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Failure in gitlab CI #9

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adavidzh opened this issue Jun 27, 2020 · 17 comments
Closed

Failure in gitlab CI #9

adavidzh opened this issue Jun 27, 2020 · 17 comments

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@adavidzh
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adavidzh commented Jun 27, 2020 •
edited

I am really excited for this extension, since it would allow a much leaner docker image in my CI runners.

The runner configuration is pretty simple:

image: python:latest

build:
  stage: build
  script:
    - pip install --no-cache-dir -r requirements.txt
    - jupyter nbconvert --to PDFviaHTML --execute example.ipynb

and of course, notebook-as-pdf is part of requirements.txt.

So I took it for a spin, but it was not a happy camper:

$ jupyter nbconvert --to PDFviaHTML --execute example.ipynb
 [NbConvertApp] Converting notebook example.ipynb to PDFviaHTML
 [NbConvertApp] Executing notebook with kernel: python3
 [NbConvertApp] Executing notebook with kernel: python3
 [W:pyppeteer.chromium_downloader] start chromium download.
 Download may take a few minutes.
 100%|██████████| 108773488/108773488 [00:01<00:00, 105172481.75it/s]
 [W:pyppeteer.chromium_downloader] 
 chromium download done.
 [W:pyppeteer.chromium_downloader] chromium extracted to: /root/.local/share/pyppeteer/local-chromium/588429
 Traceback (most recent call last):
<snip>
 Traceback (most recent call last):
   File "/usr/local/lib/python3.8/site-packages/pyppeteer/launcher.py", line 151, in _close_process
     self._loop.run_until_complete(self.killChrome())
   File "/usr/local/lib/python3.8/asyncio/base_events.py", line 591, in run_until_complete
     self._check_closed()
   File "/usr/local/lib/python3.8/asyncio/base_events.py", line 508, in _check_closed
     raise RuntimeError('Event loop is closed')
 RuntimeError: Event loop is closed
 sys:1: RuntimeWarning: coroutine 'Launcher.killChrome' was never awaited
 RuntimeWarning: Enable tracemalloc to get the object allocation traceback

I'm wondering if my requirements.txt needs something else (why is chromium installed on demand?) but instead of blindly trying things out, I thought I should report it first.

