminfo[0].strides’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  54362 |   __Pyx_LocalBuf_ND __pyx_pybuffernd_idatetimes;
        |                     ^~~~~~~~~~~~~~~~~~~~~~~~~~~
  pandas/lib.c:55235:19: warning: ‘__pyx_pybuffernd_idatetimes.diminfo[0].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  55235 |         } else if (unlikely(__pyx_t_29 >= __pyx_pybuffernd_idatetimes.diminfo[0].shape)) __pyx_t_7 = 0;
        |                   ^
  gcc -pthread -shared -B /home/tlc/anaconda3/envs/pgcn/compiler_compat -L/home/tlc/anaconda3/envs/pgcn/lib -Wl,-rpath=/home/tlc/anaconda3/envs/pgcn/lib -Wl,--no-as-needed -Wl,--sysroot=/ build/temp.linux-x86_64-3.6/pandas/lib.o -o build/lib.linux-x86_64-3.6/pandas/lib.cpython-36m-x86_64-linux-gnu.so
  skipping 'pandas/hashtable.c' Cython extension (up-to-date)
  building 'pandas.hashtable' extension
  gcc -pthread -B /home/tlc/anaconda3/envs/pgcn/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -Ipandas/src/klib -Ipandas/src -I/home/tlc/anaconda3/envs/pgcn/lib/python3.6/site-packages/numpy/core/include -I/home/tlc/anaconda3/envs/pgcn/include/python3.6m -c pandas/hashtable.c -o build/temp.linux-x86_64-3.6/pandas/hashtable.o -Wno-unused-function
  In file included from /home/tlc/anaconda3/envs/pgcn/lib/python3.6/site-packages/numpy/core/include/numpy/ndarraytypes.h:1822,
                   from /home/tlc/anaconda3/envs/pgcn/lib/python3.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:12,
                   from /home/tlc/anaconda3/envs/pgcn/lib/python3.6/site-packages/numpy/core/include/numpy/arrayobject.h:4,
                   from pandas/hashtable.c:243:
  /home/tlc/anaconda3/envs/pgcn/lib/python3.6/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
     17 | #warning "Using deprecated NumPy API, disable it with " \
        |  ^~~~~~~
  In file included from pandas/hashtable.c:246:
  pandas/src/numpy_helper.h: In function ‘transfer_object_column’:
  pandas/src/numpy_helper.h:152:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
    152 |     for (i = 0; i < length; ++i)
        |                   ^
  pandas/hashtable.c: In function ‘__pyx_fuse_0__pyx_f_6pandas_9hashtable_value_count_scalar64’:
  pandas/hashtable.c:17785:39: warning: comparison of integer expressions of different signedness: ‘int’ and ‘khint_t’ {aka ‘unsigned int’} [-Wsign-compare]
  17785 |         for (__pyx_t_8 = 0; __pyx_t_8 < __pyx_t_7; __pyx_t_8+=1) {
        |                                       ^
  pandas/hashtable.c: In function ‘__pyx_fuse_1__pyx_f_6pandas_9hashtable_value_count_scalar64’:
  pandas/hashtable.c:18229:39: warning: comparison of integer expressions of different signedness: ‘int’ and ‘khint_t’ {aka ‘unsigned int’} [-Wsign-compare]
  18229 |         for (__pyx_t_9 = 0; __pyx_t_9 < __pyx_t_8; __pyx_t_9+=1) {
        |                                       ^
  pandas/hashtable.c: In function ‘__pyx_f_6pandas_9hashtable_value_count_object’:
  pandas/hashtable.c:18913:33: warning: comparison of integer expressions of different signedness: ‘int’ and ‘khint_t’ {aka ‘unsigned int’} [-Wsign-compare]
  18913 |   for (__pyx_t_7 = 0; __pyx_t_7 < __pyx_t_6; __pyx_t_7+=1) {
        |                                 ^
  pandas/hashtable.c: In function ‘__pyx_pf_6pandas_9hashtable_4mode_object’:
  pandas/hashtable.c:19390:33: warning: comparison of integer expressions of different signedness: ‘int’ and ‘khint_t’ {aka ‘unsigned int’} [-Wsign-compare]
  19390 |   for (__pyx_t_7 = 0; __pyx_t_7 < __pyx_t_11; __pyx_t_7+=1) {
        |                                 ^
  pandas/hashtable.c: In function ‘__pyx_pf_6pandas_9hashtable_6mode_int64’:
  pandas/hashtable.c:19769:39: warning: comparison of integer expressions of different signedness: ‘int’ and ‘khint_t’ {aka ‘unsigned int’} [-Wsign-compare]
  19769 |         for (__pyx_t_7 = 0; __pyx_t_7 < __pyx_t_11; __pyx_t_7+=1) {
        |                                       ^
  pandas/hashtable.c: In function ‘__pyx_pf_6pandas_9hashtable_8duplicated_int64’:
  pandas/hashtable.c:20462:37: warning: comparison of integer expressions of different signedness: ‘int’ and ‘khint_t’ {aka ‘unsigned int’} [-Wsign-compare]
  20462 |             __pyx_t_9 = ((__pyx_v_k != __pyx_v_table->n_buckets) != 0);
        |                                     ^~
  gcc -pthread -shared -B /home/tlc/anaconda3/envs/pgcn/compiler_compat -L/home/tlc/anaconda3/envs/pgcn/lib -Wl,-rpath=/home/tlc/anaconda3/envs/pgcn/lib -Wl,--no-as-needed -Wl,--sysroot=/ build/temp.linux-x86_64-3.6/pandas/hashtable.o -o build/lib.linux-x86_64-3.6/pandas/hashtable.cpython-36m-x86_64-linux-gnu.so
  skipping 'pandas/tslib.c' Cython extension (up-to-date)
  building 'pandas.tslib' extension
  creating build/temp.linux-x86_64-3.6/pandas/src
  creating build/temp.linux-x86_64-3.6/pandas/src/datetime
  gcc -pthread -B /home/tlc/anaconda3/envs/pgcn/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -Ipandas/src/klib -Ipandas/src -I/home/tlc/anaconda3/envs/pgcn/lib/python3.6/site-packages/numpy/core/include -I/home/tlc/anaconda3/envs/pgcn/include/python3.6m -c pandas/tslib.c -o build/temp.linux-x86_64-3.6/pandas/tslib.o -Wno-unused-function
  In file included from /home/tlc/anaconda3/envs/pgcn/lib/python3.6/site-packages/numpy/core/include/numpy/ndarraytypes.h:1822,
                   from /home/tlc/anaconda3/envs/pgcn/lib/python3.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:12,
                   from /home/tlc/anaconda3/envs/pgcn/lib/python3.6/site-packages/numpy/core/include/numpy/arrayobject.h:4,
                   from pandas/tslib.c:242:
  /home/tlc/anaconda3/envs/pgcn/lib/python3.6/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
     17 | #warning "Using deprecated NumPy API, disable it with " \
        |  ^~~~~~~
  In file included from pandas/tslib.c:246:
  pandas/src/datetime_helper.h:7: warning: "PyInt_AS_LONG" redefined
      7 | #define PyInt_AS_LONG PyLong_AsLong
        |
  pandas/tslib.c:141: note: this is the location of the previous definition
    141 |   #define PyInt_AS_LONG                PyLong_AS_LONG
        |
  In file included from pandas/tslib.c:248:
  pandas/src/numpy_helper.h: In function ‘transfer_object_column’:
  pandas/src/numpy_helper.h:152:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
    152 |     for (i = 0; i < length; ++i)
        |                   ^
  pandas/tslib.c: In function ‘__pyx_f_6pandas_5tslib__check_dts_bounds’:
  pandas/tslib.c:29015:17: warning: implicit declaration of function ‘cmp_pandas_datetimestruct’ [-Wimplicit-function-declaration]
  29015 |   __pyx_t_2 = ((cmp_pandas_datetimestruct(__pyx_v_dts, (&__pyx_v_6pandas_5tslib__NS_MIN_DTS)) == -1L) != 0);
        |                 ^~~~~~~~~~~~~~~~~~~~~~~~~
  pandas/tslib.c: In function ‘__pyx_f_6pandas_5tslib__parse_dateabbr_string’:
  pandas/tslib.c:33472:51: warning: ‘__pyx_v_quarter’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  33472 |           __pyx_v_month = (((__pyx_v_quarter - 1) * 3) + 1);
        |                            ~~~~~~~~~~~~~~~~~~~~~~~^~~~
  pandas/tslib.c:33443:26: warning: ‘__pyx_v_year’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  33443 |             __pyx_v_year = (__pyx_v_year - 1);
        |             ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~
  pandas/tslib.c: In function ‘__pyx_pf_6pandas_5tslib_76tz_localize_to_utc.isra.0’:
  pandas/tslib.c:64730:21: warning: ‘__pyx_pybuffernd_dst_hours.diminfo[0].strides’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  64730 |   __Pyx_LocalBuf_ND __pyx_pybuffernd_dst_hours;
        |                     ^~~~~~~~~~~~~~~~~~~~~~~~~~
  gcc -pthread -B /home/tlc/anaconda3/envs/pgcn/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -Ipandas/src/klib -Ipandas/src -I/home/tlc/anaconda3/envs/pgcn/lib/python3.6/site-packages/numpy/core/include -I/home/tlc/anaconda3/envs/pgcn/include/python3.6m -c pandas/src/datetime/np_datetime.c -o build/temp.linux-x86_64-3.6/pandas/src/datetime/np_datetime.o -Wno-unused-function
  In file included from /home/tlc/anaconda3/envs/pgcn/lib/python3.6/site-packages/numpy/core/include/numpy/ndarraytypes.h:1822,
                   from /home/tlc/anaconda3/envs/pgcn/lib/python3.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:12,
                   from /home/tlc/anaconda3/envs/pgcn/lib/python3.6/site-packages/numpy/core/include/numpy/arrayobject.h:4,
                   from pandas/src/datetime/np_datetime.c:18:
  /home/tlc/anaconda3/envs/pgcn/lib/python3.6/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
     17 | #warning "Using deprecated NumPy API, disable it with " \
        |  ^~~~~~~
  In file included from pandas/src/datetime/np_datetime.c:10:
  /home/tlc/anaconda3/envs/pgcn/include/python3.6m/datetime.h:200:25: warning: ‘PyDateTimeAPI’ defined but not used [-Wunused-variable]
    200 | static PyDateTime_CAPI *PyDateTimeAPI = NULL;
        |                         ^~~~~~~~~~~~~
  gcc -pthread -B /home/tlc/anaconda3/envs/pgcn/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -Ipandas/src/klib -Ipandas/src -I/home/tlc/anaconda3/envs/pgcn/lib/python3.6/site-packages/numpy/core/include -I/home/tlc/anaconda3/envs/pgcn/include/python3.6m -c pandas/src/datetime/np_datetime_strings.c -o build/temp.linux-x86_64-3.6/pandas/src/datetime/np_datetime_strings.o -Wno-unused-function
  In file included from /home/tlc/anaconda3/envs/pgcn/lib/python3.6/site-packages/numpy/core/include/numpy/ndarraytypes.h:1822,
                   from /home/tlc/anaconda3/envs/pgcn/lib/python3.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:12,
                   from /home/tlc/anaconda3/envs/pgcn/lib/python3.6/site-packages/numpy/core/include/numpy/arrayobject.h:4,
                   from pandas/src/datetime/np_datetime_strings.c:17:
  /home/tlc/anaconda3/envs/pgcn/lib/python3.6/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
     17 | #warning "Using deprecated NumPy API, disable it with " \
        |  ^~~~~~~
  pandas/src/datetime/np_datetime_strings.c: In function ‘parse_iso_8601_datetime’:
  pandas/src/datetime/np_datetime_strings.c:463:18: warning: comparison of integer expressions of different signedness: ‘PANDAS_DATETIMEUNIT’ {aka ‘enum <anonymous>’} and ‘int’ [-Wsign-compare]
    463 |         if (unit != -1 && !can_cast_datetime64_units(bestunit, unit,
        |                  ^~
  pandas/src/datetime/np_datetime_strings.c:506:18: warning: comparison of integer expressions of different signedness: ‘PANDAS_DATETIMEUNIT’ {aka ‘enum <anonymous>’} and ‘int’ [-Wsign-compare]
