installation in windows 10 about hmsc

[jarioksa]

I set up the alternative repository (jarioksa.github.io) yesterday, and it may be that it has some incompatibility with Windows. I tried by adding an (empty) index: please re-try. I just tested this (with Mac), and everything worked OK.

[sashavas3]

Hello,

I've also been trying to install Hmsc in Windows 10, but haven't managed yet. This is the message I receive:

install_github("hmsc-r/HMSC", build_opts = c("--no-resave-data", "--no-manual"))

Downloading GitHub repo hmsc-r/HMSC@master
These packages have more recent versions available.
Which would you like to update?

 1: All                                   
 2: CRAN packages only                    
 3: None                                  
 4: ggplot2    (3.1.0   -> 3.2.1  ) [CRAN]
 5: Rcpp       (0.12.19 -> 1.0.2  ) [CRAN]
 6: digest     (0.6.18  -> 0.6.20 ) [CRAN]
 7: gtable     (0.2.0   -> 0.3.0  ) [CRAN]
 8: lazyeval   (0.2.1   -> 0.2.2  ) [CRAN]
 9: rlang      (0.3.0.1 -> 0.4.0  ) [CRAN]
10: tibble     (1.4.2   -> 2.1.3  ) [CRAN]
11: quantreg   (5.36    -> 5.51   ) [CRAN]
12: stringr    (1.3.1   -> 1.4.0  ) [CRAN]
13: glue       (1.3.0   -> 1.3.1  ) [CRAN]
14: stringi    (1.2.4   -> 1.4.3  ) [CRAN]
15: R6         (2.3.0   -> 2.4.0  ) [CRAN]
16: colorspace (1.3-2   -> 1.4-1  ) [CRAN]
17: pillar     (1.3.0   -> 1.4.2  ) [CRAN]
18: assertthat (0.2.0   -> 0.2.1  ) [CRAN]
19: backports  (1.1.2   -> 1.1.4  ) [CRAN]
20: curl       (3.2     -> 4.0    ) [CRAN]
21: igraph     (1.2.2   -> 1.2.4.1) [CRAN]

Enter one or more numbers, or an empty line to skip updates:

Installing 28 packages: coda, ape, fields, FNN, MCMCpack, mvtnorm, pdist, pROC, 
phytools, statmod, truncnorm, spam, maps, mcmc, animation, clusterGeneration, 
combinat, expm, mnormt, phangorn, plotrix, dotCall64, vctrs, ellipsis, zeallot, magick, 
quadprog, fastmatch
Installing packages into ‘C:/Users/Sasha/Documents/R/win-library/3.5’
(as ‘lib’ is unspecified)
Error: Failed to install 'Hmsc' from GitHub:
  (converted from warning) unable to access index for repository jarioksa.github.io/drat/src/contrib:
  scheme not supported in URL 'jarioksa.github.io/drat/src/contrib/PACKAGES'

[jarioksa]

The purpose of having that drat repository was to make life easier (and to pass CRAN submission tests): you would automatically get all needed packages instead of separate installations from archived CRAN packages. It also worked like a charm in my test system (macOS) and also passed CRAN tests. I haven't found any reason for the failures: CRAN seems to use exactly similar structure with PACKAGES file. However, I will revert this change if I don't find a solution soon.

[jarioksa]

I got some pieces of advice, and tried to fix the issue. Please see if it works now, and report in either case.

[sashavas3]

Hello again,

Unfortunately it still doesn't seem to be working:

Downloading GitHub repo hmsc-r/HMSC@master
These packages have more recent versions available.
Which would you like to update?

