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cfce / chilin

ChIP-seq DC and QC Pipeline
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got an error when installing #14

Closed mhjiang97 closed 3 years ago

mhjiang97 commented 3 years ago

Hi, maybe I need some guidance. Thank you very much!~ what I ran: python setup.py install the error:

running install
running build
running build_py
running build_ext
skipping 'lib/count.c' Cython extension (up-to-date)
running build_scripts
running install_lib
running install_scripts
changing mode of /home/mjiang/miniconda3/envs/chilin/bin/MDSeqPos.py to 755
changing mode of /home/mjiang/miniconda3/envs/chilin/bin/MotifScan.py to 755
running install_egg_info
Removing /home/mjiang/miniconda3/envs/chilin/lib/python2.7/site-packages/mdseqpos-1.01-py2.7.egg-info
Writing /home/mjiang/miniconda3/envs/chilin/lib/python2.7/site-packages/mdseqpos-1.01-py2.7.egg-info
/home/mjiang/miniconda3/envs/chilin/bin/R

R version 3.4.1 (2017-06-30) -- "Single Candle"
Copyright (C) 2017 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R是自由软件，不带任何担保。
在某些条件下你可以将其自由散布。
用'license()'或'licence()'来看散布的详细条件。

R是个合作计划，有许多人为之做出了贡献.
用'contributors()'来看合作者的详细情况
用'citation()'会告诉你如何在出版物中正确地引用R或R程序包。

用'demo()'来看一些示范程序，用'help()'来阅读在线帮助文件，或
用'help.start()'通过HTML浏览器来看帮助文件。
用'q()'退出R.

> source('http://bioconductor.org/biocLite.R');biocLite('seqLogo');library(seqLogo)
Installing package into ‘/u6/home/mjiang/doc/Rlibrary3’
(as ‘lib’ is unspecified)
试开URL’https://bioconductor.org/packages/3.6/bioc/src/contrib/BiocInstaller_1.28.0.tar.gz'
Content type 'application/x-gzip' length 18624 bytes (18 KB)
==================================================
downloaded 18 KB

* installing *source* package ‘BiocInstaller’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
Bioconductor version 3.6 (BiocInstaller 1.28.0), ?biocLite for help
A new version of Bioconductor is available after installing the most recent
  version of R; see http://bioconductor.org/install
* DONE (BiocInstaller)

The downloaded source packages are in
    ‘/u6/home/mjiang/tmp/RtmpQ8fOjH/downloaded_packages’
Bioconductor version 3.6 (BiocInstaller 1.28.0), ?biocLite for help
A new version of Bioconductor is available after installing the most recent
  version of R; see http://bioconductor.org/install
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.6 (BiocInstaller 1.28.0), R 3.4.1 (2017-06-30).
Installing package(s) ‘seqLogo’
试开URL’https://bioconductor.org/packages/3.6/bioc/src/contrib/seqLogo_1.44.0.tar.gz'
Content type 'application/x-gzip' length 272637 bytes (266 KB)
==================================================
downloaded 266 KB

* installing *source* package ‘seqLogo’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (seqLogo)

