PATH and RETICULATE_PATH are ignored when setting up Python virtual environment

[sage-bionetworks]

PATH and RETICULATE_PATH are ignored when setting up Python virtual environment

[thomasyu888]

HI @pvo93 ,

Thanks for using synapser. Can you try doing this:

require(reticulate)
reticulate::use_python("/usr/local/biotools/python/3.10.7/bin/python")
install.packages("synapser", repos = c("http://ran.synapse.org/", "http://cran.fhcrc.org/"))

[pvo93]

It still seems to be looking for Python 2.7 libraries.

require(reticulate)
Loading required package: reticulate
install.packages("synapser", repos = c("http://ran.synapse.org/", "http://cran.fhcrc.org/"))
Installing package into ‘/usr/local/biotools/rpackages/R-4.2.2-2023-02-01’
(as ‘lib’ is unspecified)
trying URL 'http://ran.synapse.org/src/contrib/synapser_1.2.0.143.tar.gz'
Content type 'application/x-tar' length 156600 bytes (152 KB)
==================================================
downloaded 152 KB

• installing source package ‘synapser’ ...
  ** using staged installation
  Error: PyType_GetFlags - /usr/lib64/libpython2.7.so.1.0: undefined symbol: PyType_GetFlags
  In addition: Warning message:
  In py_initialize(config$python, config$libpython, config$pythonhome, :
  Python 2 reached EOL on January 1, 2020. Python 2 compatability will be removed in an upcoming reticulate release.
  Execution halted
  [1] "*** Using Python Configuration:"
  virtualenv: r-reticulate
  Using virtual environment '/home/mayo/wa02042/.virtualenvs/r-reticulate' ...

• /home/mayo/wa02042/.virtualenvs/r-reticulate/bin/python -m pip install --upgrade --no-user 'requests<3' 'pandas~=2.0.0' pysftp jinja2 markupsafe
  DEPRECATION: Python 2.7 reached the end of its life on January 1st, 2020. Please upgrade your Python as Python 2.7 is no longer maintained. pip 21.0 will drop support for Python 2.7 in January 2021. More details about Python 2 support in pip can be found at https://pip.pypa.io/en/latest/development/release-process/#python-2-support pip 21.0 will remove support for this functionality.
  Collecting requests<3
  Using cached requests-2.27.1-py2.py3-none-any.whl (63 kB)
  ERROR: Could not find a version that satisfies the requirement pandas~=2.0.0 (from versions: 0.1, 0.2, 0.3.0, 0.4.0, 0.4.1, 0.4.2, 0.4.3, 0.5.0, 0.6.0, 0.6.1, 0.7.0, 0.7.1, 0.7.2, 0.7.3, 0.8.0, 0.8.1, 0.9.0, 0.9.1, 0.10.0, 0.10.1, 0.11.0, 0.12.0, 0.13.0, 0.13.1, 0.14.0, 0.14.1, 0.15.0, 0.15.1, 0.15.2, 0.16.0, 0.16.1, 0.16.2, 0.17.0, 0.17.1, 0.18.0, 0.18.1, 0.19.0, 0.19.1, 0.19.2, 0.20.0, 0.20.1, 0.20.2, 0.20.3, 0.21.0, 0.21.1, 0.22.0, 0.23.0, 0.23.1, 0.23.2, 0.23.3, 0.23.4, 0.24.0, 0.24.1, 0.24.2)
  ERROR: No matching distribution found for pandas~=2.0.0
  Error: Error installing package(s): "'requests<3'", "'pandas~=2.0.0'", "pysftp", "jinja2", "markupsafe"
  Execution halted
  ERROR: configuration failed for package ‘synapser’

• removing ‘/usr/local/biotools/rpackages/R-4.2.2-2023-02-01/synapser’
• restoring previous ‘/usr/local/biotools/rpackages/R-4.2.2-2023-02-01/synapser’

The downloaded source packages are in
‘/tmp/RtmpE09Aui/downloaded_packages’
Warning message:
In install.packages("synapser", repos = c("http://ran.synapse.org/", :
installation of package ‘synapser’ had non-zero exit status

[thomasyu888]

HI @pvo93

Did you run this command before installing?

reticulate::use_python("/usr/local/biotools/python/3.10.7/bin/python")

[pvo93]