Click to toggle the full log. 
Running with gitlab-runner 13.0.1 (21cb397c)
   on default-runner-7f9b6f57bc-t25l7 JXQu29S9
Preparing the "docker" executor
00:06
 Using Docker executor with image python:latest ...
 WARNING: Container based cache volumes creation is disabled. Will not create volume for "/cache"
 Pulling docker image python:latest ...
 Using docker image sha256:7f5b6ccd03e9da5e02a20ea4377ae61f6ae1b935b05c1bd52fdafe4b958b5e50 for python:latest ...
Preparing environment
00:02
 Running on runner-jxqu29s9-project-94480-concurrent-0 via default-runner-7f9b6f57bc-t25l7...
Getting source from Git repository
00:02
 Fetching changes with git depth set to 50...
 Initialized empty Git repository in /builds/adavid/mylittlelark/.git/
 Created fresh repository.
 From https://gitlab.cern.ch/adavid/mylittlelark
  * [new ref]         refs/pipelines/1751602 -> refs/pipelines/1751602
  * [new branch]      master                 -> origin/master
 Checking out 48add964 as master...
 Skipping Git submodules setup
Restoring cache
00:01
Downloading artifacts
00:02
Running before_script and script
01:23
 $ pip install --no-cache-dir -r requirements.txt
 Collecting jupyter
   Downloading jupyter-1.0.0-py2.py3-none-any.whl (2.7 kB)
 Collecting pympler
   Downloading Pympler-0.8.tar.gz (175 kB)
 Collecting lark-parser
   Downloading lark-parser-0.8.9.tar.gz (294 kB)
 Collecting tqdm
   Downloading tqdm-4.46.1-py2.py3-none-any.whl (63 kB)
 Collecting tables
   Downloading tables-3.6.1-cp38-cp38-manylinux1_x86_64.whl (4.3 MB)
 Collecting notebook-as-pdf
   Downloading notebook_as_pdf-0.2.0-py3-none-any.whl (5.2 kB)
 Collecting ipywidgets
   Downloading ipywidgets-7.5.1-py2.py3-none-any.whl (121 kB)
 Collecting nbconvert
   Downloading nbconvert-5.6.1-py2.py3-none-any.whl (455 kB)
 Collecting jupyter-console
   Downloading jupyter_console-6.1.0-py2.py3-none-any.whl (21 kB)
 Collecting ipykernel
   Downloading ipykernel-5.3.0-py3-none-any.whl (119 kB)
 Collecting notebook
   Downloading notebook-6.0.3-py3-none-any.whl (9.7 MB)
 Collecting qtconsole
   Downloading qtconsole-4.7.5-py2.py3-none-any.whl (118 kB)
 Collecting numexpr>=2.6.2
   Downloading numexpr-2.7.1-cp38-cp38-manylinux1_x86_64.whl (164 kB)
 Collecting numpy>=1.9.3
   Downloading numpy-1.19.0-cp38-cp38-manylinux2010_x86_64.whl (14.6 MB)
 Collecting pyppeteer
   Downloading pyppeteer-0.2.2-py3-none-any.whl (145 kB)
 Collecting PyPDF2
   Downloading PyPDF2-1.26.0.tar.gz (77 kB)
 Collecting widgetsnbextension~=3.5.0
   Downloading widgetsnbextension-3.5.1-py2.py3-none-any.whl (2.2 MB)
 Collecting ipython>=4.0.0; python_version >= "3.3"
   Downloading ipython-7.16.1-py3-none-any.whl (785 kB)
 Collecting traitlets>=4.3.1
   Downloading traitlets-4.3.3-py2.py3-none-any.whl (75 kB)
 Collecting nbformat>=4.2.0
   Downloading nbformat-5.0.7-py3-none-any.whl (170 kB)
 Collecting defusedxml
   Downloading defusedxml-0.6.0-py2.py3-none-any.whl (23 kB)
 Collecting pygments
   Downloading Pygments-2.6.1-py3-none-any.whl (914 kB)
 Collecting jupyter-core
   Downloading jupyter_core-4.6.3-py2.py3-none-any.whl (83 kB)
 Collecting entrypoints>=0.2.2
   Downloading entrypoints-0.3-py2.py3-none-any.whl (11 kB)
 Collecting pandocfilters>=1.4.1
   Downloading pandocfilters-1.4.2.tar.gz (14 kB)
 Collecting mistune<2,>=0.8.1
   Downloading mistune-0.8.4-py2.py3-none-any.whl (16 kB)
 Collecting jinja2>=2.4
   Downloading Jinja2-2.11.2-py2.py3-none-any.whl (125 kB)
 Collecting testpath
   Downloading testpath-0.4.4-py2.py3-none-any.whl (163 kB)
 Collecting bleach
   Downloading bleach-3.1.5-py2.py3-none-any.whl (151 kB)
 Collecting jupyter-client
   Downloading jupyter_client-6.1.3-py3-none-any.whl (106 kB)
 Collecting prompt-toolkit!=3.0.0,!=3.0.1,<3.1.0,>=2.0.0
   Downloading prompt_toolkit-3.0.5-py3-none-any.whl (351 kB)
 Collecting tornado>=4.2
   Downloading tornado-6.0.4.tar.gz (496 kB)
 Collecting pyzmq>=17
   Downloading pyzmq-19.0.1-cp38-cp38-manylinux1_x86_64.whl (1.1 MB)
 Collecting prometheus-client
   Downloading prometheus_client-0.8.0-py2.py3-none-any.whl (53 kB)
 Collecting Send2Trash
   Downloading Send2Trash-1.5.0-py3-none-any.whl (12 kB)
 Collecting terminado>=0.8.1
   Downloading terminado-0.8.3-py2.py3-none-any.whl (33 kB)
 Collecting ipython-genutils
   Downloading ipython_genutils-0.2.0-py2.py3-none-any.whl (26 kB)
 Collecting qtpy
   Downloading QtPy-1.9.0-py2.py3-none-any.whl (54 kB)
 Collecting appdirs<2.0.0,>=1.4.3
   Downloading appdirs-1.4.4-py2.py3-none-any.whl (9.6 kB)
 Collecting urllib3<2.0.0,>=1.25.8
   Downloading urllib3-1.25.9-py2.py3-none-any.whl (126 kB)
 Collecting websockets<9.0,>=8.1
   Downloading websockets-8.1-cp38-cp38-manylinux2010_x86_64.whl (78 kB)
 Collecting pyee<8.0.0,>=7.0.1
   Downloading pyee-7.0.2-py2.py3-none-any.whl (12 kB)
 Collecting jedi>=0.10
   Downloading jedi-0.17.1-py2.py3-none-any.whl (1.4 MB)
 Collecting pexpect; sys_platform != "win32"
   Downloading pexpect-4.8.0-py2.py3-none-any.whl (59 kB)
 Requirement already satisfied: setuptools>=18.5 in /usr/local/lib/python3.8/site-packages (from ipython>=4.0.0; python_version >= "3.3"->ipywidgets->jupyter->-r requirements.txt (line 1)) (47.1.1)
 Collecting pickleshare
   Downloading pickleshare-0.7.5-py2.py3-none-any.whl (6.9 kB)
 Collecting backcall
   Downloading backcall-0.2.0-py2.py3-none-any.whl (11 kB)
 Collecting decorator
   Downloading decorator-4.4.2-py2.py3-none-any.whl (9.2 kB)
 Collecting six
   Downloading six-1.15.0-py2.py3-none-any.whl (10 kB)
 Collecting jsonschema!=2.5.0,>=2.4
   Downloading jsonschema-3.2.0-py2.py3-none-any.whl (56 kB)
 Collecting MarkupSafe>=0.23
   Downloading MarkupSafe-1.1.1-cp38-cp38-manylinux1_x86_64.whl (32 kB)
 Collecting packaging
   Downloading packaging-20.4-py2.py3-none-any.whl (37 kB)
 Collecting webencodings
   Downloading webencodings-0.5.1-py2.py3-none-any.whl (11 kB)
 Collecting python-dateutil>=2.1
   Downloading python_dateutil-2.8.1-py2.py3-none-any.whl (227 kB)
 Collecting wcwidth
   Downloading wcwidth-0.2.5-py2.py3-none-any.whl (30 kB)
 Collecting ptyprocess; os_name != "nt"
   Downloading ptyprocess-0.6.0-py2.py3-none-any.whl (39 kB)
 Collecting parso<0.8.0,>=0.7.0
   Downloading parso-0.7.0-py2.py3-none-any.whl (100 kB)
 Collecting pyrsistent>=0.14.0
   Downloading pyrsistent-0.16.0.tar.gz (108 kB)
 Collecting attrs>=17.4.0
   Downloading attrs-19.3.0-py2.py3-none-any.whl (39 kB)
 Collecting pyparsing>=2.0.2
   Downloading pyparsing-2.4.7-py2.py3-none-any.whl (67 kB)
 Building wheels for collected packages: pympler, lark-parser, PyPDF2, pandocfilters, tornado, pyrsistent
   Building wheel for pympler (setup.py): started
   Building wheel for pympler (setup.py): finished with status 'done'
   Created wheel for pympler: filename=Pympler-0.8-py3-none-any.whl size=164713 sha256=3e8ab23edf19d99c51f5b7a9a1bf74ebbb9f947a6d9ebade2ff8c0a7ad75083f
   Stored in directory: /tmp/pip-ephem-wheel-cache-pivp50fy/wheels/2c/09/38/7c8c5dc224099d3a7194d154a99093d429bb4bda18c241c4b5
   Building wheel for lark-parser (setup.py): started
   Building wheel for lark-parser (setup.py): finished with status 'done'
   Created wheel for lark-parser: filename=lark_parser-0.8.9-py2.py3-none-any.whl size=75357 sha256=990a32661454b7b77d1df1858328ea40daa9bac5ce84bebc0be6cb43a5246b33
   Stored in directory: /tmp/pip-ephem-wheel-cache-pivp50fy/wheels/5c/55/8c/91a8363366ada1c946e50d5c030e63129a2d8f3120e1975997
   Building wheel for PyPDF2 (setup.py): started
   Building wheel for PyPDF2 (setup.py): finished with status 'done'
   Created wheel for PyPDF2: filename=PyPDF2-1.26.0-py3-none-any.whl size=61084 sha256=b1f7402d283104baebace712c6dd94abb940019a8acd38feaf5903eb11954f19
   Stored in directory: /tmp/pip-ephem-wheel-cache-pivp50fy/wheels/b1/1a/8f/a4c34be976825a2f7948d0fa40907598d69834f8ab5889de11