The downloaded source packages are in
    ‘/u6/home/mjiang/tmp/RtmpQ8fOjH/downloaded_packages’
载入需要的程辑包：grid
>
>
running install
running bdist_egg
running egg_info
writing requirements to chilin2.egg-info/requires.txt
writing chilin2.egg-info/PKG-INFO
writing top-level names to chilin2.egg-info/top_level.txt
writing dependency_links to chilin2.egg-info/dependency_links.txt
writing entry points to chilin2.egg-info/entry_points.txt
reading manifest file 'chilin2.egg-info/SOURCES.txt'
writing manifest file 'chilin2.egg-info/SOURCES.txt'
installing library code to build/bdist.linux-x86_64/egg
running install_lib
running build_py
copying chilin2/modules/config/chilin.conf -> build/lib/chilin2/modules/config
creating build/bdist.linux-x86_64/egg
creating build/bdist.linux-x86_64/egg/chilin2
copying build/lib/chilin2/__init__.py -> build/bdist.linux-x86_64/egg/chilin2
creating build/bdist.linux-x86_64/egg/chilin2/modules
copying build/lib/chilin2/modules/__init__.py -> build/bdist.linux-x86_64/egg/chilin2/modules
creating build/bdist.linux-x86_64/egg/chilin2/modules/bwa
copying build/lib/chilin2/modules/bwa/__init__.py -> build/bdist.linux-x86_64/egg/chilin2/modules/bwa
copying build/lib/chilin2/modules/bwa/dc.py -> build/bdist.linux-x86_64/egg/chilin2/modules/bwa
copying build/lib/chilin2/modules/bwa/qc.py -> build/bdist.linux-x86_64/egg/chilin2/modules/bwa
copying build/lib/chilin2/modules/bwa/tex.py -> build/bdist.linux-x86_64/egg/chilin2/modules/bwa
copying build/lib/chilin2/modules/bwa/bwa.tex -> build/bdist.linux-x86_64/egg/chilin2/modules/bwa
creating build/bdist.linux-x86_64/egg/chilin2/modules/bowtie
copying build/lib/chilin2/modules/bowtie/__init__.py -> build/bdist.linux-x86_64/egg/chilin2/modules/bowtie
copying build/lib/chilin2/modules/bowtie/dc.py -> build/bdist.linux-x86_64/egg/chilin2/modules/bowtie
creating build/bdist.linux-x86_64/egg/chilin2/modules/ceas
copying build/lib/chilin2/modules/ceas/__init__.py -> build/bdist.linux-x86_64/egg/chilin2/modules/ceas
copying build/lib/chilin2/modules/ceas/bedAnnotate.py -> build/bdist.linux-x86_64/egg/chilin2/modules/ceas
copying build/lib/chilin2/modules/ceas/dc.py -> build/bdist.linux-x86_64/egg/chilin2/modules/ceas
copying build/lib/chilin2/modules/ceas/qc.py -> build/bdist.linux-x86_64/egg/chilin2/modules/ceas
creating build/bdist.linux-x86_64/egg/chilin2/modules/config
copying build/lib/chilin2/modules/config/__init__.py -> build/bdist.linux-x86_64/egg/chilin2/modules/config
copying build/lib/chilin2/modules/config/config.py -> build/bdist.linux-x86_64/egg/chilin2/modules/config
copying build/lib/chilin2/modules/config/helpers.py -> build/bdist.linux-x86_64/egg/chilin2/modules/config
copying build/lib/chilin2/modules/config/chilin.conf -> build/bdist.linux-x86_64/egg/chilin2/modules/config
creating build/bdist.linux-x86_64/egg/chilin2/modules/conservation
copying build/lib/chilin2/modules/conservation/__init__.py -> build/bdist.linux-x86_64/egg/chilin2/modules/conservation
copying build/lib/chilin2/modules/conservation/conservation_onebw_plot.py -> build/bdist.linux-x86_64/egg/chilin2/modules/conservation
copying build/lib/chilin2/modules/conservation/conservation_plot.py -> build/bdist.linux-x86_64/egg/chilin2/modules/conservation
copying build/lib/chilin2/modules/conservation/dc.py -> build/bdist.linux-x86_64/egg/chilin2/modules/conservation
copying build/lib/chilin2/modules/conservation/qc.py -> build/bdist.linux-x86_64/egg/chilin2/modules/conservation
copying build/lib/chilin2/modules/conservation/tex.py -> build/bdist.linux-x86_64/egg/chilin2/modules/conservation
copying build/lib/chilin2/modules/conservation/conservation.tex -> build/bdist.linux-x86_64/egg/chilin2/modules/conservation
creating build/bdist.linux-x86_64/egg/chilin2/modules/enrichment
copying build/lib/chilin2/modules/enrichment/__init__.py -> build/bdist.linux-x86_64/egg/chilin2/modules/enrichment
copying build/lib/chilin2/modules/enrichment/dc.py -> build/bdist.linux-x86_64/egg/chilin2/modules/enrichment
creating build/bdist.linux-x86_64/egg/chilin2/modules/macs2_fragment
copying build/lib/chilin2/modules/macs2_fragment/__init__.py -> build/bdist.linux-x86_64/egg/chilin2/modules/macs2_fragment
