GHA MacOS: bgzip executable could be identified.

[bschilder]

Missing a system dependency? Might be able to circumvent this with one of the echotabix alternatives:
https://github.com/RajLabMSSM/echolocatoR/actions/runs/3357812148/jobs/5563951744#step:21:1

Run options(crayon.enabled = TRUE)
Loading required package: sessioninfo
── R CMD build ─────────────────────────────────────────────────────────────────
* checking for file ‘.../DESCRIPTION’ ... OK
* preparing ‘echolocatoR’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
Error: --- re-building ‘BD_GWAS.Rmd’ using rmarkdown
--- finished re-building ‘BD_GWAS.Rmd’
--- re-building ‘echolocatoR.Rmd’ using rmarkdown
Quitting from lines 85-95 (echolocatoR.Rmd) 
Error: Error: processing vignette 'echolocatoR.Rmd' failed with diagnostics:
bgzip executable could be identified.
--- failed re-building ‘echolocatoR.Rmd’
--- re-building ‘finemapping_portal.Rmd’ using rmarkdown
Downloading: https://github.com/RajLabMSSM/Fine_Mapping_Shiny/raw/master/www/data/GWAS/Nalls23andMe_2019/ASXL3/multi_finemap/ASXL3.UKB.multi_finemap.csv.gz
trying URL 'https://github.com/RajLabMSSM/Fine_Mapping_Shiny/raw/master/www/data/GWAS/Nalls23andMe_2019/ASXL3/multi_finemap/ASXL3.UKB.multi_finemap.csv.gz'
Content type 'application/octet-stream' length 157348 bytes (153 KB)
==================================================
downloaded 153 KB
Downloading: https://github.com/RajLabMSSM/Fine_Mapping_Shiny/raw/master/www/data/GWAS/Nalls23andMe_2019/BIN3/multi_finemap/BIN3.UKB.multi_finemap.csv.gz
trying URL 'https://github.com/RajLabMSSM/Fine_Mapping_Shiny/raw/master/www/data/GWAS/Nalls23andMe_2019/BIN3/multi_finemap/BIN3.UKB.multi_finemap.csv.gz'
Content type 'application/octet-stream' length 230[37](https://github.com/RajLabMSSM/echolocatoR/actions/runs/3357812148/jobs/5563951744#step:21:38)0 bytes (224 KB)
==================================================
downloaded 224 KB
Downloading: https://github.com/RajLabMSSM/Fine_Mapping_Shiny/raw/master/www/data/GWAS/Nalls23andMe_2019/ASXL3/LD/ASXL3.UKB.LD.csv.gz
trying URL 'https://github.com/RajLabMSSM/Fine_Mapping_Shiny/raw/master/www/data/GWAS/Nalls23andMe_2019/ASXL3/LD/ASXL3.UKB.LD.csv.gz'
Content type 'application/octet-stream' length 66098 bytes (64 KB)
==================================================
downloaded 64 KB
Downloading: https://github.com/RajLabMSSM/Fine_Mapping_Shiny/raw/master/www/data/GWAS/Nalls23andMe_2019/BIN3/LD/BIN3.UKB.LD.csv.gz
trying URL 'https://github.com/RajLabMSSM/Fine_Mapping_Shiny/raw/master/www/data/GWAS/Nalls23andMe_2019/BIN3/LD/BIN3.UKB.LD.csv.gz'
Content type 'application/octet-stream' length 100237 bytes (97 KB)
==================================================
downloaded 97 KB
--- finished re-building ‘finemapping_portal.Rmd’
--- re-building ‘plot_locus.Rmd’ using rmarkdown
Failed with error:  'there is no package called 'pals''
Failed with error:  'there is no package called 'pals''
The magick package is required to crop "/private/var/folders/24/8k48jl6d249_n_qfxwsl6xvm0000gn/T/RtmpBvAYS5/Rbuildabab4d92368a/echolocatoR/vignettes/plot_locus_files/figure-html/trk_plot-1.png" but not available.
Failed with error:  'there is no package called 'pals''
Failed with error:  'there is no package called 'pals''
The magick package is required to crop "/private/var/folders/24/8k48jl6d249_n_qfxwsl6xvm0000gn/T/RtmpBvAYS5/Rbuildabab4d92368a/echolocatoR/vignettes/plot_locus_files/figure-html/modify track-1.png" but not available.
Failed with error:  'there is no package called 'pals''
Failed with error:  'there is no package called 'pals''
The magick package is required to crop "/private/var/folders/24/8k48jl6d249_n_qfxwsl6xvm0000gn/T/RtmpBvAYS5/Rbuildabab4d92368a/echolocatoR/vignettes/plot_locus_files/figure-html/trk_plot.xgr-1.png" but not available.
Failed with error:  'there is no package called 'pals''
Failed with error:  'there is no package called 'pals''
The magick package is required to crop "/private/var/folders/24/8k48jl6d249_n_qfxwsl6xvm0000gn/T/RtmpBvAYS5/Rbuildabab4d92368a/echolocatoR/vignettes/plot_locus_files/figure-html/trk_plot.QTL-1.png" but not available.
--- finished re-building ‘plot_locus.Rmd’
--- re-building ‘QTLs.Rmd’ using rmarkdown
[tabix] the index file exists. Please use '-f' to overwrite.
Failed with error:  'there is no package called 'seqminer''
Quitting from lines 74-83 (QTLs.Rmd) 
Error: Error: processing vignette 'QTLs.Rmd' failed with diagnostics:
there is no package called 'seqminer'
--- failed re-building ‘QTLs.Rmd’
--- re-building ‘summarise.Rmd’ using rmarkdown
The magick package is required to crop "/private/var/folders/24/8k[48](https://github.com/RajLabMSSM/echolocatoR/actions/runs/3357812148/jobs/5563951744#step:21:49)jl6d249_n_qfxwsl6xvm0000gn/T/RtmpBvAYS5/Rbuildabab4d92368a/echolocatoR/vignettes/summarise_files/figure-html/super_summary_plot()-1.png" but not available.
--- finished re-building ‘summarise.Rmd’
SUMMARY: processing the following files failed:
  ‘echolocatoR.Rmd’ ‘QTLs.Rmd’
Error: Error: Vignette re-building failed.
Execution halted
Error: Error in proc$get_built_file() : Build process failed
Calls: <Anonymous> ... build_package -> with_envvar -> force -> <Anonymous>
Execution halted
Error: Process completed with exit code 1.

[bschilder]

Actually, this is coming directly from echotabix:
https://rdrr.io/github/RajLabMSSM/echotabix/src/R/get_bgzip.R

I'll implement some alternative bgzip options.

Also, the error should read: "gzip executable could NOT be identified"