   Building wheel for pandocfilters (setup.py): started
   Building wheel for pandocfilters (setup.py): finished with status 'done'
   Created wheel for pandocfilters: filename=pandocfilters-1.4.2-py3-none-any.whl size=7856 sha256=75791b53889332212a9cbf41d5ba54a30932ae76bec3902bc753298f58305841
   Stored in directory: /tmp/pip-ephem-wheel-cache-pivp50fy/wheels/f6/08/65/e4636b703d0e870cd62692dafd6b47db27287fe80cea433722
   Building wheel for tornado (setup.py): started
   Building wheel for tornado (setup.py): finished with status 'done'
   Created wheel for tornado: filename=tornado-6.0.4-cp38-cp38-linux_x86_64.whl size=427821 sha256=978cecc354d37b4422e9f08fe5949afad94728628d849b74d1c6870ac25c0171
   Stored in directory: /tmp/pip-ephem-wheel-cache-pivp50fy/wheels/88/79/e5/598ba17e85eccf2626eab62e4ee8452895636cd542650d450d
   Building wheel for pyrsistent (setup.py): started
   Building wheel for pyrsistent (setup.py): finished with status 'done'
   Created wheel for pyrsistent: filename=pyrsistent-0.16.0-cp38-cp38-linux_x86_64.whl size=126675 sha256=87e75b33c767b74b59c2ae526d335a2be64aab5cf3b983c519171a6aaceff172
   Stored in directory: /tmp/pip-ephem-wheel-cache-pivp50fy/wheels/17/be/0f/727fb20889ada6aaaaba861f5f0eb21663533915429ad43f28
 Successfully built pympler lark-parser PyPDF2 pandocfilters tornado pyrsistent
 Installing collected packages: six, python-dateutil, tornado, ipython-genutils, decorator, traitlets, jupyter-core, pyzmq, jupyter-client, MarkupSafe, jinja2, defusedxml, pygments, entrypoints, pandocfilters, mistune, testpath, pyrsistent, attrs, jsonschema, nbformat, pyparsing, packaging, webencodings, bleach, nbconvert, parso, jedi, ptyprocess, pexpect, pickleshare, backcall, wcwidth, prompt-toolkit, ipython, ipykernel, prometheus-client, Send2Trash, terminado, notebook, widgetsnbextension, ipywidgets, jupyter-console, qtpy, qtconsole, jupyter, pympler, lark-parser, tqdm, numpy, numexpr, tables, appdirs, urllib3, websockets, pyee, pyppeteer, PyPDF2, notebook-as-pdf
 Successfully installed MarkupSafe-1.1.1 PyPDF2-1.26.0 Send2Trash-1.5.0 appdirs-1.4.4 attrs-19.3.0 backcall-0.2.0 bleach-3.1.5 decorator-4.4.2 defusedxml-0.6.0 entrypoints-0.3 ipykernel-5.3.0 ipython-7.16.1 ipython-genutils-0.2.0 ipywidgets-7.5.1 jedi-0.17.1 jinja2-2.11.2 jsonschema-3.2.0 jupyter-1.0.0 jupyter-client-6.1.3 jupyter-console-6.1.0 jupyter-core-4.6.3 lark-parser-0.8.9 mistune-0.8.4 nbconvert-5.6.1 nbformat-5.0.7 notebook-6.0.3 notebook-as-pdf-0.2.0 numexpr-2.7.1 numpy-1.19.0 packaging-20.4 pandocfilters-1.4.2 parso-0.7.0 pexpect-4.8.0 pickleshare-0.7.5 prometheus-client-0.8.0 prompt-toolkit-3.0.5 ptyprocess-0.6.0 pyee-7.0.2 pygments-2.6.1 pympler-0.8 pyparsing-2.4.7 pyppeteer-0.2.2 pyrsistent-0.16.0 python-dateutil-2.8.1 pyzmq-19.0.1 qtconsole-4.7.5 qtpy-1.9.0 six-1.15.0 tables-3.6.1 terminado-0.8.3 testpath-0.4.4 tornado-6.0.4 tqdm-4.46.1 traitlets-4.3.3 urllib3-1.25.9 wcwidth-0.2.5 webencodings-0.5.1 websockets-8.1 widgetsnbextension-3.5.1
 $ jupyter nbconvert --to html --execute example.ipynb
 [NbConvertApp] Converting notebook example.ipynb to html
 [NbConvertApp] Executing notebook with kernel: python3
 [NbConvertApp] Writing 342781 bytes to example.html
 $ jupyter nbconvert --to PDFviaHTML --execute example.ipynb
 [NbConvertApp] Converting notebook example.ipynb to PDFviaHTML
 [NbConvertApp] Executing notebook with kernel: python3
 [NbConvertApp] Executing notebook with kernel: python3
 [W:pyppeteer.chromium_downloader] start chromium download.
 Download may take a few minutes.
 100%|██████████| 108773488/108773488 [00:01<00:00, 105172481.75it/s]
 [W:pyppeteer.chromium_downloader] 
 chromium download done.
 [W:pyppeteer.chromium_downloader] chromium extracted to: /root/.local/share/pyppeteer/local-chromium/588429
 Traceback (most recent call last):
   File "/usr/local/bin/jupyter-nbconvert", line 8, in <module>
     sys.exit(main())
   File "/usr/local/lib/python3.8/site-packages/jupyter_core/application.py", line 270, in launch_instance
     return super(JupyterApp, cls).launch_instance(argv=argv, **kwargs)
   File "/usr/local/lib/python3.8/site-packages/traitlets/config/application.py", line 664, in launch_instance
     app.start()
   File "/usr/local/lib/python3.8/site-packages/nbconvert/nbconvertapp.py", line 340, in start
     self.convert_notebooks()
   File "/usr/local/lib/python3.8/site-packages/nbconvert/nbconvertapp.py", line 510, in convert_notebooks
     self.convert_single_notebook(notebook_filename)
   File "/usr/local/lib/python3.8/site-packages/nbconvert/nbconvertapp.py", line 481, in convert_single_notebook
     output, resources = self.export_single_notebook(notebook_filename, resources, input_buffer=input_buffer)
   File "/usr/local/lib/python3.8/site-packages/nbconvert/nbconvertapp.py", line 410, in export_single_notebook
     output, resources = self.exporter.from_filename(notebook_filename, resources=resources)
   File "/usr/local/lib/python3.8/site-packages/nbconvert/exporters/exporter.py", line 179, in from_filename
     return self.from_file(f, resources=resources, **kw)
   File "/usr/local/lib/python3.8/site-packages/nbconvert/exporters/exporter.py", line 197, in from_file
     return self.from_notebook_node(nbformat.read(file_stream, as_version=4), resources=resources, **kw)
   File "/usr/local/lib/python3.8/site-packages/notebook_as_pdf/__init__.py", line 148, in from_notebook_node
     self.pool.submit(
   File "/usr/local/lib/python3.8/concurrent/futures/_base.py", line 439, in result
     return self.__get_result()
   File "/usr/local/lib/python3.8/concurrent/futures/_base.py", line 388, in __get_result
     raise self._exception
   File "/usr/local/lib/python3.8/concurrent/futures/thread.py", line 57, in run
     result = self.fn(*self.args, **self.kwargs)
   File "/usr/local/lib/python3.8/asyncio/runners.py", line 43, in run
     return loop.run_until_complete(main)
   File "/usr/local/lib/python3.8/asyncio/base_events.py", line 616, in run_until_complete
     return future.result()
   File "/usr/local/lib/python3.8/site-packages/notebook_as_pdf/__init__.py", line 107, in notebook_to_pdf
     await html_to_pdf(f.name, pdf_path)
   File "/usr/local/lib/python3.8/site-packages/notebook_as_pdf/__init__.py", line 24, in html_to_pdf
     browser = await launch(handleSIGINT=False, handleSIGTERM=False, handleSIGHUP=False)
   File "/usr/local/lib/python3.8/site-packages/pyppeteer/launcher.py", line 305, in launch
     return await Launcher(options, **kwargs).launch()
   File "/usr/local/lib/python3.8/site-packages/pyppeteer/launcher.py", line 166, in launch
     self.browserWSEndpoint = get_ws_endpoint(self.url)
   File "/usr/local/lib/python3.8/site-packages/pyppeteer/launcher.py", line 225, in get_ws_endpoint
     raise BrowserError('Browser closed unexpectedly:\n')
 pyppeteer.errors.BrowserError: Browser closed unexpectedly:
 Error in atexit._run_exitfuncs:
 Traceback (most recent call last):
   File "/usr/local/lib/python3.8/site-packages/pyppeteer/launcher.py", line 151, in _close_process
     self._loop.run_until_complete(self.killChrome())
   File "/usr/local/lib/python3.8/asyncio/base_events.py", line 591, in run_until_complete
     self._check_closed()
   File "/usr/local/lib/python3.8/asyncio/base_events.py", line 508, in _check_closed
     raise RuntimeError('Event loop is closed')
 RuntimeError: Event loop is closed
 sys:1: RuntimeWarning: coroutine 'Launcher.killChrome' was never awaited
 RuntimeWarning: Enable tracemalloc to get the object allocation traceback
Running after_script
00:02
Uploading artifacts for failed job
00:03
 ERROR: Job failed: exit code 1
@betatim
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Owner