    506 |         if (unit != -1 && !can_cast_datetime64_units(bestunit, unit,
        |                  ^~
  pandas/src/datetime/np_datetime_strings.c:978:14: warning: comparison of integer expressions of different signedness: ‘PANDAS_DATETIMEUNIT’ {aka ‘enum <anonymous>’} and ‘int’ [-Wsign-compare]
    978 |     if (unit != -1 && !can_cast_datetime64_units(bestunit, unit,
        |              ^~
  pandas/src/datetime/np_datetime_strings.c: In function ‘get_datetime_iso_8601_strlen’:
  pandas/src/datetime/np_datetime_strings.c:1009:14: warning: comparison of integer expressions of different signedness: ‘PANDAS_DATETIMEUNIT’ {aka ‘enum <anonymous>’} and ‘int’ [-Wsign-compare]
   1009 |     if (base == -1) {
        |              ^~
  pandas/src/datetime/np_datetime_strings.c: In function ‘make_iso_8601_datetime’:
  pandas/src/datetime/np_datetime_strings.c:1150:14: warning: comparison of integer expressions of different signedness: ‘PANDAS_DATETIMEUNIT’ {aka ‘enum <anonymous>’} and ‘int’ [-Wsign-compare]
   1150 |     if (base == -1) {
        |              ^~
  gcc -pthread -B /home/tlc/anaconda3/envs/pgcn/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -Ipandas/src/klib -Ipandas/src -I/home/tlc/anaconda3/envs/pgcn/lib/python3.6/site-packages/numpy/core/include -I/home/tlc/anaconda3/envs/pgcn/include/python3.6m -c pandas/src/period_helper.c -o build/temp.linux-x86_64-3.6/pandas/src/period_helper.o -Wno-unused-function
  In file included from /home/tlc/anaconda3/envs/pgcn/lib/python3.6/site-packages/numpy/core/include/numpy/ndarraytypes.h:1822,
                   from pandas/src/period_helper.h:12,
                   from pandas/src/period_helper.c:1:
  /home/tlc/anaconda3/envs/pgcn/lib/python3.6/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
     17 | #warning "Using deprecated NumPy API, disable it with " \
        |  ^~~~~~~
  gcc -pthread -shared -B /home/tlc/anaconda3/envs/pgcn/compiler_compat -L/home/tlc/anaconda3/envs/pgcn/lib -Wl,-rpath=/home/tlc/anaconda3/envs/pgcn/lib -Wl,--no-as-needed -Wl,--sysroot=/ build/temp.linux-x86_64-3.6/pandas/tslib.o build/temp.linux-x86_64-3.6/pandas/src/datetime/np_datetime.o build/temp.linux-x86_64-3.6/pandas/src/datetime/np_datetime_strings.o build/temp.linux-x86_64-3.6/pandas/src/period_helper.o -o build/lib.linux-x86_64-3.6/pandas/tslib.cpython-36m-x86_64-linux-gnu.so
  skipping 'pandas/src/period.c' Cython extension (up-to-date)
  building 'pandas._period' extension
  gcc -pthread -B /home/tlc/anaconda3/envs/pgcn/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -Ipandas/src/klib -Ipandas/src -I/home/tlc/anaconda3/envs/pgcn/lib/python3.6/site-packages/numpy/core/include -I/home/tlc/anaconda3/envs/pgcn/include/python3.6m -c pandas/src/period.c -o build/temp.linux-x86_64-3.6/pandas/src/period.o -Wno-unused-function
  In file included from /home/tlc/anaconda3/envs/pgcn/lib/python3.6/site-packages/numpy/core/include/numpy/ndarraytypes.h:1822,
                   from /home/tlc/anaconda3/envs/pgcn/lib/python3.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:12,
                   from /home/tlc/anaconda3/envs/pgcn/lib/python3.6/site-packages/numpy/core/include/numpy/arrayobject.h:4,
                   from pandas/src/period.c:243:
  /home/tlc/anaconda3/envs/pgcn/lib/python3.6/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
     17 | #warning "Using deprecated NumPy API, disable it with " \
        |  ^~~~~~~
  In file included from pandas/src/period.c:245:
  pandas/src/datetime_helper.h:7: warning: "PyInt_AS_LONG" redefined
      7 | #define PyInt_AS_LONG PyLong_AsLong
        |
  pandas/src/period.c:141: note: this is the location of the previous definition
    141 |   #define PyInt_AS_LONG                PyLong_AS_LONG
        |
  In file included from pandas/src/period.c:249:
  pandas/src/numpy_helper.h: In function ‘transfer_object_column’:
  pandas/src/numpy_helper.h:152:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
    152 |     for (i = 0; i < length; ++i)
        |                   ^
  gcc -pthread -B /home/tlc/anaconda3/envs/pgcn/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -Ipandas/src/klib -Ipandas/src -I/home/tlc/anaconda3/envs/pgcn/lib/python3.6/site-packages/numpy/core/include -I/home/tlc/anaconda3/envs/pgcn/include/python3.6m -c pandas/src/datetime/np_datetime.c -o build/temp.linux-x86_64-3.6/pandas/src/datetime/np_datetime.o -Wno-unused-function
  In file included from /home/tlc/anaconda3/envs/pgcn/lib/python3.6/site-packages/numpy/core/include/numpy/ndarraytypes.h:1822,
                   from /home/tlc/anaconda3/envs/pgcn/lib/python3.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:12,
                   from /home/tlc/anaconda3/envs/pgcn/lib/python3.6/site-packages/numpy/core/include/numpy/arrayobject.h:4,
                   from pandas/src/datetime/np_datetime.c:18:
  /home/tlc/anaconda3/envs/pgcn/lib/python3.6/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
     17 | #warning "Using deprecated NumPy API, disable it with " \
        |  ^~~~~~~
  In file included from pandas/src/datetime/np_datetime.c:10:
  /home/tlc/anaconda3/envs/pgcn/include/python3.6m/datetime.h:200:25: warning: ‘PyDateTimeAPI’ defined but not used [-Wunused-variable]
    200 | static PyDateTime_CAPI *PyDateTimeAPI = NULL;
        |                         ^~~~~~~~~~~~~
  gcc -pthread -B /home/tlc/anaconda3/envs/pgcn/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -Ipandas/src/klib -Ipandas/src -I/home/tlc/anaconda3/envs/pgcn/lib/python3.6/site-packages/numpy/core/include -I/home/tlc/anaconda3/envs/pgcn/include/python3.6m -c pandas/src/datetime/np_datetime_strings.c -o build/temp.linux-x86_64-3.6/pandas/src/datetime/np_datetime_strings.o -Wno-unused-function
  In file included from /home/tlc/anaconda3/envs/pgcn/lib/python3.6/site-packages/numpy/core/include/numpy/ndarraytypes.h:1822,
                   from /home/tlc/anaconda3/envs/pgcn/lib/python3.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:12,
                   from /home/tlc/anaconda3/envs/pgcn/lib/python3.6/site-packages/numpy/core/include/numpy/arrayobject.h:4,
                   from pandas/src/datetime/np_datetime_strings.c:17:
  /home/tlc/anaconda3/envs/pgcn/lib/python3.6/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
     17 | #warning "Using deprecated NumPy API, disable it with " \
        |  ^~~~~~~
  pandas/src/datetime/np_datetime_strings.c: In function ‘parse_iso_8601_datetime’:
  pandas/src/datetime/np_datetime_strings.c:463:18: warning: comparison of integer expressions of different signedness: ‘PANDAS_DATETIMEUNIT’ {aka ‘enum <anonymous>’} and ‘int’ [-Wsign-compare]
    463 |         if (unit != -1 && !can_cast_datetime64_units(bestunit, unit,
        |                  ^~
  pandas/src/datetime/np_datetime_strings.c:506:18: warning: comparison of integer expressions of different signedness: ‘PANDAS_DATETIMEUNIT’ {aka ‘enum <anonymous>’} and ‘int’ [-Wsign-compare]
    506 |         if (unit != -1 && !can_cast_datetime64_units(bestunit, unit,
        |                  ^~
  pandas/src/datetime/np_datetime_strings.c:978:14: warning: comparison of integer expressions of different signedness: ‘PANDAS_DATETIMEUNIT’ {aka ‘enum <anonymous>’} and ‘int’ [-Wsign-compare]
    978 |     if (unit != -1 && !can_cast_datetime64_units(bestunit, unit,
        |              ^~
  pandas/src/datetime/np_datetime_strings.c: In function ‘get_datetime_iso_8601_strlen’:
  pandas/src/datetime/np_datetime_strings.c:1009:14: warning: comparison of integer expressions of different signedness: ‘PANDAS_DATETIMEUNIT’ {aka ‘enum <anonymous>’} and ‘int’ [-Wsign-compare]
   1009 |     if (base == -1) {
        |              ^~
  pandas/src/datetime/np_datetime_strings.c: In function ‘make_iso_8601_datetime’:
  pandas/src/datetime/np_datetime_strings.c:1150:14: warning: comparison of integer expressions of different signedness: ‘PANDAS_DATETIMEUNIT’ {aka ‘enum <anonymous>’} and ‘int’ [-Wsign-compare]
   1150 |     if (base == -1) {
        |              ^~
  gcc -pthread -B /home/tlc/anaconda3/envs/pgcn/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -Ipandas/src/klib -Ipandas/src -I/home/tlc/anaconda3/envs/pgcn/lib/python3.6/site-packages/numpy/core/include -I/home/tlc/anaconda3/envs/pgcn/include/python3.6m -c pandas/src/period_helper.c -o build/temp.linux-x86_64-3.6/pandas/src/period_helper.o -Wno-unused-function
  In file included from /home/tlc/anaconda3/envs/pgcn/lib/python3.6/site-packages/numpy/core/include/numpy/ndarraytypes.h:1822,
                   from pandas/src/period_helper.h:12,
                   from pandas/src/period_helper.c:1:
  /home/tlc/anaconda3/envs/pgcn/lib/python3.6/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
     17 | #warning "Using deprecated NumPy API, disable it with " \
        |  ^~~~~~~
  gcc -pthread -shared -B /home/tlc/anaconda3/envs/pgcn/compiler_compat -L/home/tlc/anaconda3/envs/pgcn/lib -Wl,-rpath=/home/tlc/anaconda3/envs/pgcn/lib -Wl,--no-as-needed -Wl,--sysroot=/ build/temp.linux-x86_64-3.6/pandas/src/period.o build/temp.linux-x86_64-3.6/pandas/src/datetime/np_datetime.o build/temp.linux-x86_64-3.6/pandas/src/datetime/np_datetime_strings.o build/temp.linux-x86_64-3.6/pandas/src/period_helper.o -o build/lib.linux-x86_64-3.6/pandas/_period.cpython-36m-x86_64-linux-gnu.so
  skipping 'pandas/index.c' Cython extension (up-to-date)
  building 'pandas.index' extension
  gcc -pthread -B /home/tlc/anaconda3/envs/pgcn/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -Ipandas/src/klib -Ipandas/src -I/home/tlc/anaconda3/envs/pgcn/lib/python3.6/site-packages/numpy/core/include -I/home/tlc/anaconda3/envs/pgcn/include/python3.6m -c pandas/index.c -o build/temp.linux-x86_64-3.6/pandas/index.o -Wno-unused-function
  In file included from /home/tlc/anaconda3/envs/pgcn/lib/python3.6/site-packages/numpy/core/include/numpy/ndarraytypes.h:1822,
                   from /home/tlc/anaconda3/envs/pgcn/lib/python3.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:12,
                   from /home/tlc/anaconda3/envs/pgcn/lib/python3.6/site-packages/numpy/core/include/numpy/arrayobject.h:4,
                   from pandas/index.c:242:
  /home/tlc/anaconda3/envs/pgcn/lib/python3.6/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
     17 | #warning "Using deprecated NumPy API, disable it with " \
        |  ^~~~~~~
