sage-bionetworks/synapser

An R package providing programmatic access to Synapse

synapser

The synapser package provides an interface to Synapse, a collaborative workspace for reproducible data intensive research projects, providing support for:

• integrated presentation of data, code and text
• fine grained access control
• provenance tracking

The synapser package lets you communicate with the Synapse platform to create collaborative data analysis projects and access data using the R programming language. Other Synapse clients exist for Python, Java, and the web browser.

Requirements

• R version 4.1.3 or higher
• Python version 3.8 or higher
• Synapse account

Installation

synapser is available as a ready-built package for Microsoft Windows and Mac OSX. For Linux systems, it is available to install from source. Please also check out our System Dependencies article for instructions on how to install system dependencies on Linux environments.

synapser can be installed or upgraded using the standard install.packages() command, adding the Sage Bionetworks R Archive Network (RAN) to the repository list, e.g.:

install.packages("synapser", repos=c("http://ran.synapse.org", "http://cran.fhcrc.org"))

Alternatively, edit your ~/.Rprofile and configure your default repositories:

options(repos=c("http://ran.synapse.org", "http://cran.fhcrc.org"))

after which you may run install.packages without specifying the repositories:

install.packages("synapser")

If you have been asked to validate a release candidate, please use:

install.packages("synapser", repos=c("http://staging-ran.synapse.org"))

Under the hood, synapser uses reticulate and the synapsePythonClient, which is why you are required to have an installation of Python if you don't already. See instructions below on installing/upgrading Python below.

Usage

To get started, try logging into Synapse. If you don’t already have a Synapse account, register here:

library(synapser)
synLogin()

Please visit the synapser docs site or view our vignettes for using the synapser package:

browseVignettes(package = "synapser")

Usage Examples

knit2synapse

Knit RMarkdown files to Synapse wikis

syndccutils

Code for managing data coordinating operations (e.g., development of the CSBC/PS-ON Knowledge Portal and individual Center pages) for Sage-supported communities through Synapse.

How to Upgrade Python

On Windows

• Download the Python installer from the Official Website of Python here.

• Install the Downloaded Python Installer

• check Install Python and Check the “Add python.ext to PATH”, then click on the “Install Now” button.

• Verify the Update

  python --version

• Note If it still shows the old version, you may restart your system. Or uninstall the old version from the control panel.

On macOS

• Both python 2x and 3x can stay installed in a MAC. Mac comes with python 2x version. To check the default python version in your MAC, open the terminal and type

  python --version
  python3 --version

• If you don't then go ahead and install it with the installer. Go the the python's official site here.

• Now restart the terminal and check again with both commands python —version

  python3 --version

• Or use to install last version

  brew install python3 && cp /usr/local/bin/python3 /usr/local/bin/python

On Linux

• Add the repository and update

  sudo add-apt-repository ppa:deadsnakes/ppa
  sudo apt-get update

• Update the package list

  apt-get update

• Verify the updated Python packages list

  apt list | grep python3.10

• Install the Python 3.10 package using apt-get

  sudo apt-get install python3.10

• Add Python 3.8 & Python 3.10 to update-alternatives

  sudo update-alternatives --install /usr/bin/python3 python3 /usr/bin/python3.8 1
  sudo update-alternatives --install /usr/bin/python3 python3 /usr/bin/python3.10 2

• Update Python 3 for point to Python 3.10

  sudo update-alternatives --config python3

How to Upgrade R

• Verify R version
  • Open RStudio > At the top of the Console you will see session info > The first line tells you which version of R you are using.
  • or write in console >'R.version.string' to print out the R version.
  • go to Tools > Check for Package Updates. If there's an update available for tidyverse, install it.

On Windows

• To update R on Windows, try using the package installer (only for Windows).
• Got to Tools (at the top) > Check for package updates. If tidyverse shows up on the list, select it, then click “Install Updates.”

On Mac

• Go to here.
• Click the link you need to update R pkg
• When the file finishes downloading, double-click to install. You should be able to click “Next” to all dialogs to finish the installation.
• From within RStudio, go to Help > Check for Updates to install newer version of RStudio (if available, optional).
• To update packages, go to Tools > Check for Package Updates. If updates are available, select All (or just tidyverse), and click Install Updates.

synapser's Issues

Installation issue

Hi developers!

I have some installation issues.

My OS is 18.04.1-Ubuntu. Yesterday I've tried to install synapser after having installed all the system dependencies as required for Ubuntu in the documentation. But I have been unsuccessful.
Reading some previous issues and posts I've thought to remove reticulate since I am not using it and the compatibility issues.

Now when I try to install synapser I get the following:

install.packages("synapser", repos = c("http://ran.synapse.org", "http://cran.fhcrc.org"))
Installing package into ‘/home/francesco/R/x86_64-pc-linux-gnu-library/4.0’
(as ‘lib’ is unspecified)
also installing the dependency ‘PythonEmbedInR’

[...]

Error in loadNamespace(name) : there is no package called ‘reticulate’
Calls: :: ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Warning in install.packages :
installation of package ‘PythonEmbedInR’ had non-zero exit status
Error in loadNamespace(name) : there is no package called ‘reticulate’
Calls: :: ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Warning in install.packages :
installation of package ‘synapser’ had non-zero exit status

The downloaded source packages are in
‘/tmp/RtmpaLllNY/downloaded_packages’

I don't understand the meaning of the error.

sessionInfo()
R version 4.0.2 (2020-06-22)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 18.04.4 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=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8
[4] LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C LC_ADDRESS=C
[10] LC_TELEPHONE=C LC_MEASUREMENT=en_US.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_4.0.2 tools_4.0.2

Can you help me?

Thank you
Francesco

Error installing in Anaconda environment

Operating system

macOS Mojave, version 10.14.1 (18B75)

Description of the problem

Attempting to install synapser within an Anaconda (i.e., conda) environment fails with an error seemingly related to libssl and PythonEmbedInR.

$ conda create -n synapser r-base
$ conda activate synapser
$ Rscript -e 'install.packages("synapser", repos=c("https://sage-bionetworks.github.io/ran", "http://cran.fhcrc.org"))'

Note: Anaconda installation details (before conda activate step):

$ conda info

     active environment : None
            shell level : 0
       user config file : /Users/jaeddy/.condarc
 populated config files : /Users/jaeddy/.condarc
          conda version : 4.5.12
    conda-build version : 2.1.3
         python version : 3.6.7.final.0
       base environment : /Users/jaeddy/anaconda  (writable)
           channel URLs : https://conda.anaconda.org/bioconda/osx-64
                          https://conda.anaconda.org/bioconda/noarch
                          https://conda.anaconda.org/r/osx-64
                          https://conda.anaconda.org/r/noarch
                          https://repo.anaconda.com/pkgs/main/osx-64
                          https://repo.anaconda.com/pkgs/main/noarch
                          https://repo.anaconda.com/pkgs/free/osx-64
                          https://repo.anaconda.com/pkgs/free/noarch
                          https://repo.anaconda.com/pkgs/r/osx-64
                          https://repo.anaconda.com/pkgs/r/noarch
                          https://repo.anaconda.com/pkgs/pro/osx-64
                          https://repo.anaconda.com/pkgs/pro/noarch
                          https://conda.anaconda.org/conda-forge/osx-64
                          https://conda.anaconda.org/conda-forge/noarch
          package cache : /Users/jaeddy/anaconda/pkgs
                          /Users/jaeddy/.conda/pkgs
       envs directories : /Users/jaeddy/anaconda/envs
                          /Users/jaeddy/.conda/envs
               platform : osx-64
             user-agent : conda/4.5.12 requests/2.18.4 CPython/3.6.7 Darwin/18.2.0 OSX/10.14.1
                UID:GID : 503:20
             netrc file : None
           offline mode : False

Expected behavior

Successful installation of package.

Actual behavior

$ Rscript -e 'install.packages("synapser", repos=c("https://sage-bionetworks.github.io/ran", "http://cran.fhcrc.org"))'

Terminal output

also installing the dependency ‘PythonEmbedInR’
also installing the dependencies ‘R6’, ‘rjson’, ‘pack’, ‘PythonEmbedInR’

trying URL 'http://cran.fhcrc.org/src/contrib/R6_2.3.0.tar.gz'
Content type 'application/x-gzip' length 30968 bytes (30 KB)
==================================================
downloaded 30 KB

trying URL 'http://cran.fhcrc.org/src/contrib/rjson_0.2.20.tar.gz'
Content type 'application/x-gzip' length 99600 bytes (97 KB)
==================================================
downloaded 97 KB

trying URL 'http://cran.fhcrc.org/src/contrib/pack_0.1-1.tar.gz'
Content type 'application/x-gzip' length 4061 bytes
==================================================
downloaded 4061 bytes

trying URL 'https://sage-bionetworks.github.io/ran/src/contrib/PythonEmbedInR_0.3.25.tar.gz'
Content type 'application/gzip' length 93845 bytes (91 KB)
==================================================
downloaded 91 KB

trying URL 'https://sage-bionetworks.github.io/ran/src/contrib/synapser_0.4.41.tar.gz'
Content type 'application/gzip' length 110220 bytes (107 KB)
==================================================
downloaded 107 KB

* installing *source* package ‘R6’ ...
** package ‘R6’ successfully unpacked and MD5 sums checked
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (R6)
* installing *source* package ‘rjson’ ...
** package ‘rjson’ successfully unpacked and MD5 sums checked
** libs
x86_64-apple-darwin13.4.0-clang++  -I"/Users/jaeddy/anaconda/envs/synapser/lib/R/include" -DNDEBUG   -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/Users/jaeddy/anaconda/envs/synapser/include   -fPIC  -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc++ -fvisibility-inlines-hidden  -fmessage-length=0 -I/Users/jaeddy/anaconda/envs/synapser/include -fdebug-prefix-map==/usr/local/src/conda/- -fdebug-prefix-map==/usr/local/src/conda-prefix  -c dump.cpp -o dump.o
x86_64-apple-darwin13.4.0-clang -I"/Users/jaeddy/anaconda/envs/synapser/lib/R/include" -DNDEBUG   -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/Users/jaeddy/anaconda/envs/synapser/include   -fPIC  -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -I/Users/jaeddy/anaconda/envs/synapser/include -fdebug-prefix-map==/usr/local/src/conda/- -fdebug-prefix-map==/usr/local/src/conda-prefix  -c parser.c -o parser.o
parser.c:112:40: warning: '&' within '|' [-Wbitwise-op-parentheses]
                s[ 1 ] = (MASKBYTE | ( input >> 12 ) & MASKBITS );
                                   ~ ~~~~~~~~~~~~~~~~^~~~~~~~~~
parser.c:112:40: note: place parentheses around the '&' expression to silence this warning
                s[ 1 ] = (MASKBYTE | ( input >> 12 ) & MASKBITS );
                                     ~~~~~~~~~~~~~~~~^~~~~~~~~~
1 warning generated.
x86_64-apple-darwin13.4.0-clang -I"/Users/jaeddy/anaconda/envs/synapser/lib/R/include" -DNDEBUG   -D_FORTIFY_SOURCE=2 -mmacosx-version-min=10.9 -I/Users/jaeddy/anaconda/envs/synapser/include   -fPIC  -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -I/Users/jaeddy/anaconda/envs/synapser/include -fdebug-prefix-map==/usr/local/src/conda/- -fdebug-prefix-map==/usr/local/src/conda-prefix  -c register.c -o register.o
x86_64-apple-darwin13.4.0-clang++ -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Users/jaeddy/anaconda/envs/synapser/lib/R/lib -Wl,-pie -Wl,-headerpad_max_install_names -Wl,-dead_strip_dylibs -Wl,-rpath,/Users/jaeddy/anaconda/envs/synapser/lib -L/Users/jaeddy/anaconda/envs/synapser/lib -o rjson.so dump.o parser.o register.o -L/Users/jaeddy/anaconda/envs/synapser/lib/R/lib -lR -Wl,-framework -Wl,CoreFoundation
ld: warning: -pie being ignored. It is only used when linking a main executable
ld: warning: ignoring file /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/System/Library/Frameworks//CoreFoundation.framework/CoreFoundation.tbd, file was built for unsupported file format ( 0x2D 0x2D 0x2D 0x20 0x21 0x74 0x61 0x70 0x69 0x2D 0x74 0x62 0x64 0x2D 0x76 0x33 ) which is not the architecture being linked (x86_64): /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/System/Library/Frameworks//CoreFoundation.framework/CoreFoundation.tbd
ld: warning: ignoring file /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/usr/lib/libSystem.tbd, file was built for unsupported file format ( 0x2D 0x2D 0x2D 0x20 0x21 0x74 0x61 0x70 0x69 0x2D 0x74 0x62 0x64 0x2D 0x76 0x33 ) which is not the architecture being linked (x86_64): /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.14.sdk/usr/lib/libSystem.tbd
installing to /Users/jaeddy/anaconda/envs/synapser/lib/R/library/rjson/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (rjson)
* installing *source* package ‘pack’ ...
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (pack)
* installing *source* package ‘PythonEmbedInR’ ...
./configure: line 32: wget: command not found
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
100 19.6M  100 19.6M    0     0   316k      0  0:01:03  0:01:03 --:--:--  336k
Mac specific configuration
error: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/install_name_tool: can't open input file: /private/var/folders/xt/2mpzwr2972g3_yqgjz5dbsg40000gq/T/RtmpgiZfEI/R.INSTALL737855a1deb3/PythonEmbedInR/inst/lib/libssl.1.0.0.dylib for writing (Permission denied)
error: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/install_name_tool: can't lseek to offset: 0 in file: /private/var/folders/xt/2mpzwr2972g3_yqgjz5dbsg40000gq/T/RtmpgiZfEI/R.INSTALL737855a1deb3/PythonEmbedInR/inst/lib/libssl.1.0.0.dylib for writing (Bad file descriptor)
error: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/install_name_tool: can't write new headers in file: /private/var/folders/xt/2mpzwr2972g3_yqgjz5dbsg40000gq/T/RtmpgiZfEI/R.INSTALL737855a1deb3/PythonEmbedInR/inst/lib/libssl.1.0.0.dylib (Bad file descriptor)
error: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/install_name_tool: can't close written on input file: /private/var/folders/xt/2mpzwr2972g3_yqgjz5dbsg40000gq/T/RtmpgiZfEI/R.INSTALL737855a1deb3/PythonEmbedInR/inst/lib/libssl.1.0.0.dylib (Bad file descriptor)
ERROR: configuration failed for package ‘PythonEmbedInR’
* removing ‘/Users/jaeddy/anaconda/envs/synapser/lib/R/library/PythonEmbedInR’
ERROR: dependency ‘PythonEmbedInR’ is not available for package ‘synapser’
* removing ‘/Users/jaeddy/anaconda/envs/synapser/lib/R/library/synapser’