betatim commented Jun 27, 2020

Do you know which container image your runner is using (python:latest is what it says but what exactly does that correspond to in terms of OS and version?)?

My guess is that you need to install the APT packages listed in https://github.com/betatim/notebook-as-pdf/blob/master/binder/apt.txt as well. the packages listed there work on the current Ubuntu LTS version.

Chromium is installed on demand by pyppeteer thefirst time you use it. The conversion to PDF is done by chromium.

@adavidzh
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adavidzh commented Jun 29, 2020 •
edited

Do you know which container image your runner is using (python:latest is what it says but what exactly does that correspond to in terms of OS and version?)?

The relevant Dockerfile uses buildpack-deps:buster which, through some hoops, tracks back to debian:bullseye.

My guess is that you need to install the APT packages listed in https://github.com/betatim/notebook-as-pdf/blob/master/binder/apt.txt as well. the packages listed there work on the current Ubuntu LTS version.

So, AFAICT the following in .gitlab-ci.yml installs all the packages correctly:

    - apt-get update && apt-get install -y --no-install-recommends apt-utils
    - xargs -a apt.txt apt-get install -y

but there's still a pyppeteer.errors.BrowserError: Browser closed unexpectedly.

Click to toggle the full log. 
 Running with gitlab-runner 13.0.1 (21cb397c)
   on default-runner-7f9b6f57bc-gx47f FX16rjWh
Preparing the "docker" executor
 Using Docker executor with image python:latest ...
 WARNING: Container based cache volumes creation is disabled. Will not create volume for "/cache"
 Pulling docker image python:latest ...
 Using docker image sha256:7f5b6ccd03e9da5e02a20ea4377ae61f6ae1b935b05c1bd52fdafe4b958b5e50 for python:latest ...
Preparing environment
00:03
 Running on runner-fx16rjwh-project-94480-concurrent-0 via default-runner-7f9b6f57bc-gx47f...
Getting source from Git repository
00:02
 Fetching changes with git depth set to 50...
 Initialized empty Git repository in /builds/adavid/mylittlelark/.git/
 Created fresh repository.
 From https://gitlab.cern.ch/adavid/mylittlelark
  * [new ref]         refs/pipelines/1754405 -> refs/pipelines/1754405
  * [new branch]      master                 -> origin/master
 Checking out 697bb730 as master...
 Skipping Git submodules setup
Restoring cache
00:01
Downloading artifacts
00:02
Running before_script and script
 $ apt-get update && apt-get install -y --no-install-recommends apt-utils
 Get:1 http://security.debian.org/debian-security buster/updates InRelease [65.4 kB]
 Get:2 http://deb.debian.org/debian buster InRelease [121 kB]
 Get:3 http://deb.debian.org/debian buster-updates InRelease [51.9 kB]
 Get:4 http://security.debian.org/debian-security buster/updates/main amd64 Packages [204 kB]
 Get:5 http://deb.debian.org/debian buster/main amd64 Packages [7905 kB]
 Get:6 http://deb.debian.org/debian buster-updates/main amd64 Packages [7868 B]
 Fetched 8355 kB in 2s (3718 kB/s)
 Reading package lists...
 Reading package lists...
 Building dependency tree...
 Reading state information...
 The following additional packages will be installed:
   libapt-inst2.0
 The following NEW packages will be installed:
   apt-utils libapt-inst2.0
 0 upgraded, 2 newly installed, 0 to remove and 1 not upgraded.
 Need to get 624 kB of archives.
 After this operation, 1650 kB of additional disk space will be used.
 Get:1 http://security.debian.org/debian-security buster/updates/main amd64 libapt-inst2.0 amd64 1.8.2.1 [203 kB]
 Get:2 http://security.debian.org/debian-security buster/updates/main amd64 apt-utils amd64 1.8.2.1 [421 kB]
 debconf: delaying package configuration, since apt-utils is not installed
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 Selecting previously unselected package libapt-inst2.0:amd64.
 (Reading database ... 24603 files and directories currently installed.)
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 Setting up libapt-inst2.0:amd64 (1.8.2.1) ...
 Setting up apt-utils (1.8.2.1) ...
 Processing triggers for libc-bin (2.28-10) ...
 $ xargs -a apt.txt apt-get install -y
 Reading package lists...
 Building dependency tree...
 Reading state information...
 libxss1 is already the newest version (1:1.2.3-1).
 libxss1 set to manually installed.
 libpangocairo-1.0-0 is already the newest version (1.42.4-8~deb10u1).
 libpangocairo-1.0-0 set to manually installed.
 The following additional packages will be installed:
   adwaita-icon-theme at-spi2-core dbus dbus-user-session
   dconf-gsettings-backend dconf-service dmsetup glib-networking
   glib-networking-common glib-networking-services gsettings-desktop-schemas
   gtk-update-icon-cache libapparmor1 libargon2-1 libasound2-data
   libatk1.0-data libatspi2.0-0 libavahi-client3 libavahi-common-data
   libavahi-common3 libcolord2 libcryptsetup12 libcups2 libdbus-1-3 libdconf1
   libdevmapper1.02.1 libepoxy0 libgtk-3-bin libgtk-3-common libidn11 libip4tc0
   libjson-c3 libjson-glib-1.0-0 libjson-glib-1.0-common libkmod2 libnspr4
   libnss-systemd libpam-systemd libproxy1v5 librest-0.7-0 libsoup-gnome2.4-1
   libsoup2.4-1 libwayland-client0 libwayland-cursor0 libwayland-egl1
   libxcomposite1 libxcursor1 libxdamage1 libxfixes3 libxi6 libxinerama1
   libxkbcommon0 systemd systemd-sysv xkb-data
 Suggested packages:
   libasound2-plugins alsa-utils colord cups-common gvfs systemd-container
   policykit-1
 The following NEW packages will be installed:
   adwaita-icon-theme at-spi2-core dbus dbus-user-session
   dconf-gsettings-backend dconf-service dmsetup glib-networking
   glib-networking-common glib-networking-services gsettings-desktop-schemas
   gtk-update-icon-cache libapparmor1 libargon2-1 libasound2 libasound2-data
   libatk-bridge2.0-0 libatk1.0-0 libatk1.0-data libatspi2.0-0 libavahi-client3
   libavahi-common-data libavahi-common3 libcolord2 libcryptsetup12 libcups2
   libdbus-1-3 libdconf1 libdevmapper1.02.1 libepoxy0 libgtk-3-0 libgtk-3-bin
   libgtk-3-common libidn11 libip4tc0 libjson-c3 libjson-glib-1.0-0
   libjson-glib-1.0-common libkmod2 libnspr4 libnss-systemd libnss3
   libpam-systemd libproxy1v5 librest-0.7-0 libsoup-gnome2.4-1 libsoup2.4-1
   libwayland-client0 libwayland-cursor0 libwayland-egl1 libx11-xcb1
   libxcomposite1 libxcursor1 libxdamage1 libxfixes3 libxi6 libxinerama1
   libxkbcommon0 libxrandr2 libxtst6 systemd systemd-sysv xkb-data
 0 upgraded, 63 newly installed, 0 to remove and 1 not upgraded.
 Need to get 29.1 MB of archives.
 After this operation, 107 MB of additional disk space will be used.
 Get:1 http://deb.debian.org/debian buster/main amd64 libapparmor1 amd64 2.13.2-10 [94.7 kB]
 Get:2 http://deb.debian.org/debian buster/main amd64 libargon2-1 amd64 0~20171227-0.2 [19.6 kB]
 Get:3 http://deb.debian.org/debian buster/main amd64 dmsetup amd64 2:1.02.155-3 [90.8 kB]
 Get:4 http://deb.debian.org/debian buster/main amd64 libdevmapper1.02.1 amd64 2:1.02.155-3 [141 kB]
 Get:5 http://deb.debian.org/debian buster/main amd64 libjson-c3 amd64 0.12.1+ds-2 [26.9 kB]
 Get:6 http://deb.debian.org/debian buster/main amd64 libcryptsetup12 amd64 2:2.1.0-5+deb10u2 [193 kB]
 Get:7 http://deb.debian.org/debian buster/main amd64 libidn11 amd64 1.33-2.2 [116 kB]
 Get:8 http://deb.debian.org/debian buster/main amd64 libip4tc0 amd64 1.8.2-4 [70.2 kB]
 Get:9 http://deb.debian.org/debian buster/main amd64 libkmod2 amd64 26-1 [52.7 kB]
 Get:10 http://deb.debian.org/debian buster/main amd64 systemd amd64 241-7~deb10u4 [3499 kB]
 Get:11 http://deb.debian.org/debian buster/main amd64 systemd-sysv amd64 241-7~deb10u4 [99.9 kB]
 Get:12 http://deb.debian.org/debian buster/main amd64 libdbus-1-3 amd64 1.12.16-1 [214 kB]
 Get:13 http://deb.debian.org/debian buster/main amd64 dbus amd64 1.12.16-1 [235 kB]
 Get:14 http://deb.debian.org/debian buster/main amd64 libnss-systemd amd64 241-7~deb10u4 [205 kB]
 Get:15 http://deb.debian.org/debian buster/main amd64 libpam-systemd amd64 241-7~deb10u4 [209 kB]
 Get:16 http://deb.debian.org/debian buster/main amd64 gtk-update-icon-cache amd64 3.24.5-1 [81.7 kB]
 Get:17 http://deb.debian.org/debian buster/main amd64 adwaita-icon-theme all 3.30.1-1 [11.7 MB]
 Get:18 http://deb.debian.org/debian buster/main amd64 libatspi2.0-0 amd64 2.30.0-7 [65.0 kB]
 Get:19 http://deb.debian.org/debian buster/main amd64 libxi6 amd64 2:1.7.9-1 [82.6 kB]
 Get:20 http://deb.debian.org/debian buster/main amd64 libxtst6 amd64 2:1.2.3-1 [27.8 kB]
 Get:21 http://deb.debian.org/debian buster/main amd64 at-spi2-core amd64 2.30.0-7 [70.7 kB]
 Get:22 http://deb.debian.org/debian buster/main amd64 dbus-user-session amd64 1.12.16-1 [93.4 kB]
 Get:23 http://deb.debian.org/debian buster/main amd64 libdconf1 amd64 0.30.1-2 [40.7 kB]
 Get:24 http://deb.debian.org/debian buster/main amd64 dconf-service amd64 0.30.1-2 [36.4 kB]
 Get:25 http://deb.debian.org/debian buster/main amd64 dconf-gsettings-backend amd64 0.30.1-2 [28.9 kB]
 Get:26 http://deb.debian.org/debian buster/main amd64 libproxy1v5 amd64 0.4.15-5 [58.1 kB]
 Get:27 http://deb.debian.org/debian buster/main amd64 glib-networking-common all 2.58.0-2 [59.3 kB]
 Get:28 http://deb.debian.org/debian buster/main amd64 glib-networking-services amd64 2.58.0-2 [13.5 kB]
 Get:29 http://deb.debian.org/debian buster/main amd64 gsettings-desktop-schemas all 3.28.1-1 [529 kB]
 Get:30 http://deb.debian.org/debian buster/main amd64 glib-networking amd64 2.58.0-2 [54.4 kB]
 Get:31 http://deb.debian.org/debian buster/main amd64 libasound2-data all 1.1.8-1 [59.6 kB]
 Get:32 http://deb.debian.org/debian buster/main amd64 libasound2 amd64 1.1.8-1 [361 kB]