Yes, I did. I ran it a second time after deleting ~/.virtualenvs/r-reticulate and forgot to include that line to paste in the output, but I had run it earlier in the session. My apologies. I just ran it again in a new session.

require(reticulate)
Loading required package: reticulate
reticulate::use_python("/usr/local/biotools/python/3.10.7/bin/python")
install.packages("synapser", repos = c("http://ran.synapse.org/", "http://cran.fhcrc.org/"))
Installing package into ‘/usr/local/biotools/rpackages/R-4.2.2-2023-02-01’
(as ‘lib’ is unspecified)
trying URL 'http://ran.synapse.org/src/contrib/synapser_1.2.0.143.tar.gz'
Content type 'application/x-tar' length 156600 bytes (152 KB)
==================================================
downloaded 152 KB

• installing source package ‘synapser’ ...
  ** using staged installation
  Error: PyType_GetFlags - /usr/lib64/libpython2.7.so.1.0: undefined symbol: PyType_GetFlags
  In addition: Warning message:
  In py_initialize(config$python, config$libpython, config$pythonhome, :
  Python 2 reached EOL on January 1, 2020. Python 2 compatability will be removed in an upcoming reticulate release.
  Execution halted
  [1] "*** Using Python Configuration:"
  virtualenv: r-reticulate
  Using virtual environment '/home/mayo/wa02042/.virtualenvs/r-reticulate' ...

• /home/mayo/wa02042/.virtualenvs/r-reticulate/bin/python -m pip install --upgrade --no-user 'requests<3' 'pandas~=2.0.0' pysftp jinja2 markupsafe
  DEPRECATION: Python 2.7 reached the end of its life on January 1st, 2020. Please upgrade your Python as Python 2.7 is no longer maintained. pip 21.0 will drop support for Python 2.7 in January 2021. More details about Python 2 support in pip can be found at https://pip.pypa.io/en/latest/development/release-process/#python-2-support pip 21.0 will remove support for this functionality.
  Collecting requests<3
  Using cached requests-2.27.1-py2.py3-none-any.whl (63 kB)
  ERROR: Could not find a version that satisfies the requirement pandas~=2.0.0 (from versions: 0.1, 0.2, 0.3.0, 0.4.0, 0.4.1, 0.4.2, 0.4.3, 0.5.0, 0.6.0, 0.6.1, 0.7.0, 0.7.1, 0.7.2, 0.7.3, 0.8.0, 0.8.1, 0.9.0, 0.9.1, 0.10.0, 0.10.1, 0.11.0, 0.12.0, 0.13.0, 0.13.1, 0.14.0, 0.14.1, 0.15.0, 0.15.1, 0.15.2, 0.16.0, 0.16.1, 0.16.2, 0.17.0, 0.17.1, 0.18.0, 0.18.1, 0.19.0, 0.19.1, 0.19.2, 0.20.0, 0.20.1, 0.20.2, 0.20.3, 0.21.0, 0.21.1, 0.22.0, 0.23.0, 0.23.1, 0.23.2, 0.23.3, 0.23.4, 0.24.0, 0.24.1, 0.24.2)
  ERROR: No matching distribution found for pandas~=2.0.0
  Error: Error installing package(s): "'requests<3'", "'pandas~=2.0.0'", "pysftp", "jinja2", "markupsafe"
  Execution halted
  ERROR: configuration failed for package ‘synapser’

• removing ‘/usr/local/biotools/rpackages/R-4.2.2-2023-02-01/synapser’
• restoring previous ‘/usr/local/biotools/rpackages/R-4.2.2-2023-02-01/synapser’

The downloaded source packages are in
‘/tmp/RtmpJvldw0/downloaded_packages’
Warning message:
In install.packages("synapser", repos = c("http://ran.synapse.org/", :
installation of package ‘synapser’ had non-zero exit status

[thomasyu888]

Hi @pvo93 ,

Apologies for the delays in response - I have found the bug and am attempting to fix it for the upcoming release. In the meantime, a not as ideal way to interact with the client in R can be found here: https://github.com/Sage-Bionetworks/synapsePythonClient/blob/develop/docs/articles/reticulate.rst.

You would use reticulate directly to install the client:

require(reticulate)
reticulate::use_python("/usr/local/biotools/python/3.10.7/bin/python")
reticulate::py_install("synapseclient")

The rest of the instructions can be found in the link above. Please let me know if that doesn't work while I attempt to fix the issue.