The downloaded source packages are in
	‘/private/var/folders/xt/2mpzwr2972g3_yqgjz5dbsg40000gq/T/RtmplleVbq/downloaded_packages’
Updating HTML index of packages in '.Library'
Making 'packages.html' ... done
Warning messages:
1: In install.packages("synapser", repos = c("https://sage-bionetworks.github.io/ran",  :
  installation of package ‘PythonEmbedInR’ had non-zero exit status
2: In install.packages("synapser", repos = c("https://sage-bionetworks.github.io/ran",  :
  installation of package ‘synapser’ had non-zero exit status

Output of sessionInfo()

$ Rscript -e 'sessionInfo()'

R version 3.5.1 (2018-07-02)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: macOS  10.14.1

Matrix products: default
BLAS/LAPACK: /Users/jaeddy/anaconda/envs/synapser/lib/R/lib/libRblas.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

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

loaded via a namespace (and not attached):
[1] compiler_3.5.1

need to install ffi

Operating system

Ubuntu

Description of the problem

I needed to install libffi in order to install synapser (presumably the broken software dependencies link indicates this). On ubuntu I did:

sudo apt-get install build-essential libssl-dev libffi-dev python-dev

Expected behavior

When I attempted to install synapser
install.packages("synapser", repos=c("http://ran.synapse.org", "http://cran.fhcrc.org"))
I got the error message:
Package libffi was not found in the pkg-config search path.
Perhaps you should add the directory containing `libffi.pc'
to the PKG_CONFIG_PATH environment variable
No package 'libffi' found

What did you expect to happen?

Output of sessionInfo()

sessionInfo()
R version 3.6.0 (2019-04-26)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 18.04.2 LTS

Matrix products: default
BLAS: /usr/local/lib/R/lib/libRblas.so
LAPACK: /usr/local/lib/R/lib/libRlapack.so

locale:
[1] LC_CTYPE=C.UTF-8 LC_NUMERIC=C LC_TIME=C.UTF-8
[4] LC_COLLATE=C.UTF-8 LC_MONETARY=C.UTF-8 LC_MESSAGES=C.UTF-8
[7] LC_PAPER=C.UTF-8 LC_NAME=C LC_ADDRESS=C
[10] LC_TELEPHONE=C LC_MEASUREMENT=C.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_3.6.0 tools_3.6.0

Can't log in with .synapseConfig

Operating system

Windows 11
My Home directory is a OneDrive (ugh) folder, not sure if that is relevant

Description of the problem

I just installed the latest {synapser} on my new laptop. I got a personal auth token from Synapse and created a .synapseConfig file in my Home directory, but synLogin() returns Error in value[[3L]](cond) : No credentials provided.

I am able to log in with synLogin(authToken = "<my_token>") so the token seems to be working.

My .synapseConfig file looks like this:

[authentication]
authtoken = eyJ0eXAiOiJKV1QiLCJra..etc. [no quotes]

Output of sessionInfo()

R version 4.3.2 (2023-10-31 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 11 x64 (build 22631)

Matrix products: default


locale:
[1] LC_COLLATE=English_United States.utf8  LC_CTYPE=English_United States.utf8   
[3] LC_MONETARY=English_United States.utf8 LC_NUMERIC=C                          
[5] LC_TIME=English_United States.utf8    

time zone: America/Los_Angeles
tzcode source: internal

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

other attached packages:
[1] synapser_2.0.0.200

loaded via a namespace (and not attached):
 [1] utf8_1.2.4        codetools_0.2-19  Matrix_1.6-1.1    lattice_0.21-9   
 [5] rjson_0.2.21      reticulate_1.35.0 glue_1.7.0        png_0.1-8        
 [9] lifecycle_1.0.4   cli_3.6.2         fansi_1.0.6       vctrs_0.6.5      
[13] grid_4.3.2        compiler_4.3.2    rstudioapi_0.15.0 tools_4.3.2      
[17] pillar_1.9.0      Rcpp_1.0.12       rlang_1.1.3       jsonlite_1.8.8   

Trial Issue

Trial Issue Comment

Cannot install synapser due to a problem with MarkupSafe

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   

synQuery() does not seem to retrieve complex annotations

Operating system

Ubuntu 18.04 LTS

Description of the problem

Consider syn16780473, which is an example file containing a complex annotation Field1:

When calling synQuery( 'select id,Field1 from entity where parentId=="syn12180284" and Field2==123' ), the result seems to only contain "abc".

Expected behavior

If the result of synQuery() above was stored into a variable named r, we expect that r$results[[1]]$entity.Field1 would be list( "abc", "def" ) to match synGetAnnotations( "syn16780473" )$Field1.

Actual behavior

library( synapser )
#> 
#> TERMS OF USE NOTICE:
#>   When using Synapse, remember that the terms and conditions of use require that you:
#>   1) Attribute data contributors when discussing these data or results from these data.
#>   2) Not discriminate, identify, or recontact individuals or groups represented by the data.
#>   3) Use and contribute only data de-identified to HIPAA standards.
#>   4) Redistribute data only under these same terms of use.
synLogin()
#> Welcome, Artem Sokolov!
#> NULL

# synGetAnnotations() correctly retrieves both "abc" and "def"
str(synGetAnnotations( "syn16780473" ))
#> List of 2
#>  $ Field1:List of 2
#>   ..$ : chr "abc"
#>   ..$ : chr "def"
#>  $ Field2:List of 1
#>   ..$ : num 123

# synQuery() on the other hand retrieves only "abc"
str(synQuery( 'select id,Field1 from entity where parentId=="syn12180284" and Field2==123' ))
#> List of 2
#>  $ results             :List of 1
#>   ..$ :List of 2
#>   .. ..$ entity.id    : chr "syn16780473"
#>   .. ..$ entity.Field1:List of 1
#>   .. .. ..$ : chr "abc"
#>  $ totalNumberOfResults: num 1

Created on 2018-08-31 by the reprex package (v0.2.0).

Output of sessionInfo()

R version 3.5.1 (2018-07-02)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 18.04.1 LTS

Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/openblas/libblas.so.3
LAPACK: /usr/lib/x86_64-linux-gnu/libopenblasp-r0.2.20.so

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

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

other attached packages:
[1] synapser_0.3.40

loaded via a namespace (and not attached):
[1] compiler_3.5.1        R6_2.2.2              tools_3.5.1          
[4] pack_0.1-1            PythonEmbedInR_0.2.24

Installation of synapser failed after updating R to 3.5.2

Operating system

R version 3.5.2 (2018-12-20)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Mojave 10.14.1

Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib

Description of the problem

Installation of synapser failed after updating R to 3.5.2

Expected behavior

install.packages("synapser", repos=c("https://sage-bionetworks.github.io/ran", "http://cran.fhcrc.org"))
No errors

Actual behavior

rying URL 'https://sage-bionetworks.github.io/ran/bin/macosx/el-capitan/contrib/3.5/synapser_0.4.41.tgz'
Warning in install.packages :
cannot open URL 'https://sage-bionetworks.github.io/ran/bin/macosx/el-capitan/contrib/3.5/synapser_0.4.41.tgz': HTTP status was '503 Service Unavailable'
Error in download.file(url, destfile, method, mode = "wb", ...) :
cannot open URL 'https://sage-bionetworks.github.io/ran/bin/macosx/el-capitan/contrib/3.5/synapser_0.4.41.tgz'

Output of sessionInfo()

R version 3.5.2 (2018-12-20)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Mojave 10.14.1

Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

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

other attached packages:
[1] tableone_0.9.3 ggthemes_4.0.1 gridExtra_2.3 forcats_0.3.0
[5] stringr_1.3.1 dplyr_0.7.8 purrr_0.2.5 readr_1.3.1
[9] tidyr_0.8.2 tibble_1.4.2 ggplot2_3.1.0 tidyverse_1.2.1
[13] gdata_2.18.0 data.table_1.11.8 install.load_1.2.1

loaded via a namespace (and not attached):
[1] gtools_3.8.1 tidyselect_0.2.5 splines_3.5.2 haven_2.0.0
[5] lattice_0.20-38 colorspace_1.3-2 generics_0.0.2 yaml_2.2.0
[9] survival_2.43-3 rlang_0.3.0.1 pillar_1.3.1 glue_1.3.0
[13] withr_2.1.2 modelr_0.1.2 readxl_1.2.0 bindrcpp_0.2.2
[17] bindr_0.1.1 plyr_1.8.4 munsell_0.5.0 gtable_0.2.0
[21] cellranger_1.1.0 rvest_0.3.2 broom_0.5.1 Rcpp_1.0.0
[25] scales_1.0.0 backports_1.1.3 jsonlite_1.6 hms_0.4.2
[29] stringi_1.2.4 survey_3.35 grid_3.5.2 cli_1.0.1
[33] tools_3.5.2 magrittr_1.5 lazyeval_0.2.1 crayon_1.3.4
[37] pkgconfig_2.0.2 Matrix_1.2-15 xml2_1.2.0 lubridate_1.7.4
[41] assertthat_0.2.0 httr_1.4.0 rstudioapi_0.8 R6_2.3.0
[45] nlme_3.1-137 compiler_3.5.2

Streaming upload and Google storage.

Hi,
Is it possible to upload a file to Synapse by streaming it? Or do I need to have it on my local machine.
I need to upload files stored in GCP and I would like to avoid having to localize them.

Thank you,
E.

package ‘synapser’ is not available (for R version 3.6.2)

Operating system

Google Cloud Platform - AI Hub - Debian - Jupyter Notebook for R

Description of the problem

“package ‘synapser’ is not available (for R version 3.6.2)”.
R 3.6.2 is default version for GCP Jupyter Notebook for R

Desired Actions

Can a version of the synapster library be released for R 3.6.2?

Output of sessionInfo()

R version 3.6.2 (2019-12-12)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Debian GNU/Linux 9 (stretch)

Matrix products: default
BLAS: /usr/lib/openblas-base/libblas.so.3
LAPACK: /usr/lib/libopenblasp-r0.2.19.so

locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.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_3.6.2 IRdisplay_0.7.0 pbdZMQ_0.3-3 tools_3.6.2
[5] htmltools_0.4.0 pillar_1.4.2 base64enc_0.1-3 crayon_1.3.4
[9] Rcpp_1.0.3 uuid_0.1-2 IRkernel_1.1 jsonlite_1.6
[13] digest_0.6.23 repr_1.0.1 rlang_0.4.2 evaluate_0.14

Warnings print "PythonEmbedInR"

Operating system

OS X and CentOS 6.9 with R 3.5.1 and synapse 0.4.41

Description of the problem

Minimal reproducible example: Running very simple code prints many warnings

library(GenomicRanges)
library(synapser)
gr = GRanges(rep(1, 2), IRanges(1:2, 1:2))

This results in output:

Found more than one class "DataFrame" in cache; using the first, from namespace 'S4Vectors'
Also defined by ‘PythonEmbedInR’
Found more than one class "DataFrame" in cache; using the first, from namespace 'S4Vectors'
Also defined by ‘PythonEmbedInR’
Found more than one class "DataFrame" in cache; using the first, from namespace 'S4Vectors'
Also defined by ‘PythonEmbedInR’

This only happens when synapser is loaded.

The real issue is when I use GRanges store large sets of genome intervals. Then R prints this warning thousands of times and takes over my console.

I realized it was due to synapses based on:
https://sagebionetworks.jira.com/browse/SYNR-1318?page=com.atlassian.jira.plugin.system.issuetabpanels%3Aall-tabpanel

Output of sessionInfo()

R version 3.5.1 (2018-07-02)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS  10.14

Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] parallel  stats4    stats     graphics  grDevices datasets  utils
[8] methods   base

other attached packages:
[1] synapser_0.4.41      GenomicRanges_1.34.0 GenomeInfoDb_1.18.0
[4] IRanges_2.16.0       S4Vectors_0.20.0     BiocGenerics_0.28.0

loaded via a namespace (and not attached):
[1] zlibbioc_1.28.0        compiler_3.5.1         R6_2.3.0
[4] XVector_0.22.0         GenomeInfoDbData_1.2.0 RCurl_1.95-4.11
[7] pack_0.1-1             PythonEmbedInR_0.3.25  bitops_1.0-6

Error installing on Debian

Operating system

Distributor ID: Debian
Description: Debian GNU/Linux 9.6 (stretch)
Release: 9.6
Codename: stretch

Description of the problem

When I run

install.packages("synapser", repos=c("https://sage-bionetworks.github.io/ran", "http://cran.fhcrc.org"))

in RStudio, synapser fails to install.