  In file included from pandas/index.c:244:
  pandas/src/numpy_helper.h: In function ‘transfer_object_column’:
  pandas/src/numpy_helper.h:152:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
    152 |     for (i = 0; i < length; ++i)
        |                   ^
  In file included from pandas/index.c:249:
  pandas/src/datetime_helper.h: At top level:
  pandas/src/datetime_helper.h:7: warning: "PyInt_AS_LONG" redefined
      7 | #define PyInt_AS_LONG PyLong_AsLong
        |
  pandas/index.c:141: note: this is the location of the previous definition
    141 |   #define PyInt_AS_LONG                PyLong_AS_LONG
        |
  pandas/index.c: In function ‘__pyx_f_6pandas_5index_11IndexEngine_get_loc’:
  pandas/index.c:139:40: warning: ‘__pyx_v_mid’ may be used uninitialized in this function [-Wmaybe-uninitialized]
    139 |   #define PyInt_FromSsize_t            PyLong_FromSsize_t
        |                                        ^~~~~~~~~~~~~~~~~~
  pandas/index.c:9125:14: note: ‘__pyx_v_mid’ was declared here
   9125 |   Py_ssize_t __pyx_v_mid;
        |              ^~~~~~~~~~~
  gcc -pthread -B /home/tlc/anaconda3/envs/pgcn/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -Ipandas/src/klib -Ipandas/src -I/home/tlc/anaconda3/envs/pgcn/lib/python3.6/site-packages/numpy/core/include -I/home/tlc/anaconda3/envs/pgcn/include/python3.6m -c pandas/src/datetime/np_datetime.c -o build/temp.linux-x86_64-3.6/pandas/src/datetime/np_datetime.o -Wno-unused-function
  In file included from /home/tlc/anaconda3/envs/pgcn/lib/python3.6/site-packages/numpy/core/include/numpy/ndarraytypes.h:1822,
                   from /home/tlc/anaconda3/envs/pgcn/lib/python3.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:12,
                   from /home/tlc/anaconda3/envs/pgcn/lib/python3.6/site-packages/numpy/core/include/numpy/arrayobject.h:4,
                   from pandas/src/datetime/np_datetime.c:18:
  /home/tlc/anaconda3/envs/pgcn/lib/python3.6/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
     17 | #warning "Using deprecated NumPy API, disable it with " \
        |  ^~~~~~~
  In file included from pandas/src/datetime/np_datetime.c:10:
  /home/tlc/anaconda3/envs/pgcn/include/python3.6m/datetime.h:200:25: warning: ‘PyDateTimeAPI’ defined but not used [-Wunused-variable]
    200 | static PyDateTime_CAPI *PyDateTimeAPI = NULL;
        |                         ^~~~~~~~~~~~~
  gcc -pthread -B /home/tlc/anaconda3/envs/pgcn/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -Ipandas/src/klib -Ipandas/src -I/home/tlc/anaconda3/envs/pgcn/lib/python3.6/site-packages/numpy/core/include -I/home/tlc/anaconda3/envs/pgcn/include/python3.6m -c pandas/src/datetime/np_datetime_strings.c -o build/temp.linux-x86_64-3.6/pandas/src/datetime/np_datetime_strings.o -Wno-unused-function
  In file included from /home/tlc/anaconda3/envs/pgcn/lib/python3.6/site-packages/numpy/core/include/numpy/ndarraytypes.h:1822,
                   from /home/tlc/anaconda3/envs/pgcn/lib/python3.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:12,
                   from /home/tlc/anaconda3/envs/pgcn/lib/python3.6/site-packages/numpy/core/include/numpy/arrayobject.h:4,
                   from pandas/src/datetime/np_datetime_strings.c:17:
  /home/tlc/anaconda3/envs/pgcn/lib/python3.6/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
     17 | #warning "Using deprecated NumPy API, disable it with " \
        |  ^~~~~~~
  pandas/src/datetime/np_datetime_strings.c: In function ‘parse_iso_8601_datetime’:
  pandas/src/datetime/np_datetime_strings.c:463:18: warning: comparison of integer expressions of different signedness: ‘PANDAS_DATETIMEUNIT’ {aka ‘enum <anonymous>’} and ‘int’ [-Wsign-compare]
    463 |         if (unit != -1 && !can_cast_datetime64_units(bestunit, unit,
        |                  ^~
  pandas/src/datetime/np_datetime_strings.c:506:18: warning: comparison of integer expressions of different signedness: ‘PANDAS_DATETIMEUNIT’ {aka ‘enum <anonymous>’} and ‘int’ [-Wsign-compare]
    506 |         if (unit != -1 && !can_cast_datetime64_units(bestunit, unit,
        |                  ^~
  pandas/src/datetime/np_datetime_strings.c:978:14: warning: comparison of integer expressions of different signedness: ‘PANDAS_DATETIMEUNIT’ {aka ‘enum <anonymous>’} and ‘int’ [-Wsign-compare]
    978 |     if (unit != -1 && !can_cast_datetime64_units(bestunit, unit,
        |              ^~
  pandas/src/datetime/np_datetime_strings.c: In function ‘get_datetime_iso_8601_strlen’:
  pandas/src/datetime/np_datetime_strings.c:1009:14: warning: comparison of integer expressions of different signedness: ‘PANDAS_DATETIMEUNIT’ {aka ‘enum <anonymous>’} and ‘int’ [-Wsign-compare]
   1009 |     if (base == -1) {
        |              ^~
  pandas/src/datetime/np_datetime_strings.c: In function ‘make_iso_8601_datetime’:
  pandas/src/datetime/np_datetime_strings.c:1150:14: warning: comparison of integer expressions of different signedness: ‘PANDAS_DATETIMEUNIT’ {aka ‘enum <anonymous>’} and ‘int’ [-Wsign-compare]
   1150 |     if (base == -1) {
        |              ^~
  gcc -pthread -shared -B /home/tlc/anaconda3/envs/pgcn/compiler_compat -L/home/tlc/anaconda3/envs/pgcn/lib -Wl,-rpath=/home/tlc/anaconda3/envs/pgcn/lib -Wl,--no-as-needed -Wl,--sysroot=/ build/temp.linux-x86_64-3.6/pandas/index.o build/temp.linux-x86_64-3.6/pandas/src/datetime/np_datetime.o build/temp.linux-x86_64-3.6/pandas/src/datetime/np_datetime_strings.o -o build/lib.linux-x86_64-3.6/pandas/index.cpython-36m-x86_64-linux-gnu.so
  skipping 'pandas/algos.c' Cython extension (up-to-date)
  building 'pandas.algos' extension
  gcc -pthread -B /home/tlc/anaconda3/envs/pgcn/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -Ipandas/src/klib -Ipandas/src -I/home/tlc/anaconda3/envs/pgcn/lib/python3.6/site-packages/numpy/core/include -I/home/tlc/anaconda3/envs/pgcn/include/python3.6m -c pandas/algos.c -o build/temp.linux-x86_64-3.6/pandas/algos.o -Wno-unused-function
  In file included from /home/tlc/anaconda3/envs/pgcn/lib/python3.6/site-packages/numpy/core/include/numpy/ndarraytypes.h:1822,
                   from /home/tlc/anaconda3/envs/pgcn/lib/python3.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:12,
                   from /home/tlc/anaconda3/envs/pgcn/lib/python3.6/site-packages/numpy/core/include/numpy/arrayobject.h:4,
                   from pandas/algos.c:242:
  /home/tlc/anaconda3/envs/pgcn/lib/python3.6/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
     17 | #warning "Using deprecated NumPy API, disable it with " \
        |  ^~~~~~~
  In file included from pandas/algos.c:244:
  pandas/src/numpy_helper.h: In function ‘transfer_object_column’:
  pandas/src/numpy_helper.h:152:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
    152 |     for (i = 0; i < length; ++i)
        |                   ^
  In file included from pandas/algos.c:252:
  pandas/src/datetime_helper.h: At top level:
  pandas/src/datetime_helper.h:7: warning: "PyInt_AS_LONG" redefined
      7 | #define PyInt_AS_LONG PyLong_AsLong
        |
  pandas/algos.c:141: note: this is the location of the previous definition
    141 |   #define PyInt_AS_LONG                PyLong_AS_LONG
        |
  pandas/algos.c: In function ‘__pyx_pf_6pandas_5algos_404group_last_int64’:
  pandas/algos.c:139621:40: warning: self-comparison always evaluates to true [-Wtautological-compare]
  139621 |             __pyx_t_22 = ((__pyx_v_val == __pyx_v_val) != 0);
         |                                        ^~
  pandas/algos.c: In function ‘__pyx_pf_6pandas_5algos_410group_nth_int64’:
  pandas/algos.c:141829:40: warning: self-comparison always evaluates to true [-Wtautological-compare]
  141829 |             __pyx_t_22 = ((__pyx_v_val == __pyx_v_val) != 0);
         |                                        ^~
  pandas/algos.c: In function ‘__pyx_pf_6pandas_5algos_416group_min_int64’:
  pandas/algos.c:144507:42: warning: self-comparison always evaluates to true [-Wtautological-compare]
  144507 |               __pyx_t_20 = ((__pyx_v_val == __pyx_v_val) != 0);
         |                                          ^~
  pandas/algos.c:144661:40: warning: self-comparison always evaluates to true [-Wtautological-compare]
  144661 |             __pyx_t_20 = ((__pyx_v_val == __pyx_v_val) != 0);
         |                                        ^~
  pandas/algos.c: In function ‘__pyx_pf_6pandas_5algos_422group_max_int64’:
  pandas/algos.c:147345:42: warning: self-comparison always evaluates to true [-Wtautological-compare]
  147345 |               __pyx_t_20 = ((__pyx_v_val == __pyx_v_val) != 0);
         |                                          ^~
  pandas/algos.c:147499:40: warning: self-comparison always evaluates to true [-Wtautological-compare]
  147499 |             __pyx_t_20 = ((__pyx_v_val == __pyx_v_val) != 0);
         |                                        ^~
  pandas/algos.c: In function ‘__pyx_pf_6pandas_5algos_518group_cumsum’:
  pandas/algos.c:150047:40: warning: self-comparison always evaluates to true [-Wtautological-compare]
  150047 |             __pyx_t_11 = ((__pyx_v_val == __pyx_v_val) != 0);
         |                                        ^~
  pandas/algos.c: In function ‘__pyx_pf_6pandas_5algos_520group_cumsum’:
  pandas/algos.c:150459:40: warning: self-comparison always evaluates to true [-Wtautological-compare]
  150459 |             __pyx_t_11 = ((__pyx_v_val == __pyx_v_val) != 0);
         |                                        ^~
  pandas/algos.c: In function ‘__pyx_pf_6pandas_5algos_522group_cumsum’:
  pandas/algos.c:150871:40: warning: self-comparison always evaluates to true [-Wtautological-compare]
  150871 |             __pyx_t_11 = ((__pyx_v_val == __pyx_v_val) != 0);
         |                                        ^~
  pandas/algos.c: In function ‘__pyx_pf_6pandas_5algos_524group_cumsum’:
  pandas/algos.c:151283:40: warning: self-comparison always evaluates to true [-Wtautological-compare]
  151283 |             __pyx_t_11 = ((__pyx_v_val == __pyx_v_val) != 0);
         |                                        ^~
  pandas/algos.c: In function ‘__pyx_pf_6pandas_5algos_526group_cumsum’:
  pandas/algos.c:151695:40: warning: self-comparison always evaluates to true [-Wtautological-compare]
  151695 |             __pyx_t_11 = ((__pyx_v_val == __pyx_v_val) != 0);
         |                                        ^~
  pandas/algos.c: In function ‘__pyx_pf_6pandas_5algos_528group_cumsum’:
  pandas/algos.c:152107:40: warning: self-comparison always evaluates to true [-Wtautological-compare]
  152107 |             __pyx_t_11 = ((__pyx_v_val == __pyx_v_val) != 0);
         |                                        ^~
  pandas/algos.c: In function ‘__pyx_pf_6pandas_5algos_530group_cumsum’:
  pandas/algos.c:152519:40: warning: self-comparison always evaluates to true [-Wtautological-compare]
  152519 |             __pyx_t_11 = ((__pyx_v_val == __pyx_v_val) != 0);
         |                                        ^~
  pandas/algos.c: In function ‘__pyx_pf_6pandas_5algos_532group_cumsum’:
  pandas/algos.c:152931:40: warning: self-comparison always evaluates to true [-Wtautological-compare]
  152931 |             __pyx_t_11 = ((__pyx_v_val == __pyx_v_val) != 0);
         |                                        ^~
  pandas/algos.c: In function ‘__pyx_pf_6pandas_5algos_50roll_window.isra.0’:
  pandas/algos.c:41642:167: warning: ‘__pyx_pybuffernd_tot_wgt.diminfo[0].strides’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  41642 |           *__Pyx_BufPtrStrided1d(__pyx_t_5numpy_double_t *, __pyx_pybuffernd_tot_wgt.rcbuffer->pybuffer.buf, __pyx_t_20, __pyx_pybuffernd_tot_wgt.diminfo[0].strides) += __pyx_v_val_win;
        |                                                                                                                                                                       ^~
  pandas/algos.c:41637:21: warning: ‘__pyx_pybuffernd_tot_wgt.diminfo[0].shape’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  41637 |           } else if (unlikely(__pyx_t_20 >= __pyx_pybuffernd_tot_wgt.diminfo[0].shape)) __pyx_t_7 = 0;
        |                     ^
  pandas/algos.c: In function ‘__pyx_pw_6pandas_5algos_431group_shift_indexer’:
  pandas/algos.c:153935:7: warning: ‘__pyx_v_offset’ may be used uninitialized in this function [-Wmaybe-uninitialized]
  153935 |   int __pyx_v_offset;
         |       ^~~~~~~~~~~~~~
  gcc -pthread -shared -B /home/tlc/anaconda3/envs/pgcn/compiler_compat -L/home/tlc/anaconda3/envs/pgcn/lib -Wl,-rpath=/home/tlc/anaconda3/envs/pgcn/lib -Wl,--no-as-needed -Wl,--sysroot=/ build/temp.linux-x86_64-3.6/pandas/algos.o -o build/lib.linux-x86_64-3.6/pandas/algos.cpython-36m-x86_64-linux-gnu.so
  skipping 'pandas/parser.c' Cython extension (up-to-date)
  building 'pandas.parser' extension
  creating build/temp.linux-x86_64-3.6/pandas/src/parser
  gcc -pthread -B /home/tlc/anaconda3/envs/pgcn/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -Ipandas/src/klib -Ipandas/src -I/home/tlc/anaconda3/envs/pgcn/lib/python3.6/site-packages/numpy/core/include -I/home/tlc/anaconda3/envs/pgcn/include/python3.6m -c pandas/parser.c -o build/temp.linux-x86_64-3.6/pandas/parser.o -Wno-unused-function
  In file included from /home/tlc/anaconda3/envs/pgcn/lib/python3.6/site-packages/numpy/core/include/numpy/ndarraytypes.h:1822,
                   from /home/tlc/anaconda3/envs/pgcn/lib/python3.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:12,
                   from /home/tlc/anaconda3/envs/pgcn/lib/python3.6/site-packages/numpy/core/include/numpy/arrayobject.h:4,
                   from pandas/parser.c:243:
  /home/tlc/anaconda3/envs/pgcn/lib/python3.6/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
     17 | #warning "Using deprecated NumPy API, disable it with " \
        |  ^~~~~~~
  In file included from pandas/parser.c:245:
  pandas/src/numpy_helper.h: In function ‘transfer_object_column’:
  pandas/src/numpy_helper.h:152:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
    152 |     for (i = 0; i < length; ++i)
        |                   ^
  pandas/parser.c: In function ‘__pyx_f_6pandas_6parser_10TextReader__get_header’:
  pandas/parser.c:6483:49: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
   6483 |       __pyx_t_2 = ((__pyx_v_self->parser->lines < (__pyx_v_hr + 1)) != 0);
        |                                                 ^
  pandas/parser.c:6551:49: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
   6551 |       __pyx_t_2 = ((__pyx_v_self->parser->lines < (__pyx_v_hr + 1)) != 0);
        |                                                 ^
  pandas/parser.c:7540:45: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
   7540 |   __pyx_t_8 = ((__pyx_v_self->parser->lines < (__pyx_v_data_line + 1)) != 0);
        |                                             ^
  pandas/parser.c:7599:23: warning: comparison of integer expressions of different signedness: ‘Py_ssize_t’ {aka ‘long int’} and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
   7599 |       if (((__pyx_t_4 > __pyx_t_7) != 0)) {
        |                       ^
  pandas/parser.c:7670:34: warning: comparison of integer expressions of different signedness: ‘Py_ssize_t’ {aka ‘long int’} and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
   7670 |       __pyx_t_2 = ((__pyx_v_nuse == __pyx_v_passed_count) != 0);
        |                                  ^~
  pandas/parser.c:7706:35: warning: comparison of integer expressions of different signedness: ‘Py_ssize_t’ {aka ‘long int’} and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
   7706 |       __pyx_t_17 = ((__pyx_v_nuse < __pyx_v_passed_count) != 0);
        |                                   ^
  pandas/parser.c: In function ‘__pyx_f_6pandas_6parser__string_box_factorize’:
  pandas/parser.c:17999:35: warning: comparison of integer expressions of different signedness: ‘Py_ssize_t’ {aka ‘long int’} and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  17999 |   for (__pyx_t_12 = 0; __pyx_t_12 < __pyx_t_11; __pyx_t_12+=1) {
        |                                   ^
  pandas/parser.c: In function ‘__pyx_f_6pandas_6parser__string_box_utf8’:
  pandas/parser.c:18449:35: warning: comparison of integer expressions of different signedness: ‘Py_ssize_t’ {aka ‘long int’} and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  18449 |   for (__pyx_t_12 = 0; __pyx_t_12 < __pyx_t_11; __pyx_t_12+=1) {
        |                                   ^
  pandas/parser.c: In function ‘__pyx_f_6pandas_6parser__string_box_decode’:
  pandas/parser.c:18910:35: warning: comparison of integer expressions of different signedness: ‘Py_ssize_t’ {aka ‘long int’} and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  18910 |   for (__pyx_t_12 = 0; __pyx_t_12 < __pyx_t_11; __pyx_t_12+=1) {
        |                                   ^
  pandas/parser.c: In function ‘__pyx_f_6pandas_6parser__apply_converter’:
  pandas/parser.c:25457:37: warning: comparison of integer expressions of different signedness: ‘Py_ssize_t’ {aka ‘long int’} and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  25457 |     for (__pyx_t_14 = 0; __pyx_t_14 < __pyx_t_13; __pyx_t_14+=1) {
        |                                     ^
  pandas/parser.c:25577:37: warning: comparison of integer expressions of different signedness: ‘Py_ssize_t’ {aka ‘long int’} and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  25577 |     for (__pyx_t_14 = 0; __pyx_t_14 < __pyx_t_13; __pyx_t_14+=1) {
        |                                     ^
  pandas/parser.c:25671:37: warning: comparison of integer expressions of different signedness: ‘Py_ssize_t’ {aka ‘long int’} and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
  25671 |     for (__pyx_t_14 = 0; __pyx_t_14 < __pyx_t_13; __pyx_t_14+=1) {
        |                                     ^
  pandas/parser.c: In function ‘__pyx_f_6pandas_6parser__fill_structured_column’:
  pandas/parser.c:26520:35: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
  26520 |     for (__pyx_t_3 = 0; __pyx_t_3 < __pyx_t_2; __pyx_t_3+=1) {
        |                                   ^
  pandas/parser.c: In function ‘__pyx_f_6pandas_6parser_10TextReader__get_header’:
  pandas/parser.c:6332:10: warning: ‘__pyx_v_data_line’ may be used uninitialized in this function [-Wmaybe-uninitialized]
   6332 |   size_t __pyx_v_data_line;
        |          ^~~~~~~~~~~~~~~~~
  gcc -pthread -B /home/tlc/anaconda3/envs/pgcn/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -Ipandas/src/klib -Ipandas/src -I/home/tlc/anaconda3/envs/pgcn/lib/python3.6/site-packages/numpy/core/include -I/home/tlc/anaconda3/envs/pgcn/include/python3.6m -c pandas/src/parser/tokenizer.c -o build/temp.linux-x86_64-3.6/pandas/src/parser/tokenizer.o -Wno-unused-function
  pandas/src/parser/tokenizer.c: In function ‘tokenize_delimited’:
  pandas/src/parser/tokenizer.c:670:39: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
    670 |     if (line_limit > 0 && self->lines == start_lines + line_limit) {    \
        |                                       ^~
  pandas/src/parser/tokenizer.c:691:20: note: in expansion of macro ‘END_LINE_STATE’
    691 | #define END_LINE() END_LINE_STATE(START_RECORD)
        |                    ^~~~~~~~~~~~~~
  pandas/src/parser/tokenizer.c:748:17: note: in expansion of macro ‘END_LINE’
    748 |                 END_LINE();
        |                 ^~~~~~~~
  pandas/src/parser/tokenizer.c:670:39: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
    670 |     if (line_limit > 0 && self->lines == start_lines + line_limit) {    \
        |                                       ^~
  pandas/src/parser/tokenizer.c:691:20: note: in expansion of macro ‘END_LINE_STATE’
    691 | #define END_LINE() END_LINE_STATE(START_RECORD)
        |                    ^~~~~~~~~~~~~~
  pandas/src/parser/tokenizer.c:760:21: note: in expansion of macro ‘END_LINE’
    760 |                     END_LINE();
        |                     ^~~~~~~~
  pandas/src/parser/tokenizer.c:670:39: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
    670 |     if (line_limit > 0 && self->lines == start_lines + line_limit) {    \
        |                                       ^~
  pandas/src/parser/tokenizer.c:691:20: note: in expansion of macro ‘END_LINE_STATE’
    691 | #define END_LINE() END_LINE_STATE(START_RECORD)
        |                    ^~~~~~~~~~~~~~
  pandas/src/parser/tokenizer.c:772:21: note: in expansion of macro ‘END_LINE’
    772 |                     END_LINE();
        |                     ^~~~~~~~
  pandas/src/parser/tokenizer.c:670:39: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
    670 |     if (line_limit > 0 && self->lines == start_lines + line_limit) {    \
        |                                       ^~
  pandas/src/parser/tokenizer.c:691:20: note: in expansion of macro ‘END_LINE_STATE’