 Get:33 http://deb.debian.org/debian buster/main amd64 libatk1.0-data all 2.30.0-2 [145 kB]
 Get:34 http://deb.debian.org/debian buster/main amd64 libatk1.0-0 amd64 2.30.0-2 [50.6 kB]
 Get:35 http://deb.debian.org/debian buster/main amd64 libatk-bridge2.0-0 amd64 2.30.0-5 [61.6 kB]
 Get:36 http://deb.debian.org/debian buster/main amd64 libavahi-common-data amd64 0.7-4+b1 [122 kB]
 Get:37 http://deb.debian.org/debian buster/main amd64 libavahi-common3 amd64 0.7-4+b1 [54.6 kB]
 Get:38 http://deb.debian.org/debian buster/main amd64 libavahi-client3 amd64 0.7-4+b1 [58.1 kB]
 Get:39 http://deb.debian.org/debian buster/main amd64 libcolord2 amd64 1.4.3-4 [141 kB]
 Get:40 http://deb.debian.org/debian buster/main amd64 libcups2 amd64 2.2.10-6+deb10u3 [324 kB]
 Get:41 http://deb.debian.org/debian buster/main amd64 libepoxy0 amd64 1.5.3-0.1 [190 kB]
 Get:42 http://deb.debian.org/debian buster/main amd64 libjson-glib-1.0-common all 1.4.4-2 [52.3 kB]
 Get:43 http://deb.debian.org/debian buster/main amd64 libjson-glib-1.0-0 amd64 1.4.4-2 [61.2 kB]
 Get:44 http://deb.debian.org/debian buster/main amd64 libsoup2.4-1 amd64 2.64.2-2 [253 kB]
 Get:45 http://deb.debian.org/debian buster/main amd64 libsoup-gnome2.4-1 amd64 2.64.2-2 [18.0 kB]
 Get:46 http://deb.debian.org/debian buster/main amd64 librest-0.7-0 amd64 0.8.1-1 [33.7 kB]
 Get:47 http://deb.debian.org/debian buster/main amd64 libwayland-client0 amd64 1.16.0-1 [26.4 kB]
 Get:48 http://deb.debian.org/debian buster/main amd64 libwayland-cursor0 amd64 1.16.0-1 [14.1 kB]
 Get:49 http://deb.debian.org/debian buster/main amd64 libwayland-egl1 amd64 1.16.0-1 [8204 B]
 Get:50 http://deb.debian.org/debian buster/main amd64 libxcomposite1 amd64 1:0.4.4-2 [16.5 kB]
 Get:51 http://deb.debian.org/debian buster/main amd64 libxfixes3 amd64 1:5.0.3-1 [21.9 kB]
 Get:52 http://deb.debian.org/debian buster/main amd64 libxcursor1 amd64 1:1.1.15-2 [36.6 kB]
 Get:53 http://deb.debian.org/debian buster/main amd64 libxdamage1 amd64 1:1.1.4-3+b3 [14.9 kB]
 Get:54 http://deb.debian.org/debian buster/main amd64 libxinerama1 amd64 2:1.1.4-2 [17.7 kB]
 Get:55 http://deb.debian.org/debian buster/main amd64 xkb-data all 2.26-2 [681 kB]
 Get:56 http://deb.debian.org/debian buster/main amd64 libxkbcommon0 amd64 0.8.2-1 [123 kB]
 Get:57 http://deb.debian.org/debian buster/main amd64 libxrandr2 amd64 2:1.5.1-1 [37.5 kB]
 Get:58 http://deb.debian.org/debian buster/main amd64 libgtk-3-common all 3.24.5-1 [3678 kB]
 Get:59 http://deb.debian.org/debian buster/main amd64 libgtk-3-0 amd64 3.24.5-1 [2580 kB]
 Get:60 http://deb.debian.org/debian buster/main amd64 libgtk-3-bin amd64 3.24.5-1 [114 kB]
 Get:61 http://deb.debian.org/debian buster/main amd64 libnspr4 amd64 2:4.20-1 [112 kB]
 Get:62 http://deb.debian.org/debian buster/main amd64 libnss3 amd64 2:3.42.1-1+deb10u2 [1160 kB]
 Get:63 http://deb.debian.org/debian buster/main amd64 libx11-xcb1 amd64 2:1.6.7-1 [190 kB]
 debconf: unable to initialize frontend: Dialog
 debconf: (TERM is not set, so the dialog frontend is not usable.)
 debconf: falling back to frontend: Readline
 debconf: unable to initialize frontend: Readline
 debconf: (This frontend requires a controlling tty.)
 debconf: falling back to frontend: Teletype
 dpkg-preconfigure: unable to re-open stdin: 
 Fetched 29.1 MB in 1s (20.8 MB/s)
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 Setting up libip4tc0:amd64 (1.8.2-4) ...
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 Setting up libdevmapper1.02.1:amd64 (2:1.02.155-3) ...
 Setting up libcryptsetup12:amd64 (2:2.1.0-5+deb10u2) ...
 Setting up systemd (241-7~deb10u4) ...
 Created symlink /etc/systemd/system/getty.target.wants/getty@tty1.service → /lib/systemd/system/getty@.service.
 Created symlink /etc/systemd/system/multi-user.target.wants/remote-fs.target → /lib/systemd/system/remote-fs.target.
 Created symlink /etc/systemd/system/dbus-org.freedesktop.timesync1.service → /lib/systemd/system/systemd-timesyncd.service.
 Created symlink /etc/systemd/system/sysinit.target.wants/systemd-timesyncd.service → /lib/systemd/system/systemd-timesyncd.service.
 Setting up dmsetup (2:1.02.155-3) ...
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 No diversion 'diversion of /usr/sbin/update-icon-caches to /usr/sbin/update-icon-caches.gtk2 by libgtk-3-bin', none removed.
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 Setting up glib-networking:amd64 (2.58.0-2) ...
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 $ pip install --no-cache-dir -r requirements.txt
 Collecting jupyter
   Downloading jupyter-1.0.0-py2.py3-none-any.whl (2.7 kB)
 Collecting pympler
   Downloading Pympler-0.8.tar.gz (175 kB)
 Collecting lark-parser
   Downloading lark-parser-0.8.9.tar.gz (294 kB)
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   Downloading tqdm-4.47.0-py2.py3-none-any.whl (66 kB)
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   Downloading tables-3.6.1-cp38-cp38-manylinux1_x86_64.whl (4.3 MB)
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   Downloading notebook_as_pdf-0.2.0-py3-none-any.whl (5.2 kB)
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   Downloading ipywidgets-7.5.1-py2.py3-none-any.whl (121 kB)
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   Downloading nbconvert-5.6.1-py2.py3-none-any.whl (455 kB)
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   Downloading notebook-6.0.3-py3-none-any.whl (9.7 MB)
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   Downloading jupyter_console-6.1.0-py2.py3-none-any.whl (21 kB)
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   Downloading qtconsole-4.7.5-py2.py3-none-any.whl (118 kB)
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   Downloading ipykernel-5.3.0-py3-none-any.whl (119 kB)
 Collecting numexpr>=2.6.2
   Downloading numexpr-2.7.1-cp38-cp38-manylinux1_x86_64.whl (164 kB)
 Collecting numpy>=1.9.3
   Downloading numpy-1.19.0-cp38-cp38-manylinux2010_x86_64.whl (14.6 MB)
 Collecting pyppeteer
   Downloading pyppeteer-0.2.2-py3-none-any.whl (145 kB)
 Collecting PyPDF2
   Downloading PyPDF2-1.26.0.tar.gz (77 kB)
 Collecting nbformat>=4.2.0
   Downloading nbformat-5.0.7-py3-none-any.whl (170 kB)
 Collecting traitlets>=4.3.1
   Downloading traitlets-4.3.3-py2.py3-none-any.whl (75 kB)
 Collecting widgetsnbextension~=3.5.0
   Downloading widgetsnbextension-3.5.1-py2.py3-none-any.whl (2.2 MB)
 Collecting ipython>=4.0.0; python_version >= "3.3"
   Downloading ipython-7.16.1-py3-none-any.whl (785 kB)
 Collecting entrypoints>=0.2.2
   Downloading entrypoints-0.3-py2.py3-none-any.whl (11 kB)
 Collecting pandocfilters>=1.4.1
   Downloading pandocfilters-1.4.2.tar.gz (14 kB)
 Collecting pygments
   Downloading Pygments-2.6.1-py3-none-any.whl (914 kB)
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   Downloading Jinja2-2.11.2-py2.py3-none-any.whl (125 kB)
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   Downloading jupyter_core-4.6.3-py2.py3-none-any.whl (83 kB)
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   Downloading testpath-0.4.4-py2.py3-none-any.whl (163 kB)
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   Downloading bleach-3.1.5-py2.py3-none-any.whl (151 kB)
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   Downloading defusedxml-0.6.0-py2.py3-none-any.whl (23 kB)
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   Downloading mistune-0.8.4-py2.py3-none-any.whl (16 kB)
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   Downloading prometheus_client-0.8.0-py2.py3-none-any.whl (53 kB)
 Collecting pyzmq>=17
   Downloading pyzmq-19.0.1-cp38-cp38-manylinux1_x86_64.whl (1.1 MB)
 Collecting ipython-genutils
   Downloading ipython_genutils-0.2.0-py2.py3-none-any.whl (26 kB)
 Collecting terminado>=0.8.1
   Downloading terminado-0.8.3-py2.py3-none-any.whl (33 kB)
 Collecting jupyter-client>=5.3.4
   Downloading jupyter_client-6.1.3-py3-none-any.whl (106 kB)
 Collecting tornado>=5.0
   Downloading tornado-6.0.4.tar.gz (496 kB)
 Collecting Send2Trash
   Downloading Send2Trash-1.5.0-py3-none-any.whl (12 kB)
 Collecting prompt-toolkit!=3.0.0,!=3.0.1,<3.1.0,>=2.0.0
   Downloading prompt_toolkit-3.0.5-py3-none-any.whl (351 kB)
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   Downloading QtPy-1.9.0-py2.py3-none-any.whl (54 kB)
 Collecting urllib3<2.0.0,>=1.25.8
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 Collecting websockets<9.0,>=8.1
   Downloading websockets-8.1-cp38-cp38-manylinux2010_x86_64.whl (78 kB)
 Collecting appdirs<2.0.0,>=1.4.3
   Downloading appdirs-1.4.4-py2.py3-none-any.whl (9.6 kB)
 Collecting pyee<8.0.0,>=7.0.1
   Downloading pyee-7.0.2-py2.py3-none-any.whl (12 kB)
 Collecting jsonschema!=2.5.0,>=2.4
   Downloading jsonschema-3.2.0-py2.py3-none-any.whl (56 kB)
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   Downloading six-1.15.0-py2.py3-none-any.whl (10 kB)
 Collecting decorator
   Downloading decorator-4.4.2-py2.py3-none-any.whl (9.2 kB)
 Collecting pexpect; sys_platform != "win32"
   Downloading pexpect-4.8.0-py2.py3-none-any.whl (59 kB)
 Collecting pickleshare
   Downloading pickleshare-0.7.5-py2.py3-none-any.whl (6.9 kB)
 Collecting jedi>=0.10
   Downloading jedi-0.17.1-py2.py3-none-any.whl (1.4 MB)
 Requirement already satisfied: setuptools>=18.5 in /usr/local/lib/python3.8/site-packages (from ipython>=4.0.0; python_version >= "3.3"->ipywidgets->jupyter->-r requirements.txt (line 1)) (47.1.1)
 Collecting backcall
   Downloading backcall-0.2.0-py2.py3-none-any.whl (11 kB)
 Collecting MarkupSafe>=0.23
   Downloading MarkupSafe-1.1.1-cp38-cp38-manylinux1_x86_64.whl (32 kB)