Actual behavior

Error message:

error: The 'keyrings.alt' distribution was not found and is required by synapseclient
Warning in install.packages :
  installation of package ‘synapser’ had non-zero exit status

Output of sessionInfo()

> sessionInfo()
R version 3.5.1 (2018-07-02)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Debian GNU/Linux 9 (stretch)

Matrix products: default
BLAS: /usr/lib/openblas-base/libblas.so.3
LAPACK: /usr/lib/libopenblasp-r0.2.19.so

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=en_US.UTF-8       
 [4] LC_COLLATE=en_US.UTF-8     LC_MONETARY=en_US.UTF-8    LC_MESSAGES=C             
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                  LC_ADDRESS=C              
[10] LC_TELEPHONE=C             LC_MEASUREMENT=en_US.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_3.5.1 tools_3.5.1    yaml_2.2.0   

Cloud Drive Mapper Causing Error with Synapser

Operating system

Which operating system are you working on? E.g., Ubuntu Linux, Max OSX, Windows 10, etc.

Windows 10 Enterprise, Version 20H2

Description of the problem

Provide a description of the problem, and if possible a minimal reproducible example.

Our team has previously used the below code to pull data from Synapse into R. However, our institution recently installed OneDrive and a OneDrive Cloud Mapper to map OneDrive files to a network path and it appears that the program iam cloud Cloud Drive Mapper (Version 2.9.5.2) interferes with the synapser package. When we sign out of the Cloud Drive Mapper, this error is resolved. We would prefer to be logged into the cloud drive mapper and be able to use synapser simultaneously, if possible.

library(synapser)

# source in login info since credentials won't save with OneDrive cloud mapper
source("synapse_pw.R")

synLogin("my_email", synapse_pw)

# load derived data files corresponding to GENIE BPC NSCLC public release
derived_data_file_synapse <- synGet("syn22299362", version = 44)
load(derived_data_file_synapse$path)

Expected behavior

What did you expect to happen?

I expected the code to pull the file corresponding to syn22299362 from Synapse into R.

Actual behavior

What actually happened? Provide output or error messages from the console, if applicable.

Error in value[3L] : [WinError 87] The parameter is incorrect

Output of sessionInfo()

Copy the output of running sessionInfo() to get a listing of your R environment.
R version 4.2.2 (2022-10-31 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19042)

Matrix products: default

locale:
[1] LC_COLLATE=English_United States.utf8 LC_CTYPE=English_United States.utf8 LC_MONETARY=English_United States.utf8
[4] LC_NUMERIC=C LC_TIME=English_United States.utf8

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

other attached packages:
[1] synapser_0.15.35

loaded via a namespace (and not attached):
[1] Rcpp_1.0.9 PythonEmbedInR_0.12.79 plyr_1.8.8 pillar_1.8.1 compiler_4.2.2
[6] tools_4.2.2 digest_0.6.30 lubridate_1.9.0 lifecycle_1.0.3 tibble_3.1.8
[11] gtable_0.3.1 timechange_0.1.1 pkgconfig_2.0.3 rlang_1.0.6 DBI_1.1.3
[16] cli_3.5.0 rstudioapi_0.14 fastmap_1.1.0 httr_1.4.4 cbioportalR_1.0.1.9000
[21] dplyr_1.0.10 stringr_1.5.0 janitor_2.1.0 generics_0.1.3 vctrs_0.5.1
[26] mskRvis_0.3.2 rprojroot_2.0.3 grid_4.2.2 tidyselect_1.2.0 glue_1.6.2
[31] snakecase_0.11.0 here_1.0.1 R6_2.5.1 fansi_1.0.3 arsenal_3.6.3
[36] purrr_1.0.0 ggplot2_3.4.0 magrittr_2.0.3 codetools_0.2-18 scales_1.2.1
[41] htmltools_0.5.3 assertthat_0.2.1 gt_0.8.0 colorspace_2.0-3 utf8_1.2.2
[46] stringi_1.7.8 pack_0.1-1 munsell_0.5.0

broken link to software dependencies

The following link to software dependencies under install:

https://github.com/Sage-Bionetworks/synapser/blob/master/articles/systemDependencies.html

is broken.

R client installation fails: No module named 'pip'

I already installed the Synapse R client successfully on another machine running R version 3.4.1 (2017-06-30) on x86_64, linux-gnu system. But installation fails on the current machine, which is also a x86_64, linux-gnu system but is running R version 3.4.4 (2018-03-15).

I run the code for installation specified in the Getting Started doc and I get the following error:

No module named 'pip'
Error in pyExec("import pip") : 
  An error has occurred while executing Python code. See traceback above.

But the latest pip is installed on the system. And I verified that import pip worked in the python REPL shell. And on the present machine the Python client could be installed without any problems. Any ideas what could cause this issue?

Installation Fails on R 4.1.0

Details

Running fresh installation of R 4.1.0 on Windows 10.

Description

synapser installation fails on R 4.1.0 with the following error:

Error: package or namespace load failed for 'synapser' in library.dynam(lib, package, package.lib):
 DLL 'PythonEmbedInR' not found: maybe not installed for this architecture?
Error: loading failed
Execution halted
*** arch - x64
ERROR: loading failed for 'i386'

However, I previously installed PythonEmbedInR successfully with the following:

install.packages("PythonEmbedInR", repos=c("http://cran.fhcrc.org", "http://ran.synapse.org"))

Indeed, the PythonEmbedInR package loads successfully:

> library(PythonEmbedInR)
Loading required package: R6
Loading required package: rjson

sessionInfo() Output

R version 4.1.0 (2021-05-18)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19042)

Matrix products: default

locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252    LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C                           LC_TIME=English_United States.1252    

attached base packages:
[1] parallel  stats4    stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] PythonEmbedInR_0.7.80 rjson_0.2.20          R6_2.5.0              devtools_2.4.1        usethis_2.0.1         GO.db_3.13.0         
 [7] AnnotationDbi_1.54.0  IRanges_2.26.0        S4Vectors_0.30.0      Biobase_2.52.0        BiocGenerics_0.38.0   remotes_2.3.0    

Not able to authenticate using all possible ways

Operating system

Windows 10
R is installed in ~/laptop/OneDrive/Documents/R/R-4.1.3
.synapseConfig is saved under ~

Description of the problem

I registered a synapse account, and installed "synapser" package in R . I created a token with full permission including view, and tried all the ways mentioned in https://r-docs.synapse.org/articles/manageSynapseCredentials.html#kimyen-ladia to authenticate using synLogin(), but failed with error message "Error in value[3L] :
HTTPSConnectionPool(host='repo-prod.prod.sagebase.org', port=443): Max retries exceeded with url: /repo/v1/userProfile (Caused by SSLError(SSLError(1, '[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed (_ssl.c:852)'),))"

Expected behavior

Be able to authenticate

Actual behavior

failed

Output of sessionInfo()

sessionInfo()
R version 4.1.3 (2022-03-10)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19043)

Matrix products: default

locale:
[1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 LC_MONETARY=English_United States.1252 LC_NUMERIC=C
[5] LC_TIME=English_United States.1252

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

other attached packages:
[1] synapser_0.11.7

loaded via a namespace (and not attached):
[1] Rcpp_1.0.8.3 knitr_1.38 magrittr_2.0.2 tidyselect_1.1.2 R6_2.5.1 rlang_1.0.2 fastmap_1.1.0
[8] fansi_1.0.3 dplyr_1.0.8 tools_4.1.3 xfun_0.30 utf8_1.2.2 cli_3.2.0 DBI_1.1.2
[15] htmltools_0.5.2 ellipsis_0.3.2 yaml_2.3.5 assertthat_0.2.1 digest_0.6.29 tibble_3.1.6 lifecycle_1.0.1
[22] crayon_1.5.1 zip_2.2.0 PythonEmbedInR_0.8.4 purrr_0.3.4 codetools_0.2-18 vctrs_0.3.8 glue_1.6.2
[29] evaluate_0.15 rmarkdown_2.13 openxlsx_4.2.5 stringi_1.7.6 compiler_4.1.3 pillar_1.7.0 pack_0.1-1
[36] generics_0.1.2 pkgconfig_2.0.3

Thank you very much!
Wendy

installPythonClient.py cannot find existing setuptools

Description of the problem

Installation fails with ImportError in installPythonClient.py on R 3.5.2, ubuntu 18.04. The error message says No module named 'setuptools'. But setuptools is in fact installed both for python2.7 and for python3.6; I verified this with pip show setuptools and pip3 show setuptools and I can import setuptools in my interactive Python shell.

Details

Below is the full output of install.packages

> install.packages("synapser", repos = c("https://sage-bionetworks.github.io/ran", "http://cran.fhcrc.org"))
Installing package into ‘/home/attila/R/library’
(as ‘lib’ is unspecified)
trying URL 'https://sage-bionetworks.github.io/ran/src/contrib/synapser_0.5.45.tar.gz'
Content type 'application/gzip' length 129333 bytes (126 KB)
==================================================
downloaded 126 KB

* installing *source* package ‘synapser’ ...
Loading required package: R6
Loading required package: rjson
Loading required package: R6
Loading required package: rjson
Traceback (most recent call last):

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

  File "/tmp/RtmpEhtLqv/R.INSTALL31961930fc22/synapser/inst/python/installPythonClient.py", line 11, in <module>

    
from setuptools.command.install import install
ImportError
: 
No module named 'setuptools'
Error in pyExec(sprintf("import %s", import)) : 
  An error has occurred while executing Python code. See traceback above.
Calls: <Anonymous> -> pyExec
Execution halted
ERROR: configuration failed for package ‘synapser’
* removing ‘/home/attila/R/library/synapser’

The downloaded source packages are in
        ‘/tmp/RtmptJtRIx/downloaded_packages’
Warning message:
In install.packages("synapser", repos = c("https://sage-bionetworks.github.io/ran",  :
  installation of package ‘synapser’ had non-zero exit status

Output of sessionInfo()

> sessionInfo()
R version 3.5.2 (2018-12-20)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 18.04.2 LTS

Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/openblas/libblas.so.3
LAPACK: /usr/lib/x86_64-linux-gnu/libopenblasp-r0.2.20.so

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

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

other attached packages:
[1] knitr_1.21

loaded via a namespace (and not attached):
[1] compiler_3.5.2 tools_3.5.2    xfun_0.5      

synapser 0.8.71 fails on load

I just computed R 4.0.3 from source on my Mac. When I install synapser with

install.packages("synapser", repos=c("http://ran.synapse.org", "http://cran.fhcrc.org"), type="mac.binary")

and then load the package in an empty R session I get:

library(synapser)

 *** caught segfault ***
address 0x18, cause 'memory not mapped'

Traceback:
 1: pyIsConnected()
 2: pyConnect()
 3: fun(libname, pkgname)
 4: doTryCatch(return(expr), name, parentenv, handler)
 5: tryCatchOne(expr, names, parentenv, handlers[[1L]])
 6: tryCatchList(expr, classes, parentenv, handlers)
 7: tryCatch(fun(libname, pkgname), error = identity)
 8: runHook(".onLoad", env, package.lib, package)
 9: loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
10: namespaceImport(ns, loadNamespace(i, c(lib.loc, .libPaths()),     versionCheck = vI[[i]]), from = package)
11: loadNamespace(package, lib.loc)
12: doTryCatch(return(expr), name, parentenv, handler)
13: tryCatchOne(expr, names, parentenv, handlers[[1L]])
14: tryCatchList(expr, classes, parentenv, handlers)
15: tryCatch({    attr(package, "LibPath") <- which.lib.loc    ns <- loadNamespace(package, lib.loc)    env <- attachNamespace(ns, pos = pos, deps, exclude, include.only)}, error = function(e) {    P <- if (!is.null(cc <- conditionCall(e)))         paste(" in", deparse(cc)[1L])    else ""    msg <- gettextf("package or namespace load failed for %s%s:\n %s",         sQuote(package), P, conditionMessage(e))    if (logical.return)         message(paste("Error:", msg), domain = NA)    else stop(msg, call. = FALSE, domain = NA)})
16: library(synapser)

Possible actions:
1: abort (with core dump, if enabled)
2: normal R exit
3: exit R without saving workspace
4: exit R saving workspace
Selection: 

Here is my system info:

 sessionInfo()
R version 4.0.3 (2020-10-10)
Platform: x86_64-apple-darwin19.6.0 (64-bit)
Running under: macOS Catalina 10.15.7

Matrix products: default
BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libLAPACK.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

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

loaded via a namespace (and not attached):
[1] compiler_4.0.3 R6_2.5.0       pack_0.1-1

 packageVersion('synapser')
[1] ‘0.8.71’

Thanks,
Gabriel

PATH and RETICULATE_PATH are ignored when setting up Python virtual environment

Operating system

Linux RHEL8 in a shared research high performance computing environment (Mayo Clinic) where I don't have root privileges.

