devtools installation fails

[Jason-Conner-NOAA]

Trying to install FishStatsUtils to overwrite version 2.2.0: devtools::install_github("james-thorson/FishStatsUtils", force=T)

Fails with this error (similar error with Namespace happens when attempting to compile from source): Downloading GitHub repo james-thorson/FishStatsUtils@master √ checking for file 'C:\Users\Jason.Conner\AppData\Local\Temp\Rtmp4GpjTb\remotesca1c50201014\James-Thorson-NOAA-FishStatsUtils-2154071/DESCRIPTION' (362ms)

• preparing 'FishStatsUtils': (1.1s) √ checking DESCRIPTION meta-information ...
• checking for LF line-endings in source and make files and shell scripts (600ms)
• checking for empty or unneeded directories
• looking to see if a 'data/datalist' file should be added
• building 'FishStatsUtils_2.3.0.tar.gz' (3.4s)

Installing package into ‘C:/Users/Jason.Conner/Documents/R/win-library/3.5’ (as ‘lib’ is unspecified)

• installing source package 'FishStatsUtils' ... R data moving datasets to lazyload DB byte-compile and prepare package for lazy loading help installing help indices building package indices testing if installed package can be loaded Downloading GitHub repo kaskr/TMB_contrib_R@master Error: package or namespace load failed for 'FishStatsUtils': .onAttach failed in attachNamespace() for 'FishStatsUtils', details: call: utils::download.file(url, path, method = download_method(), quiet = quiet, error: cannot open URL 'https://api.github.com/repos/kaskr/TMB_contrib_R/tarball/master' Error: loading failed Execution halted ERROR: loading failed
• removing 'C:/Users/Jason.Conner/Documents/R/win-library/3.5/FishStatsUtils'
• restoring previous 'C:/Users/Jason.Conner/Documents/R/win-library/3.5/FishStatsUtils' In R CMD INSTALL Error in i.p(...) : (converted from warning) installation of package ‘C:/Users/JASON~1.CON/AppData/Local/Temp/Rtmp4GpjTb/fileca1c52ad4feb/FishStatsUtils_2.3.0.tar.gz’ had non-zero exit status

[Jason-Conner-NOAA]

R version MRAN 3.5.3, VAST version 3.1.0

[James-Thorson-NOAA]

Some versions of R on our gov machines are having a problem with installing stuff using devtools, and the symptom is an error about utils::download.file which occurs when installing anything from GitHub (e.g., TMB_contrib_R\TMBhelper in your case). I don't know if its a problem with our IT privileges or devtools, and really someone (not me) should look into it generically for AFSC users.

The solution for now is to bypass utils::download.file by either:

1. Downloading each github package individually as a ZIP, e.g., by going to https://github.com/kaskr/TMB_contrib_R and clicking "Clone or download" and then using devtools::install_local(.) to install that ZIP
2. Doing the same thing, but cloning locally using a git client, and then using devtools::install_local(.) on that directory.

Could you update to confirm whether this works or not?

[Jason-Conner-NOAA]

Thanks Jim, that worked. For the record, I am running this on a clean install of Win 10, without any AFSC configuration. I think this actually may be a permissions issue for the repo on kaskr, perhaps a download limit?

[James-Thorson-NOAA]

Can you confirm whether you have the same issue for any other GitHub package installed using devtools::install_github, or which packages you've installed from GitHub that way without a problem?

On Tuesday, October 1, 2019, Jason Conner notifications@github.com wrote:

Thanks Jim, that worked. For the record, I am running this on a clean install of Win 10, without any AFSC configuration. I think this actually may be a permissions issue for the repo on kaskr, perhaps a download limit?

— You are receiving this because you modified the open/close state. Reply to this email directly, view it on GitHub https://github.com/James-Thorson-NOAA/FishStatsUtils/issues/21?email_source=notifications&email_token=AL62VMRLDT5CWME7D2AKFCDQMN6XBA5CNFSM4I4L5R72YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEAB7DVY#issuecomment-537129431, or mute the thread https://github.com/notifications/unsubscribe-auth/AL62VMUS5HTL3HKWBVVAVW3QMN6XBANCNFSM4I4L5R7Q .

-- James Thorson

Program leader, Habitat and Ecosystem Process Research (HEPR) Alaska Fisheries Science Center, NMFS Affiliate Faculty, University of Washington and Oregon State University

The contents of this message are mine personally and do not necessarily reflect any position of NOAA.

[James-Thorson]

what is the output when you try installing?

I recommend installing INLA separately first, and please try installing their testing version using instructions here: https://www.r-inla.org/download-install

On Thu, Sep 21, 2023 at 7:11 PM Hoang Huy Huynh @.***> wrote:

Dear Dr. James Thorson,

Despite my repeated attempts and diverse approaches, I have been unsuccessful in installing the "VAST" package using the guidelines provided in your GitHub repository (https://github.com/James-Thorson-NOAA/VAST). I have tried various computers and R versions, but unfortunately, the package remains elusive.

Here is what I tried in Rstudio version 4.3.1 [ > library(VAST) Error in library(VAST): there is no package called ‘VAST’ ]

I am eagerly looking forward to your valuable guidance. All the best, Huy

— Reply to this email directly, view it on GitHub https://github.com/James-Thorson-NOAA/FishStatsUtils/issues/21#issuecomment-1730708485, or unsubscribe https://github.com/notifications/unsubscribe-auth/AB46UTJ4L622FOG3T66GYSLX3TXVFANCNFSM4I4L5R7Q . You are receiving this because you are subscribed to this thread.Message ID: @.***>