 Collecting webencodings
   Downloading webencodings-0.5.1-py2.py3-none-any.whl (11 kB)
 Collecting packaging
   Downloading packaging-20.4-py2.py3-none-any.whl (37 kB)
 Collecting ptyprocess; os_name != "nt"
   Downloading ptyprocess-0.6.0-py2.py3-none-any.whl (39 kB)
 Collecting python-dateutil>=2.1
   Downloading python_dateutil-2.8.1-py2.py3-none-any.whl (227 kB)
 Collecting wcwidth
   Downloading wcwidth-0.2.5-py2.py3-none-any.whl (30 kB)
 Collecting attrs>=17.4.0
   Downloading attrs-19.3.0-py2.py3-none-any.whl (39 kB)
 Collecting pyrsistent>=0.14.0
   Downloading pyrsistent-0.16.0.tar.gz (108 kB)
 Collecting parso<0.8.0,>=0.7.0
   Downloading parso-0.7.0-py2.py3-none-any.whl (100 kB)
 Collecting pyparsing>=2.0.2
   Downloading pyparsing-2.4.7-py2.py3-none-any.whl (67 kB)
 Building wheels for collected packages: pympler, lark-parser, PyPDF2, pandocfilters, tornado, pyrsistent
   Building wheel for pympler (setup.py): started
   Building wheel for pympler (setup.py): finished with status 'done'
   Created wheel for pympler: filename=Pympler-0.8-py3-none-any.whl size=164713 sha256=8687c2cba848a998ca3c382eaebb40d3f4c237126a98e2f7ea237c86d893d1ce
   Stored in directory: /tmp/pip-ephem-wheel-cache-9xvt7yiv/wheels/2c/09/38/7c8c5dc224099d3a7194d154a99093d429bb4bda18c241c4b5
   Building wheel for lark-parser (setup.py): started
   Building wheel for lark-parser (setup.py): finished with status 'done'
   Created wheel for lark-parser: filename=lark_parser-0.8.9-py2.py3-none-any.whl size=75357 sha256=4064750ada68815a698f20c2e004897b56b489dc16ef099621219d6faeaa468e
   Stored in directory: /tmp/pip-ephem-wheel-cache-9xvt7yiv/wheels/5c/55/8c/91a8363366ada1c946e50d5c030e63129a2d8f3120e1975997
   Building wheel for PyPDF2 (setup.py): started
   Building wheel for PyPDF2 (setup.py): finished with status 'done'
   Created wheel for PyPDF2: filename=PyPDF2-1.26.0-py3-none-any.whl size=61084 sha256=e6180338e2967be51311c889dba65ad577f061c1a114be4fceddebe9703bdd94
   Stored in directory: /tmp/pip-ephem-wheel-cache-9xvt7yiv/wheels/b1/1a/8f/a4c34be976825a2f7948d0fa40907598d69834f8ab5889de11
   Building wheel for pandocfilters (setup.py): started
   Building wheel for pandocfilters (setup.py): finished with status 'done'
   Created wheel for pandocfilters: filename=pandocfilters-1.4.2-py3-none-any.whl size=7856 sha256=20ef2df286088ae82b07087621f275199011e9c4484b9e1810d20e78a6299bd3
   Stored in directory: /tmp/pip-ephem-wheel-cache-9xvt7yiv/wheels/f6/08/65/e4636b703d0e870cd62692dafd6b47db27287fe80cea433722
   Building wheel for tornado (setup.py): started
   Building wheel for tornado (setup.py): finished with status 'done'
   Created wheel for tornado: filename=tornado-6.0.4-cp38-cp38-linux_x86_64.whl size=427816 sha256=1108d56966f59c5370206b5f73d74ed424469bfcabf83040e18ea276a7405dea
   Stored in directory: /tmp/pip-ephem-wheel-cache-9xvt7yiv/wheels/88/79/e5/598ba17e85eccf2626eab62e4ee8452895636cd542650d450d
   Building wheel for pyrsistent (setup.py): started
   Building wheel for pyrsistent (setup.py): finished with status 'done'
   Created wheel for pyrsistent: filename=pyrsistent-0.16.0-cp38-cp38-linux_x86_64.whl size=126681 sha256=63540c806f41714295504782e15bcb66ec815d4d7b4e66ed5ab06eb6cb0b02be
   Stored in directory: /tmp/pip-ephem-wheel-cache-9xvt7yiv/wheels/17/be/0f/727fb20889ada6aaaaba861f5f0eb21663533915429ad43f28
 Successfully built pympler lark-parser PyPDF2 pandocfilters tornado pyrsistent
 Installing collected packages: ipython-genutils, six, attrs, pyrsistent, jsonschema, decorator, traitlets, jupyter-core, nbformat, tornado, wcwidth, prompt-toolkit, pygments, ptyprocess, pexpect, pickleshare, parso, jedi, backcall, ipython, pyzmq, python-dateutil, jupyter-client, ipykernel, entrypoints, pandocfilters, MarkupSafe, jinja2, testpath, webencodings, pyparsing, packaging, bleach, defusedxml, mistune, nbconvert, prometheus-client, terminado, Send2Trash, notebook, widgetsnbextension, ipywidgets, jupyter-console, qtpy, qtconsole, jupyter, pympler, lark-parser, tqdm, numpy, numexpr, tables, urllib3, websockets, appdirs, pyee, pyppeteer, PyPDF2, notebook-as-pdf
 Successfully installed MarkupSafe-1.1.1 PyPDF2-1.26.0 Send2Trash-1.5.0 appdirs-1.4.4 attrs-19.3.0 backcall-0.2.0 bleach-3.1.5 decorator-4.4.2 defusedxml-0.6.0 entrypoints-0.3 ipykernel-5.3.0 ipython-7.16.1 ipython-genutils-0.2.0 ipywidgets-7.5.1 jedi-0.17.1 jinja2-2.11.2 jsonschema-3.2.0 jupyter-1.0.0 jupyter-client-6.1.3 jupyter-console-6.1.0 jupyter-core-4.6.3 lark-parser-0.8.9 mistune-0.8.4 nbconvert-5.6.1 nbformat-5.0.7 notebook-6.0.3 notebook-as-pdf-0.2.0 numexpr-2.7.1 numpy-1.19.0 packaging-20.4 pandocfilters-1.4.2 parso-0.7.0 pexpect-4.8.0 pickleshare-0.7.5 prometheus-client-0.8.0 prompt-toolkit-3.0.5 ptyprocess-0.6.0 pyee-7.0.2 pygments-2.6.1 pympler-0.8 pyparsing-2.4.7 pyppeteer-0.2.2 pyrsistent-0.16.0 python-dateutil-2.8.1 pyzmq-19.0.1 qtconsole-4.7.5 qtpy-1.9.0 six-1.15.0 tables-3.6.1 terminado-0.8.3 testpath-0.4.4 tornado-6.0.4 tqdm-4.47.0 traitlets-4.3.3 urllib3-1.25.9 wcwidth-0.2.5 webencodings-0.5.1 websockets-8.1 widgetsnbextension-3.5.1
 $ jupyter nbconvert --to html --execute example.ipynb
 [NbConvertApp] Converting notebook example.ipynb to html
 [NbConvertApp] Executing notebook with kernel: python3
 [NbConvertApp] Writing 342781 bytes to example.html
 $ jupyter nbconvert --to PDFviaHTML --execute example.ipynb
 [NbConvertApp] Converting notebook example.ipynb to PDFviaHTML
 [NbConvertApp] Executing notebook with kernel: python3
 [NbConvertApp] Executing notebook with kernel: python3
 [W:pyppeteer.chromium_downloader] start chromium download.
 Download may take a few minutes.
 100%|██████████| 108773488/108773488 [00:00<00:00, 198338391.82it/s]
 [W:pyppeteer.chromium_downloader] 
 chromium download done.
 [W:pyppeteer.chromium_downloader] chromium extracted to: /root/.local/share/pyppeteer/local-chromium/588429
 Traceback (most recent call last):
   File "/usr/local/bin/jupyter-nbconvert", line 8, in <module>
     sys.exit(main())
   File "/usr/local/lib/python3.8/site-packages/jupyter_core/application.py", line 270, in launch_instance
     return super(JupyterApp, cls).launch_instance(argv=argv, **kwargs)
   File "/usr/local/lib/python3.8/site-packages/traitlets/config/application.py", line 664, in launch_instance
     app.start()
   File "/usr/local/lib/python3.8/site-packages/nbconvert/nbconvertapp.py", line 340, in start
     self.convert_notebooks()
   File "/usr/local/lib/python3.8/site-packages/nbconvert/nbconvertapp.py", line 510, in convert_notebooks
     self.convert_single_notebook(notebook_filename)
   File "/usr/local/lib/python3.8/site-packages/nbconvert/nbconvertapp.py", line 481, in convert_single_notebook
     output, resources = self.export_single_notebook(notebook_filename, resources, input_buffer=input_buffer)
   File "/usr/local/lib/python3.8/site-packages/nbconvert/nbconvertapp.py", line 410, in export_single_notebook
     output, resources = self.exporter.from_filename(notebook_filename, resources=resources)
   File "/usr/local/lib/python3.8/site-packages/nbconvert/exporters/exporter.py", line 179, in from_filename
     return self.from_file(f, resources=resources, **kw)
   File "/usr/local/lib/python3.8/site-packages/nbconvert/exporters/exporter.py", line 197, in from_file
     return self.from_notebook_node(nbformat.read(file_stream, as_version=4), resources=resources, **kw)
   File "/usr/local/lib/python3.8/site-packages/notebook_as_pdf/__init__.py", line 148, in from_notebook_node
     self.pool.submit(
   File "/usr/local/lib/python3.8/concurrent/futures/_base.py", line 439, in result
     return self.__get_result()
   File "/usr/local/lib/python3.8/concurrent/futures/_base.py", line 388, in __get_result
     raise self._exception
   File "/usr/local/lib/python3.8/concurrent/futures/thread.py", line 57, in run
     result = self.fn(*self.args, **self.kwargs)
   File "/usr/local/lib/python3.8/asyncio/runners.py", line 43, in run
     return loop.run_until_complete(main)
   File "/usr/local/lib/python3.8/asyncio/base_events.py", line 616, in run_until_complete
     return future.result()
   File "/usr/local/lib/python3.8/site-packages/notebook_as_pdf/__init__.py", line 107, in notebook_to_pdf
     await html_to_pdf(f.name, pdf_path)
   File "/usr/local/lib/python3.8/site-packages/notebook_as_pdf/__init__.py", line 24, in html_to_pdf
     browser = await launch(handleSIGINT=False, handleSIGTERM=False, handleSIGHUP=False)
   File "/usr/local/lib/python3.8/site-packages/pyppeteer/launcher.py", line 305, in launch
     return await Launcher(options, **kwargs).launch()
   File "/usr/local/lib/python3.8/site-packages/pyppeteer/launcher.py", line 166, in launch
     self.browserWSEndpoint = get_ws_endpoint(self.url)
   File "/usr/local/lib/python3.8/site-packages/pyppeteer/launcher.py", line 225, in get_ws_endpoint
     raise BrowserError('Browser closed unexpectedly:\n')
 pyppeteer.errors.BrowserError: Browser closed unexpectedly:
 Error in atexit._run_exitfuncs:
 Traceback (most recent call last):
   File "/usr/local/lib/python3.8/site-packages/pyppeteer/launcher.py", line 151, in _close_process
     self._loop.run_until_complete(self.killChrome())
   File "/usr/local/lib/python3.8/asyncio/base_events.py", line 591, in run_until_complete
     self._check_closed()
   File "/usr/local/lib/python3.8/asyncio/base_events.py", line 508, in _check_closed
     raise RuntimeError('Event loop is closed')
 RuntimeError: Event loop is closed
 sys:1: RuntimeWarning: coroutine 'Launcher.killChrome' was never awaited
 RuntimeWarning: Enable tracemalloc to get the object allocation traceback

