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James-Thorson-NOAA / VAST

Spatio-temporal analysis of univariate or multivariate data, e.g., standardizing data for multiple species or stages
http://www.FishStats.org
GNU General Public License v3.0
124 stars 53 forks source link

installation issue #179

Open andybeet opened 5 years ago

andybeet commented 5 years ago

installed TMB and INLA just fine

> devtools::install_github("james-thorson/VAST")
Error: Failed to install 'unknown package' from GitHub:
  cannot open URL 'https://api.github.com/repos/james-thorson/VAST/contents/DESCRIPTION?ref=master'

If i clone your repo and try to build it, it fails. Looks like it is looking for FishStatsUtils which doesn't seem to be an existing repo.

Error: package or namespace load failed for 'VAST':
 .onAttach failed in attachNamespace() for 'VAST', details:
  call: NULL
  error: Failed to install 'unknown package' from GitHub:
  cannot open URL 'https://api.github.com/repos/james-thorson/FishStatsUtils/contents/DESCRIPTION?ref=2.1.0'
Error: loading failed
Execution halted
ERROR: loading failed
* removing 'C:/~/R/win-library/3.5/VAST'
In R CMD INSTALL

Exited with status 1.
James-Thorson-NOAA commented 5 years ago

I can't sort out what's happening from that level of detail. But FishStatsUtils is certainly a package, please see: https://github.com/James-Thorson/FishStatsUtils. Note that in my limited experience, GitHub auto-directs that link to the new name https://github.com/James-Thorson-NOAA/FishStatsUtils, following new NOAA naming policies, and I'm doubtful that the name change is what's causing the issue.

Vladicon commented 5 years ago

Hello Jim! Probably the same issue with FishStatsUtils:

ERROR: hard-coded installation path: please report to the package maintainer and use '--no-staged-install'

James-Thorson-NOAA commented 5 years ago

What OS and version of R are you using? And what version of devtools?

On Sunday, July 28, 2019, Vladimir notifications@github.com wrote:

Hello Jim! Probably the same issue with FishStatsUtils:

ERROR: hard-coded installation path: please report to the package maintainer and use '--no-staged-install'

  • removing 'E:/Docs/R/win-library/3.6/00LOCK-VAST/00new/FishStatsUtils' Error: package or namespace load failed for 'VAST': .onAttach failed in attachNamespace() for 'VAST', details: call: NULL error: Failed to install 'FishStatsUtils' from GitHub: (converted from warning) installation of package 'C:/Users/ADMIN~1.KUL/AppData/Local/Temp/RtmpU3ljs1/file45a45a9a5690/FishStatsUtils_2.2.0.tar.gz' had non-zero exit status Error: loading failed Execution halted *** arch - x64

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/James-Thorson-NOAA/VAST/issues/179?email_source=notifications&email_token=AL62VMTWYCQ76GRQ4C4YCDTQBYZN3A5CNFSM4IG4OIWKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD27JR4Y#issuecomment-515807475, or mute the thread https://github.com/notifications/unsubscribe-auth/AL62VMS6MJHLKG6P7KJUFETQBYZN3ANCNFSM4IG4OIWA .

-- James Thorson

Program leader, Habitat and Ecosystem Process Research (HEPR) Alaska Fisheries Science Center, NMFS Affiliate Faculty, University of Washington and Oregon State University Associate Editor, Canadian Journal of Fisheries and Aquatic Sciences

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

Vladicon commented 5 years ago

What OS and version of R are you using? And what version of devtools? … Windows 10 64 bit (ver 1903) and R gave the same error in Microsoft R Open 3.5.3 and R-3.6.1 for Windows (32/64 bit)

Vladicon commented 5 years ago

in MRO devtools is 2.0.2 and in R-3.6.1 devtools is 2.1.0

Vladicon commented 5 years ago

What OS and version of R are you using? And what version of devtools? … On Sunday, July 28, 2019, Vladimir @.> wrote: Hello Jim! Probably the same issue with FishStatsUtils: ERROR: hard-coded installation path: please report to the package maintainer and use '--no-staged-install' - removing 'E:/Docs/R/win-library/3.6/00LOCK-VAST/00new/FishStatsUtils' Error: package or namespace load failed for 'VAST': .onAttach failed in attachNamespace() for 'VAST', details: call: NULL error: Failed to install 'FishStatsUtils' from GitHub: (converted from warning) installation of package 'C:/Users/ADMIN~1.KUL/AppData/Local/Temp/RtmpU3ljs1/file45a45a9a5690/FishStatsUtils_2.2.0.tar.gz' had non-zero exit status Error: loading failed Execution halted arch - x64 — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#179?email_source=notifications&email_token=AL62VMTWYCQ76GRQ4C4YCDTQBYZN3A5CNFSM4IG4OIWKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD27JR4Y#issuecomment-515807475>, or mute the thread https://github.com/notifications/unsubscribe-auth/AL62VMS6MJHLKG6P7KJUFETQBYZN3ANCNFSM4IG4OIWA . -- James Thorson Program leader, Habitat and Ecosystem Process Research (HEPR) Alaska Fisheries Science Center, NMFS Affiliate Faculty, University of Washington and Oregon State University Associate Editor, Canadian Journal of Fisheries and Aquatic Sciences The contents of this message are mine personally and do not necessarily reflect any position of NOAA.

Ubuntu 18.04 and devtools 2.1.0 have the same error: ERROR: hard-coded installation path: please report to the package maintainer and use ‘--no-staged-install’

Vladicon commented 5 years ago

While the issue is not resolved (in Windows 10 and Ubuntu 18.04 with clean R installation) I've found a way to install the latest VAST (after install.packages("TMB") install.packages("INLA", repos=c(getOption("repos"), INLA="https://inla.r-inla-download.org/R/stable"), dep=TRUE) of course): devtools::install_github("james-thorson/FishStatsUtils", ref="2.2.0") devtools::install_github("james-thorson/VAST") So, if FishStatsUtils are installed beforehand then VAST finishes installation without errors in Windows 10 and Ubuntu 18.04.

With best wishes and hope that this info will help you.