copying build/lib/chilin2/modules/macs2_fragment/dc.py -> build/bdist.linux-x86_64/egg/chilin2/modules/macs2_fragment
copying build/lib/chilin2/modules/macs2_fragment/qc.py -> build/bdist.linux-x86_64/egg/chilin2/modules/macs2_fragment
creating build/bdist.linux-x86_64/egg/chilin2/modules/contamination
copying build/lib/chilin2/modules/contamination/__init__.py -> build/bdist.linux-x86_64/egg/chilin2/modules/contamination
copying build/lib/chilin2/modules/contamination/dc.py -> build/bdist.linux-x86_64/egg/chilin2/modules/contamination
copying build/lib/chilin2/modules/contamination/qc.py -> build/bdist.linux-x86_64/egg/chilin2/modules/contamination
copying build/lib/chilin2/modules/contamination/tex.py -> build/bdist.linux-x86_64/egg/chilin2/modules/contamination
copying build/lib/chilin2/modules/contamination/contamination.tex -> build/bdist.linux-x86_64/egg/chilin2/modules/contamination
creating build/bdist.linux-x86_64/egg/chilin2/modules/dbaccessor
copying build/lib/chilin2/modules/dbaccessor/__init__.py -> build/bdist.linux-x86_64/egg/chilin2/modules/dbaccessor
copying build/lib/chilin2/modules/dbaccessor/caller.py -> build/bdist.linux-x86_64/egg/chilin2/modules/dbaccessor
copying build/lib/chilin2/modules/dbaccessor/ChiLinQC.db -> build/bdist.linux-x86_64/egg/chilin2/modules/dbaccessor
copying build/lib/chilin2/modules/dbaccessor/Histone_centers.txt -> build/bdist.linux-x86_64/egg/chilin2/modules/dbaccessor
copying build/lib/chilin2/modules/dbaccessor/TF_centers.txt -> build/bdist.linux-x86_64/egg/chilin2/modules/dbaccessor
creating build/bdist.linux-x86_64/egg/chilin2/modules/fastqc
copying build/lib/chilin2/modules/fastqc/__init__.py -> build/bdist.linux-x86_64/egg/chilin2/modules/fastqc
copying build/lib/chilin2/modules/fastqc/dc.py -> build/bdist.linux-x86_64/egg/chilin2/modules/fastqc
copying build/lib/chilin2/modules/fastqc/qc.py -> build/bdist.linux-x86_64/egg/chilin2/modules/fastqc
copying build/lib/chilin2/modules/fastqc/tex.py -> build/bdist.linux-x86_64/egg/chilin2/modules/fastqc
copying build/lib/chilin2/modules/fastqc/fastqc.tex -> build/bdist.linux-x86_64/egg/chilin2/modules/fastqc
copying build/lib/chilin2/modules/fastqc/fastqc_gc.tex -> build/bdist.linux-x86_64/egg/chilin2/modules/fastqc
creating build/bdist.linux-x86_64/egg/chilin2/modules/frip
copying build/lib/chilin2/modules/frip/__init__.py -> build/bdist.linux-x86_64/egg/chilin2/modules/frip
copying build/lib/chilin2/modules/frip/dc.py -> build/bdist.linux-x86_64/egg/chilin2/modules/frip
copying build/lib/chilin2/modules/frip/qc.py -> build/bdist.linux-x86_64/egg/chilin2/modules/frip
copying build/lib/chilin2/modules/frip/tex.py -> build/bdist.linux-x86_64/egg/chilin2/modules/frip
copying build/lib/chilin2/modules/frip/frip.tex -> build/bdist.linux-x86_64/egg/chilin2/modules/frip
creating build/bdist.linux-x86_64/egg/chilin2/modules/interface
copying build/lib/chilin2/modules/interface/__init__.py -> build/bdist.linux-x86_64/egg/chilin2/modules/interface
copying build/lib/chilin2/modules/interface/dc.py -> build/bdist.linux-x86_64/egg/chilin2/modules/interface
copying build/lib/chilin2/modules/interface/filter_pe_sam_faster.py -> build/bdist.linux-x86_64/egg/chilin2/modules/interface
copying build/lib/chilin2/modules/interface/sampling_pe_sam.py -> build/bdist.linux-x86_64/egg/chilin2/modules/interface
copying build/lib/chilin2/modules/interface/tojson.py -> build/bdist.linux-x86_64/egg/chilin2/modules/interface
creating build/bdist.linux-x86_64/egg/chilin2/modules/library
copying build/lib/chilin2/modules/library/__init__.py -> build/bdist.linux-x86_64/egg/chilin2/modules/library
copying build/lib/chilin2/modules/library/dc.py -> build/bdist.linux-x86_64/egg/chilin2/modules/library
copying build/lib/chilin2/modules/library/qc.py -> build/bdist.linux-x86_64/egg/chilin2/modules/library
creating build/bdist.linux-x86_64/egg/chilin2/modules/macs
copying build/lib/chilin2/modules/macs/__init__.py -> build/bdist.linux-x86_64/egg/chilin2/modules/macs
copying build/lib/chilin2/modules/macs/dc.py -> build/bdist.linux-x86_64/egg/chilin2/modules/macs
copying build/lib/chilin2/modules/macs/qc.py -> build/bdist.linux-x86_64/egg/chilin2/modules/macs