Description of the problem

When I try to install synapser, it always uses /usr/bin/python2.7 even though that's not the python in my PATH or RETICULATE_PATH. This leads to multiple warnings that 2.7 is deprecated. Then the installation fails because it can't find a recent enough version of pandas. Even after I hack the code to get around that, it can't install the python client version 3.0.0 as specified in your installPythonClient.R file.

Expected behavior

I expect it to use the python specified in PATH or RETICULATE_PATH

Actual behavior

[wa02042@mforgehn4 synapser]$ R --vanilla

R version 4.2.2 (2022-10-31) -- "Innocent and Trusting"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

.libPaths("/usr/local/biotools/rpackages/R-4.2.2-2023-02-01")
system("which python")
/usr/local/biotools/python/3.10.7/bin/python
system("\rm -rf ~/.virtualenvs/r-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
  [1] "*** Using Python Configuration:"
  Using Python: /usr/bin/python2.7
  Creating virtual environment 'r-reticulate' ...

• /usr/bin/python2.7 -m virtualenv -p '/usr/bin/python2.7' /home/mayo/wa02042/.virtualenvs/r-reticulate
  created virtual environment CPython2.7.18.final.0-64 in 5297ms
  creator CPython2Posix(dest=/home/mayo/wa02042/.virtualenvs/r-reticulate, clear=False, no_vcs_ignore=False, global=False)
  seeder FromAppData(download=False, pip=bundle, wheel=bundle, setuptools=bundle, via=copy, app_data_dir=/home/mayo/wa02042/.local/share/virtualenv)
  added seed packages: pip==20.3.4, setuptools==44.1.1, wheel==0.37.1
  activators NushellActivator,PythonActivator,FishActivator,CShellActivator,PowerShellActivator,BashActivator
  Done!
  Installing packages: pip, wheel, setuptools
• /home/mayo/wa02042/.virtualenvs/r-reticulate/bin/python -m pip install --upgrade pip wheel setuptools
  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.
  Requirement already up-to-date: pip in /home/mayo/wa02042/.virtualenvs/r-reticulate/lib/python2.7/site-packages (20.3.4)
  Requirement already up-to-date: wheel in /home/mayo/wa02042/.virtualenvs/r-reticulate/lib/python2.7/site-packages (0.37.1)
  Requirement already up-to-date: setuptools in /home/mayo/wa02042/.virtualenvs/r-reticulate/lib/python2.7/site-packages (44.1.1)
  Installing packages: numpy
• /home/mayo/wa02042/.virtualenvs/r-reticulate/bin/python -m pip install --upgrade --no-user numpy
  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 numpy
  Using cached numpy-1.16.6-cp27-cp27mu-manylinux1_x86_64.whl (17.0 MB)
  Installing collected packages: numpy
  Successfully installed numpy-1.16.6
  Virtual environment 'r-reticulate' successfully created.
  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

Output of sessionInfo()

sessionInfo()
R version 4.2.2 (2022-10-31)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Red Hat Enterprise Linux 8.8 (Ootpa)

Matrix products: default
BLAS: /usr/lib64/libblas.so.3.8.0
LAPACK: /usr/lib64/liblapack.so.3.8.0

locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=C
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.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_4.2.2 tools_4.2.2

pip.main returned 1 when installing synapseclient==2.2.2

Operating system and R/tidyverse environment

Ubuntu 20.04 LTS
R 4.0.1
tidyverse 1.3.0

Description of the problem

Installing the package raises the following exception:

Command "/usr/local/lib/R/site-library/PythonEmbedInR/bin/python3.6 -u -c "import setuptools, tokenize;__file__='/tmp/pip-install-h7p9rsdy/cryptography/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" install --record /tmp/pip-record-qm7qj3cw/install-record.txt --single-version-externally-managed --compile --home=/tmp/pip-target-jfbt0sgm" failed with error code 1 in /tmp/pip-install-h7p9rsdy/cryptography/
You are using pip version 18.1, however version 21.0.1 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/RtmpwDzp01/R.INSTALL2fba53de384b/synapser/inst/python/installPythonClient.py", line 129, in main


_install_pip(["synapseclient=={}".format(SYNAPSE_CLIENT_PACKAGE_VERSION)], localSitePackages)
  File "/tmp/RtmpwDzp01/R.INSTALL2fba53de384b/synapser/inst/python/installPythonClient.py", line 175, in _install_pip


raise Exception("pip.main returned {} when installing {}".format(rc, package))
Exception
:
pip.main returned 1 when installing synapseclient==2.2.2
Error in PythonEmbedInR::pyExec(command) :
  An error has occurred while executing Python code. See traceback above.
Execution halted
ERROR: configuration failed for package ‘synapser’
* removing ‘/usr/local/lib/R/site-library/synapser’

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

The issue can be reproduced with a Docker container:

$ docker run --rm -it rocker/tidyverse:4.0.1 /bin/bash
root@0cd3d28b5e97:/# R -e 'install.packages( "synapser", repos=c("http://ran.synapse.org", "http://cran.fhcrc.org") )'

synSetAnnotations not accessible in MacOS/Windows but works fine on Linux

Operating system

NOT an issue on Ubuntu Linux, but an issue on Mac OSX and Windows 10.

• synapseclient==4.0.0
• synapser version ‘2.0.0.200’ (obtained with install.packages("synapser", repos = "http://ran.synapse.org"))

Description of the problem

> synapser::synSetAnnotations("syn51811164", annotations=list(foo="bar", baz=1))
Error: 'synSetAnnotations' is not an exported object from 'namespace:synapser'

Expected behavior

Works fine on Linux. Submits and prints the annotations as a list.

Actual behavior

> synapser::synSetAnnotations("syn51811164", annotations=list(foo="bar", baz=1))
Error: 'synSetAnnotations' is not an exported object from 'namespace:synapser'

Output of sessionInfo()R version 4.2.1 (2022-06-23)

Platform: aarch64-apple-darwin20 (64-bit)
Running under: macOS 14.3.1

Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

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

other attached packages:
[1] synapser_2.0.0.200

loaded via a namespace (and not attached):
 [1] compiler_4.2.1   rjson_0.2.21     here_1.0.1       Matrix_1.6-5     rprojroot_2.0.4 
 [6] tools_4.2.1      Rcpp_1.0.12      reticulate_1.28  codetools_0.2-18 grid_4.2.1      
[11] jsonlite_1.8.8   png_0.1-8        lattice_0.22-5  

Cannot be enabled after installation

Operating system

• R 4.2.2
• Windows 10 * 64
• Python 3.9

Description of the problem

• ModuleNotFoundError: No module named 'synapseclient' when library this package after installation, and I installed the 'synapseclient' package in the corresponding Python environment, how to solve it now? Thank you!

Expected behavior

*I hope I can library this package successfully.

Actual behavior

*Error: package or namespace load failed for ‘synapser’:
loadNamespace()里算'synapser'时.onLoad失败了，详细内容：
调用: NULL
错误: ModuleNotFoundError: No module named 'synapseclient'

Output of sessionInfo()

*R version 4.2.2 (2022-10-31 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 22000)

Matrix products: default

locale:
[1] LC_COLLATE=Chinese (Simplified)_China.utf8 LC_CTYPE=Chinese (Simplified)_China.utf8 LC_MONETARY=Chinese (Simplified)_China.utf8 LC_NUMERIC=C
[5] LC_TIME=Chinese (Simplified)_China.utf8

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

loaded via a namespace (and not attached):
[1] reticulate_1.28 xfun_0.36 remotes_2.4.2 purrr_1.0.0 lattice_0.20-45 vctrs_0.5.1 miniUI_0.1.1.1 htmltools_0.5.4 usethis_2.1.6
[10] yaml_2.3.6 rlang_1.0.6 pkgbuild_1.4.0 later_1.3.0 urlchecker_1.0.1 glue_1.6.2 sessioninfo_1.2.2 lifecycle_1.0.3 stringr_1.5.0
[19] devtools_2.4.5 htmlwidgets_1.6.0 memoise_2.0.1 evaluate_0.19 knitr_1.42 callr_3.7.3 fastmap_1.1.0 httpuv_1.6.7 ps_1.7.2
[28] Rcpp_1.0.9 xtable_1.8-4 promises_1.2.0.1 BiocManager_1.30.19 cachem_1.0.6 pkgload_1.3.2 jsonlite_1.8.4 mime_0.12 fs_1.5.2
[37] rjson_0.2.21 png_0.1-8 digest_0.6.31 stringi_1.7.8 processx_3.8.0 shiny_1.7.4 grid_4.2.2 rprojroot_2.0.3 here_1.0.1
[46] cli_3.4.1 tools_4.2.2 magrittr_2.0.3 profvis_0.3.7 crayon_1.5.2 ellipsis_0.3.2 Matrix_1.5-3 rsconnect_0.8.28 prettyunits_1.1.1
[55] rmarkdown_2.19 rstudioapi_0.14 R6_2.5.1 compiler_4.2.2

`synSetAnnotations()` does not work on entities before they are uploaded

Operating system

Ubuntu 16.04 LTS

Description of the problem

It would be helpful to be able to set annotations on a File entity before uploading it to Synapse. Currently, synSetAnnotations() applied to a local File entity produces a "couldn't find id of File" error. See below for a reproducible example.

Expected behavior

synSetAnnotations( f, ... ) correctly sets annotations for File entity f even if f has not been synStore()d yet.

Actual behavior

library( synapser )
#> 
#> TERMS OF USE NOTICE:
#>   When using Synapse, remember that the terms and conditions of use require that you:
#>   1) Attribute data contributors when discussing these data or results from these data.
#>   2) Not discriminate, identify, or recontact individuals or groups represented by the data.
#>   3) Use and contribute only data de-identified to HIPAA standards.
#>   4) Redistribute data only under these same terms of use.
synLogin()
#> Welcome, Artem Sokolov!
#> NULL

## Save the built-in dataset mtcars to a file
readr::write_csv( mtcars, "mtcars.csv" )

## Ensure that the file is present locally
list.files( pattern="csv" )
#> [1] "mtcars.csv"

## Create a Synapse File entity
## syn12180284 is a test project
f <- File( "mtcars.csv", parent="syn12180284" )

## Attempt to set annotations
## Produces an error
synSetAnnotations( f, list(type = "dataset") )
#> Error in value[[3L]](cond): Invalid parameters: couldn't find id of File: mtcars.csv (-)
#>   md5=None
#>   fileSize=None
#>   contentType=None
#>   externalURL=None
#>   cacheDir=
#>   files=['mtcars.csv']
#>   path=mtcars.csv
#>   synapseStore=True
#> properties:
#>   concreteType=org.sagebionetworks.repo.model.FileEntity
#>   name=mtcars.csv
#>   parentId=syn12180284
#> annotations:

## Upload the file
s <- synStore(f)
#> ################################################## Uploading file to Synapse storage ##################################################
Uploading [####################]100.00%   1.3kB/1.3kB  mtcars.csv Done...

## Attempt to set annotations on the uploaded entity
## This works
synSetAnnotations( s$properties$id, list(type = "dataset") )
#> $type
#> $type[[1]]
#> [1] "dataset"

Created on 2018-08-13 by the reprex package (v0.2.0).

Output of sessionInfo()

R version 3.4.4 (2018-03-15)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.5 LTS

Matrix products: default
BLAS: /usr/lib/openblas-base/libblas.so.3
LAPACK: /usr/lib/libopenblasp-r0.2.18.so

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

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

other attached packages:
[1] synapser_0.2.38

loaded via a namespace (and not attached):
 [1] readr_1.1.1           compiler_3.4.4        R6_2.2.2             
 [4] hms_0.4.2             tools_3.4.4           pillar_1.2.1         
 [7] tibble_1.4.2          Rcpp_0.12.18          codetools_0.2-15     
[10] pack_0.1-1            pkgconfig_2.0.1       rlang_0.2.1          
[13] PythonEmbedInR_0.2.24

Issue installing synapser on mac13

Operating system

• Which operating system are you working on? E.g., Ubuntu Linux, Max OSX, Windows 10, etc.*
  mac13 (ventura)

Description of the problem

#316 (comment)

Expected behavior

Ability to install

Actual behavior

See linked ticket

Numeric NA values read in as -2147483648 on Windows

Operating system

Windows 10

Description of the problem

When reading in data, numeric variables that have NA values are not read in as NA but are instead read in as -2147483648

Expected behavior

Columns are numeric, with missing values coded as NA

Actual behavior

No errors, warnings, or messages.
Columns are numeric, but missing values are coded as -2147483648

Output of sessionInfo()

R version 4.1.2 (2021-11-01)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19045)

Matrix products: default

locale:
[1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C
[5] LC_TIME=English_United States.1252

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

other attached packages:
[1] synapser_1.0.0

loaded via a namespace (and not attached):
[1] Rcpp_1.0.9 pillar_1.8.1 compiler_4.1.2 plyr_1.8.8 tools_4.1.2 digest_0.6.30
[7] jsonlite_1.8.4 evaluate_0.20 lifecycle_1.0.3 tibble_3.1.8 lattice_0.20-45 pkgconfig_2.0.3
[13] png_0.1-8 rlang_1.1.1 Matrix_1.5-3 cli_3.4.1 rstudioapi_0.14 yaml_2.3.7
[19] xfun_0.37 fastmap_1.1.0 withr_2.5.0 dplyr_1.1.0 knitr_1.42 generics_0.1.3
[25] vctrs_0.6.3 rprojroot_2.0.3 grid_4.1.2 tidyselect_1.2.0 reticulate_1.28 glue_1.6.2
[31] here_1.0.1 R6_2.5.1 fansi_1.0.4 rmarkdown_2.23 magrittr_2.0.3 codetools_0.2-18
[37] htmltools_0.5.3 utf8_1.2.3 rjson_0.2.21

