fail to install phyloscannerR from GitHub

BDI-pathogens / phyloscanner

Phylogenetics between and within hosts at once, all along the genome.

GNU General Public License v3.0

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fail to install phyloscannerR from GitHub #59

Closed BT896 closed 3 years ago

BT896 commented 3 years ago

Hi,

I'm getting an exit status after attempting installation of phyloscannerR to R 4.0.3. Install command is install_github("BDI-pathogens/phyloscanner/phyloscannerR", dependencies = T).

The error occurs at the same HTML link produce.pairwise.graphs2.

Error reads: C:../Local/Temp/RtmpEVaLHH/R.INSTALL434820413b15/phyloscannerR/man/produce.pairwise.graphs2.Rd:51: Bad \link text

removing 'C:../Documents/R/win-library/4.0/phyloscannerR' Error: Failed to install 'phyloscannerR' from GitHub: (converted from warning) installation of package ‘C:../Local/Temp/RtmpmkqZMh/file31603193268f/phyloscannerR_1.8.0.tar.gz’ had non-zero exit status

Is this something you've come across before?

Thanks, Ben

mdhall272 commented 3 years ago

I can't seem to replicate this but I don't have easy access to a Windows machine. I don't suppose updating roxygen2 helps?

BT896 commented 3 years ago

I've updated roxygen2 but still comes up with the same error message at produce.pairwise.graphs2.Rd:51.

Should '\link{\code{classify.pairwise.relationships}}' read '\code{\link{classify.pairwise.relationships}} ?

mdhall272 commented 3 years ago

Seems unlikely to me - like I say, this works fine on a Mac. Try cloning the repository and using install? You can just delete those @seealso lines at a pinch.

BT896 commented 3 years ago

Deleted @seealso and now fully installed. Thanks for your help!

mdhall272 commented 3 years ago

Was it just that @seealso, or all of them?

BT896 commented 3 years ago

Just that one

On Tue, 22 Dec 2020, 16:58 Matthew Hall, notifications@github.com wrote:

Was it just that @seealso, or all of them?

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