 1: All                                   
 2: CRAN packages only                    
 3: None                                  
 4: ggplot2    (3.1.0   -> 3.2.1  ) [CRAN]
 5: Rcpp       (0.12.19 -> 1.0.2  ) [CRAN]
 6: digest     (0.6.18  -> 0.6.20 ) [CRAN]
 7: gtable     (0.2.0   -> 0.3.0  ) [CRAN]
 8: lazyeval   (0.2.1   -> 0.2.2  ) [CRAN]
 9: rlang      (0.3.0.1 -> 0.4.0  ) [CRAN]
10: tibble     (1.4.2   -> 2.1.3  ) [CRAN]
11: quantreg   (5.36    -> 5.51   ) [CRAN]
12: stringr    (1.3.1   -> 1.4.0  ) [CRAN]
13: glue       (1.3.0   -> 1.3.1  ) [CRAN]
14: stringi    (1.2.4   -> 1.4.3  ) [CRAN]
15: R6         (2.3.0   -> 2.4.0  ) [CRAN]
16: colorspace (1.3-2   -> 1.4-1  ) [CRAN]
17: pillar     (1.3.0   -> 1.4.2  ) [CRAN]
18: assertthat (0.2.0   -> 0.2.1  ) [CRAN]
19: backports  (1.1.2   -> 1.1.4  ) [CRAN]
20: curl       (3.2     -> 4.0    ) [CRAN]
21: igraph     (1.2.2   -> 1.2.4.1) [CRAN]

Enter one or more numbers, or an empty line to skip updates:

Installing 28 packages: coda, ape, fields, FNN, MCMCpack, mvtnorm, pdist, pROC, phytools,
statmod, truncnorm, spam, maps, mcmc, animation, clusterGeneration, combinat, expm,
mnormt, phangorn, plotrix, dotCall64, vctrs, ellipsis, zeallot, magick, quadprog, fastmatch

Installing packages into ‘C:/Users/Sasha/Documents/R/win-library/3.5’
(as ‘lib’ is unspecified)
also installing the dependency ‘rlang’

Error: Failed to install 'Hmsc' from GitHub:
  (converted from warning) unable to access index for repository https://jarioksa.github.io/drat/bin/windows/contrib/3.5:
  cannot open URL 'https://jarioksa.github.io/drat/bin/windows/contrib/3.5/PACKAGES'

[jarioksa]

@sashavas3 Your problem was that there were no packages for the old R release (version 3.5). There is now: see if it works.

[sashavas3]

Thanks, it has now worked!

[chnpenny]

it worked for me the next day. Sorry I didn't update till now.

[DiegoPavonJordan]

Huomenta,

I am experiencing similar problems. I ran these ok:

require(devtools)
require(grDevices)
install_url('https://cran.r-project.org/src/contrib/Archive/BayesLogit/BayesLogit_0.6.tar.gz')

But when I ran this:

install_github("hmsc-r/HMSC", build_opts = c("--no-resave-data", "--no-manual"))

I get the following error:
** byte-compile and prepare package for lazy loading
Error: (converted from warning) package 'coda' was built under R version 3.6.1
Execution halted
ERROR: lazy loading failed for package 'Hmsc'

• removing 'C:/Programs/R/R-3.6.0/library/Hmsc'
  Error: Failed to install 'Hmsc' from GitHub:
  (converted from warning) installation of package ‘C:/Users/DIEGO~1.PAV/AppData/Local/Temp/Rtmpsr9qqX/file1cc43bf036aa/Hmsc_0.4.3.2.tar.gz’ had non-zero exit status

Do you have any advice on how to overcome this error and get the HMSC installed?

My session info:

session_info()

• Session info -----------------------------------------------------------------------------------------------------------
  setting value
  version R version 3.6.0 (2019-04-26)
  os Windows 10 x64
  system x86_64, mingw32
  ui RStudio
  language (EN)
  collate Norwegian Bokmål_Norway.1252
  ctype Norwegian Bokmål_Norway.1252
  tz Europe/Berlin
  date 2019-09-17

