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dynverse / dyno

Inferring, interpreting and visualising trajectories using a streamlined set of packages 🦕
https://dynverse.github.io/dyno
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installation of dyno fails since dynwrap is called twice #33

Closed abotzki closed 5 years ago

abotzki commented 5 years ago

Hi the installation of the dyno package fails at the point where dynwrap is called again - @devel dynfeature (NA -> 88274ff88...) [GitHub] dynguidel... (NA -> d177eb719...) [GitHub] dynmethods (NA -> fbac20a1a...) [GitHub] dynplot (NA -> 87717ae06...) [GitHub] dynwrap (NA -> dee7f681b...) [GitHub] BH (NA -> 1.66.0-1 ) [CRAN] bindr (NA -> 0.1.1 ) [CRAN] bindrcpp (NA -> 0.2.2 ) [CRAN] dplyr (NA -> 0.7.8 ) [CRAN] fansi (NA -> 0.4.0 ) [CRAN] pillar (NA -> 1.3.1 ) [CRAN] pkgconfig (NA -> 2.0.2 ) [CRAN] plogr (NA -> 0.2.0 ) [CRAN] plyr (NA -> 1.8.4 ) [CRAN] praise (NA -> 1.0.0 ) [CRAN] purrr (NA -> 0.2.5 ) [CRAN] ranger (NA -> 0.10.1 ) [CRAN] RcppEigen (NA -> 0.3.3.5.0 ) [CRAN] reshape2 (NA -> 1.4.3 ) [CRAN] stringi (NA -> 1.2.4 ) [CRAN] stringr (NA -> 1.3.1 ) [CRAN] testthat (NA -> 2.0.1 ) [CRAN] tibble (NA -> 1.4.2 ) [CRAN] tidyr (NA -> 0.8.2 ) [CRAN] tidyselect (NA -> 0.2.5 ) [CRAN] utf8 (NA -> 1.1.4 ) [CRAN] dynutils (NA -> 051f64ef5...) [GitHub] dynwrap (NA -> dee7f681b...) [GitHub] dyneval (NA -> 72948e12a...) [GitHub] dynwrap (dee7f681b... -> 887a5b927...) [GitHub]

...
Downloading GitHub repo dynverse/dyneval@master
Installing package into ‘/usr/local/lib/R/site-library’
(as ‘lib’ is unspecified)
* installing *source* package ‘dyneval’ ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** testing if installed package can be loaded
* DONE (dyneval)
Downloading GitHub repo dynverse/dynwrap@devel
Skipping dynwrap, it is already being installed
Error in vapply(remotes, install_remote, ..., FUN.VALUE = character(1)) :
  values must be type 'character',
 but FUN(X[[2]]) result is type 'logical'
Calls: <Anonymous> ... update -> update.package_deps -> install_remotes -> vapply
Execution halted
...
rcannood commented 5 years ago

Thanks for trying out dyno! Discussing with @zouter , this seems related to r-lib/remotes#225. This is a bug from remotes that probably occurs because one package requires dynwrap@master, while another package requires dynwrap@devel. I'm changing the depending packages so that they only require dynwrap@master, since the @devel dependency was included by mistake. I'll keep you posted!

zouter commented 5 years ago

This should now be fixed with dynverse/dynguidelines#49 . @abotzki, can you confirm? Thanks!

abotzki commented 5 years ago

Hmm I just tried from scratch again: the installation stops immediately.

> devtools::install_github('dynverse/dyno')
Error: HTTP error 403.
  API rate limit exceeded for 35.241.173.168. (But here's the good news: Authenticated requests get a higher rate limit. Check out the documentation for more details.)

  Rate limit remaining: 0/60
  Rate limit reset at: 2018-12-18 14:56:52 UTC

  To increase your GitHub API rate limit
  - Use `usethis::browse_github_pat()` to create a Personal Access Token.
  - Use `usethis::edit_r_environ()` and add the token as `GITHUB_PAT`.

executing usethis::browse_github_pat() does not create a token, so automated installation remains difficult.

rcannood commented 5 years ago

This error is because your IP address has been making too many github api requests.

A good solution would be to create a PAT and add a GITHUB_PAT=<xx_your_pat_here_xx> entry to your ~/.Renviron file (which you can access in Rstudio with usethis::edit_r_environ()).

abotzki commented 5 years ago

Yes, I followed the suggestion and this works when I do it manually. I will see whether I can fix this by using an ansible script. It still looks like a workaround but I also understand that the issue with the r-lib remotes is beyond your control.

sjkoelle commented 4 years ago

I am still getting this error even when using the authentication token. The installation seems to have failed in the middle

... (installing)... ** testing if installed package keeps a record of temporary installation path

Some dynverse packages appear to have installed successfully, but I get the rate limit error if I try to restart.

rcannood commented 4 years ago

Your issue is definitely separate from that Alexander, so please create a separate github issue. I also don't have enough information to know what your problem is. Do you have a GITHUB_PAT defined somewhere? Could you provide the full log?

sjkoelle commented 4 years ago

got it resolved. thanks.