copying build/lib/chilin2/modules/macs/tex.py -> build/bdist.linux-x86_64/egg/chilin2/modules/macs
creating build/bdist.linux-x86_64/egg/chilin2/modules/mdseqpos
copying build/lib/chilin2/modules/mdseqpos/__init__.py -> build/bdist.linux-x86_64/egg/chilin2/modules/mdseqpos
copying build/lib/chilin2/modules/mdseqpos/dc.py -> build/bdist.linux-x86_64/egg/chilin2/modules/mdseqpos
copying build/lib/chilin2/modules/mdseqpos/qc.py -> build/bdist.linux-x86_64/egg/chilin2/modules/mdseqpos
copying build/lib/chilin2/modules/mdseqpos/tex.py -> build/bdist.linux-x86_64/egg/chilin2/modules/mdseqpos
copying build/lib/chilin2/modules/mdseqpos/motif.tex -> build/bdist.linux-x86_64/egg/chilin2/modules/mdseqpos
creating build/bdist.linux-x86_64/egg/chilin2/modules/regulatory
copying build/lib/chilin2/modules/regulatory/RegPotential.py -> build/bdist.linux-x86_64/egg/chilin2/modules/regulatory
copying build/lib/chilin2/modules/regulatory/__init__.py -> build/bdist.linux-x86_64/egg/chilin2/modules/regulatory
copying build/lib/chilin2/modules/regulatory/dc.py -> build/bdist.linux-x86_64/egg/chilin2/modules/regulatory
creating build/bdist.linux-x86_64/egg/chilin2/modules/star
copying build/lib/chilin2/modules/star/__init__.py -> build/bdist.linux-x86_64/egg/chilin2/modules/star
creating build/bdist.linux-x86_64/egg/chilin2/modules/replicates
copying build/lib/chilin2/modules/replicates/__init__.py -> build/bdist.linux-x86_64/egg/chilin2/modules/replicates
copying build/lib/chilin2/modules/replicates/dc.py -> build/bdist.linux-x86_64/egg/chilin2/modules/replicates
copying build/lib/chilin2/modules/replicates/qc.py -> build/bdist.linux-x86_64/egg/chilin2/modules/replicates
creating build/bdist.linux-x86_64/egg/chilin2/modules/summary
copying build/lib/chilin2/modules/summary/__init__.py -> build/bdist.linux-x86_64/egg/chilin2/modules/summary
copying build/lib/chilin2/modules/summary/qc_json_summary.py -> build/bdist.linux-x86_64/egg/chilin2/modules/summary
copying build/lib/chilin2/modules/summary/qc_summary_table.py -> build/bdist.linux-x86_64/egg/chilin2/modules/summary
copying build/lib/chilin2/modules/summary/begin.tex -> build/bdist.linux-x86_64/egg/chilin2/modules/summary
copying build/lib/chilin2/modules/summary/end.tex -> build/bdist.linux-x86_64/egg/chilin2/modules/summary
copying build/lib/chilin2/modules/summary/instructions.tex -> build/bdist.linux-x86_64/egg/chilin2/modules/summary
copying build/lib/chilin2/modules/summary/qc_report.tex -> build/bdist.linux-x86_64/egg/chilin2/modules/summary
copying build/lib/chilin2/modules/summary/summary_table.tex -> build/bdist.linux-x86_64/egg/chilin2/modules/summary
copying build/lib/chilin2/modules/summary/R_culmulative_plot.R -> build/bdist.linux-x86_64/egg/chilin2/modules/summary
copying build/lib/chilin2/modules/summary/bmcart.cls -> build/bdist.linux-x86_64/egg/chilin2/modules/summary
copying build/lib/chilin2/modules/summary/CFCE_Logo_Final.jpg -> build/bdist.linux-x86_64/egg/chilin2/modules/summary
creating build/bdist.linux-x86_64/egg/chilin2/modules/washU
copying build/lib/chilin2/modules/washU/__init__.py -> build/bdist.linux-x86_64/egg/chilin2/modules/washU
copying build/lib/chilin2/modules/washU/dc.py -> build/bdist.linux-x86_64/egg/chilin2/modules/washU
creating build/bdist.linux-x86_64/egg/chilin2/modules/phantompeak
copying build/lib/chilin2/modules/phantompeak/phan.tex -> build/bdist.linux-x86_64/egg/chilin2/modules/phantompeak
creating build/bdist.linux-x86_64/egg/samflow
copying build/lib/samflow/__init__.py -> build/bdist.linux-x86_64/egg/samflow
copying build/lib/samflow/command.py -> build/bdist.linux-x86_64/egg/samflow
copying build/lib/samflow/helper.py -> build/bdist.linux-x86_64/egg/samflow
copying build/lib/samflow/workflow.py -> build/bdist.linux-x86_64/egg/samflow
byte-compiling build/bdist.linux-x86_64/egg/chilin2/__init__.py to __init__.pyc
byte-compiling build/bdist.linux-x86_64/egg/chilin2/modules/__init__.py to __init__.pyc
byte-compiling build/bdist.linux-x86_64/egg/chilin2/modules/bwa/__init__.py to __init__.pyc
byte-compiling build/bdist.linux-x86_64/egg/chilin2/modules/bwa/dc.py to dc.pyc
byte-compiling build/bdist.linux-x86_64/egg/chilin2/modules/bwa/qc.py to qc.pyc