Test code from meeting with @thomasyu888 today

# pull code other than as.data.frame()
test1 <- synTableQuery(sprintf("SELECT * FROM %s", paste0("syn21446700", ".", synGet("syn21446700")$properties$versionNumber - 1)))

View(as.data.frame(test1))

View(test1$asDataFrame())

# look at where file was temporarily saved
test1$filepath

# schema is NULL
test1$schema

# hybrid_death_int is recorded as an integer
test1$headers

# CsvFileTable is correct
class(test1)

# with read.csv it's read in correctly
test2 <- read.csv("c:/users/laveryj/.synapsecache/284/129372284/synapse_table_query_129372284.csv")

# with pandas read csv it's also read in correctly
library(reticulate)
pd <- reticulate::import("pandas")
test3 <- pd$read_csv("c:/users/laveryj/.synapsecache/284/129372284/synapse_table_query_129372284.csv")

# this is the problem - for some reason there is an issue converting to df
test1$asDataFrame() %>% select(contains("hybrid_death")) %>% view()

# no issues - numeric correctly NA
test4 <- read.csv("c:/users/laveryj/.synapsecache/284/129372284/synapse_table_query_129372284.csv",
                  encoding = "UTF-8",
                  stringsAsFactors = FALSE,
                  check.names = FALSE,
                  na.strings = c(""),
                  colClasses = "character")

test4 %>% select(contains("hybrid_death")) %>% view()

# these have correct NA
as.integer(test4$hybrid_death_int)
as.numeric(test4$hybrid_death_int)

# reproduces the error
test5 <- synapser::as.data.frame(test1)

test5 %>% select(contains("hybrid_death")) %>% view()

# this doesn't replicate the error, NAs are correct
# sourced functions from: https://github.com/Sage-Bionetworks/synapser/blob/8b2d310ca11c56d2514fb8d719edeb2a1cecc475/R/table.R#L120-L131
test6 <- .readCsvBasedOnSchema(test1)

test6 %>% select(contains("hybrid_death")) %>% view()

could not find function "synLogin"

Operating system

Windows 10, etc.

Description of the problem

*after typing :synLogin(email , password ）,it shows error:could not find function "synLogin" *

R4.2.1.
Thanks.

please add back synSetAnnotations or similar

Operating system

Mac OS X

Description of the problem

as described in #331, synSetAnnotations has been removed. Our nfportalutils package (github.com/nf-osi/nfportalutils) depends on this function in several places. Can it be added back, or can a workaround be suggested?

Here's another new issue

Operating system

Which operating system are you working on? E.g., Ubuntu Linux, Max OSX, Windows 10, etc.

Description of the problem

Provide a description of the problem, and if possible a minimal reproducible example.

Expected behavior

What did you expect to happen?

Actual behavior

What actually happened? Provide output or error messages from the console, if applicable.

Output of sessionInfo()

Copy the output of running sessionInfo() to get a listing of your R environment.

Timestamp in request is out of date.

Operating system

Linux

Description of the problem

When trying to log in the R package, (library(synapser)) I get the following error:

Error in value[[3L]](cond) : 401 Client Error: 
Timestamp in request, 2021-08-06T10:59:06.000Z, is out of date.

Any syggestion?

Output of sessionInfo()

R version 3.6.1 (2019-07-05)
Platform: x86_64-conda_cos6-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)

Matrix products: default
BLAS/LAPACK: /home/hpc/xenofon.giannoulis/anaconda3/lib/R/lib/libRblas.so

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

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

other attached packages:
[1] synapser_0.11.7 data.table_1.14.0

loaded via a namespace (and not attached):
[1] compiler_3.6.1 R6_2.5.0 tools_3.6.1
[4] codetools_0.2-18 pack_0.1-1 PythonEmbedInR_0.8.4

arm64 binary for M1 Mac not available

Operating system

Which operating system are you working on? E.g., Ubuntu Linux, Max OSX, Windows 10, etc.
macOS 11.5.2

Description of the problem

synapser does not appear to be available for the M1 Mac. Are there known issues with running synapser on M1 Macs? if not, can the Linux instructions for compiling from scratch be used?

SSL error trying to login

Operating system

MacOS

Description of the problem

Similar to #204, but here when I put in my credentials it fails. syn_ are my credentials as character objects.

synLogin(syn_username,syn_pwd)

Error in value[[3L]](cond) : 
  HTTPSConnectionPool(host='auth-prod.prod.sagebase.org', port=443): Max retries exceeded with url: /auth/v1/session (Caused by SSLError(SSLError(1, '[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed (_ssl.c:720)'),))

Expected behavior

Login. 😄

Actual behavior

Error in value[[3L]](cond) : 
  HTTPSConnectionPool(host='auth-prod.prod.sagebase.org', port=443): Max retries exceeded with url: /auth/v1/session (Caused by SSLError(SSLError(1, '[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed (_ssl.c:720)'),))

Output of sessionInfo()

R version 3.5.0 (2018-04-23)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS High Sierra 10.13.6

Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

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

other attached packages:
 [1] synapserutils_0.1.4 synapser_0.5.45     forcats_0.3.0      
 [4] stringr_1.3.1       dplyr_0.8.0.1       purrr_0.3.0        
 [7] readr_1.3.1         tidyr_0.8.2         tibble_2.0.1       
[10] ggplot2_3.1.0       tidyverse_1.2.1    

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.0            lubridate_1.7.4       lattice_0.20-38      
 [4] prettyunits_1.0.2     ps_1.3.0              assertthat_0.2.0     
 [7] rprojroot_1.3-2       digest_0.6.18         packrat_0.5.0        
[10] R6_2.4.0              cellranger_1.1.0      plyr_1.8.4           
[13] backports_1.1.3       httr_1.4.0            pillar_1.3.1         
[16] rlang_0.3.1.9000      lazyeval_0.2.1        curl_3.3             
[19] readxl_1.2.0          rstudioapi_0.9.0      callr_3.1.1          
[22] desc_1.2.0            devtools_2.0.1        munsell_0.5.0        
[25] broom_0.5.1           compiler_3.5.0        modelr_0.1.2         
[28] xfun_0.4              pkgconfig_2.0.2       pack_0.1-1           
[31] pkgbuild_1.0.2        tidyselect_0.2.5      codetools_0.2-16     
[34] crayon_1.3.4          withr_2.1.2           grid_3.5.0           
[37] nlme_3.1-137          jsonlite_1.6          gtable_0.2.0         
[40] magrittr_1.5          scales_1.0.0          cli_1.0.1            
[43] stringi_1.2.4         PythonEmbedInR_0.3.25 fs_1.2.6             
[46] remotes_2.0.2         testthat_2.0.1        xml2_1.2.0           
[49] generics_0.0.2        tools_3.5.0           glue_1.3.0           
[52] hms_0.4.2             processx_3.2.1        pkgload_1.0.2        
[55] yaml_2.2.0            colorspace_1.4-0      sessioninfo_1.1.1    
[58] rvest_0.3.2           memoise_1.1.0         knitr_1.21           
[61] haven_2.0.0           usethis_1.4.0 

synGet() hangs when retrieving files as non-root (macOS 10.15)

Operating system

macOS Catalina 10.15.7
R version 4.0.3

Description of the problem

I'm unable to retrieve files using synGet() without errors.
When I use the default path, as in below:

> library('synapser')
> synapser::synLogin(
+   "my_user_name",
+   "top_secret_password"
+ )


> fh <- synGet("syn1906479", downloadFile=T)`
   Error in value[[3L]](cond) : `
  [Errno 13] Permission denied: '/Users/myusername/.synapseCache/969'`
> 

When I change the path, the file is successfully retrieved (and has the correct md5) however the command gets "stuck" and never completes.

> fh <- synGet("syn1906479", downloadFile=T, downloadLocation="/Users/myusername/Desktop")

Deleting the file does not end the command and return the console prompt

If I delete the file, and then send a single interrupt (either "ctrl-c" in the terminal, or the "stop" button in RStudio), the file is re-downloaded, but R remains stuck on the call to synGet().

Sending several interrupts in rapid succession kills the call to synGet() and returns the following error

In RStudio:

> fh <- synGet("syn1906479", downloadFile=T, downloadLocation="/Users/adam/Desktop")





Error in value[[3L]](cond) : keyboard interrupt received
>

In a terminal R Session

> fh <- synGet("syn1906479", downloadFile=T, downloadLocation="/Users/adam/Desktop")
^C
^C
^C
^C
^C
Error in value[[3L]](cond) : keyboard interrupt received

I also observed a different error that I could not reproduce

> fh <- synGet("syn1906479", downloadFile=T, downloadLocation="/Users/adam/Desktop")
^C
^C
^C
Error in value[[3L]](cond) : 
  Could not obtain a lock on the file cache within timeout: 0:01:10  Please try again later
> 

Provide a description of the problem, and if possible a minimal reproducible example.

Expected behavior

I expected the file to be downloaded, and the file handle stored in an R object

Actual behavior

Command gets stuck and in some cases the target file fails to download

Output of sessionInfo()

 sessionInfo()
R version 4.0.3 (2020-10-10)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Catalina 10.15.7

Matrix products: default
BLAS:   /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRblas.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

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

other attached packages:
[1] synapser_0.9.77

loaded via a namespace (and not attached):
[1] compiler_4.0.3        R6_2.5.0              tools_4.0.3          
[4] codetools_0.2-18      pack_0.1-1            PythonEmbedInR_0.6.76

Copy the output of running sessionInfo() to get a listing of your R environment.

Failed to install PythonEmbedInR

Operating system

Max OSX 12.3.1

Description of the problem

One collaborator reported unsuccessful installation of synapser by running install.packages("synapser", repos=c("http://ran.synapse.org/", "http://cran.fhcrc.org/")). It looks like the /usr/local/opt/openssl/lib/libcrypto.1*.dylib couldn't be found when installing the PythonEmbedInR package (full errors are listed below).

Expected behavior

synapser should be installed successfully.

Actual behavior

 install.packages("synapser", repos=c("http://ran.synapse.org/", "http://cran.fhcrc.org/"))
also installing the dependency 'PythonEmbedInR'

Warning in install.packages :
  unable to access index for repository http://ran.synapse.org/bin/macosx/contrib/4.2:
  cannot open URL 'http://ran.synapse.org/bin/macosx/contrib/4.2/PACKAGES'
Package which is only available in source form, and may need compilation of C/C++/Fortran:
  'PythonEmbedInR'
Do you want to attempt to install these from sources? (Yes/no/cancel) yes
installing the source packages 'PythonEmbedInR', 'synapser'

trying URL 'http://ran.synapse.org/src/contrib/PythonEmbedInR_0.8.4.tar.gz'
Content type 'application/x-tar' length 95306 bytes (93 KB)
==================================================
downloaded 93 KB

trying URL 'http://ran.synapse.org/src/contrib/synapser_0.11.7.tar.gz'
Content type 'application/x-tar' length 134168 bytes (131 KB)
==================================================
downloaded 131 KB

* installing *source* package 'PythonEmbedInR' ...
** using staged installation
                                 ...
 22450K .......... ..........                                 100% 23.5M=1.0s
2022-06-01 12:31:46 (22.3 MB/s) - 'Python-3.6.8.tgz' saved [23010188/23010188]
Mac specific configuration
ls: /usr/local/opt/openssl/lib/libcrypto.1*.dylib: No such file or directory
ERROR: configuration failed for package 'PythonEmbedInR'
* removing '/Library/Frameworks/R.framework/Versions/4.2/Resources/library/PythonEmbedInR'
Warning in install.packages :
  installation of package 'PythonEmbedInR' had non-zero exit status
ERROR: dependency 'PythonEmbedInR' is not available for package 'synapser'
* removing '/Library/Frameworks/R.framework/Versions/4.2/Resources/library/synapser'
Warning in install.packages :
  installation of package 'synapser' had non-zero exit status

The downloaded source packages are in
	'/private/var/folders/yw/z16m_yvs4sgg4nt4jcg8y5txvlw4tj/T/Rtmp9hGe5V/downloaded_packages'

Output of sessionInfo()

No module named 'pysftp'

Operating system

Max OSX

Description of the problem

Cannot upload data using the package. It says: No module named 'pysftp', but pysftp is installed for Python 3.6.4.

fileEntity <- synGet("syn18265702")
file <- File(path ="~/Downloads/merged_metadata.csv", parent = fileEntity)
file <- synStore(file)

Expected behavior

File upload

Actual behavior

Error in value[[3L]](cond) : No module named 'pysftp'

Output of sessionInfo()

> sessionInfo()
R version 3.5.1 (2018-07-02)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS  10.14

Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

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

other attached packages:
[1] synapserutils_0.1.4 synapser_0.5.45

loaded via a namespace (and not attached):
[1] compiler_3.5.1        R6_2.3.0              codetools_0.2-16
[4] pack_0.1-1            PythonEmbedInR_0.3.25

Set synapseCache location

Operating system

Redhat Linux

Description of the problem

default synapseCache is at user home
how to set it to a specified location

I tried to set CACHE_ROOT at .Renviron or .synapseConfig or Sys.setenv() but it was not picked up by synapser

Expected behavior

provide a function synCacheDir()

@brucehoff

can't login in

library(synapser)
synLogin()
Error in value[3L] : No credentials provided.