• Packages ---------------------------------------------------------------------------------------------------------------
  package * version date lib source
  assertthat 0.2.1 2019-03-21 [1] CRAN (R 3.6.1)
  backports 1.1.4 2019-04-10 [1] CRAN (R 3.6.0)
  callr 3.3.1 2019-07-18 [1] CRAN (R 3.6.1)
  cli 1.1.0 2019-03-19 [1] CRAN (R 3.6.1)
  crayon 1.3.4 2017-09-16 [1] CRAN (R 3.6.1)
  curl 4.1 2019-09-16 [1] CRAN (R 3.6.0)
  desc 1.2.0 2018-05-01 [1] CRAN (R 3.6.1)
  devtools * 2.2.0 2019-09-07 [1] CRAN (R 3.6.1)
  digest 0.6.20 2019-07-04 [1] CRAN (R 3.6.1)
  DT 0.8 2019-08-07 [1] CRAN (R 3.6.1)
  ellipsis 0.2.0.1 2019-07-02 [1] CRAN (R 3.6.1)
  fs 1.3.1 2019-05-06 [1] CRAN (R 3.6.1)
  glue 1.3.1 2019-03-12 [1] CRAN (R 3.6.1)
  htmltools 0.3.6 2017-04-28 [1] CRAN (R 3.6.1)
  htmlwidgets 1.3 2018-09-30 [1] CRAN (R 3.6.1)
  magrittr 1.5 2014-11-22 [1] CRAN (R 3.6.1)
  memoise 1.1.0 2017-04-21 [1] CRAN (R 3.6.1)
  pkgbuild 1.0.5 2019-08-26 [1] CRAN (R 3.6.1)
  pkgload 1.0.2 2018-10-29 [1] CRAN (R 3.6.1)
  prettyunits 1.0.2 2015-07-13 [1] CRAN (R 3.6.1)
  processx 3.4.1 2019-07-18 [1] CRAN (R 3.6.1)
  ps 1.3.0 2018-12-21 [1] CRAN (R 3.6.1)
  R6 2.4.0 2019-02-14 [1] CRAN (R 3.6.1)
  Rcpp 1.0.2 2019-07-25 [1] CRAN (R 3.6.1)
  remotes 2.1.0 2019-06-24 [1] CRAN (R 3.6.1)
  rlang 0.4.0 2019-06-25 [1] CRAN (R 3.6.1)
  rprojroot 1.3-2 2018-01-03 [1] CRAN (R 3.6.1)
  rstudioapi 0.10 2019-03-19 [1] CRAN (R 3.6.1)
  sessioninfo 1.1.1 2018-11-05 [1] CRAN (R 3.6.1)
  testthat 2.2.1 2019-07-25 [1] CRAN (R 3.6.1)
  usethis * 1.5.1 2019-07-04 [1] CRAN (R 3.6.1)
  withr 2.1.2 2018-03-15 [1] CRAN (R 3.6.1)

[1] C:/Programs/R/R-3.6.0/library

Kiitos avusta!

[Lks22]

@DiegoPavonJordan Try to download the newest R version 3.6.1 and see if that works.

[jarioksa]

Both Hmsc and BayesLogit are now in CRAN, and you can install Hmsc as any other R package, and BayesLogit will be installed automatically. There probably is a problem with old R release in Windows (older than R 3.6.0) because BayesLogit binary is not available for old R in Windows (there seems to be no problem in older R in macOS).

[sashavas3]

Thank you for the update!

…

On Sun, 13 Oct 2019 at 18:36, Jari Oksanen ***@***.***> wrote: Both *Hmsc* and *BayesLogit* are now in CRAN, and you can install *Hmsc* as any other *R* package, and *BayesLogit* will be installed automatically. There probably is a problem with old *R* release in Windows (older than *R* 3.6.0) because *BayesLogit* binary is not available for old *R* in Windows (there seems to be no problem in older *R* in macOS). — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#22?email_source=notifications&email_token=ANAPFKT57RROGRRE3PEYSRDQONMDVA5CNFSM4IQCENSKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEBC3K4Y#issuecomment-541439347>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ANAPFKX5CDG4H4SUHNBKXN3QONMDVANCNFSM4IQCENSA> .

-- Sasha Vasconcelos PhD student CIBIO/InBIO, Research Center in Biodiversity and Genetic Resources, Associate Laboratory Instituto Superior de Agronomia Tapada da Ajuda 1349-017 Lisbon, Portugal ResearchGate <https://www.researchgate.net/profile/Sasha_Vasconcelos> ResearcherID <https://publons.com/researcher/2593829/sasha-vasconcelos/publications/>