    691 | #define END_LINE() END_LINE_STATE(START_RECORD)
        |                    ^~~~~~~~~~~~~~
  pandas/src/parser/tokenizer.c:803:17: note: in expansion of macro ‘END_LINE’
    803 |                 END_LINE();
        |                 ^~~~~~~~
  pandas/src/parser/tokenizer.c:670:39: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
    670 |     if (line_limit > 0 && self->lines == start_lines + line_limit) {    \
        |                                       ^~
  pandas/src/parser/tokenizer.c:691:20: note: in expansion of macro ‘END_LINE_STATE’
    691 | #define END_LINE() END_LINE_STATE(START_RECORD)
        |                    ^~~~~~~~~~~~~~
  pandas/src/parser/tokenizer.c:888:17: note: in expansion of macro ‘END_LINE’
    888 |                 END_LINE();
        |                 ^~~~~~~~
  pandas/src/parser/tokenizer.c:670:39: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
    670 |     if (line_limit > 0 && self->lines == start_lines + line_limit) {    \
        |                                       ^~
  pandas/src/parser/tokenizer.c:691:20: note: in expansion of macro ‘END_LINE_STATE’
    691 | #define END_LINE() END_LINE_STATE(START_RECORD)
        |                    ^~~~~~~~~~~~~~
  pandas/src/parser/tokenizer.c:960:17: note: in expansion of macro ‘END_LINE’
    960 |                 END_LINE();
        |                 ^~~~~~~~
  pandas/src/parser/tokenizer.c:670:39: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
    670 |     if (line_limit > 0 && self->lines == start_lines + line_limit) {    \
        |                                       ^~
  pandas/src/parser/tokenizer.c:691:20: note: in expansion of macro ‘END_LINE_STATE’
    691 | #define END_LINE() END_LINE_STATE(START_RECORD)
        |                    ^~~~~~~~~~~~~~
  pandas/src/parser/tokenizer.c:981:17: note: in expansion of macro ‘END_LINE’
    981 |                 END_LINE();
        |                 ^~~~~~~~
  pandas/src/parser/tokenizer.c:670:39: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
    670 |     if (line_limit > 0 && self->lines == start_lines + line_limit) {    \
        |                                       ^~
  pandas/src/parser/tokenizer.c:691:20: note: in expansion of macro ‘END_LINE_STATE’
    691 | #define END_LINE() END_LINE_STATE(START_RECORD)
        |                    ^~~~~~~~~~~~~~
  pandas/src/parser/tokenizer.c:989:17: note: in expansion of macro ‘END_LINE’
    989 |                 END_LINE();
        |                 ^~~~~~~~
  pandas/src/parser/tokenizer.c:686:39: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
    686 |     if (line_limit > 0 && self->lines == start_lines + line_limit) {    \
        |                                       ^~
  pandas/src/parser/tokenizer.c:993:17: note: in expansion of macro ‘END_LINE_AND_FIELD_STATE’
    993 |                 END_LINE_AND_FIELD_STATE(START_FIELD);
        |                 ^~~~~~~~~~~~~~~~~~~~~~~~
  pandas/src/parser/tokenizer.c:1008:51: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
   1008 |                 if (line_limit > 0 && self->lines == start_lines + line_limit) {
        |                                                   ^~
  pandas/src/parser/tokenizer.c: In function ‘tokenize_delim_customterm’:
  pandas/src/parser/tokenizer.c:670:39: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
    670 |     if (line_limit > 0 && self->lines == start_lines + line_limit) {    \
        |                                       ^~
  pandas/src/parser/tokenizer.c:691:20: note: in expansion of macro ‘END_LINE_STATE’
    691 | #define END_LINE() END_LINE_STATE(START_RECORD)
        |                    ^~~~~~~~~~~~~~
  pandas/src/parser/tokenizer.c:1086:17: note: in expansion of macro ‘END_LINE’
   1086 |                 END_LINE();
        |                 ^~~~~~~~
  pandas/src/parser/tokenizer.c:670:39: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
    670 |     if (line_limit > 0 && self->lines == start_lines + line_limit) {    \
        |                                       ^~
  pandas/src/parser/tokenizer.c:691:20: note: in expansion of macro ‘END_LINE_STATE’
    691 | #define END_LINE() END_LINE_STATE(START_RECORD)
        |                    ^~~~~~~~~~~~~~
  pandas/src/parser/tokenizer.c:1095:21: note: in expansion of macro ‘END_LINE’
   1095 |                     END_LINE();
        |                     ^~~~~~~~
  pandas/src/parser/tokenizer.c:670:39: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
    670 |     if (line_limit > 0 && self->lines == start_lines + line_limit) {    \
        |                                       ^~
  pandas/src/parser/tokenizer.c:691:20: note: in expansion of macro ‘END_LINE_STATE’
    691 | #define END_LINE() END_LINE_STATE(START_RECORD)
        |                    ^~~~~~~~~~~~~~
  pandas/src/parser/tokenizer.c:1107:21: note: in expansion of macro ‘END_LINE’
   1107 |                     END_LINE();
        |                     ^~~~~~~~
  pandas/src/parser/tokenizer.c:670:39: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
    670 |     if (line_limit > 0 && self->lines == start_lines + line_limit) {    \
        |                                       ^~
  pandas/src/parser/tokenizer.c:691:20: note: in expansion of macro ‘END_LINE_STATE’
    691 | #define END_LINE() END_LINE_STATE(START_RECORD)
        |                    ^~~~~~~~~~~~~~
  pandas/src/parser/tokenizer.c:1127:17: note: in expansion of macro ‘END_LINE’
   1127 |                 END_LINE();
        |                 ^~~~~~~~
  pandas/src/parser/tokenizer.c:670:39: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
    670 |     if (line_limit > 0 && self->lines == start_lines + line_limit) {    \
        |                                       ^~
  pandas/src/parser/tokenizer.c:691:20: note: in expansion of macro ‘END_LINE_STATE’
    691 | #define END_LINE() END_LINE_STATE(START_RECORD)
        |                    ^~~~~~~~~~~~~~
  pandas/src/parser/tokenizer.c:1196:17: note: in expansion of macro ‘END_LINE’
   1196 |                 END_LINE();
        |                 ^~~~~~~~
  pandas/src/parser/tokenizer.c:670:39: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
    670 |     if (line_limit > 0 && self->lines == start_lines + line_limit) {    \
        |                                       ^~
  pandas/src/parser/tokenizer.c:691:20: note: in expansion of macro ‘END_LINE_STATE’
    691 | #define END_LINE() END_LINE_STATE(START_RECORD)
        |                    ^~~~~~~~~~~~~~
  pandas/src/parser/tokenizer.c:1262:17: note: in expansion of macro ‘END_LINE’
   1262 |                 END_LINE();
        |                 ^~~~~~~~
  pandas/src/parser/tokenizer.c:670:39: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
    670 |     if (line_limit > 0 && self->lines == start_lines + line_limit) {    \
        |                                       ^~
  pandas/src/parser/tokenizer.c:691:20: note: in expansion of macro ‘END_LINE_STATE’
    691 | #define END_LINE() END_LINE_STATE(START_RECORD)
        |                    ^~~~~~~~~~~~~~
  pandas/src/parser/tokenizer.c:1286:17: note: in expansion of macro ‘END_LINE’
   1286 |                 END_LINE();
        |                 ^~~~~~~~
  pandas/src/parser/tokenizer.c: In function ‘tokenize_whitespace’:
  pandas/src/parser/tokenizer.c:670:39: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
    670 |     if (line_limit > 0 && self->lines == start_lines + line_limit) {    \
        |                                       ^~
  pandas/src/parser/tokenizer.c:691:20: note: in expansion of macro ‘END_LINE_STATE’
    691 | #define END_LINE() END_LINE_STATE(START_RECORD)
        |                    ^~~~~~~~~~~~~~
  pandas/src/parser/tokenizer.c:1350:17: note: in expansion of macro ‘END_LINE’
   1350 |                 END_LINE();
        |                 ^~~~~~~~
  pandas/src/parser/tokenizer.c:670:39: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
    670 |     if (line_limit > 0 && self->lines == start_lines + line_limit) {    \
        |                                       ^~
  pandas/src/parser/tokenizer.c:691:20: note: in expansion of macro ‘END_LINE_STATE’
    691 | #define END_LINE() END_LINE_STATE(START_RECORD)
        |                    ^~~~~~~~~~~~~~
  pandas/src/parser/tokenizer.c:1372:17: note: in expansion of macro ‘END_LINE’
   1372 |                 END_LINE();
        |                 ^~~~~~~~
  pandas/src/parser/tokenizer.c:670:39: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
    670 |     if (line_limit > 0 && self->lines == start_lines + line_limit) {    \
        |                                       ^~
  pandas/src/parser/tokenizer.c:691:20: note: in expansion of macro ‘END_LINE_STATE’
    691 | #define END_LINE() END_LINE_STATE(START_RECORD)
        |                    ^~~~~~~~~~~~~~
  pandas/src/parser/tokenizer.c:1392:21: note: in expansion of macro ‘END_LINE’
   1392 |                     END_LINE();
        |                     ^~~~~~~~
  pandas/src/parser/tokenizer.c:670:39: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
    670 |     if (line_limit > 0 && self->lines == start_lines + line_limit) {    \
        |                                       ^~
  pandas/src/parser/tokenizer.c:691:20: note: in expansion of macro ‘END_LINE_STATE’
    691 | #define END_LINE() END_LINE_STATE(START_RECORD)
        |                    ^~~~~~~~~~~~~~
  pandas/src/parser/tokenizer.c:1403:21: note: in expansion of macro ‘END_LINE’
   1403 |                     END_LINE();
        |                     ^~~~~~~~
  pandas/src/parser/tokenizer.c:670:39: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
    670 |     if (line_limit > 0 && self->lines == start_lines + line_limit) {    \
        |                                       ^~
  pandas/src/parser/tokenizer.c:691:20: note: in expansion of macro ‘END_LINE_STATE’
    691 | #define END_LINE() END_LINE_STATE(START_RECORD)
        |                    ^~~~~~~~~~~~~~
  pandas/src/parser/tokenizer.c:1433:17: note: in expansion of macro ‘END_LINE’
   1433 |                 END_LINE();
        |                 ^~~~~~~~
  pandas/src/parser/tokenizer.c:670:39: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
    670 |     if (line_limit > 0 && self->lines == start_lines + line_limit) {    \
        |                                       ^~
  pandas/src/parser/tokenizer.c:691:20: note: in expansion of macro ‘END_LINE_STATE’