byte-compiling build/bdist.linux-x86_64/egg/chilin2/modules/bwa/tex.py to tex.pyc
byte-compiling build/bdist.linux-x86_64/egg/chilin2/modules/bowtie/__init__.py to __init__.pyc
byte-compiling build/bdist.linux-x86_64/egg/chilin2/modules/bowtie/dc.py to dc.pyc
byte-compiling build/bdist.linux-x86_64/egg/chilin2/modules/ceas/__init__.py to __init__.pyc
byte-compiling build/bdist.linux-x86_64/egg/chilin2/modules/ceas/bedAnnotate.py to bedAnnotate.pyc
byte-compiling build/bdist.linux-x86_64/egg/chilin2/modules/ceas/dc.py to dc.pyc
byte-compiling build/bdist.linux-x86_64/egg/chilin2/modules/ceas/qc.py to qc.pyc
byte-compiling build/bdist.linux-x86_64/egg/chilin2/modules/config/__init__.py to __init__.pyc
byte-compiling build/bdist.linux-x86_64/egg/chilin2/modules/config/config.py to config.pyc
byte-compiling build/bdist.linux-x86_64/egg/chilin2/modules/config/helpers.py to helpers.pyc
byte-compiling build/bdist.linux-x86_64/egg/chilin2/modules/conservation/__init__.py to __init__.pyc
byte-compiling build/bdist.linux-x86_64/egg/chilin2/modules/conservation/conservation_onebw_plot.py to conservation_onebw_plot.pyc
byte-compiling build/bdist.linux-x86_64/egg/chilin2/modules/conservation/conservation_plot.py to conservation_plot.pyc
byte-compiling build/bdist.linux-x86_64/egg/chilin2/modules/conservation/dc.py to dc.pyc
byte-compiling build/bdist.linux-x86_64/egg/chilin2/modules/conservation/qc.py to qc.pyc
byte-compiling build/bdist.linux-x86_64/egg/chilin2/modules/conservation/tex.py to tex.pyc
byte-compiling build/bdist.linux-x86_64/egg/chilin2/modules/enrichment/__init__.py to __init__.pyc
byte-compiling build/bdist.linux-x86_64/egg/chilin2/modules/enrichment/dc.py to dc.pyc
byte-compiling build/bdist.linux-x86_64/egg/chilin2/modules/macs2_fragment/__init__.py to __init__.pyc
byte-compiling build/bdist.linux-x86_64/egg/chilin2/modules/macs2_fragment/dc.py to dc.pyc
byte-compiling build/bdist.linux-x86_64/egg/chilin2/modules/macs2_fragment/qc.py to qc.pyc
byte-compiling build/bdist.linux-x86_64/egg/chilin2/modules/contamination/__init__.py to __init__.pyc
byte-compiling build/bdist.linux-x86_64/egg/chilin2/modules/contamination/dc.py to dc.pyc
byte-compiling build/bdist.linux-x86_64/egg/chilin2/modules/contamination/qc.py to qc.pyc
byte-compiling build/bdist.linux-x86_64/egg/chilin2/modules/contamination/tex.py to tex.pyc
byte-compiling build/bdist.linux-x86_64/egg/chilin2/modules/dbaccessor/__init__.py to __init__.pyc
byte-compiling build/bdist.linux-x86_64/egg/chilin2/modules/dbaccessor/caller.py to caller.pyc
byte-compiling build/bdist.linux-x86_64/egg/chilin2/modules/fastqc/__init__.py to __init__.pyc
byte-compiling build/bdist.linux-x86_64/egg/chilin2/modules/fastqc/dc.py to dc.pyc
byte-compiling build/bdist.linux-x86_64/egg/chilin2/modules/fastqc/qc.py to qc.pyc
byte-compiling build/bdist.linux-x86_64/egg/chilin2/modules/fastqc/tex.py to tex.pyc
byte-compiling build/bdist.linux-x86_64/egg/chilin2/modules/frip/__init__.py to __init__.pyc
byte-compiling build/bdist.linux-x86_64/egg/chilin2/modules/frip/dc.py to dc.pyc
byte-compiling build/bdist.linux-x86_64/egg/chilin2/modules/frip/qc.py to qc.pyc
byte-compiling build/bdist.linux-x86_64/egg/chilin2/modules/frip/tex.py to tex.pyc
byte-compiling build/bdist.linux-x86_64/egg/chilin2/modules/interface/__init__.py to __init__.pyc
byte-compiling build/bdist.linux-x86_64/egg/chilin2/modules/interface/dc.py to dc.pyc
byte-compiling build/bdist.linux-x86_64/egg/chilin2/modules/interface/filter_pe_sam_faster.py to filter_pe_sam_faster.pyc
byte-compiling build/bdist.linux-x86_64/egg/chilin2/modules/interface/sampling_pe_sam.py to sampling_pe_sam.pyc
byte-compiling build/bdist.linux-x86_64/egg/chilin2/modules/interface/tojson.py to tojson.pyc
byte-compiling build/bdist.linux-x86_64/egg/chilin2/modules/library/__init__.py to __init__.pyc
byte-compiling build/bdist.linux-x86_64/egg/chilin2/modules/library/dc.py to dc.pyc
byte-compiling build/bdist.linux-x86_64/egg/chilin2/modules/library/qc.py to qc.pyc
byte-compiling build/bdist.linux-x86_64/egg/chilin2/modules/macs/__init__.py to __init__.pyc
byte-compiling build/bdist.linux-x86_64/egg/chilin2/modules/macs/dc.py to dc.pyc
