Hello,
This is Wendy Wu from Arvinas. I am a newly registered synapse member, and interested to access synapse data using R. I installed R package ?synapser? and followed the instruction from https://r-docs.synapse.org/articles/manageSynapseCredentials.html to authenticate. However, none of them worked for me, even using my username and password that I can successfully log into my synapse account.
Can you please help with it? The details are shown below.
**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
Created by Wenhui Wu guodudou Hello @thomas.yu ,
Thank you very much for the suggestion. Yes, I am able to log in using my home computer. I think my work internet blocked the access. I will contact our IT group to solve the issue.
By the way, I have a couple of questions about how to format .synapseConfig file for which the online template is as below:
```
[authentication]
# either authtoken OR username and password
authtoken =
username =
password =
```
1. Do I write the corresponding information between <> or "" or nothing?
2. What if I want to use API key, do I put it at ?
Thank you very much!
Wendy
hello @guodudou ,
Thanks. Are you hitting this error at work or at your home network? If you are at work, can you try this command when you are at home?
Best,
Tom Hello @thomas.yu
Thank you very much for your help. I just tried using my email and password but still get the same error message.
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:852)'),))
I look forward to your advice!
Best,
Wendy Hello @guodudou
Sorry for your troubles. Can you try:
```r
library(synapser)
synLogin(email="email", password="yourpassword")
```
Do you get an error from this, and if so can you paste the error? NOTE: Please make sure to redact your password if pasting the commands.
Best,
Tom
Drop files to upload
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