I have registered a Synapse account. But when I run the code, I got this error. How can I get the place to login in to my account.

Cannot install synapser due to problems with MarkupSafe

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   

Cannot install package

Operating system

Ubuntu Linux 16.04

Actual behavior

rc = pip.main(['install', packageName,  '--upgrade', '--quiet', '--target', target])
AttributeError
: 
module 'pip' has no attribute 'main'

Pip version

pip 10.0.1 (python 3.5)

Output of sessionInfo()

─ Session info ───────────────────────────────────────────────────────────────
 setting  value                       
 version  R version 3.4.3 (2017-11-30)
 os       Ubuntu 16.04.3 LTS          
 system   x86_64, linux-gnu           
 ui       X11                         
 language (EN)                        
 collate  en_US.UTF-8                 
 tz       Europe/San_Marino           
 date     2018-04-23                  

─ Packages ───────────────────────────────────────────────────────────────────
 package       * version     date       source                            
 assertthat      0.2.0       2017-04-11 CRAN (R 3.4.3)                    
 backports       1.1.2       2017-12-13 CRAN (R 3.4.3)                    
 BiocInstaller * 1.28.0      2018-02-09 Bioconductor                      
 callr           2.0.2.9002  2018-04-05 Github (r-lib/callr@9c38827)      
 cli             1.0.0       2017-11-05 cran (@1.0.0)                     
 clisymbols      1.2.0       2017-05-21 cran (@1.2.0)                     
 colorout      * 1.2-0       2018-02-15 Github (jalvesaq/colorout@2fd35ab)
 crayon          1.3.4       2017-09-16 cran (@1.3.4)                     
 debugme         1.1.0       2017-10-22 cran (@1.1.0)                     
 desc            1.1.1       2017-08-03 CRAN (R 3.4.3)                    
 devtools      * 1.13.5.9000 2018-04-05 Github (r-lib/devtools@5a1b9d9)   
 digest          0.6.15      2018-01-28 CRAN (R 3.4.3)                    
 magrittr        1.5         2014-11-22 cran (@1.5)                       
 memoise         1.1.0       2017-04-21 CRAN (R 3.4.3)                    
 pkgbuild        1.0.0       2018-04-05 Github (r-lib/pkgbuild@015f7f6)   
 pkgload         1.0.0       2018-04-05 Github (r-lib/pkgload@bd40696)    
 R6              2.2.2       2017-06-17 CRAN (R 3.4.3)                    
 rlang           0.2.0       2018-02-20 cran (@0.2.0)                     
 rprojroot       1.3-2       2018-01-03 CRAN (R 3.4.3)                    
 sessioninfo     1.0.0       2017-06-21 cran (@1.0.0)                     
 testthat        2.0.0       2017-12-13 CRAN (R 3.4.3)                    
 usethis       * 1.3.0       2018-02-24 cran (@1.3.0)                     
 withr           2.1.2       2018-03-15 cran (@2.1.2)          

Configuration fails because module `pip` has no attribute `main`

Operating system

Debian GNU/Linux 10 (buster)

Description of the problem

Where the error occurs:

install.packages("synapser", repos=c("https://sage-bionetworks.github.io/ran", "http://cran.fhcrc.org"))    
...
rc = pip.main(['install', packageName, '--upgrade', '--quiet', '--target', target])                                                           
AttributeError
:
module 'pip' has no attribute 'main'
Error in PythonEmbedInR::pyExec(command) :
  An error has occurred while executing Python code. See traceback above.                                                                     
Execution halted
ERROR: configuration failed for package ‘synapser’

Expected behavior

Error-free installation.

Actual behavior

> install.packages("synapser", repos=c("https://sage-bionetworks.github.io/ran", "http://cran.fhcrc.org"))                                    
Installing package into ‘/home/attila/R/library’
(as ‘lib’ is unspecified)
trying URL 'https://sage-bionetworks.github.io/ran/src/contrib/synapser_0.6.54.tar.gz'                                                        
Content type 'application/gzip' length 132790 bytes (129 KB)
==================================================
downloaded 129 KB

* installing *source* package ‘synapser’ ...
Loading required package: R6
Loading required package: rjson
Loading required package: R6
Loading required package: rjson
Traceback (most recent call last):

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

  File "/tmp/RtmpCrpmKQ/R.INSTALL6a5a2855c492/synapser/inst/python/installPythonClient.py", line 57, in main                                  


call_pip('pandas==0.22', localSitePackages)
  File "/tmp/RtmpCrpmKQ/R.INSTALL6a5a2855c492/synapser/inst/python/installPythonClient.py", line 106, in call_pip                             


rc = pip.main(['install', packageName, '--upgrade', '--quiet', '--target', target])                                                           
AttributeError
:
module 'pip' has no attribute 'main'
Error in PythonEmbedInR::pyExec(command) :
  An error has occurred while executing Python code. See traceback above.                                                                     
Execution halted
ERROR: configuration failed for package ‘synapser’
* removing ‘/home/attila/R/library/synapser’

The downloaded source packages are in
        ‘/tmp/Rtmp2dN5YW/downloaded_packages’
Warning message:
In install.packages("synapser", repos = c("https://sage-bionetworks.github.io/ran",  :                                                        
  installation of package ‘synapser’ had non-zero exit status

Output of sessionInfo()

> sessionInfo()
R version 3.5.2 (2018-12-20)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Debian GNU/Linux 10 (buster)

Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/openblas/libblas.so.3
LAPACK: /usr/lib/x86_64-linux-gnu/libopenblasp-r0.3.5.so

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.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_3.5.2 tools_3.5.2

synapser doesn't work in latest Connect 1.7.2

Operating system

centos 7

Description of the problem

Hi, we are using synapser on our RStudio Connect server in a daily data-downloading script. It works well (on Connect 1.7.0) until we upgraded RStudio Connect to 1.7.2 two days ago. It looks like PythonEmbededInR can no longer pick up the correct python installation. I forced packrat to rebuild PythonEmbededInR by increasing the version number in my forked repo but it didn't work out either.

I understand this issue might be hard to replicate because RStudio Connect is another commercial product. If you guys also have Connect, you can test it out. I'm contacting rstudio support as well and will update this issue once I hear back.

Error log

03/25 11:59:46.617
Traceback (most recent call last):
03/25 11:59:46.617
File "<string>", line 1, in <module>
03/25 11:59:46.617
ImportError: No module named pip
03/25 11:59:46.620
Quitting from lines 9-16 (smartphone_update_sql.Rmd)
03/25 11:59:46.620
Error: package or namespace load failed for 'synapser':
03/25 11:59:46.620
.onLoad failed in loadNamespace() for 'PythonEmbedInR', details:
03/25 11:59:46.620
call: value[[3L]](cond)
03/25 11:59:46.620
error: ERROR: Missing system dependencies. Please make sure that your machine has the required dependencies listed in the SystemRequirements field of the DESCRIPTION file: https://github.com/Sage-Bionetworks/PythonEmbedInR/blob/master/DESCRIPTION

Output of sessionInfo()

R version 3.5.0 (2018-04-23)
Platform: x86_64-redhat-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)

Matrix products: default
BLAS/LAPACK: /usr/lib64/R/lib/libRblas.so

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=en_US.UTF-8       
 [4] LC_COLLATE=en_US.UTF-8     LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                  LC_ADDRESS=C              
[10] LC_TELEPHONE=C             LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

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

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.1        compiler_3.5.0    prettyunits_1.0.2 bitops_1.0-6     
 [5] base64enc_0.1-3   remotes_2.0.2     tools_3.5.0       testthat_2.0.1   
 [9] digest_0.6.18     packrat_0.5.0     pkgbuild_1.0.3    pkgload_1.0.2    
[13] lattice_0.20-38   jsonlite_1.6      evaluate_0.13     memoise_1.1.0    
[17] rlang_0.3.2       Matrix_1.2-14     cli_1.1.0         rstudioapi_0.10  
[21] curl_3.3          yaml_2.2.0        xfun_0.5          withr_2.1.2      
[25] stringr_1.4.0     knitr_1.22        fs_1.2.7          desc_1.2.0       
[29] askpass_1.1       devtools_2.0.1    grid_3.5.0        rprojroot_1.3-2  
[33] reticulate_1.10   glue_1.3.1        R6_2.4.0          processx_3.3.0   
[37] rmarkdown_1.12    sessioninfo_1.1.1 callr_3.2.0       magrittr_1.5     
[41] usethis_1.4.0     backports_1.1.3   ps_1.3.0          htmltools_0.3.6  
[45] rsconnect_0.8.13  assertthat_0.2.1  stringi_1.4.3     RCurl_1.95-4.12  
[49] openssl_1.3       crayon_1.3.4  

when installing urllib3 not imported

Operating system

CentOS 7

Description of the problem

python urllib3 module not found during synapser installation even though the package is already there.

Expected behavior

Python should be able to find urllib3 as I saw from running this line in a python console:

bash:mskilab01:~/software 1002 $ python
Python 3.5.2 (default, Oct 27 2016, 10:30:44)
[GCC 4.9.2 20150212 (Red Hat 4.9.2-6)] on linux
Type "help", "copyright", "credits" or "license" for more information.

import urllib3

Actual behavior

install.packages("synapser", repos = c("http://ran.synapse.org", "http://cran.fhcrc.org"))

File Edit Options Buffers Tools iESS Complete In/Out Signals Help
Using /gpfs/commons/home/xyao/.local/lib/python3.5/site-packages

Searching for urllib3==1.23

Best match: urllib3 1.23

Adding urllib3 1.23 to easy-install.pth file

Using /gpfs/commons/home/xyao/.local/lib/python3.5/site-packages

Searching for idna==2.7

Best match: idna 2.7

Adding idna 2.7 to easy-install.pth file

Using /gpfs/commons/home/xyao/.local/lib/python3.5/site-packages

Searching for chardet==3.0.4

Best match: chardet 3.0.4

Adding chardet 3.0.4 to easy-install.pth file

Installing chardetect script to /tmp/RtmpeV96TB/R.INSTALLc00a729021d7/synapser/inst/bin

Using /gpfs/commons/home/xyao/.local/lib/python3.5/site-packages

Finished processing dependencies for synapseclient==1.9.2

Traceback (most recent call last):

File "", line 1, in

File "/tmp/RtmpeV96TB/R.INSTALLc00a729021d7/synapser/inst/python/installPythonClient.py", line 82, in main

import synapseclient
File "/tmp/RtmpeV96TB/R.INSTALLc00a729021d7/synapser/inst/lib/python3.5/site-packages/synapseclient-1.9.2-py3.5.egg/s
ynapseclient/init.py", line 274, in

from .client import Synapse, login
File "/tmp/RtmpeV96TB/R.INSTALLc00a729021d7/synapser/inst/lib/python3.5/site-packages/synapseclient-1.9.2-py3.5.egg/s
ynapseclient/client.py", line 78, in

from . import cache
File "/tmp/RtmpeV96TB/R.INSTALLc00a729021d7/synapser/inst/lib/python3.5/site-packages/synapseclient-1.9.2-py3.5.egg/s
ynapseclient/cache.py", line 26, in

from synapseclient.lock import Lock
File "/tmp/RtmpeV96TB/R.INSTALLc00a729021d7/synapser/inst/lib/python3.5/site-packages/synapseclient-1.9.2-py3.5.egg/s
ynapseclient/lock.py", line 12, in

from synapseclient.exceptions import *
File "/tmp/RtmpeV96TB/R.INSTALLc00a729021d7/synapser/inst/lib/python3.5/site-packages/synapseclient-1.9.2-py3.5.egg/s
ynapseclient/exceptions.py", line 20, in

import requests
File "/tmp/RtmpeV96TB/R.INSTALLc00a729021d7/synapser/inst/lib/python3.5/site-packages/requests-2.22.0-py3.5.egg/reque
sts/init.py", line 43, in

import urllib3
ImportError
:
No module named 'urllib3'
Error in PythonEmbedInR::pyExec(command) :
An error has occurred while executing Python code. See traceback above.
Execution halted
ERROR: configuration failed for package ‘synapser’

Output of sessionInfo()

sessionInfo()
R version 3.5.1 (2018-07-02)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)

Matrix products: default
BLAS: /nfs/sw/R/R-3.5.1/lib64/R/lib/libRblas.so
LAPACK: /nfs/sw/R/R-3.5.1/lib64/R/lib/libRlapack.so

