One or more Python packages fails to install... but which?

[JThomasWatson]

Bug Report

Github issues is reserved for bug report. If you have a question, please don't use this form.
Instead, please ask your question on the Synapse Help Forum.

Operating system

Windows 10

Description of the problem

I'm trying to install the synapser R package using install.packages("synapser", repos=c("http://ran.synapse.org", "http://cran.fhcrc.org")), which appears to work without error. However, when I library(synapser) I get an error message that says there are Python package/s that failed to install. I've set dependencies=TRUE and separately installed the Python packages mentioned in the console output from the library command - requests, pandas, pysftp, jinja2, markupsafe - but the error persists.

Expected behavior

I expected the package to install and load successfully.

Actual behavior

Below is the complete console output from installing and attempting to library the synapser package.

> install.packages("synapser", repos=c("http://ran.synapse.org", "http://cran.fhcrc.org"), dependencies = TRUE)
trying URL 'http://ran.synapse.org/bin/windows/contrib/4.3/synapser_1.1.0.119.zip'
Content type 'application/zip' length 362009 bytes (353 KB)
downloaded 353 KB

package ‘synapser’ successfully unpacked and MD5 sums checked

The downloaded binary packages are in
	C:\Users\qbk7582\AppData\Local\Temp\RtmpMJDMvF\downloaded_packages
> library(synapser)
+ "C:/Users/qbk7582/AppData/Local/r-miniconda/condabin/conda.bat" "install" "--yes" "--name" "r-reticulate" "-c" "conda-forge" "requests" "pandas" "pysftp" "jinja2" "markupsafe"
Channels:
 - conda-forge
 - bioconda
 - defaults
Platform: win-64
Collecting package metadata (repodata.json): ...working... failed

# >>>>>>>>>>>>>>>>>>>>>> ERROR REPORT <<<<<<<<<<<<<<<<<<<<<<

    Traceback (most recent call last):
      File "C:\Users\qbk7582\AppData\Local\R-MINI~1\Lib\site-packages\conda\exception_handler.py", line 16, in __call__
        return func(*args, **kwargs)
               ^^^^^^^^^^^^^^^^^^^^^
      File "C:\Users\qbk7582\AppData\Local\R-MINI~1\Lib\site-packages\conda\cli\main.py", line 84, in main_subshell
        exit_code = do_call(args, p)
                    ^^^^^^^^^^^^^^^^
      File "C:\Users\qbk7582\AppData\Local\R-MINI~1\Lib\site-packages\conda\cli\conda_argparse.py", line 126, in do_call
        return getattr(module, func_name)(args, parser)
               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
      File "C:\Users\qbk7582\AppData\Local\R-MINI~1\Lib\site-packages\conda\notices\core.py", line 123, in wrapper
        return func(*args, **kwargs)
               ^^^^^^^^^^^^^^^^^^^^^
      File "C:\Users\qbk7582\AppData\Local\R-MINI~1\Lib\site-packages\conda\cli\main_install.py", line 22, in execute
        install(args, parser, "install")
      File "C:\Users\qbk7582\AppData\Local\R-MINI~1\Lib\site-packages\conda\cli\install.py", line 309, in install
        unlink_link_transaction = solver.solve_for_transaction(
                                  ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
      File "C:\Users\qbk7582\AppData\Local\R-MINI~1\Lib\site-packages\conda\core\solve.py", line 153, in solve_for_transaction
        unlink_precs, link_precs = self.solve_for_diff(
                                   ^^^^^^^^^^^^^^^^^^^^
      File "C:\Users\qbk7582\AppData\Local\R-MINI~1\Lib\site-packages\conda\core\solve.py", line 214, in solve_for_diff
        final_precs = self.solve_final_state(
                      ^^^^^^^^^^^^^^^^^^^^^^^