byte-compiling build/bdist.linux-x86_64/egg/chilin2/modules/macs/qc.py to qc.pyc
byte-compiling build/bdist.linux-x86_64/egg/chilin2/modules/macs/tex.py to tex.pyc
byte-compiling build/bdist.linux-x86_64/egg/chilin2/modules/mdseqpos/__init__.py to __init__.pyc
byte-compiling build/bdist.linux-x86_64/egg/chilin2/modules/mdseqpos/dc.py to dc.pyc
byte-compiling build/bdist.linux-x86_64/egg/chilin2/modules/mdseqpos/qc.py to qc.pyc
byte-compiling build/bdist.linux-x86_64/egg/chilin2/modules/mdseqpos/tex.py to tex.pyc
byte-compiling build/bdist.linux-x86_64/egg/chilin2/modules/regulatory/RegPotential.py to RegPotential.pyc
byte-compiling build/bdist.linux-x86_64/egg/chilin2/modules/regulatory/__init__.py to __init__.pyc
byte-compiling build/bdist.linux-x86_64/egg/chilin2/modules/regulatory/dc.py to dc.pyc
byte-compiling build/bdist.linux-x86_64/egg/chilin2/modules/star/__init__.py to __init__.pyc
byte-compiling build/bdist.linux-x86_64/egg/chilin2/modules/replicates/__init__.py to __init__.pyc
byte-compiling build/bdist.linux-x86_64/egg/chilin2/modules/replicates/dc.py to dc.pyc
byte-compiling build/bdist.linux-x86_64/egg/chilin2/modules/replicates/qc.py to qc.pyc
byte-compiling build/bdist.linux-x86_64/egg/chilin2/modules/summary/__init__.py to __init__.pyc
byte-compiling build/bdist.linux-x86_64/egg/chilin2/modules/summary/qc_json_summary.py to qc_json_summary.pyc
byte-compiling build/bdist.linux-x86_64/egg/chilin2/modules/summary/qc_summary_table.py to qc_summary_table.pyc
byte-compiling build/bdist.linux-x86_64/egg/chilin2/modules/washU/__init__.py to __init__.pyc
byte-compiling build/bdist.linux-x86_64/egg/chilin2/modules/washU/dc.py to dc.pyc
byte-compiling build/bdist.linux-x86_64/egg/samflow/__init__.py to __init__.pyc
byte-compiling build/bdist.linux-x86_64/egg/samflow/command.py to command.pyc
byte-compiling build/bdist.linux-x86_64/egg/samflow/helper.py to helper.pyc
byte-compiling build/bdist.linux-x86_64/egg/samflow/workflow.py to workflow.pyc
creating build/bdist.linux-x86_64/egg/EGG-INFO
installing scripts to build/bdist.linux-x86_64/egg/EGG-INFO/scripts
running install_scripts
running build_scripts
creating build/bdist.linux-x86_64/egg/EGG-INFO/scripts
copying build/scripts-2.7/meta_info.sh -> build/bdist.linux-x86_64/egg/EGG-INFO/scripts
changing mode of build/bdist.linux-x86_64/egg/EGG-INFO/scripts/meta_info.sh to 755
copying chilin2.egg-info/PKG-INFO -> build/bdist.linux-x86_64/egg/EGG-INFO
copying chilin2.egg-info/SOURCES.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
copying chilin2.egg-info/dependency_links.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
copying chilin2.egg-info/entry_points.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
copying chilin2.egg-info/not-zip-safe -> build/bdist.linux-x86_64/egg/EGG-INFO
copying chilin2.egg-info/requires.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
copying chilin2.egg-info/top_level.txt -> build/bdist.linux-x86_64/egg/EGG-INFO
creating 'dist/chilin2-2.0.0-py2.7.egg' and adding 'build/bdist.linux-x86_64/egg' to it
removing 'build/bdist.linux-x86_64/egg' (and everything under it)
Processing chilin2-2.0.0-py2.7.egg
removing '/u6/home/mjiang/miniconda3/envs/chilin/lib/python2.7/site-packages/chilin2-2.0.0-py2.7.egg' (and everything under it)
creating /u6/home/mjiang/miniconda3/envs/chilin/lib/python2.7/site-packages/chilin2-2.0.0-py2.7.egg
Extracting chilin2-2.0.0-py2.7.egg to /u6/home/mjiang/miniconda3/envs/chilin/lib/python2.7/site-packages
chilin2 2.0.0 is already the active version in easy-install.pth
Installing meta_info.sh script to /home/mjiang/miniconda3/envs/chilin/bin
Installing conservation_onebw_plot.py script to /home/mjiang/miniconda3/envs/chilin/bin
Installing RegPotential.py script to /home/mjiang/miniconda3/envs/chilin/bin
Installing filter_pe_sam_faster.py script to /home/mjiang/miniconda3/envs/chilin/bin
Installing conservation_plot.py script to /home/mjiang/miniconda3/envs/chilin/bin
Installing sampling_pe_sam.py script to /home/mjiang/miniconda3/envs/chilin/bin
Installing chilin script to /home/mjiang/miniconda3/envs/chilin/bin
Installing bedAnnotate.py script to /home/mjiang/miniconda3/envs/chilin/bin

