Is there a way to get gitcreds working on RStudio server (linux)?
lcolladotor opened this issue · 3 comments
Hi,
I'm having a bit of a problem with gitcreds on an RStudio Server 1.4.1103 that I'm using for teaching a class this week. I'm able to create a GitHub token and store it with gitcreds.
> usethis::create_github_token()
● Call `gitcreds::gitcreds_set()` to register this token in the local Git credential store
It is also a great idea to store this token in any password-management software that you use
✓ Opening URL 'https://github.com/settings/tokens/new?scopes=repo,user,gist,workflow&description=R:GITHUB_PAT'
> gitcreds::gitcreds_set()
? Enter password or token: a358aac525e5b498editedETCETERA
-> Adding new credentials...
-> Removing credetials from cache...
-> Done.
> gitcreds::gitcreds_get("https://github.com")
<gitcreds>
protocol: https
host : github.com
username: PersonalAccessToken
password: <-- hidden -->
> gitcreds::gitcreds_get("https://github.com")$password
[1] "a358aac525e5b498editedETCETERA"I can change R projects, restart R, and well, I get the same info back from gitcreds::gitcreds_get("https://github.com").
> gitcreds::gitcreds_get("https://github.com")
<gitcreds>
protocol: https
host : github.com
username: PersonalAccessToken
password: <-- hidden -->
> gitcreds::gitcreds_cache_envvar("https://github.com")
[1] "GITHUB_PAT_GITHUB_COM"
> gitcreds::gitcreds_list_helpers()
[1] "cache"
> gitcreds::gitcreds_list()
Error in gitcreds$throw(gitcreds$new_error("gitcreds_unknown_helper", :
Unknown credential helper: `cache`, cannot list credentialsHowever, at some point, I'm no longer able to retrieve the information. It's almost like wherever the token is cached gets deleted. Is there a way to find what would the cache location be? I haven't been able to figure out what triggers the break in behavior. I mean, after gitcreds::gitcreds_set() I really only use commands like usethis::use_github() and none of the gitcreds commands.
> Sys.getenv("GITHUB_PAT_GITHUB_COM")
[1] "protocol:https:host:github.com:username:PersonalAccessToken:password:a358aac525e5b498editedETCETERA"After reading https://gitcreds.r-lib.org/reference/gitcreds_get.html#arguments (Credential helpers section) I see that but most Linux distributions do not set up a default credential helper. which makes me guess that at some point the environment variable GITHUB_PAT_GITHUB_COM gets un-set. For now I told students to use usethis::edit_r_environ() although I'm aware that this is no longer the suggested setup. Though hmm, maybe I'm missing something else that could be done to get gitcreds working on this linux environment.
(at some point this happens:)
> gitcreds::gitcreds_get("https://github.com")
Error in throw(new_error("gitcreds_no_credentials", url = url)) :
Could not find any credentials
> traceback()
4: stop(cond)
3: throw(new_error("gitcreds_no_credentials", url = url))
2: gitcreds_parse_output(out, url)
1: gitcreds::gitcreds_get("https://github.com")Let me know if there's any other information I can provide that would be useful.
Best,
Leo
Related to lcolladotor/rnaseq_LCG-UNAM_2021@e15bb0f.
> options(width = 120)
> sessioninfo::session_info()
─ Session info ───────────────────────────────────────────────────────────────────────────────────────────────────────
setting value
version R version 4.0.3 (2020-10-10)
os Ubuntu 20.04.1 LTS
system x86_64, linux-gnu
ui RStudio
language (EN)
collate en_US.UTF-8
ctype en_US.UTF-8
tz America/Mexico_City
date 2021-02-23
─ Packages ───────────────────────────────────────────────────────────────────────────────────────────────────────────
package * version date lib source
assertthat 0.2.1 2019-03-21 [2] CRAN (R 4.0.3)
bookdown 0.21 2020-10-13 [2] CRAN (R 4.0.3)
cli 2.3.0 2021-01-31 [2] CRAN (R 4.0.3)
data.table 1.14.0 2021-02-21 [2] CRAN (R 4.0.3)
digest 0.6.27 2020-10-24 [2] CRAN (R 4.0.3)
ellipsis 0.3.1 2020-05-15 [2] CRAN (R 4.0.3)
evaluate 0.14 2019-05-28 [2] CRAN (R 4.0.3)
generics 0.1.0 2020-10-31 [2] CRAN (R 4.0.3)
gitcreds 0.1.1 2020-12-04 [2] CRAN (R 4.0.3)
glue 1.4.2 2020-08-27 [2] CRAN (R 4.0.3)
hms 1.0.0 2021-01-13 [1] CRAN (R 4.0.3)
htmltools 0.5.1.1 2021-01-22 [2] CRAN (R 4.0.3)
knitr 1.31 2021-01-27 [2] CRAN (R 4.0.3)
lifecycle 0.2.0 2020-03-06 [2] CRAN (R 4.0.3)
lubridate 1.7.9.2 2020-11-13 [1] CRAN (R 4.0.3)
magrittr 2.0.1 2020-11-17 [2] CRAN (R 4.0.3)
pkgconfig 2.0.3 2019-09-22 [2] CRAN (R 4.0.3)
Rcpp 1.0.6 2021-01-15 [2] CRAN (R 4.0.3)
rlang 0.4.10 2020-12-30 [2] CRAN (R 4.0.3)
rmarkdown 2.7 2021-02-19 [2] CRAN (R 4.0.3)
rsthemes 0.2.1.9000 2021-02-23 [1] Github (gadenbuie/rsthemes@521572b)
rstudioapi 0.13 2020-11-12 [2] CRAN (R 4.0.3)
sessioninfo 1.1.1 2018-11-05 [2] CRAN (R 4.0.3)
suncalc 0.5.0 2019-04-03 [1] CRAN (R 4.0.3)
vctrs 0.3.6 2020-12-17 [2] CRAN (R 4.0.3)
withr 2.4.1 2021-01-26 [2] CRAN (R 4.0.3)
xfun 0.20 2021-01-06 [2] CRAN (R 4.0.3)
yaml 2.2.1 2020-02-01 [2] CRAN (R 4.0.3)
[1] /home/compu2/R/x86_64-pc-linux-gnu-library/4.0
[2] /usr/local/lib/R/site-library
[3] /usr/lib/R/site-library
[4] /usr/lib/R/library
> system("git --version")
git version 2.25.1RStudio Server
Version 1.4.1103
© 2009-2021 RStudio, PBC
"Wax Begonia" (458706c3, 2021-01-06) for Ubuntu Bionic
Mozilla/5.0 (Windows NT 10.0; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/88.0.4324.182 Safari/537.36
Yes, on Linux you often don't have a proper credential store, especially on a server. In your case
> gitcreds::gitcreds_list_helpers()
[1] "cache"means that you are using the cache credential helper: https://git-scm.com/docs/git-credential-cache
This credential helper stores the credentials in memory, so they are lost after a reboot. It also has a timeout, defaulting to 900 seconds.
If you can use an .Renviron file on RStudio server, then it is probably simplest to set up the token as an environment variable in .Renviron. You can set GITHUB_PAT_GITHUB_COM or just GITHUB_PAT, and gitcreds (and thus usethis, etc.) still picks these up.
Thank you very much for the explanation Gábor!
Best,
Leo
NP, we'll try to explain this better in the gitcreds and/or usethis docs.