    691 | #define END_LINE() END_LINE_STATE(START_RECORD)
        |                    ^~~~~~~~~~~~~~
  pandas/src/parser/tokenizer.c:1491:17: note: in expansion of macro ‘END_LINE’
   1491 |                 END_LINE();
        |                 ^~~~~~~~
  pandas/src/parser/tokenizer.c:670:39: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
    670 |     if (line_limit > 0 && self->lines == start_lines + line_limit) {    \
        |                                       ^~
  pandas/src/parser/tokenizer.c:691:20: note: in expansion of macro ‘END_LINE_STATE’
    691 | #define END_LINE() END_LINE_STATE(START_RECORD)
        |                    ^~~~~~~~~~~~~~
  pandas/src/parser/tokenizer.c:1563:17: note: in expansion of macro ‘END_LINE’
   1563 |                 END_LINE();
        |                 ^~~~~~~~
  pandas/src/parser/tokenizer.c:670:39: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
    670 |     if (line_limit > 0 && self->lines == start_lines + line_limit) {    \
        |                                       ^~
  pandas/src/parser/tokenizer.c:691:20: note: in expansion of macro ‘END_LINE_STATE’
    691 | #define END_LINE() END_LINE_STATE(START_RECORD)
        |                    ^~~~~~~~~~~~~~
  pandas/src/parser/tokenizer.c:1584:17: note: in expansion of macro ‘END_LINE’
   1584 |                 END_LINE();
        |                 ^~~~~~~~
  pandas/src/parser/tokenizer.c:670:39: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
    670 |     if (line_limit > 0 && self->lines == start_lines + line_limit) {    \
        |                                       ^~
  pandas/src/parser/tokenizer.c:1588:17: note: in expansion of macro ‘END_LINE_STATE’
   1588 |                 END_LINE_STATE(EAT_WHITESPACE);
        |                 ^~~~~~~~~~~~~~
  pandas/src/parser/tokenizer.c:670:39: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
    670 |     if (line_limit > 0 && self->lines == start_lines + line_limit) {    \
        |                                       ^~
  pandas/src/parser/tokenizer.c:1595:17: note: in expansion of macro ‘END_LINE_STATE’
   1595 |                 END_LINE_STATE(START_RECORD);
        |                 ^~~~~~~~~~~~~~
  pandas/src/parser/tokenizer.c:670:39: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
    670 |     if (line_limit > 0 && self->lines == start_lines + line_limit) {    \
        |                                       ^~
  pandas/src/parser/tokenizer.c:691:20: note: in expansion of macro ‘END_LINE_STATE’
    691 | #define END_LINE() END_LINE_STATE(START_RECORD)
        |                    ^~~~~~~~~~~~~~
  pandas/src/parser/tokenizer.c:1610:17: note: in expansion of macro ‘END_LINE’
   1610 |                 END_LINE();
        |                 ^~~~~~~~
  pandas/src/parser/tokenizer.c: In function ‘parser_consume_rows’:
  pandas/src/parser/tokenizer.c:1689:15: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
   1689 |     if (nrows > self->lines) {
        |               ^
  pandas/src/parser/tokenizer.c:1732:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
   1732 |     for (i = 0; i < self->lines - nrows + 1; ++i)
        |                   ^
  pandas/src/parser/tokenizer.c: In function ‘parser_trim_buffers’:
  pandas/src/parser/tokenizer.c:1765:17: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
   1765 |     if (new_cap < self->stream_cap) {
        |                 ^
  pandas/src/parser/tokenizer.c:1778:17: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
   1778 |     if (new_cap < self->words_cap) {
        |                 ^
  pandas/src/parser/tokenizer.c:1797:17: warning: comparison of integer expressions of different signedness: ‘size_t’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
   1797 |     if (new_cap < self->lines_cap) {
        |                 ^
  pandas/src/parser/tokenizer.c: In function ‘_tokenize_helper’:
  pandas/src/parser/tokenizer.c:1868:47: warning: comparison of integer expressions of different signedness: ‘int’ and ‘size_t’ {aka ‘long unsigned int’} [-Wsign-compare]
   1868 |         if (!all && self->lines - start_lines >= nrows)
        |                                               ^~
  gcc -pthread -B /home/tlc/anaconda3/envs/pgcn/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -Ipandas/src/klib -Ipandas/src -I/home/tlc/anaconda3/envs/pgcn/lib/python3.6/site-packages/numpy/core/include -I/home/tlc/anaconda3/envs/pgcn/include/python3.6m -c pandas/src/parser/io.c -o build/temp.linux-x86_64-3.6/pandas/src/parser/io.o -Wno-unused-function
  pandas/src/parser/io.c: In function ‘buffer_mmap_bytes’:
  pandas/src/parser/io.c:248:32: warning: comparison of integer expressions of different signedness: ‘long unsigned int’ and ‘off_t’ {aka ‘long int’} [-Wsign-compare]
    248 |     if (src->position + nbytes > src->last_pos) {
        |                                ^
  gcc -pthread -shared -B /home/tlc/anaconda3/envs/pgcn/compiler_compat -L/home/tlc/anaconda3/envs/pgcn/lib -Wl,-rpath=/home/tlc/anaconda3/envs/pgcn/lib -Wl,--no-as-needed -Wl,--sysroot=/ build/temp.linux-x86_64-3.6/pandas/parser.o build/temp.linux-x86_64-3.6/pandas/src/parser/tokenizer.o build/temp.linux-x86_64-3.6/pandas/src/parser/io.o -o build/lib.linux-x86_64-3.6/pandas/parser.cpython-36m-x86_64-linux-gnu.so
  skipping 'pandas/io/sas/saslib.c' Cython extension (up-to-date)
  building 'pandas.io.sas.saslib' extension
  creating build/temp.linux-x86_64-3.6/pandas/io
  creating build/temp.linux-x86_64-3.6/pandas/io/sas
  gcc -pthread -B /home/tlc/anaconda3/envs/pgcn/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -Ipandas/src/klib -Ipandas/src -I/home/tlc/anaconda3/envs/pgcn/lib/python3.6/site-packages/numpy/core/include -I/home/tlc/anaconda3/envs/pgcn/include/python3.6m -c pandas/io/sas/saslib.c -o build/temp.linux-x86_64-3.6/pandas/io/sas/saslib.o -Wno-unused-function
  In file included from /home/tlc/anaconda3/envs/pgcn/lib/python3.6/site-packages/numpy/core/include/numpy/ndarraytypes.h:1822,
                   from /home/tlc/anaconda3/envs/pgcn/lib/python3.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:12,
                   from /home/tlc/anaconda3/envs/pgcn/lib/python3.6/site-packages/numpy/core/include/numpy/arrayobject.h:4,
                   from pandas/io/sas/saslib.c:242:
  /home/tlc/anaconda3/envs/pgcn/lib/python3.6/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
     17 | #warning "Using deprecated NumPy API, disable it with " \
        |  ^~~~~~~
  pandas/io/sas/saslib.c: In function ‘__pyx_pf_6pandas_2io_3sas_6saslib_2_rdc_decompress.isra.0’:
  pandas/io/sas/saslib.c:3922:65: warning: ‘__pyx_v_ctrl_bits’ may be used uninitialized in this function [-Wmaybe-uninitialized]
   3922 |     __pyx_t_8 = (((__pyx_v_ctrl_bits & __pyx_v_ctrl_mask) == 0) != 0);
        |                 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~
  gcc -pthread -shared -B /home/tlc/anaconda3/envs/pgcn/compiler_compat -L/home/tlc/anaconda3/envs/pgcn/lib -Wl,-rpath=/home/tlc/anaconda3/envs/pgcn/lib -Wl,--no-as-needed -Wl,--sysroot=/ build/temp.linux-x86_64-3.6/pandas/io/sas/saslib.o -o build/lib.linux-x86_64-3.6/pandas/io/sas/saslib.cpython-36m-x86_64-linux-gnu.so
  skipping 'pandas/src/sparse.c' Cython extension (up-to-date)
  building 'pandas._sparse' extension
  gcc -pthread -B /home/tlc/anaconda3/envs/pgcn/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/home/tlc/anaconda3/envs/pgcn/lib/python3.6/site-packages/numpy/core/include -I/home/tlc/anaconda3/envs/pgcn/include/python3.6m -c pandas/src/sparse.c -o build/temp.linux-x86_64-3.6/pandas/src/sparse.o -Wno-unused-function
  In file included from /home/tlc/anaconda3/envs/pgcn/lib/python3.6/site-packages/numpy/core/include/numpy/ndarraytypes.h:1822,
                   from /home/tlc/anaconda3/envs/pgcn/lib/python3.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:12,
                   from /home/tlc/anaconda3/envs/pgcn/lib/python3.6/site-packages/numpy/core/include/numpy/arrayobject.h:4,
                   from pandas/src/sparse.c:242:
  /home/tlc/anaconda3/envs/pgcn/lib/python3.6/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp]
     17 | #warning "Using deprecated NumPy API, disable it with " \
        |  ^~~~~~~
  gcc -pthread -shared -B /home/tlc/anaconda3/envs/pgcn/compiler_compat -L/home/tlc/anaconda3/envs/pgcn/lib -Wl,-rpath=/home/tlc/anaconda3/envs/pgcn/lib -Wl,--no-as-needed -Wl,--sysroot=/ build/temp.linux-x86_64-3.6/pandas/src/sparse.o -lm -o build/lib.linux-x86_64-3.6/pandas/_sparse.cpython-36m-x86_64-linux-gnu.so
  skipping 'pandas/src/testing.c' Cython extension (up-to-date)
  building 'pandas._testing' extension
  gcc -pthread -B /home/tlc/anaconda3/envs/pgcn/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/home/tlc/anaconda3/envs/pgcn/lib/python3.6/site-packages/numpy/core/include -I/home/tlc/anaconda3/envs/pgcn/include/python3.6m -c pandas/src/testing.c -o build/temp.linux-x86_64-3.6/pandas/src/testing.o -Wno-unused-function
  gcc -pthread -shared -B /home/tlc/anaconda3/envs/pgcn/compiler_compat -L/home/tlc/anaconda3/envs/pgcn/lib -Wl,-rpath=/home/tlc/anaconda3/envs/pgcn/lib -Wl,--no-as-needed -Wl,--sysroot=/ build/temp.linux-x86_64-3.6/pandas/src/testing.o -lm -o build/lib.linux-x86_64-3.6/pandas/_testing.cpython-36m-x86_64-linux-gnu.so
  skipping 'pandas/msgpack/_packer.cpp' Cython extension (up-to-date)
  building 'pandas.msgpack._packer' extension
  creating build/temp.linux-x86_64-3.6/pandas/msgpack
  gcc -pthread -B /home/tlc/anaconda3/envs/pgcn/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -D__LITTLE_ENDIAN__=1 -Ipandas/src/msgpack -Ipandas/src/klib -Ipandas/src -I/home/tlc/anaconda3/envs/pgcn/lib/python3.6/site-packages/numpy/core/include -I/home/tlc/anaconda3/envs/pgcn/include/python3.6m -c pandas/msgpack/_packer.cpp -o build/temp.linux-x86_64-3.6/pandas/msgpack/_packer.o -Wno-unused-function
  gcc: fatal error: cannot execute ‘cc1plus’: execvp: No such file or directory
  compilation terminated.
  error: command 'gcc' failed with exit status 1
  ----------------------------------------
  ERROR: Failed building wheel for pandas
  Running setup.py clean for pandas
Failed to build pandas
Installing collected packages: pandas
  Attempting uninstall: pandas
    Found existing installation: pandas 1.1.5
    Uninstalling pandas-1.1.5:
      Successfully uninstalled pandas-1.1.5
    Running setup.py install for pandas: started