@betatim
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betatim commented Jun 30, 2020

Also happens on Ubuntu. Just rebuilt the docker image that mybinder.org uses and it gives same error you are reporting. If I build it locally with repo2docker I also get this.

Investigating what changed.

@betatim
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betatim commented Jun 30, 2020

It looks like I can make it work by disabling the sandbox. Can you change your nbconvert command-line to jupyter-nbconvert --PDFExporter.no_sandbox=True --to PDFviaHTML some-notebook.ipynb to see if that works?

If that fixes it I think we should make it the default.

@adavidzh
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I feel less alone now. Thanks for reproducing the issue.

So, I tried it out and it doesn't work, but perhaps because the first line I get is:

$ jupyter nbconvert --PDFExporter.no_sandbox=True --to PDFviaHTML --execute example.ipynb
 [NbConvertApp] WARNING | Config option `no_sandbox` not recognized by `PDFExporter`.
 [NbConvertApp] Converting notebook example.ipynb to PDFviaHTML
 [NbConvertApp] Executing notebook with kernel: python3
<snip>

I have no versions in my requirements.txt and pip seems to be picking up

Collecting nbconvert
   Downloading nbconvert-5.6.1-py2.py3-none-any.whl (455 kB)

@betatim
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betatim commented Jun 30, 2020

Can you try without --execute and which version of notebook-as-pdf do you have installed in your CI environment? It might be that the option to turn off the sandbox was added after the last release. In which case can you install from master iwth pip install https://github.com/betatim/notebook-as-pdf/archive/master.zip?

@adavidzh
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In steps:

  • pip was pulling
Collecting notebook-as-pdf
   Downloading notebook_as_pdf-0.2.0-py3-none-any.whl (5.2 kB)
  • Removing --execute did not help:
$ jupyter nbconvert --PDFExporter.no_sandbox=True --to PDFviaHTML example.ipynb
 [NbConvertApp] WARNING | Config option `no_sandbox` not recognized by `PDFExporter`.
 [NbConvertApp] Converting notebook example.ipynb to PDFviaHTML
<snip>
  • Installing with pip install https://github.com/betatim/notebook-as-pdf/archive/master.zip works, and an interesting difference in the logs is that it installs 0.1.0 instead:
 $ pip install https://github.com/betatim/notebook-as-pdf/archive/master.zip
 Collecting https://github.com/betatim/notebook-as-pdf/archive/master.zip
   Downloading https://github.com/betatim/notebook-as-pdf/archive/master.zip
 Requirement already satisfied: nbconvert in /usr/local/lib/python3.8/site-packages (from notebook-as-pdf==0.1.0) (5.6.1)
 Collecting pyppeteer
   Downloading pyppeteer-0.2.2-py3-none-any.whl (145 kB)
 Collecting PyPDF2
   Downloading PyPDF2-1.26.0.tar.gz (77 kB)
 Requirement already satisfied: jinja2>=2.4 in /usr/local/lib/python3.8/site-packages (from nbconvert->notebook-as-pdf==0.1.0) (2.11.2)
 Requirement already satisfied: defusedxml in /usr/local/lib/python3.8/site-packages (from nbconvert->notebook-as-pdf==0.1.0) (0.6.0)
 Requirement already satisfied: entrypoints>=0.2.2 in /usr/local/lib/python3.8/site-packages (from nbconvert->notebook-as-pdf==0.1.0) (0.3)
 Requirement already satisfied: pygments in /usr/local/lib/python3.8/site-packages (from nbconvert->notebook-as-pdf==0.1.0) (2.6.1)
 Requirement already satisfied: traitlets>=4.2 in /usr/local/lib/python3.8/site-packages (from nbconvert->notebook-as-pdf==0.1.0) (4.3.3)
 Requirement already satisfied: jupyter-core in /usr/local/lib/python3.8/site-packages (from nbconvert->notebook-as-pdf==0.1.0) (4.6.3)
 Requirement already satisfied: pandocfilters>=1.4.1 in /usr/local/lib/python3.8/site-packages (from nbconvert->notebook-as-pdf==0.1.0) (1.4.2)
 Requirement already satisfied: testpath in /usr/local/lib/python3.8/site-packages (from nbconvert->notebook-as-pdf==0.1.0) (0.4.4)
 Requirement already satisfied: bleach in /usr/local/lib/python3.8/site-packages (from nbconvert->notebook-as-pdf==0.1.0) (3.1.5)
 Requirement already satisfied: nbformat>=4.4 in /usr/local/lib/python3.8/site-packages (from nbconvert->notebook-as-pdf==0.1.0) (5.0.7)
 Requirement already satisfied: mistune<2,>=0.8.1 in /usr/local/lib/python3.8/site-packages (from nbconvert->notebook-as-pdf==0.1.0) (0.8.4)
 Collecting websockets<9.0,>=8.1
   Downloading websockets-8.1-cp38-cp38-manylinux2010_x86_64.whl (78 kB)
 Requirement already satisfied: tqdm<5.0.0,>=4.42.1 in /usr/local/lib/python3.8/site-packages (from pyppeteer->notebook-as-pdf==0.1.0) (4.47.0)
 Collecting pyee<8.0.0,>=7.0.1
   Downloading pyee-7.0.2-py2.py3-none-any.whl (12 kB)
 Collecting urllib3<2.0.0,>=1.25.8
   Downloading urllib3-1.25.9-py2.py3-none-any.whl (126 kB)
 Collecting appdirs<2.0.0,>=1.4.3
   Downloading appdirs-1.4.4-py2.py3-none-any.whl (9.6 kB)
 Requirement already satisfied: MarkupSafe>=0.23 in /usr/local/lib/python3.8/site-packages (from jinja2>=2.4->nbconvert->notebook-as-pdf==0.1.0) (1.1.1)
 Requirement already satisfied: six in /usr/local/lib/python3.8/site-packages (from traitlets>=4.2->nbconvert->notebook-as-pdf==0.1.0) (1.15.0)
 Requirement already satisfied: decorator in /usr/local/lib/python3.8/site-packages (from traitlets>=4.2->nbconvert->notebook-as-pdf==0.1.0) (4.4.2)
 Requirement already satisfied: ipython-genutils in /usr/local/lib/python3.8/site-packages (from traitlets>=4.2->nbconvert->notebook-as-pdf==0.1.0) (0.2.0)
 Requirement already satisfied: webencodings in /usr/local/lib/python3.8/site-packages (from bleach->nbconvert->notebook-as-pdf==0.1.0) (0.5.1)
 Requirement already satisfied: packaging in /usr/local/lib/python3.8/site-packages (from bleach->nbconvert->notebook-as-pdf==0.1.0) (20.4)
 Requirement already satisfied: jsonschema!=2.5.0,>=2.4 in /usr/local/lib/python3.8/site-packages (from nbformat>=4.4->nbconvert->notebook-as-pdf==0.1.0) (3.2.0)
 Requirement already satisfied: pyparsing>=2.0.2 in /usr/local/lib/python3.8/site-packages (from packaging->bleach->nbconvert->notebook-as-pdf==0.1.0) (2.4.7)
 Requirement already satisfied: attrs>=17.4.0 in /usr/local/lib/python3.8/site-packages (from jsonschema!=2.5.0,>=2.4->nbformat>=4.4->nbconvert->notebook-as-pdf==0.1.0) (19.3.0)
 Requirement already satisfied: pyrsistent>=0.14.0 in /usr/local/lib/python3.8/site-packages (from jsonschema!=2.5.0,>=2.4->nbformat>=4.4->nbconvert->notebook-as-pdf==0.1.0) (0.16.0)
 Requirement already satisfied: setuptools in /usr/local/lib/python3.8/site-packages (from jsonschema!=2.5.0,>=2.4->nbformat>=4.4->nbconvert->notebook-as-pdf==0.1.0) (47.1.1)
 Building wheels for collected packages: notebook-as-pdf, PyPDF2
   Building wheel for notebook-as-pdf (setup.py): started
   Building wheel for notebook-as-pdf (setup.py): finished with status 'done'
   Created wheel for notebook-as-pdf: filename=notebook_as_pdf-0.1.0-py3-none-any.whl size=5394 sha256=5437ce2b1946010e4dee232c90eaaf8dc9119a0d7f7c3f41a6b4043ffe4a7a52
   Stored in directory: /tmp/pip-ephem-wheel-cache-gmcqdqkf/wheels/db/24/c0/da0bf437e8ab1e0926f6a3554b2f116afa9b8b514d316fe8f0
   Building wheel for PyPDF2 (setup.py): started
   Building wheel for PyPDF2 (setup.py): finished with status 'done'
   Created wheel for PyPDF2: filename=PyPDF2-1.26.0-py3-none-any.whl size=61084 sha256=b7c1da81cedd303618cf3848e67a5554820a1e35817abdbcf27799d002dab605
   Stored in directory: /root/.cache/pip/wheels/b1/1a/8f/a4c34be976825a2f7948d0fa40907598d69834f8ab5889de11
 Successfully built notebook-as-pdf PyPDF2
 Installing collected packages: websockets, pyee, urllib3, appdirs, pyppeteer, PyPDF2, notebook-as-pdf
 Successfully installed PyPDF2-1.26.0 appdirs-1.4.4 notebook-as-pdf-0.1.0 pyee-7.0.2 pyppeteer-0.2.2 urllib3-1.25.9 websockets-8.1