Installed /u6/home/mjiang/miniconda3/envs/chilin/lib/python2.7/site-packages/chilin2-2.0.0-py2.7.egg
Processing dependencies for chilin2==2.0.0
Searching for bx-python
Reading https://pypi.org/simple/bx-python/
Downloading https://files.pythonhosted.org/packages/09/06/34d30efc7ee4f94945335a1aa4c5fc461e406f3c9f9f73f6102d26bf1932/bx-python-0.8.11.tar.gz#sha256=7f26c2a5516b999f4330887f2b126608b4d96ed0f1de6e62ee59f3d066586974
Best match: bx-python 0.8.11
Processing bx-python-0.8.11.tar.gz
Writing /home/mjiang/tmp/easy_install-VYPX63/bx-python-0.8.11/setup.cfg
Running bx-python-0.8.11/setup.py -q bdist_egg --dist-dir /home/mjiang/tmp/easy_install-VYPX63/bx-python-0.8.11/egg-dist-tmp-pCwTTv
Traceback (most recent call last):
  File "setup.py", line 269, in <module>
    main()
  File "setup.py", line 266, in main
    install()
  File "setup.py", line 219, in install
    install_requires=['MarkupSafe==1.1.1', 'jinja2 ==2.9','argparse','bx-python'])
  File "/home/mjiang/miniconda3/envs/chilin/lib/python2.7/site-packages/setuptools/__init__.py", line 145, in setup
    return distutils.core.setup(**attrs)
  File "/home/mjiang/miniconda3/envs/chilin/lib/python2.7/distutils/core.py", line 151, in setup
    dist.run_commands()
  File "/home/mjiang/miniconda3/envs/chilin/lib/python2.7/distutils/dist.py", line 953, in run_commands
    self.run_command(cmd)
  File "/home/mjiang/miniconda3/envs/chilin/lib/python2.7/distutils/dist.py", line 972, in run_command
    cmd_obj.run()
  File "/home/mjiang/miniconda3/envs/chilin/lib/python2.7/site-packages/setuptools/command/install.py", line 67, in run
    self.do_egg_install()
  File "/home/mjiang/miniconda3/envs/chilin/lib/python2.7/site-packages/setuptools/command/install.py", line 117, in do_egg_install
    cmd.run(show_deprecation=False)
  File "/home/mjiang/miniconda3/envs/chilin/lib/python2.7/site-packages/setuptools/command/easy_install.py", line 424, in run
    self.easy_install(spec, not self.no_deps)
  File "/home/mjiang/miniconda3/envs/chilin/lib/python2.7/site-packages/setuptools/command/easy_install.py", line 666, in easy_install
    return self.install_item(None, spec, tmpdir, deps, True)
  File "/home/mjiang/miniconda3/envs/chilin/lib/python2.7/site-packages/setuptools/command/easy_install.py", line 713, in install_item
    self.process_distribution(spec, dist, deps)
  File "/home/mjiang/miniconda3/envs/chilin/lib/python2.7/site-packages/setuptools/command/easy_install.py", line 758, in process_distribution
    [requirement], self.local_index, self.easy_install
  File "/home/mjiang/miniconda3/envs/chilin/lib/python2.7/site-packages/pkg_resources/__init__.py", line 782, in resolve
    replace_conflicting=replace_conflicting
  File "/home/mjiang/miniconda3/envs/chilin/lib/python2.7/site-packages/pkg_resources/__init__.py", line 1065, in best_match
    return self.obtain(req, installer)
  File "/home/mjiang/miniconda3/envs/chilin/lib/python2.7/site-packages/pkg_resources/__init__.py", line 1077, in obtain
    return installer(requirement)
  File "/home/mjiang/miniconda3/envs/chilin/lib/python2.7/site-packages/setuptools/command/easy_install.py", line 685, in easy_install
    return self.install_item(spec, dist.location, tmpdir, deps)
  File "/home/mjiang/miniconda3/envs/chilin/lib/python2.7/site-packages/setuptools/command/easy_install.py", line 711, in install_item
    dists = self.install_eggs(spec, download, tmpdir)
  File "/home/mjiang/miniconda3/envs/chilin/lib/python2.7/site-packages/setuptools/command/easy_install.py", line 896, in install_eggs
    return self.build_and_install(setup_script, setup_base)
  File "/home/mjiang/miniconda3/envs/chilin/lib/python2.7/site-packages/setuptools/command/easy_install.py", line 1164, in build_and_install
    self.run_setup(setup_script, setup_base, args)
  File "/home/mjiang/miniconda3/envs/chilin/lib/python2.7/site-packages/setuptools/command/easy_install.py", line 1150, in run_setup
    run_setup(setup_script, args)
  File "/home/mjiang/miniconda3/envs/chilin/lib/python2.7/site-packages/setuptools/sandbox.py", line 253, in run_setup
    raise
  File "/home/mjiang/miniconda3/envs/chilin/lib/python2.7/contextlib.py", line 35, in __exit__
    self.gen.throw(type, value, traceback)
  File "/home/mjiang/miniconda3/envs/chilin/lib/python2.7/site-packages/setuptools/sandbox.py", line 195, in setup_context
    yield
  File "/home/mjiang/miniconda3/envs/chilin/lib/python2.7/contextlib.py", line 35, in __exit__
    self.gen.throw(type, value, traceback)
  File "/home/mjiang/miniconda3/envs/chilin/lib/python2.7/site-packages/setuptools/sandbox.py", line 166, in save_modules
    saved_exc.resume()
  File "/home/mjiang/miniconda3/envs/chilin/lib/python2.7/site-packages/setuptools/sandbox.py", line 141, in resume
    six.reraise(type, exc, self._tb)
  File "/home/mjiang/miniconda3/envs/chilin/lib/python2.7/site-packages/setuptools/sandbox.py", line 154, in save_modules
    yield saved
  File "/home/mjiang/miniconda3/envs/chilin/lib/python2.7/site-packages/setuptools/sandbox.py", line 195, in setup_context
    yield
  File "/home/mjiang/miniconda3/envs/chilin/lib/python2.7/site-packages/setuptools/sandbox.py", line 250, in run_setup
    _execfile(setup_script, ns)
  File "/home/mjiang/miniconda3/envs/chilin/lib/python2.7/site-packages/setuptools/sandbox.py", line 44, in _execfile
    code = compile(script, filename, 'exec')
  File "/home/mjiang/tmp/easy_install-VYPX63/bx-python-0.8.11/setup.py", line 38
    raise Exception(f"numpy must be installed to build: {e}")
                                                           ^
SyntaxError: invalid syntax
mhjiang97 commented 3 years ago