One reason might be pandas==0.18.0 does not support python>3.5 as in https://pandas.pydata.org/pandas-docs/version/0.18.0/install.html?

When I install pandas==1.1.5 and run python main_prioritization.py, some error occurs seems coming from pandas as:

/home/tlc/anaconda3/envs/pgcn/lib/python3.6/site-packages/tensorflow/python/framework/dtypes.py:519: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'.
  _np_qint8 = np.dtype([("qint8", np.int8, 1)])
/home/tlc/anaconda3/envs/pgcn/lib/python3.6/site-packages/tensorflow/python/framework/dtypes.py:520: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'.
  _np_quint8 = np.dtype([("quint8", np.uint8, 1)])
/home/tlc/anaconda3/envs/pgcn/lib/python3.6/site-packages/tensorflow/python/framework/dtypes.py:521: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'.
  _np_qint16 = np.dtype([("qint16", np.int16, 1)])
/home/tlc/anaconda3/envs/pgcn/lib/python3.6/site-packages/tensorflow/python/framework/dtypes.py:522: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'.
  _np_quint16 = np.dtype([("quint16", np.uint16, 1)])
/home/tlc/anaconda3/envs/pgcn/lib/python3.6/site-packages/tensorflow/python/framework/dtypes.py:523: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'.
  _np_qint32 = np.dtype([("qint32", np.int32, 1)])
/home/tlc/anaconda3/envs/pgcn/lib/python3.6/site-packages/tensorflow/python/framework/dtypes.py:528: FutureWarning: Passing (type, 1) or '1type' as a synonym of type is deprecated; in a future version of numpy, it will be understood as (type, (1,)) / '(1,)type'.
  np_resource = np.dtype([("resource", np.ubyte, 1)])