      File "C:\Users\qbk7582\AppData\Local\R-MINI~1\Lib\site-packages\conda_libmamba_solver\solver.py", line 185, in solve_final_state
        index = LibMambaIndexHelper(
                ^^^^^^^^^^^^^^^^^^^^
      File "C:\Users\qbk7582\AppData\Local\R-MINI~1\Lib\site-packages\conda_libmamba_solver\index.py", line 125, in __init__
        self._index = self._load_channels()
                      ^^^^^^^^^^^^^^^^^^^^^
      File "C:\Users\qbk7582\AppData\Local\R-MINI~1\Lib\site-packages\conda_libmamba_solver\index.py", line 248, in _load_channels
        jsons = {url: str(path) for (url, path) in executor.map(self._fetch_channel, urls)}
                ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
      File "C:\Users\qbk7582\AppData\Local\R-MINI~1\Lib\site-packages\conda_libmamba_solver\index.py", line 248, in <dictcomp>
        jsons = {url: str(path) for (url, path) in executor.map(self._fetch_channel, urls)}
                ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
      File "C:\Users\qbk7582\AppData\Local\R-MINI~1\Lib\concurrent\futures\_base.py", line 619, in result_iterator
        yield _result_or_cancel(fs.pop())
              ^^^^^^^^^^^^^^^^^^^^^^^^^^^
      File "C:\Users\qbk7582\AppData\Local\R-MINI~1\Lib\concurrent\futures\_base.py", line 317, in _result_or_cancel
        return fut.result(timeout)
               ^^^^^^^^^^^^^^^^^^^
      File "C:\Users\qbk7582\AppData\Local\R-MINI~1\Lib\concurrent\futures\_base.py", line 456, in result
        return self.__get_result()
               ^^^^^^^^^^^^^^^^^^^
      File "C:\Users\qbk7582\AppData\Local\R-MINI~1\Lib\concurrent\futures\_base.py", line 401, in __get_result
        raise self._exception
      File "C:\Users\qbk7582\AppData\Local\R-MINI~1\Lib\concurrent\futures\thread.py", line 58, in run
        result = self.fn(*self.args, **self.kwargs)
                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
      File "C:\Users\qbk7582\AppData\Local\R-MINI~1\Lib\site-packages\conda_libmamba_solver\index.py", line 214, in _fetch_channel
        json_path, _ = subdir_data.repo_fetch.fetch_latest_path()
                       ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
      File "C:\Users\qbk7582\AppData\Local\R-MINI~1\Lib\site-packages\conda\gateways\repodata\__init__.py", line 769, in fetch_latest_path
        _, state = self.fetch_latest()
                   ^^^^^^^^^^^^^^^^^^^
      File "C:\Users\qbk7582\AppData\Local\R-MINI~1\Lib\site-packages\conda\gateways\repodata\__init__.py", line 819, in fetch_latest
        cache.load_state()
      File "C:\Users\qbk7582\AppData\Local\R-MINI~1\Lib\site-packages\conda\gateways\repodata\__init__.py", line 625, in load_state
        self.load(state_only=True)
      File "C:\Users\qbk7582\AppData\Local\R-MINI~1\Lib\site-packages\conda\gateways\repodata\__init__.py", line 575, in load
        state = json.loads(state_file.read())
                ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
      File "C:\Users\qbk7582\AppData\Local\R-MINI~1\Lib\json\__init__.py", line 346, in loads
        return _default_decoder.decode(s)
               ^^^^^^^^^^^^^^^^^^^^^^^^^^
      File "C:\Users\qbk7582\AppData\Local\R-MINI~1\Lib\json\decoder.py", line 337, in decode
        obj, end = self.raw_decode(s, idx=_w(s, 0).end())
                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
      File "C:\Users\qbk7582\AppData\Local\R-MINI~1\Lib\json\decoder.py", line 355, in raw_decode
        raise JSONDecodeError("Expecting value", s, err.value) from None
    json.decoder.JSONDecodeError: Expecting value: line 1 column 1 (char 0)