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

attached base packages:
[1] parallel stats4 stats graphics grDevices utils datasets
[8] methods base

other attached packages:
[1] Flow_0.0.0.9000 gGnome_0.1
[3] gTrack_0.1.0 Matrix_1.2-17
[5] skitools_0.0.0.9000 igraph_1.2.4
[7] reshape2_1.4.3 plotly_4.8.0
[9] ggplot2_3.1.1 stringr_1.4.0
[11] gUtils_0.2.0 data.table_1.12.2
[13] usethis_1.5.0 devtools_2.0.1
[15] htmlwidgets_1.3 VariantAnnotation_1.28.13
[17] Rsamtools_1.34.1 Biostrings_2.50.2
[19] XVector_0.22.0 SummarizedExperiment_1.12.0
[21] DelayedArray_0.8.0 BiocParallel_1.16.6
[23] matrixStats_0.54.0 Biobase_2.42.0
[25] GenomicRanges_1.34.0 GenomeInfoDb_1.18.2
[27] IRanges_2.16.0 S4Vectors_0.20.1
[29] BiocGenerics_0.28.0

loaded via a namespace (and not attached):
[1] bitops_1.0-6 fs_1.2.7 bit64_0.9-7
[4] progress_1.2.0 httr_1.4.0 rprojroot_1.3-2
[7] tools_3.5.1 backports_1.1.3 R6_2.4.0
[10] DBI_1.0.0 lazyeval_0.2.2 colorspace_1.4-1
[13] withr_2.1.2 tidyselect_0.2.5 prettyunits_1.0.2
[16] processx_3.3.0 bit_1.1-14 compiler_3.5.1
[19] cli_1.1.0 desc_1.2.0 rtracklayer_1.42.2
[22] scales_1.0.0 callr_3.2.0 digest_0.6.18
[25] pkgconfig_2.0.2 htmltools_0.3.6 sessioninfo_1.1.1
[28] BSgenome_1.50.0 rlang_0.3.4 RSQLite_2.1.1
[31] jsonlite_1.6 dplyr_0.8.0.1 RCurl_1.95-4.12
[34] magrittr_1.5 GenomeInfoDbData_1.2.0 Rcpp_1.0.1
[37] munsell_0.5.0 stringi_1.4.3 zlibbioc_1.28.0
[40] pkgbuild_1.0.3 plyr_1.8.4 grid_3.5.1
[43] blob_1.1.1 crayon_1.3.4 lattice_0.20-35
[46] GenomicFeatures_1.34.7 hms_0.4.2 ps_1.3.0
[49] pillar_1.3.1 biomaRt_2.38.0 pkgload_1.0.2
[52] XML_3.98-1.19 glue_1.3.1 remotes_2.0.2
[55] testthat_2.0.1 gtable_0.3.0 purrr_0.3.2
[58] tidyr_0.8.3 assertthat_0.2.1 viridisLite_0.3.0
[61] tibble_2.1.1 GenomicAlignments_1.18.1 AnnotationDbi_1.44.0
[64] memoise_1.1.0

Error installing on OS X when R is compiled from source (plus a fix)

Operating system

OSX 10.15.5 using R 4.0.1 compiled from source

Description of the problem

When I run your install command install.packages("synapser", repos=c("http://ran.synapse.org", "http://cran.fhcrc.org")

I get the this error:

Error: package or namespace load failed for ‘PythonEmbedInR’:
 .onLoad failed in loadNamespace() for 'PythonEmbedInR', details:
  call: dyn.load(sharedObjectFile, local = FALSE)
  error: unable to load shared object '/private/var/folders/pn/84915v0n2jx0mjl1kql7fp1m0000gn/T/Rtmpdlnx72/R.INSTALLcb2333d5a8f1/PythonEmbedInR/':
  dlopen(/private/var/folders/pn/84915v0n2jx0mjl1kql7fp1m0000gn/T/Rtmpdlnx72/R.INSTALLcb2333d5a8f1/PythonEmbedInR/, 10): no suitable image found.  Did find:
	/private/var/folders/pn/84915v0n2jx0mjl1kql7fp1m0000gn/T/Rtmpdlnx72/R.INSTALLcb2333d5a8f1/PythonEmbedInR/: not a file
	/private/var/folders/pn/84915v0n2jx0mjl1kql7fp1m0000gn/T/Rtmpdlnx72/R.INSTALLcb2333d5a8f1/PythonEmbedInR: not a file
Error: loading failed
Execution halted
ERROR: loading failed
* removing ‘/Users/gabrielhoffman/prog/R-4.0.1/library/PythonEmbedInR’
* restoring previous ‘/Users/gabrielhoffman/prog/R-4.0.1/library/PythonEmbedInR’

The downloaded source packages are in
	‘/private/var/folders/pn/84915v0n2jx0mjl1kql7fp1m0000gn/T/Rtmpef1hjV/downloaded_packages’
Updating HTML index of packages in '.Library'
Making 'packages.html' ... done
Warning message:
In install.packages("PythonEmbedInR", repos = c("http://ran.synapse.org",  :
  installation of package ‘PythonEmbedInR’ had non-zero exit status

Fix

After a while it realer that installing the binary version solves the issue:

install.packages("synapser", repos=c("http://ran.synapse.org", "http://cran.fhcrc.org"), type="mac.binary")

This also addressed the same issue on another machine: OSX 10.15.5 using R 4.0.1 compiled from source

I figure I'm not the only one with this issue, so it might be useful to mention the type="mac.binary" option in you README.

Output of sessionInfo()

R version 4.0.1 (2020-06-06)
Platform: x86_64-apple-darwin19.5.0 (64-bit)
Running under: macOS Catalina 10.15.5

Matrix products: default
BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libLAPACK.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

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

loaded via a namespace (and not attached):
[1] compiler_4.0.1 tools_4.0.1

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

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]

Unable to install due to issue with synapseclient module

Operating system

Max OSX
Python 3.10.13

Description of the problem

I am experiencing issues installing the package. There seems to be an issue with calling the synapseclient module during configuration.

Actual behavior

The installation is failing with error ModuleNotFoundError: No module named 'synapseclient'. However, the output shows Requirement already satisfied: synapseclient==3.0.0 confirming the module should be installed.
Additionally, I have tried installing synapseclient directly to the virtualenv via reticulate but I still encounter this same issue.

> install.packages("synapser", repos=c("http://ran.synapse.org", "http://cran.fhcrc.org"))
Installing package into ‘/Users/richardgallardo/Library/R/arm64/4.2/library’
(as ‘lib’ is unspecified)
Warning in install.packages :
  unable to access index for repository http://ran.synapse.org/bin/macosx/big-sur-arm64/contrib/4.2:
  cannot open URL 'http://ran.synapse.org/bin/macosx/big-sur-arm64/contrib/4.2/PACKAGES'
installing the source package ‘synapser’

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
[1] "*** Using Python Configuration:"
virtualenv: r-reticulate
Using virtual environment '/Users/richardgallardo/.virtualenvs/r-reticulate' ...
+ /Users/richardgallardo/.virtualenvs/r-reticulate/bin/python -m pip install --upgrade --no-user 'requests<3' 'pandas~=2.0.0' pysftp jinja2 markupsafe
Requirement already satisfied: requests<3 in /Users/richardgallardo/.virtualenvs/r-reticulate/lib/python3.9/site-packages (2.31.0)
Requirement already satisfied: pandas~=2.0.0 in /Users/richardgallardo/.virtualenvs/r-reticulate/lib/python3.9/site-packages (2.0.3)
Requirement already satisfied: pysftp in /Users/richardgallardo/.virtualenvs/r-reticulate/lib/python3.9/site-packages (0.2.9)
Requirement already satisfied: jinja2 in /Users/richardgallardo/.virtualenvs/r-reticulate/lib/python3.9/site-packages (3.1.3)
Requirement already satisfied: markupsafe in /Users/richardgallardo/.virtualenvs/r-reticulate/lib/python3.9/site-packages (2.1.4)
Requirement already satisfied: charset-normalizer<4,>=2 in /Users/richardgallardo/.virtualenvs/r-reticulate/lib/python3.9/site-packages (from requests<3) (3.3.2)
Requirement already satisfied: idna<4,>=2.5 in /Users/richardgallardo/.virtualenvs/r-reticulate/lib/python3.9/site-packages (from requests<3) (3.6)
Requirement already satisfied: urllib3<3,>=1.21.1 in /Users/richardgallardo/.virtualenvs/r-reticulate/lib/python3.9/site-packages (from requests<3) (1.26.18)
Requirement already satisfied: certifi>=2017.4.17 in /Users/richardgallardo/.virtualenvs/r-reticulate/lib/python3.9/site-packages (from requests<3) (2023.11.17)
Requirement already satisfied: python-dateutil>=2.8.2 in /Users/richardgallardo/.virtualenvs/r-reticulate/lib/python3.9/site-packages (from pandas~=2.0.0) (2.8.2)
Requirement already satisfied: pytz>=2020.1 in /Users/richardgallardo/.virtualenvs/r-reticulate/lib/python3.9/site-packages (from pandas~=2.0.0) (2023.3.post1)
Requirement already satisfied: tzdata>=2022.1 in /Users/richardgallardo/.virtualenvs/r-reticulate/lib/python3.9/site-packages (from pandas~=2.0.0) (2023.4)
Requirement already satisfied: numpy>=1.20.3 in /Users/richardgallardo/.virtualenvs/r-reticulate/lib/python3.9/site-packages (from pandas~=2.0.0) (1.26.3)
Requirement already satisfied: paramiko>=1.17 in /Users/richardgallardo/.virtualenvs/r-reticulate/lib/python3.9/site-packages (from pysftp) (3.4.0)
Requirement already satisfied: bcrypt>=3.2 in /Users/richardgallardo/.virtualenvs/r-reticulate/lib/python3.9/site-packages (from paramiko>=1.17->pysftp) (4.1.2)
Requirement already satisfied: cryptography>=3.3 in /Users/richardgallardo/.virtualenvs/r-reticulate/lib/python3.9/site-packages (from paramiko>=1.17->pysftp) (42.0.0)
Requirement already satisfied: pynacl>=1.5 in /Users/richardgallardo/.virtualenvs/r-reticulate/lib/python3.9/site-packages (from paramiko>=1.17->pysftp) (1.5.0)
Requirement already satisfied: six>=1.5 in /Users/richardgallardo/.virtualenvs/r-reticulate/lib/python3.9/site-packages (from python-dateutil>=2.8.2->pandas~=2.0.0) (1.16.0)
Requirement already satisfied: cffi>=1.12 in /Users/richardgallardo/.virtualenvs/r-reticulate/lib/python3.9/site-packages (from cryptography>=3.3->paramiko>=1.17->pysftp) (1.16.0)
Requirement already satisfied: pycparser in /Users/richardgallardo/.virtualenvs/r-reticulate/lib/python3.9/site-packages (from cffi>=1.12->cryptography>=3.3->paramiko>=1.17->pysftp) (2.21)
Using virtual environment '/Users/richardgallardo/.virtualenvs/r-reticulate' ...
+ /Users/richardgallardo/.virtualenvs/r-reticulate/bin/python -m pip install --upgrade --no-user 'synapseclient==3.0.0'
Requirement already satisfied: synapseclient==3.0.0 in /Users/richardgallardo/.virtualenvs/r-reticulate/lib/python3.9/site-packages (3.0.0)
Requirement already satisfied: requests<3.0,>=2.22.0 in /Users/richardgallardo/.virtualenvs/r-reticulate/lib/python3.9/site-packages (from synapseclient==3.0.0) (2.31.0)
Requirement already satisfied: urllib3<2 in /Users/richardgallardo/.virtualenvs/r-reticulate/lib/python3.9/site-packages (from synapseclient==3.0.0) (1.26.18)
Requirement already satisfied: keyring<23.5,>=15 in /Users/richardgallardo/.virtualenvs/r-reticulate/lib/python3.9/site-packages (from synapseclient==3.0.0) (23.4.1)
Requirement already satisfied: deprecated<2.0,>=1.2.4 in /Users/richardgallardo/.virtualenvs/r-reticulate/lib/python3.9/site-packages (from synapseclient==3.0.0) (1.2.14)
Requirement already satisfied: wrapt<2,>=1.10 in /Users/richardgallardo/.virtualenvs/r-reticulate/lib/python3.9/site-packages (from deprecated<2.0,>=1.2.4->synapseclient==3.0.0) (1.16.0)
Requirement already satisfied: importlib-metadata>=3.6 in /Users/richardgallardo/.virtualenvs/r-reticulate/lib/python3.9/site-packages (from keyring<23.5,>=15->synapseclient==3.0.0) (7.0.1)
Requirement already satisfied: charset-normalizer<4,>=2 in /Users/richardgallardo/.virtualenvs/r-reticulate/lib/python3.9/site-packages (from requests<3.0,>=2.22.0->synapseclient==3.0.0) (3.3.2)
Requirement already satisfied: idna<4,>=2.5 in /Users/richardgallardo/.virtualenvs/r-reticulate/lib/python3.9/site-packages (from requests<3.0,>=2.22.0->synapseclient==3.0.0) (3.6)
Requirement already satisfied: certifi>=2017.4.17 in /Users/richardgallardo/.virtualenvs/r-reticulate/lib/python3.9/site-packages (from requests<3.0,>=2.22.0->synapseclient==3.0.0) (2023.11.17)
Requirement already satisfied: zipp>=0.5 in /Users/richardgallardo/.virtualenvs/r-reticulate/lib/python3.9/site-packages (from importlib-metadata>=3.6->keyring<23.5,>=15->synapseclient==3.0.0) (3.17.0)
Error in py_run_string_impl(code, local, convert) : 
  ModuleNotFoundError: No module named 'synapseclient'
Run `reticulate::py_last_error()` for details.
Calls: generateRdFiles ... getFunctionInfo -> <Anonymous> -> py_run_string_impl
Execution halted
ERROR: configuration failed for package ‘synapser’
* removing ‘/Users/richardgallardo/Library/R/arm64/4.2/library/synapser’
Warning in install.packages :
  installation of package ‘synapser’ had non-zero exit status

Output of sessionInfo()

Using a fresh session and after attempting the installation:

> sessionInfo()
R version 4.2.2 (2022-10-31)
Platform: aarch64-apple-darwin20 (64-bit)
Running under: macOS Ventura 13.6

Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

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

loaded via a namespace (and not attached):
[1] compiler_4.2.2  tools_4.2.2     rstudioapi_0.14

Additionally, my reticulate package is v1.34.0

can't load the library(synapser)

Operating system

Windows 10

Description of the problem

I can download the package alright. But when it comes to "library(synapser)", the error occurs.