Bad key savefig.frameon in file /home/tlc/anaconda3/envs/pgcn/lib/python3.6/site-packages/matplotlib/mpl-data/stylelib/_classic_test.mplstyle, line 421 ('savefig.frameon : True')
You probably need to get an updated matplotlibrc file from
https://github.com/matplotlib/matplotlib/blob/v3.3.3/matplotlibrc.template
or from the matplotlib source distribution

Bad key verbose.level in file /home/tlc/anaconda3/envs/pgcn/lib/python3.6/site-packages/matplotlib/mpl-data/stylelib/_classic_test.mplstyle, line 472 ('verbose.level  : silent      # one of silent, helpful, debug, debug-annoying')
You probably need to get an updated matplotlibrc file from
https://github.com/matplotlib/matplotlib/blob/v3.3.3/matplotlibrc.template
or from the matplotlib source distribution

Bad key verbose.fileo in file /home/tlc/anaconda3/envs/pgcn/lib/python3.6/site-packages/matplotlib/mpl-data/stylelib/_classic_test.mplstyle, line 473 ('verbose.fileo  : sys.stdout  # a log filename, sys.stdout or sys.stderr')
You probably need to get an updated matplotlibrc file from
https://github.com/matplotlib/matplotlib/blob/v3.3.3/matplotlibrc.template
or from the matplotlib source distribution
In /home/tlc/anaconda3/envs/pgcn/lib/python3.6/site-packages/matplotlib/mpl-data/stylelib/_classic_test.mplstyle: 
The text.latex.preview rcparam was deprecated in Matplotlib 3.3 and will be removed two minor releases later.
In /home/tlc/anaconda3/envs/pgcn/lib/python3.6/site-packages/matplotlib/mpl-data/stylelib/_classic_test.mplstyle: 
The mathtext.fallback_to_cm rcparam was deprecated in Matplotlib 3.3 and will be removed two minor releases later.
In /home/tlc/anaconda3/envs/pgcn/lib/python3.6/site-packages/matplotlib/mpl-data/stylelib/_classic_test.mplstyle: Support for setting the 'mathtext.fallback_to_cm' rcParam is deprecated since 3.3 and will be removed two minor releases later; use 'mathtext.fallback : 'cm' instead.
In /home/tlc/anaconda3/envs/pgcn/lib/python3.6/site-packages/matplotlib/mpl-data/stylelib/_classic_test.mplstyle: 
The validate_bool_maybe_none function was deprecated in Matplotlib 3.3 and will be removed two minor releases later.
In /home/tlc/anaconda3/envs/pgcn/lib/python3.6/site-packages/matplotlib/mpl-data/stylelib/_classic_test.mplstyle: 
The savefig.jpeg_quality rcparam was deprecated in Matplotlib 3.3 and will be removed two minor releases later.
In /home/tlc/anaconda3/envs/pgcn/lib/python3.6/site-packages/matplotlib/mpl-data/stylelib/_classic_test.mplstyle: 
The keymap.all_axes rcparam was deprecated in Matplotlib 3.3 and will be removed two minor releases later.
In /home/tlc/anaconda3/envs/pgcn/lib/python3.6/site-packages/matplotlib/mpl-data/stylelib/_classic_test.mplstyle: 
The animation.avconv_path rcparam was deprecated in Matplotlib 3.3 and will be removed two minor releases later.
In /home/tlc/anaconda3/envs/pgcn/lib/python3.6/site-packages/matplotlib/mpl-data/stylelib/_classic_test.mplstyle: 
The animation.avconv_args rcparam was deprecated in Matplotlib 3.3 and will be removed two minor releases later.
Traceback (most recent call last):
  File "main_prioritization.py", line 17, in <module>
    from skchem.metrics import bedroc_score
  File "/home/tlc/anaconda3/envs/pgcn/lib/python3.6/site-packages/skchem/__init__.py", line 19, in <module>
    from . import pandas_ext
  File "/home/tlc/anaconda3/envs/pgcn/lib/python3.6/site-packages/skchem/pandas_ext/__init__.py", line 10, in <module>
    from .structure_methods import StructureMethods
  File "/home/tlc/anaconda3/envs/pgcn/lib/python3.6/site-packages/skchem/pandas_ext/structure_methods.py", line 16, in <module>
    from pandas.core.base import NoNewAttributesMixin, AccessorProperty
ImportError: cannot import name 'AccessorProperty'

I will be really appreaciate if you can provide me some solution. Hope you well in this difficult time.

The access authority of the data

Hi, Mr. Li. Thanks so much for your work. I use the google drive url in your readme but it seems that the data is inaccessible. So could you please open it?

sine

Training code unavailable

Hi, I found your method interesting. Could you please share your training code?

How to apply this model on new disease data?

Hi,
I would like to try to use your model to prioritize genes associated with diseases that are not included in your training dataset. I have phenotype data and I can generate disease features, but since these diseases were not in your training adjacency matrix, how do I exactly use the model?

Is it even possible to apply your model on diseases that are not included in your training?

Thanks,
Hurley

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disease_gene_prioritization_gcn's Introduction

PGCN: Disease gene prioritization by disease and gene embedding through GCN

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