Cannot install synapser due to a problem with MarkupSafe

[yocra3]

Operating system

Ubuntu 18.04.5 LTS

Description of the problem

There is an error when installing MarkupSafe:

> install.packages("synapser", repos=c("http://ran.synapse.org", "http://cran.fhcrc.org"))
Installing package into ‘/home/genetica/R/x86_64-pc-linux-gnu-library/3.6’
(as ‘lib’ is unspecified)
probando la URL 'http://ran.synapse.org/src/contrib/synapser_0.8.71.tar.gz'
Content type 'application/x-tar' length 132104 bytes (129 KB)
==================================================
downloaded 129 KB

* installing *source* package ‘synapser’ ...
** using staged installation
Loading required package: R6
Loading required package: rjson
Loading required package: R6
Loading required package: rjson
You are using pip version 18.1, however version 20.2.3 is available.
You should consider upgrading via the 'pip install --upgrade pip' command.
You are using pip version 18.1, however version 20.2.3 is available.
You should consider upgrading via the 'pip install --upgrade pip' command.
You are using pip version 18.1, however version 20.2.3 is available.
You should consider upgrading via the 'pip install --upgrade pip' command.
Command "python setup.py egg_info" failed with error code 1 in /tmp/pip-install-c4ouwebu/MarkupSafe/
You are using pip version 18.1, however version 20.2.3 is available.
You should consider upgrading via the 'pip install --upgrade pip' command.
Traceback (most recent call last):

  File "<string>", line 1, in <module>

  File "/tmp/RtmpSd9Qnv/R.INSTALL8fb572759ef/synapser/inst/python/installPythonClient.py", line 137, in main

], localSitePackages)
  File "/tmp/RtmpSd9Qnv/R.INSTALL8fb572759ef/synapser/inst/python/installPythonClient.py", line 172, in _install_pip

raise Exception("pip.main returned {} when installing {}".format(rc, package))
Exception
: 
pip.main returned 1 when installing MarkupSafe==1.0
Error in PythonEmbedInR::pyExec(command) : 
  An error has occurred while executing Python code. See traceback above.
Ejecución interrumpida
ERROR: configuration failed for package ‘synapser’
* removing ‘/home/genetica/R/x86_64-pc-linux-gnu-library/3.6/synapser’

The downloaded source packages are in
    ‘/tmp/RtmpWEd6TS/downloaded_packages’
Warning message:
In install.packages("synapser", repos = c("http://ran.synapse.org",  :
  installation of package ‘synapser’ had non-zero exit status

The problem is due to that synapser is trying to install an old version of MarkupSafe. When trying to install it in command line, directly with pip, I can install MarkupSafe 1.1:

> pip3 install MarkupSafe
Collecting MarkupSafe
  Cache entry deserialization failed, entry ignored
  Using cached https://files.pythonhosted.org/packages/b2/5f/23e0023be6bb885d00ffbefad2942bc51a620328ee910f64abe5a8d18dd1/MarkupSafe-1.1.1-cp36-cp36m-manylinux1_x86_64.whl
Installing collected packages: MarkupSafe
Successfully installed MarkupSafe-1.1.1

But not MarkupSafe 1.0:

> pip3 install MarkupSafe-1.0
Collecting MarkupSafe-1.0
Exception:
Traceback (most recent call last):
  File "/usr/lib/python3/dist-packages/pip/basecommand.py", line 215, in main
    status = self.run(options, args)
  File "/usr/lib/python3/dist-packages/pip/commands/install.py", line 353, in run
    wb.build(autobuilding=True)
  File "/usr/lib/python3/dist-packages/pip/wheel.py", line 749, in build
    self.requirement_set.prepare_files(self.finder)
  File "/usr/lib/python3/dist-packages/pip/req/req_set.py", line 380, in prepare_files
    ignore_dependencies=self.ignore_dependencies))
  File "/usr/lib/python3/dist-packages/pip/req/req_set.py", line 554, in _prepare_file
    require_hashes
  File "/usr/lib/python3/dist-packages/pip/req/req_install.py", line 278, in populate_link
    self.link = finder.find_requirement(self, upgrade)
  File "/usr/lib/python3/dist-packages/pip/index.py", line 465, in find_requirement
    all_candidates = self.find_all_candidates(req.name)
  File "/usr/lib/python3/dist-packages/pip/index.py", line 423, in find_all_candidates
    for page in self._get_pages(url_locations, project_name):
  File "/usr/lib/python3/dist-packages/pip/index.py", line 568, in _get_pages
    page = self._get_page(location)
  File "/usr/lib/python3/dist-packages/pip/index.py", line 683, in _get_page
    return HTMLPage.get_page(link, session=self.session)
  File "/usr/lib/python3/dist-packages/pip/index.py", line 795, in get_page
    resp.raise_for_status()
  File "/usr/share/python-wheels/requests-2.18.4-py2.py3-none-any.whl/requests/models.py", line 935, in raise_for_status
    raise HTTPError(http_error_msg, response=self)
requests.exceptions.HTTPError: 404 Client Error: Not Found for url: https://pypi.org/simple/markupsafe-1-0/

Expected behavior

Install synapser.

Actual behavior

Synapser fails to install.

Output of sessionInfo()

> sessionInfo()
R version 3.6.3 (2020-02-29)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 18.04.5 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.7.1
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.7.1

locale:
 [1] LC_CTYPE=es_ES.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=es_ES.UTF-8        LC_COLLATE=es_ES.UTF-8    
 [5] LC_MONETARY=es_ES.UTF-8    LC_MESSAGES=es_ES.UTF-8   
 [7] LC_PAPER=es_ES.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=es_ES.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

loaded via a namespace (and not attached):
[1] compiler_3.6.3 tools_3.6.3   

[jkiang13]

Closing as.a duplicate of https://github.com/Sage-Bionetworks/synapser/issues/286