Expected behavior

library(synapser)

Actual behavior

library(synapser)
Error: package or namespace load failed for ‘synapser’:
.onLoad failed in loadNamespace() for 'synapser', details:
call: PythonEmbedInR::pyExec("syn=synapseclient.Synapse(skip_checks=True)")
error:
Traceback (most recent call last):
File "", line 1, in
File "C:/Program Files/R/R-3.6.1/library/synapser\Lib\site-packages\synapseclient-1.9.3-py3.5.egg\synapseclient\client.py", line 215, in init
self.cache = cache.Cache(cache_root_dir)
File "C:/Program Files/R/R-3.6.1/library/synapser\Lib\site-packages\synapseclient-1.9.3-py3.5.egg\synapseclient\cache.py", line 89, in init
self.cache_root_dir = cache_root_dir
File "C:/Program Files/R/R-3.6.1/library/synapser\Lib\site-packages\synapseclient-1.9.3-py3.5.egg\synapseclient\cache.py", line 83, in setattr
os.makedirs(value)
File "os.py", line 231, in makedirs
File "os.py", line 241, in makedirs
OSError: [WinError 123] The filename, directory name, or vol

Output of sessionInfo()

R version 3.6.1 (2019-07-05)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 17763)

Matrix products: default

locale:
[1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C
[5] LC_TIME=English_United States.1252

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

loaded via a namespace (and not attached):
[1] compiler_3.6.1 R6_2.4.0 tools_3.6.1 codetools_0.2-16
[5] pack_0.1-1 PythonEmbedInR_0.3.37

Unable to Install Synapser

Operating system

I am working on a Mac OSX operating on an M1 chip.

Description of the problem

I am trying to install synapser into R Studio using the
install.packages("synapser", repos=c("http://ran.synapse.org", "http://cran.fhcrc.org"))
command and I end up having a large error message detailing dependency conflicts that I am unsure of how to resolve

Expected behavior

I am not sure exactly how it should look but I do know it is supposed to download correctly.

Actual behavior

`UnsatisfiableError: The following specifications were found
to be incompatible with the existing python installation in your environment:

Specifications:

• pandas[version='<1.5'] -> python[version='2.7.|3.5.|3.6.|>=2.7,<2.8.0a0|>=3.10,<3.11.0a0|>=3.8,<3.9.0a0|>=3.9,<3.10.0a0|>=3.7,<3.8.0a0|>=3.6,<3.7.0a0|>=3.5,<3.6.0a0|3.4.|>=3.7.1,<3.8.0a0']
• pysftp -> python[version='2.7.|3.5.|3.6.|3.4.']
• pysftp -> python[version='>=2.7,<2.8.0a0|>=3.6,<3.7.0a0|>=3.8,<3.9.0a0|>=3.7,<3.8.0a0|>=3.5,<3.6.0a0']

Your python: python=3.11

If python is on the left-most side of the chain, that's the version you've asked for.
When python appears to the right, that indicates that the thing on the left is somehow
not available for the python version you are constrained to. Note that conda will not
change your python version to a different minor version unless you explicitly specify
that.

The following specifications were found to be incompatible with each other:

Output in format: Requested package -> Available versions

Package cryptography conflicts for:
requests[version='<3'] -> urllib3[version='>=1.21.1,<1.26,!=1.25.0,!=1.25.1'] -> cryptography[version='>=1.3.4']
pysftp -> paramiko[version='>=1.17.0'] -> cryptography[version='>=1.1|>=1.5|>=2.5']

Package tzdata conflicts for:
requests[version='<3'] -> python[version='>=3.10,<3.11.0a0'] -> tzdata
jinja2 -> python[version='>=3.11,<3.12.0a0'] -> tzdata
pandas[version='<1.5'] -> pypy3.9[version='>=7.3.9'] -> tzdata
markupsafe -> python[version='>=3.11,<3.12.0a0'] -> tzdata
python=3.11 -> tzdata

Package libsqlite conflicts for:
python=3.11 -> libsqlite[version='>=3.39.4,<4.0a0|>=3.40.0,<4.0a0|>=3.42.0,<4.0a0']
python=3.11 -> sqlite[version='>=3.41.2,<4.0a0'] -> libsqlite[version='3.41.2|3.42.0',build='h58db7d2_1|h58db7d2_0']

Package setuptools conflicts for:
pandas[version='<1.5'] -> numexpr[version='>=2.7.1'] -> setuptools
python=3.11 -> pip -> setuptools
jinja2 -> setuptools
pandas[version='<1.5'] -> setuptools[version='<60.0.0']

Package python_abi conflicts for:
requests[version='<3'] -> python_abi[version='2.7.|3.6.|3.6|3.8.|3.7.',build='_cp27m|_cp37m|_pypy36_pp73|_cp38|_cp36m']
requests[version='<3'] -> certifi[version='>=2017.4.17'] -> python_abi[version='3.10.|3.9|3.8|3.9.|3.7',build='_pypy37_pp73|_cp39|_pypy39_pp73|_cp310|_pypy38_pp73']
pandas[version='<1.5'] -> numpy[version='>=1.19.5,<2.0a0'] -> python_abi=3.11[build=_cp311]
markupsafe -> python_abi[version='2.7.|3.10.|3.11.|3.8|3.9.|3.9|3.8.|3.7.|3.7|3.6|3.6.',build='_cp27m|_pypy37_pp73|_cp310|_pypy39_pp73|_cp311|_pypy38_pp73|_cp39|_cp38|_cp37m|_pypy36_pp73|_cp36m']
pysftp -> python=3.6 -> python_abi==3.6[build=_pypy36_pp73]
pandas[version='<1.5'] -> python_abi[version='3.10.|3.8.|3.8|3.9|3.9.|3.7|3.7.|3.6|3.6.',build='_pypy37_pp73|_cp310|_pypy39_pp73|_pypy38_pp73|_cp39|_cp38|_cp37m|_pypy36_pp73|_cp36m']
jinja2 -> markupsafe[version='>=0.23,<2'] -> python_abi[version='2.7.|3.10.|3.7.|3.7|3.9.|3.8.|3.6|3.6.|3.8|3.9|3.11.',build='_cp311|_pypy39_pp73|_cp27m|_pypy37_pp73|_cp310|_cp37m|_cp39|_cp38|_pypy36_pp73|_cp36m|_pypy38_pp73']

Package expat conflicts for:
markupsafe -> pypy3.8[version='>=7.3.11'] -> expat[version='>=2.2.10,<3.0.0a0|>=2.4.1,<3.0a0|>=2.4.7,<3.0a0|>=2.4.8,<3.0a0|>=2.4.9,<3.0a0|>=2.5.0,<3.0a0|>=2.2.9,<3.0.0a0|>=2.3.0,<3.0a0']
pandas[version='<1.5'] -> pypy3.9[version='>=7.3.9'] -> expat[version='>=2.2.10,<3.0.0a0|>=2.3.0,<3.0a0|>=2.4.1,<3.0a0|>=2.4.8,<3.0a0|>=2.4.9,<3.0a0|>=2.5.0,<3.0a0|>=2.2.9,<3.0.0a0']

Package pypy3.9 conflicts for:
markupsafe -> pypy3.9[version='>=7.3.11|>=7.3.9|>=7.3.8']
markupsafe -> python[version='>=3.9,<3.10.0a0'] -> pypy3.9[version='7.3.|7.3.11.|7.3.9.|7.3.8.']

Package pypy3.7 conflicts for:
markupsafe -> pypy3.7[version='>=7.3.3|>=7.3.4|>=7.3.7']
markupsafe -> python[version='>=3.7,<3.8.0a0'] -> pypy3.7[version='7.3.|7.3.3.|7.3.4.|7.3.5.|7.3.7.*']

Package pypy3.8 conflicts for:
markupsafe -> python[version='>=3.8,<3.9.0a0'] -> pypy3.8[version='7.3.|7.3.11.|7.3.9.|7.3.8.']
markupsafe -> pypy3.8[version='>=7.3.11|>=7.3.9|>=7.3.8']
pandas[version='<1.5'] -> pypy3.8[version='>=7.3.9']
pandas[version='<1.5'] -> numpy[version='>=1.19.5,<2.0a0'] -> pypy3.8[version='7.3.|7.3.11.|>=7.3.11|>=7.3.8|7.3.9.|7.3.8.']
requests[version='<3'] -> certifi[version='>=2017.4.17'] -> pypy3.8[version='7.3.11.|>=7.3.8|>=7.3.9|7.3.9.|7.3.8.']
jinja2 -> setuptools -> pypy3.8[version='7.3.11.|>=7.3.11|>=7.3.8|>=7.3.9|7.3.9.|7.3.8.']

Package certifi conflicts for:
requests[version='<3'] -> certifi[version='>=2017.4.17']
pandas[version='<1.5'] -> setuptools[version='<60.0.0'] -> certifi[version='>=2016.09|>=2016.9.26']
jinja2 -> setuptools -> certifi[version='>=2016.09|>=2016.9.26']
requests[version='<3'] -> urllib3[version='>=1.21.1,<1.26,!=1.25.0,!=1.25.1'] -> certifi

Error: one or more Python packages failed to install [error code 1]
Execution halted
ERROR: configuration failed for package ‘synapser’

• removing ‘/Users/manicj/Library/R/arm64/4.2/library/synapser’
  Warning in install.packages :
  installation of package ‘synapser’ had non-zero exit status

The downloaded source packages are in
‘/private/var/folders/6_/0r963bdd7r76s46qwrn44hc4s8314r/T/RtmpdvXKJU/downloaded_`

Output of sessionInfo()

R version 4.2.2 (2022-10-31)
Platform: aarch64-apple-darwin20 (64-bit)
Running under: macOS Ventura 13.4.1

Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

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

other attached packages:
[1] cmapR_1.10.0

loaded via a namespace (and not attached):
[1] Rcpp_1.0.11 compiler_4.2.2 pillar_1.9.0
[4] cytolib_2.10.1 GenomeInfoDb_1.34.9 XVector_0.38.0
[7] MatrixGenerics_1.10.0 bitops_1.0-7 tools_4.2.2
[10] zlibbioc_1.44.0 lifecycle_1.0.3 tibble_3.2.1
[13] lattice_0.20-45 pkgconfig_2.0.3 rlang_1.1.1
[16] Matrix_1.5-1 DelayedArray_0.24.0 cli_3.6.1
[19] rstudioapi_0.15.0 GenomeInfoDbData_1.2.9 dplyr_1.1.2
[22] generics_0.1.3 S4Vectors_0.36.2 vctrs_0.6.3
[25] IRanges_2.32.0 stats4_4.2.2 grid_4.2.2
[28] tidyselect_1.2.0 glue_1.6.2 Biobase_2.58.0
[31] R6_2.5.1 fansi_1.0.4 RProtoBufLib_2.10.0
[34] magrittr_2.0.3 matrixStats_1.0.0 BiocGenerics_0.44.0
[37] GenomicRanges_1.50.2 SummarizedExperiment_1.28.0 flowCore_2.10.0
[40] utf8_1.2.3 RCurl_1.98-1.12 rjson_0.2.21

Unmet dependency on Debian 9: libffi-dev

Operating system

myprompt$ uname -a
Linux attila-ThinkS 4.9.0-8-amd64 #1 SMP Debian 4.9.130-2 (2018-10-27) x86_64 GNU/Linux

Description of the problem

On Debian 9 (Stretch) the upgrade to synapser 0.5.45 failed with the error below. Installing libffi-dev solved the problem.

Package libffi was not found in the pkg-config search path.
Perhaps you should add the directory containing `libffi.pc'
to the PKG_CONFIG_PATH environment variable
No package 'libffi' found
c/_cffi_backend.c:15:17: fatal error: ffi.h: No such file or directory
 #include <ffi.h>
                 ^
compilation terminated.
error: Setup script exited with error: command 'gcc' failed with exit status 1
ERROR: configuration failed for package ‘synapser’
* removing ‘/usr/local/lib/R/site-library/synapser’
* restoring previous ‘/usr/local/lib/R/site-library/synapser’

Output of sessionInfo()

> sessionInfo()
R version 3.4.1 (2017-06-30)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Debian GNU/Linux 9 (stretch)

Matrix products: default
BLAS: /usr/lib/openblas-base/libblas.so.3
LAPACK: /usr/lib/libopenblasp-r0.2.19.so

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8     LC_MONETARY=en_US.UTF-8   
 [6] LC_MESSAGES=en_US.UTF-8    LC_PAPER=en_US.UTF-8       LC_NAME=C                  LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
[1] knitr_1.20     setwidth_1.0-4 colorout_1.0-2

loaded via a namespace (and not attached):
[1] compiler_3.4.1 tools_3.4.1   

ENH: get API Key

Operating system

Max OSX

Description of the problem

Default in synLogin is that no credentials are given. Should add a check that

if (is.null(email) && is.null(password)) {
   if (is.null(apiKey)) {
       apiKey = Sys.getenv("SYNAPSE_API_KEY")
   }
}

so that if you have a SYNAPSE_API_KEY variable set in ~/.Renviron or environment (and using R from the terminal), then it will auto login.

Expected behavior

Login if API set in ~/.Renviron

Actual behavior

Fails if no credentials given