'apex' is missing during installation

[konopinski]

Hi,
I've been installing recently StrataG on two machines - Ubuntu and Win10. Both attempts ended in error saying package apex is not available. Luckily at least for now the package can be installed from Thibaud Jombart's git.
devtools::install_github("thibautjombart/apex")
Perhaps you should include this in your installation manual. Also building vignettes failed on Ubuntu but it didn't bother me excessively.
Cheers
Maciek

[EricArcher]

apex is listed in the Depends of the DESCRIPTION file for strataG, so it should be installed from CRAN when strataG is installed. Can you uninstall both apex and strataG and post the exact error message you get when you try to install strataG?

[marina-klemm]

Hi @EricArcher, I found the same problem as @konopinski and it was somewhat solved now that they shared their fix around apex (thanks btw!).

`> if (!require('devtools')) install.packages('devtools')
Loading required package: devtools
Loading required package: usethis

install from GitHub

devtools::install_github('ericarcher/strataG', build_vignettes = TRUE)
Downloading GitHub repo ericarcher/strataG@HEAD
Skipping 1 packages not available: apex
── R CMD build ─────────────────────────────────────────────────────────────────────────────────────────────────────────
✔ checking for file 'C:\Users\marin\AppData\Local\Temp\RtmpEf5Z6x\remotes3ce0462a3016\EricArcher-strataG-d89348c/DESCRIPTION' ...
─ preparing 'strataG':
✔ checking DESCRIPTION meta-information ...
─ cleaning src
─ installing the package to build vignettes
-----------------------------------
ERROR: dependency 'apex' is not available for package 'strataG'
─ removing 'C:/Users/marin/AppData/Local/Temp/RtmpUjNEIk/Rinst8e833617204/strataG'
-----------------------------------
ERROR: package installation failed
Error: Failed to install 'strataG' from GitHub:
! System command 'Rcmd.exe' failed`

Now that this was solved, there's yet another error I'm trying to get past:

`> devtools::install_github('ericarcher/strataG', build_vignettes = TRUE)
Downloading GitHub repo ericarcher/strataG@HEAD
── R CMD build ─────────────────────────────────────────────────────────────────────────────────────────────────────────
✔ checking for file 'C:\Users\marin\AppData\Local\Temp\RtmpEf5Z6x\remotes3ce02ffd75b7\EricArcher-strataG-d89348c/DESCRIPTION' ...
─ preparing 'strataG':
✔ checking DESCRIPTION meta-information ...
─ cleaning src
─ installing the package to build vignettes
E creating vignettes (39.8s)
--- re-building 'external.programs.Rmd' using rmarkdown
--- finished re-building 'external.programs.Rmd'

--- re-building 'gtypes.Rmd' using rmarkdown

Quitting from lines 156-158 [unnamed-chunk-13] (gtypes.Rmd)
Error: processing vignette 'gtypes.Rmd' failed with diagnostics:
ℹ In argument: value = fun(.data$allele, ...).
ℹ In group 1: locus = "D11t".
Caused by error:
! 'diversity' is not an exported object from 'namespace:sprex'
--- failed re-building 'gtypes.Rmd'

--- re-building 'sequences.Rmd' using rmarkdown

Quitting from lines 76-78 [unnamed-chunk-9] (sequences.Rmd)
Error: processing vignette 'sequences.Rmd' failed with diagnostics:
'diversity' is not an exported object from 'namespace:sprex'
--- failed re-building 'sequences.Rmd'

--- re-building 'summaries.Rmd' using rmarkdown

Quitting from lines 45-50 [unnamed-chunk-7] (summaries.Rmd)
Error: processing vignette 'summaries.Rmd' failed with diagnostics:
ℹ In argument: value = fun(.data$allele, ...).
ℹ In group 1: locus = "D11t".
Caused by error:
! 'diversity' is not an exported object from 'namespace:sprex'
--- failed re-building 'summaries.Rmd'

SUMMARY: processing the following files failed:
'gtypes.Rmd' 'sequences.Rmd' 'summaries.Rmd'

Error: Vignette re-building failed.
Execution halted
Error: Failed to install 'strataG' from GitHub:
! System command 'Rcmd.exe' failed`

Any help is appreciated, thank you!

[EricArcher]

It looks like apex is no longer available on CRAN.
The vignette issue is due to some changes I made in the diversity function.
Fixing both of these will have to wait until I have time to devote to this package again.

[marina-klemm]

Hi @EricArcher , thank you for replying so quickly. I found that the apex fix suggested by @konopinski and the way to install strataG mentioned in another thread (added down here for reference) worked out beautifully together.
Thank you!

`# Enable this universe
options(repos = c(
zkamvar = 'https://zkamvar.r-universe.dev',
CRAN = 'https://cloud.r-project.org'))

Install some packages

install.packages('strataG')`