SSL certificate problem

[huyvuong]

I tried the BasespaceR package but the Client_id and Client_secret I got from MyApps dashboard don't work. Here's the error: aAuth <- AppAuth(client_id="xxxxxxxxxxxxxxxxxxxx", client_secret="7d82d559330f4ceba232cdd36e14644e", scope="create global") Error in function (type, msg, asError = TRUE) : SSL certificate problem, verify that the CA cert is OK. Details: error:14090086:SSL routines:SSL3_GET_SERVER_CERTIFICATE:certificate verify failed

Would you please let me know why? Thank you.

[adrianalexa]

Hi huyvuong,

Thanks for the report. It seems to be a problem with the 'curl' installation that propagates through RCurl. You can get more details on this from the RCurl FAQ: http://www.omegahat.org/RCurl/FAQ.html (search for "When I try to interact with a URL via https, I get an error of the form"). It seems that the library cannot access a certificate from a signed agent.

There are some options if you use RCurl functions directly, but I'll have to do some internal changes to BaseSpaceR package. Problem is that I cannot replicate this problem on my machines so is hard to test the changes.

Can you please send me the R session details (type 'sessionInfo() within R), the details of the computer you are running the code from? Are you on a Windows platform? Would it be possible to use a different machine/R installation?

Kind regards, Adrian Alexa

[huyvuong]

Hi Adrian,

Thank for the information. It would be great if I can test it for you. Here's the sessionInfo(). I use windows 7, 64 bit. I will try the linux machine later this afternoon.

sessionInfo() R version 2.15.2 (2012-10-26) Platform: x86_64-w64-mingw32/x64 (64-bit)

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] stats graphics grDevices utils datasets methods base

other attached packages: [1] BaseSpaceR_0.1.4 RJSONIO_1.0-1 RCurl_1.95-3 bitops_1.0-5

loaded via a namespace (and not attached): [1] tools_2.15.2

Best regards, Huy

On Mon, Mar 4, 2013 at 10:21 AM, adrianalexa notifications@github.comwrote:

Hi huyvuong,

Thanks for the report. It seems to be a problem with the 'curl' installation that propagates through RCurl. You can get more details on this from the RCurl FAQ: http://www.omegahat.org/RCurl/FAQ.html (search for "When I try to interact with a URL via https, I get an error of the form"). It seems that the library cannot access a certificate from a signed agent.

There are some options if you use RCurl functions directly, but I'll have to do some internal changes to BaseSpaceR package. Problem is that I cannot replicate this problem on my machines so is hard to test the changes.

Can you please send me the R session details (type 'sessionInfo() within R), the details of the computer you are running the code from? Are you on a Windows platform? Would it be possible to use a different machine/R installation?

Kind regards, Adrian Alexa

— Reply to this email directly or view it on GitHubhttps://github.com/basespace/basespace-r-sdk/issues/1#issuecomment-14389177 .

[adrianalexa]

Hi Huy,

there is a new version of the package available. There are some new nice feature and a redesign of the API which should provide easier navigation through the BaseSpace resources. Also I implemented a solution for the SSL certificate problem under Windows.

You can try the new version and let me know if you encounter the same problem. Also I didn't have time to update the documentation on the BaseSpace developer site, but until then you can take a look at the package vignette under the 'inst/doc' directory (https://github.com/basespace/basespace-r-sdk/blob/master/BaseSpaceR/inst/doc/BaseSpaceR-QscoreApp.pdf).

Looking forward to hear how it works for you.

Cheers, Adrian

[huyvuong]

Hi Adrian,

Sorry for the delay. Just an update that it is working now after I upgrade the RCurl package and the reinstall the new version of API.

Thank very much, Huy

On Sat, Mar 9, 2013 at 2:19 PM, adrianalexa notifications@github.comwrote:

Hi Huy,

there is a new version of the package available. There are some new nice feature and a redesign of the API which should provide easier navigation through the BaseSpace resources. Also I implemented a solution for the SSL certificate problem under Windows.

You can try the new version and let me know if you encounter the same problem. Also I didn't have time to update the documentation on the BaseSpace developer site, but until then you can take a look at the package vignette under the 'inst/doc' directory ( https://github.com/basespace/basespace-r-sdk/blob/master/BaseSpaceR/inst/doc/BaseSpaceR-QscoreApp.pdf ).

Looking forward to hear how it works for you.

Cheers, Adrian

— Reply to this email directly or view it on GitHubhttps://github.com/basespace/basespace-r-sdk/issues/1#issuecomment-14669794 .

[huyvuong]

Hi Adrian,

I have got the access token and passed the authorization but I didn't see any projects and runs from my account (run listProjects(aAuth) and listRuns(aAuth) returned empty response collection.

Would you please let me know why? Thanks.

Best regards, Huy

On Thu, Mar 28, 2013 at 2:26 PM, Huy Vuong huy.vuong@gmail.com wrote:

Hi Adrian,

Sorry for the delay. Just an update that it is working now after I upgrade the RCurl package and the reinstall the new version of API.

Thank very much, Huy

On Sat, Mar 9, 2013 at 2:19 PM, adrianalexa notifications@github.comwrote:

Hi Huy,

there is a new version of the package available. There are some new nice feature and a redesign of the API which should provide easier navigation through the BaseSpace resources. Also I implemented a solution for the SSL certificate problem under Windows.

You can try the new version and let me know if you encounter the same problem. Also I didn't have time to update the documentation on the BaseSpace developer site, but until then you can take a look at the package vignette under the 'inst/doc' directory ( https://github.com/basespace/basespace-r-sdk/blob/master/BaseSpaceR/inst/doc/BaseSpaceR-QscoreApp.pdf ).

Looking forward to hear how it works for you.

Cheers, Adrian

— Reply to this email directly or view it on GitHubhttps://github.com/basespace/basespace-r-sdk/issues/1#issuecomment-14669794 .

[adrianalexa]

Hi Huy,

this looks wired, you should be able to see at least two public projects. If you create a new project using BaseSpace dashboard would you see that?

Could you send me an e-mail (see e-mail address in the DESCRIPTION file) with your session info and if possible the access token you got (or you can save the AppAuth instance and send that). This would allow me to pinpoint the problem.

Lastly, if you are using the 'aAuth' data as shown in the package vignette, would you be able to see any project/run?

Regards, Adrian