Error when install HybridChenck form githup

[yexiaying]

I installed HybridCheck failed from githup. The error messages are as follows: You mentioned a windows GUI version can be get from HybridCheck website in your supporting file Appendix S2, but I can not find it. where can I get this version.

[TransGirlCodes]

Do you have Biostrings, and IRanges installed from BioConductor? They are required for HybridCheck to work.

I've been looking for a while for a solution to the problem of Bioconductor dependencies, since they have their own little system for installing and managing packages.

I think there is a solution. If instead of using devtools::install_github, you use remotes::install_github to install HybridCheck, it should make sure you have all the dependencies, including the Bioconductor ones.

Try

install.packages("remotes")
library(remotes)
remotes::install_github("BenJWard/HybridCheck", build_vignettes = T)

See if that works. If not it means the vignette is not building for some other reason we'll have to figure out.

[yexiaying]

I tried the way you mentioned but failed. I have install the Biostrings and IRanges from BioConductor, and I can load these packages sucessfully in my Rstudio. But it still showed that these two packages not available when install the HybridCheck package. the R version I used is 3.6.2.

[TransGirlCodes]

@yexiaying Ok this is what I could expect to see on my machine:

The downloaded binary packages are in
    /var/folders/h0/fmczc7390c7f_ddk7yxc47h801tjlx/T//Rtmpht3xas/downloaded_packages
   checking for file ‘/private/var/folders/h0/fmczc7390c7f_ddk7yxc47h801tjlx/T/Rtmpht3xas/remotes✔  checking for file ‘/private/var/folders/h0/fmczc7390c7f_ddk7yxc47h801tjlx/T/Rtmpht3xas/remotesb61523b2e11c/BenJWard-HybridCheck-9203bac/DESCRIPTION’
─  preparing ‘HybridCheck’:
✔  checking DESCRIPTION meta-information ...
─  installing the package to build vignettes
✔  creating vignettes (1m 11.2s)
─  checking for LF line-endings in source and make files and shell scripts
─  checking for empty or unneeded directories
─  looking to see if a ‘data/datalist’ file should be added
─  building ‘HybridCheck_1.0.1.tar.gz’

But it looks like your process stalls when trying to build the user manual. So my next suggestion would be to make sure that packages like 'knitr' are installed, as they are what are used now to build vignettes... it often comes with RStudio. You can also try remotes::install_github("BenJWard/HybridCheck", build_vignettes = F) which would skip trying to build the user manual vignette. If that command works, then we have succesfully found the issue is the packages you need to build the manual.

[yexiaying]

I tried remotes::install_github("BenJWard/HybridCheck", build_vignettes = F) and it worked. Thank you very much!

[TransGirlCodes]

Great! If you need to build the manual, try ensuring knitr is installed first.