conda list:

# packages in environment at /home/mjiang/miniconda3/envs/chilin:
#
# Name                    Version                   Build  Channel
_libgcc_mutex             0.1                 conda_forge    conda-forge
_openmp_mutex             4.5                      1_llvm    conda-forge
_r-mutex                  1.0.1               anacondar_1    conda-forge
alsa-lib                  1.2.3                h516909a_0    conda-forge
bedtools                  2.17.0                        0    bioconda
binutils_impl_linux-64    2.31.1               h6176602_1    anaconda
binutils_linux-64         2.31.1               h6176602_9    anaconda
bioconductor-seqlogo      1.46.0                   r341_0    bioconda
blas                      2.17                   openblas    conda-forge
bwa                       0.7.13                        1    bioconda
bwidget                   1.9.11                        1    anaconda
bzip2                     1.0.8                h7b6447c_0    anaconda
ca-certificates           2020.10.14                    0    anaconda
cairo                     1.14.12              h77bcde2_0    anaconda
certifi                   2019.11.28               py27_0    anaconda
chilin2                   2.0.0                    pypi_0    pypi
curl                      7.69.1               hbc83047_0    anaconda
cython                    0.29.14          py27he6710b0_0    anaconda
fastqc                    0.11.9               hdfd78af_1    bioconda
font-ttf-dejavu-sans-mono 2.37                 h6964260_0    anaconda
fontconfig                2.12.6               h49f89f6_0    anaconda
freetype                  2.8                  h52ed37b_0    anaconda
fribidi                   1.0.10               h7b6447c_0    anaconda
gcc_impl_linux-64         7.3.0                habb00fd_1    anaconda
gcc_linux-64              7.3.0                h553295d_9    anaconda
gettext                   0.19.8.1             h9b4dc7a_1    anaconda
gfortran_impl_linux-64    7.3.0                hdf63c60_1    anaconda
gfortran_linux-64         7.3.0                h553295d_9    anaconda
giflib                    5.2.1                h7b6447c_0    anaconda
glib                      2.53.6               hc861d11_1    anaconda
graphite2                 1.3.14               h23475e2_0    anaconda
gsl                       2.6                  hf94e986_0    conda-forge
gxx_impl_linux-64         7.3.0                hdf63c60_1    anaconda
gxx_linux-64              7.3.0                h553295d_9    anaconda
harfbuzz                  1.7.6                hc5b324e_0    anaconda
icu                       58.2                 he6710b0_3    anaconda
jpeg                      9d                   h36c2ea0_0    conda-forge
krb5                      1.17.1               h2fd8d38_0    conda-forge
libblas                   3.8.0               17_openblas    conda-forge
libcblas                  3.8.0               17_openblas    conda-forge
libcurl                   7.69.1               h20c2e04_0    anaconda
libedit                   3.1.20170329                  0    conda-forge
libffi                    3.2.1             hf484d3e_1007    anaconda
libgcc                    7.2.0                h69d50b8_2    anaconda
libgcc-ng                 9.1.0                hdf63c60_0    anaconda
libgfortran-ng            7.3.0                hdf63c60_0    anaconda
libiconv                  1.15                 h63c8f33_5    anaconda
liblapack                 3.8.0               17_openblas    conda-forge
liblapacke                3.8.0               17_openblas    conda-forge
libopenblas               0.3.10               h5a2b251_0    anaconda
libpng                    1.6.34               hb9fc6fc_0    anaconda
libssh2                   1.9.0                h1ba5d50_1    anaconda
libstdcxx-ng              9.1.0                hdf63c60_0    anaconda
libtiff                   4.0.9                he85c1e1_2    anaconda
libuuid                   2.32.1            h14c3975_1000    conda-forge
libxcb                    1.14                 h7b6447c_0    anaconda
libxml2                   2.9.10               hb55368b_3    anaconda
llvm-openmp               11.1.0               h4bd325d_1    conda-forge
lz4-c                     1.9.2                heb0550a_3    anaconda
macs2                     2.1.0                         0    bioconda
make                      4.2.1                h1bed415_1    anaconda
mdseqpos                  1.01                     pypi_0    pypi
mysql-connector-c         6.1.11               h597af5e_1    anaconda
ncurses                   5.9                          10    conda-forge
numpy                     1.16.6           py27h30dfecb_0    anaconda
numpy-base                1.16.6           py27h2f8d375_0    anaconda
openjdk                   11.0.1            h516909a_1016    conda-forge
openssl                   1.1.1h               h7b6447c_0    anaconda
pango                     1.40.11              hedb6d6b_0    anaconda
pcre                      8.39                          0    conda-forge
pcre2                     10.35                h14c3975_1    anaconda
perl                      5.26.2               h14c3975_0    anaconda
pip                       19.3.1                   py27_0    anaconda
pixman                    0.38.0               h7b6447c_0    anaconda
python                    2.7.15            h721da81_1008    conda-forge
r-base                    3.4.1                         4    conda-forge
readline                  7.0                           0    conda-forge
samtools                  0.1.19                        3    bioconda
sed                       4.8                  h7b6447c_0    anaconda
seqtk                     1.3                  hed695b0_2    bioconda
setuptools                44.0.0                   py27_0    anaconda
sqlite                    3.26.0               h7b6447c_0    anaconda
tk                        8.6.10               hbc83047_0    anaconda
tktable                   2.10                 h14c3975_0    anaconda
ucsc-bedclip              357                           1    bioconda
ucsc-bedgraphtobigwig     357                           1    bioconda
ucsc-wigcorrelate         357                           1    bioconda
ucsc-wigtobigwig          357                           1    bioconda
wheel                     0.35.1                     py_0    anaconda
xorg-fixesproto           5.0               h14c3975_1002    conda-forge
xorg-inputproto           2.3.2             h14c3975_1002    conda-forge
xorg-kbproto              1.0.7             h14c3975_1002    conda-forge
xorg-libice               1.0.10               h516909a_0    conda-forge
xorg-libsm                1.2.3             h84519dc_1000    conda-forge
xorg-libx11               1.6.12               h516909a_0    conda-forge
xorg-libxext              1.3.4                h516909a_0    conda-forge
xorg-libxfixes            5.0.3             h516909a_1004    conda-forge
xorg-libxi                1.7.10               h516909a_0    conda-forge
xorg-libxrender           0.9.10            h516909a_1002    conda-forge
xorg-libxtst              1.2.3             h516909a_1002    conda-forge
xorg-recordproto          1.14.2            h516909a_1002    conda-forge
xorg-renderproto          0.11.1            h14c3975_1002    conda-forge
xorg-xextproto            7.3.0             h14c3975_1002    conda-forge
xorg-xproto               7.0.31            h14c3975_1007    conda-forge
xz                        5.2.5                h7b6447c_0    anaconda
zlib                      1.2.11               h7b6447c_3    anaconda
zstd                      1.4.4                h0b5b093_3    anaconda
qinqian commented 3 years ago

Sorry to reply so late! somehow this issue fell outside of my radar. The possible solution will be:

  1. Could you please use the conda environment python to install the MDSeqPos.py?
  2. Could you please use the docker version to install ChiLin image?
  3. Could you please also give it a try for cidc_chips (https://bitbucket.org/plumbers/cidc_chips/src), which is a descendant of ChiLin pipeline? This version fixed several issues with a more robust Snakemake framework.

Thanks, Best wishes, Qian