`$ C:\Users\qbk7582\AppData\Local\R-MINI~1\Scripts\conda-script.py install --yes --name r-reticulate -c conda-forge requests pandas pysftp jinja2 markupsafe`

  environment variables:
                 CIO_TEST=<not set>
                CONDA_EXE=C:\Users\qbk7582\AppData\Local\R-MINI~1\condabin\..\Scripts\conda.exe
               CONDA_EXES="C:\Users\qbk7582\AppData\Local\R-
                          MINI~1\condabin\..\Scripts\conda.exe"
               CONDA_ROOT=C:\Users\qbk7582\AppData\Local\R-MINI~1
                CUDA_PATH=C:\Program Files\NVIDIA GPU Computing Toolkit\CUDA\v11.8
           CURL_CA_BUNDLE=C:/Users/qbk7582/AppData/Local/Programs/R/R-4.3.0/etc/curl-ca-
                          bundle.crt
                 HOMEPATH=\Users\qbk7582
               LD_PRELOAD=<not set>
          NVTOOLSEXT_PATH=C:\Program Files\NVIDIA Corporation\NvToolsExt\
                     PATH=C:\Users\qbk7582\AppData\Local\r-
                          miniconda\condabin;C:\Users\qbk7582\AppData\Local\r-
                          miniconda\Scripts;C:\Users\qbk7582\AppData\Local\r-
                          miniconda\Library\bin;C:\Users\qbk7582\AppData\Local\Programs\Python\P
                          ython311;C:\Users\qbk7582\AppData\Local\Programs\Python\Python311\Scri
                          pts;C:\rtools43\x86_64-w64-
                          mingw32.static.posix\bin;C:\rtools43\usr\bin;C:\Users\qbk7582\AppData\
                          Local\Programs\R\R-4.3.0\bin\x64;C:\Program Files\NVIDIA GPU Computing
                          Toolkit\CUDA\v11.8\bin;C:\Program Files\NVIDIA GPU Computing
                          Toolkit\CUDA\v11.8\libnvvp;C:\Program Files\Common
                          Files\Oracle\Java\javapath_target_958656;C:\Program Files (x86)\Common
                          Files\Oracle\Java\javapath_target_22315328;C:\Windows\System32;C:\Wind
                          ows;C:\Windows\System32\wbem;C:\Windows\System32\WindowsPowerShell\v1.
                          0;C:\Windows\System32\OpenSSH;C:\Program Files
                          (x86)\Sennheiser\SoftphoneSDK;C:\Program Files\PuTTY;C:\Program
                          Files\Git\cmd;C:\Program Files\Docker\Docker\resources\bin;C:\Program
                          Files\NVIDIA Corporation\Nsight Compute 2022.3.0;C:\Program Files
                          (x86)\NVIDIA Corporation\PhysX\Common;C:\Users\qbk7582\AppData\Local\M
                          icrosoft\WindowsApps;C:\Users\qbk7582\AppData\Local\Programs\Git\cmd;C
                          :\Users\qbk7582\AppData\Local;C:\Users\qbk7582\AppData\Local\GitHubDes
                          ktop\bin;C:\Users\qbk7582\AppData\Local\Programs\Microsoft VS
                          Code\bin;C:\Program
                          Files\RStudio\resources\app\bin\quarto\bin;C:\Program
                          Files\RStudio\resources\app\bin\postback
             PSMODULEPATH=C:\Program Files\WindowsPowerShell\Modules;C:\windows\system32\Windows
                          PowerShell\v1.0\Modules
         PYTHONIOENCODING=utf-8
       REQUESTS_CA_BUNDLE=<not set>
   RMARKDOWN_MATHJAX_PATH=C:/Program Files/RStudio/resources/app/resources/mathjax-27
        RS_RPOSTBACK_PATH=C:/Program Files/RStudio/resources/app/bin/rpostback.exe
          R_RTOOLS43_PATH=C:\rtools43/x86_64-w64-mingw32.static.posix/bin;C:\rtools43/usr/bin
            SSL_CERT_FILE=<not set>

     active environment : None
       user config file : C:\Users\qbk7582\.condarc
 populated config files : C:\Users\qbk7582\.condarc
          conda version : 23.5.2
    conda-build version : not installed
         python version : 3.11.4.final.0
       virtual packages : __archspec=1=x86_64
                          __cuda=11.8=0
                          __win=0=0
       base environment : C:\Users\qbk7582\AppData\Local\R-MINI~1  (writable)
      conda av data dir : C:\Users\qbk7582\AppData\Local\R-MINI~1\etc\conda
  conda av metadata url : None
           channel URLs : https://conda.anaconda.org/conda-forge/win-64
                          https://conda.anaconda.org/conda-forge/noarch
                          https://conda.anaconda.org/bioconda/win-64
                          https://conda.anaconda.org/bioconda/noarch
                          https://repo.anaconda.com/pkgs/main/win-64
                          https://repo.anaconda.com/pkgs/main/noarch
                          https://repo.anaconda.com/pkgs/r/win-64
                          https://repo.anaconda.com/pkgs/r/noarch
                          https://repo.anaconda.com/pkgs/msys2/win-64
                          https://repo.anaconda.com/pkgs/msys2/noarch
          package cache : C:\Users\qbk7582\AppData\Local\R-MINI~1\pkgs
                          C:\Users\qbk7582\.conda\pkgs
                          C:\Users\qbk7582\AppData\Local\conda\conda\pkgs
       envs directories : C:\Users\qbk7582\AppData\Local\R-MINI~1\envs
                          C:\Users\qbk7582\.conda\envs
                          C:\Users\qbk7582\AppData\Local\conda\conda\envs
               platform : win-64
             user-agent : conda/23.5.2 requests/2.29.0 CPython/3.11.4 Windows/10 Windows/10.0.19045 solver/libmamba conda-libmamba-solver/23.5.0 libmambapy/1.4.1
          administrator : False
             netrc file : None
           offline mode : False


An unexpected error has occurred. Conda has prepared the above report.

Upload successful.
Error: package or namespace load failed for ‘synapser’:
 .onLoad failed in loadNamespace() for 'synapser', details:
  call: NULL
  error: one or more Python packages failed to install [error code 1]

[thomasyu888]

Hi @JThomasWatson , I will open up a ticket within synapser to track this issue.

By the looks of it, it seems like your R environment is using conda to try to install it's python dependencies when using reticulate which could be an issue. Let me dig into this more.

[JThomasWatson]

Hi, @thomasyu888. I ended up using the command line to bypass the issue altogether, and was able to download the files I needed.

[thomasyu888]

Hi @JThomasWatson ,

Thanks for letting us know - glad the command line client worked out for you.

We are still investigating this issue, but I will shift this to another github repo.