Good morning
I am trying to download the syn13894145.2 data. When trying in R, the error 'Warning in install.packages :
package ?synapser? is not available (for R version 3.5.1)' occurs when I try to install synapser.
When trying in python, the error 'ModuleNotFoundError: No module named 'synapseclient' ' occurs.
Please advise.
Created by cvanderm I have a DUC through Synapse as well as a separate DUA directly with Rush that was approved. Sorry for the frustration with this. To help us investigate can you please let us know if you have a DUA directly with Rush, or if you requested access by submitting a DUC through Synapse Yes, terms of use was accepted. But there is still an 'unmet conditions' tab, which when I click on that says I need to request access. Which has already been done and approved. @cvanderm there is a clickwrap agreement asking you to acknowledge data providers in publications. Have you agreed to this? To check that go here and see if you have agreed to this "Publications generated using data accessed through the AMP-AD Knowledge Portal must acknowledge and cite both the data contributor(s) and the AMP-AD consortium as described on the Data Use Requirements Page": https://www.synapse.org/#!AccessRequirements:ID=syn3219045&TYPE=ENTITY @amap -
Can you please help? It says I need to request access to the data. but i have already requested access and it has been approved. so i am not able to download it. please advise. The easiest way to find the data for a particular study is to follow the [Browse Data by Study](https://www.synapse.org/#!Synapse:syn2580853/wiki/409853) link from the wiki. From there you can use the subsetting tool on the left panel to select the study data that you're interested in. In your case, you'll want to select "ROSMAP" from the Study category. The Client Documentation page can help you with detailed instructions for downloading data once you've decided files you're interested in. Hi. I am still not able to download ROSMAP dataset. Please send me instructions on how to do so once I have installed synapser. Where can I find detailed information on how to download ROSMAP? i updated R and now it has worked - thanks. Hi @kimyenAdmin
I am still getting the same error. When I run install.packages("synapser", repos=c("http://ran.synapse.org", "http://cran.fhcrc.org")) the package seems to install correctly (although some of the warnings may be the problem):
> install.packages("synapser", repos=c("http://ran.synapse.org", "http://cran.fhcrc.org"))
also installing the dependency ?PythonEmbedInR?
trying URL 'http://ran.synapse.org/src/contrib/PythonEmbedInR_0.3.37.tar.gz'
Content type 'application/x-tar' length 93833 bytes (91 KB)
==================================================
downloaded 91 KB
trying URL 'http://ran.synapse.org/src/contrib/synapser_0.6.58.tar.gz'
Content type 'application/x-tar' length 126645 bytes (123 KB)
==================================================
downloaded 123 KB
* 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
14 19.6M 14 2901k 0 0 20 19.6M 20 4069k 25 19.6M 25 5237k 0 0 1153k 0:00:01 100 19.6M 100 19.6M 0 0 1168k 0 0:00:17 0:00:17
Mac specific configuration
cp: /usr/local/opt/openssl/lib/libcrypto.a: No such file or directory
ERROR: configuration failed for package ?PythonEmbedInR?
* removing ?/anaconda3/lib/R/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 ?/anaconda3/lib/R/library/synapser?
Warning in install.packages :
installation of package ?synapser? had non-zero exit status
The downloaded source packages are in
?/private/var/folders/0q/mq3c3lyd2f180qyts8hzdz_m2ykwdh/T/RtmpvVlLDC/downloaded_packages?
Updating HTML index of packages in '.Library'
Making 'packages.html' ... done
I then run library("synapser") and get Error in library("synapser") : there is no package called ?synapser? Hello @cvanderm ,
Like @sieberts said, `synapser` is available at our RAN (http://ran.synapse.org). In your command, you were pointing to a different RAN endpoint.
Please use:
```
install.packages("synapser", repos=c("http://ran.synapse.org", "http://cran.fhcrc.org"))
```
Please let us know if you found this command on one of our documentation, so that we can update the link. If someone gave you this command, please notify them about the change on the RAN URL.
@kimyen, can you help? When I run the following in R:
install.packages("synapser", repos=c("https://sage-bionetworks.github.io/ran", "http://cran.fhcrc.org"))
install.packages("synapser")
library("synapser")
This error still comes up:
Error in library("synapser") : there is no package called ?synapser?
A colleague also tried to run and got the same error.
Synapser is newly available (as of yesterday afternoon) for R 3.5 via http://ran.synapse.org. When did you try to install? Hi! You need to install one of the Synapse clients in order to download from Synapse. You can read more about installing these clients here:
https://docs.synapse.org/articles/getting_started_clients.html