  • Putting back --execute is still ok after the above.

  • So then, I moved the installation of notebook-as-pdf back into requirements.txt so as to get

Collecting notebook-as-pdf==0.1.0
   Downloading notebook_as_pdf-0.1.0-py3-none-any.whl (5.3 kB)

but that generates a

   File "/usr/local/lib/python3.8/site-packages/notebook_as_pdf/__init__.py", line 17, in <module>
     import pikepdf
   File "/usr/local/lib/python3.8/site-packages/pikepdf/__init__.py", line 48, in <module>
     from .models import (
   File "/usr/local/lib/python3.8/site-packages/pikepdf/models/__init__.py", line 11, in <module>
     from .image import PdfImage, PdfInlineImage, UnsupportedImageTypeError
   File "/usr/local/lib/python3.8/site-packages/pikepdf/models/image.py", line 17, in <module>
     from pikepdf import (
   File "/usr/local/lib/python3.8/site-packages/pikepdf/jbig2.py", line 11, in <module>
     from PIL import Image
 ModuleNotFoundError: No module named 'PIL'

  • One other thing I tried was to skip the apt-get step, but that was also not a happy camper (unsurprisingly).

  • Finally, the PDF coming out the other side is a long single-page document, which is a little hard to navigate. But, of course, that may just be a feature.

@betatim betatim mentioned this issue Jun 30, 2020
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@betatim
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betatim commented Jun 30, 2020

Thanks a lot!

The v0.1.0 when you install from master is because someone (coughcough) forgot to update the contents of the setup.py so it still shows 0.1.0.

I've added todo items to #12 which should fix the problem you had (--no-sandbox not being turned on).

The one page PDF is very much a feature 😀 If you don't need to print it, why limit yourself to weird A4 pages with all the "how do we split content across page breaks" problems. If you do want to print the notebook onto paper, you probably need a different extension. For navigation help checkout the stretch goal in #12.

I'll close this now.

@betatim betatim closed this as completed Jun 30, 2020
@adavidzh
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adavidzh commented Jul 1, 2020

Grand. Thanks for helping out someone who's a newb (cough cough).

For navigation help [...]

This is exactly what I had in mind when I asked about it.

I agree that pages are arbitrary, but https://site/file.pdf#page=N is a staple for me when sharing information, but I wonder if one could make use of a more granular way.

@betatim
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betatim commented Jul 1, 2020

I think if we can make the TOC thing work there will be "destinations" in the PDF. Not sure yet how people would discover their name but it would allow you to link to a heading. I'll keep you posted.

@adavidzh
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adavidzh commented Jul 1, 2020

I think if we can make the TOC thing work there will be "destinations" in the PDF. Not sure yet how people would discover their name but it would allow you to link to a heading. I'll keep you posted.

Your comment just crossed my comment in #12.

@snmhas
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snmhas commented Jul 8, 2020

I installed the 0.3.1 version but i have the same error when i run the commands below

jupyter-nbconvert --to PDFviaHTML histogram.ipynb
jupyter-nbconvert --execute --to PDFviaHTML histogram.ipynb

Traceback (most recent call last):
File "/usr/local/bin/jupyter-nbconvert", line 8, in
sys.exit(main())
File "/usr/local/lib/python3.7/dist-packages/jupyter_core/application.py", line 270, in launch_instance
return super(JupyterApp, cls).launch_instance(argv=argv, **kwargs)
File "/usr/local/lib/python3.7/dist-packages/traitlets/config/application.py", line 664, in launch_instance
app.start()
File "/usr/local/lib/python3.7/dist-packages/nbconvert/nbconvertapp.py", line 340, in start
self.convert_notebooks()
File "/usr/local/lib/python3.7/dist-packages/nbconvert/nbconvertapp.py", line 510, in convert_notebooks
self.convert_single_notebook(notebook_filename)
File "/usr/local/lib/python3.7/dist-packages/nbconvert/nbconvertapp.py", line 481, in convert_single_notebook
output, resources = self.export_single_notebook(notebook_filename, resources, input_buffer=input_buffer)
File "/usr/local/lib/python3.7/dist-packages/nbconvert/nbconvertapp.py", line 410, in export_single_notebook
output, resources = self.exporter.from_filename(notebook_filename, resources=resources)
File "/usr/local/lib/python3.7/dist-packages/nbconvert/exporters/exporter.py", line 179, in from_filename
return self.from_file(f, resources=resources, **kw)
File "/usr/local/lib/python3.7/dist-packages/nbconvert/exporters/exporter.py", line 197, in from_file
return self.from_notebook_node(nbformat.read(file_stream, as_version=4), resources=resources, **kw)
File "/usr/local/lib/python3.7/dist-packages/notebook_as_pdf/init.py", line 235, in from_notebook_node
**kwargs,
File "/usr/lib/python3.7/concurrent/futures/_base.py", line 435, in result
return self.__get_result()
File "/usr/lib/python3.7/concurrent/futures/_base.py", line 384, in __get_result
raise self._exception
File "/usr/lib/python3.7/concurrent/futures/thread.py", line 57, in run
result = self.fn(*self.args, **self.kwargs)
File "/usr/lib/python3.7/asyncio/runners.py", line 43, in run
return loop.run_until_complete(main)
File "/usr/lib/python3.7/asyncio/base_events.py", line 587, in run_until_complete
return future.result()
File "/usr/local/lib/python3.7/dist-packages/notebook_as_pdf/init.py", line 180, in notebook_to_pdf
heading_positions = await html_to_pdf(f.name, pdf_path, pyppeteer_args)
File "/usr/local/lib/python3.7/dist-packages/notebook_as_pdf/init.py", line 28, in html_to_pdf
args=pyppeteer_args or [],
File "/usr/local/lib/python3.7/dist-packages/pyppeteer/launcher.py", line 305, in launch
return await Launcher(options, **kwargs).launch()
File "/usr/local/lib/python3.7/dist-packages/pyppeteer/launcher.py", line 166, in launch
self.browserWSEndpoint = get_ws_endpoint(self.url)
File "/usr/local/lib/python3.7/dist-packages/pyppeteer/launcher.py", line 225, in get_ws_endpoint
raise BrowserError('Browser closed unexpectedly:\n')
pyppeteer.errors.BrowserError: Browser closed unexpectedly:

Error in atexit._run_exitfuncs:
Traceback (most recent call last):
File "/usr/local/lib/python3.7/dist-packages/pyppeteer/launcher.py", line 151, in _close_process
self._loop.run_until_complete(self.killChrome())
File "/usr/lib/python3.7/asyncio/base_events.py", line 562, in run_until_complete
self._check_closed()
File "/usr/lib/python3.7/asyncio/base_events.py", line 479, in _check_closed
raise RuntimeError('Event loop is closed')
RuntimeError: Event loop is closed
sys:1: RuntimeWarning: coroutine 'Launcher.killChrome' was never awaited
RuntimeWarning: Enable tracemalloc to get the object allocation traceback

@betatim
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betatim commented Jul 8, 2020

Did you install the packages listed in https://github.com/betatim/notebook-as-pdf/blob/master/binder/apt.txt ?

If yes, what happens if you run jupyter-nbconvert --PDFExporter.no_sandbox=True --to PDFviaHTML some-notebook.ipynb?

@snmhas
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snmhas commented Jul 8, 2020

Yest, it works. I tried to install apt packages but i was getting some errors. Now i am able to install apt packages. Sorry to bother you.

@betatim
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betatim commented Jul 8, 2020

What do you mean with "it works"? Did it start working after you installed the APT packages or after you tried with the no_sandbox command line flag?

@snmhas
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snmhas commented Jul 8, 2020

After I installed the apt packages I run the command below and it worked.

jupyter-nbconvert --to PDFviaHTML histogram.ipynb

@betatim
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betatim commented Jul 9, 2020

Thanks for trying out this package and sharing what worked/didn't work :)

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