search

thackl / gggenomes

A grammar of graphics for comparative genomics
https://thackl.github.io/gggenomes/
Other
581 stars 64 forks source link

Issue with installation (Mac OS, XCode) #95

Closed awalling closed 2 years ago

awalling commented 2 years ago

Hello,

I am attempting to install gggenomes. When I run the following lines of code, I get the following errors:

`devtools::install_github("thackl/thacklr") Downloading GitHub repo thackl/thacklr@HEAD Error: Failed to install 'thacklr' from GitHub: Command failed (1) In addition: Warning message: In system(full, intern = TRUE, ignore.stderr = quiet) : running command ''/usr/bin/git' ls-remote https://git.bioconductor.org/packages/ggtree RELEASE_3_14 2>/dev/null' had status 1

devtools::install_github("thackl/gggenomes") Downloading GitHub repo thackl/gggenomes@HEAD Error: Failed to install 'gggenomes' from GitHub: Command failed (1) In addition: Warning message: In system(full, intern = TRUE, ignore.stderr = quiet) : running command ''/usr/bin/git' ls-remote https://git.bioconductor.org/packages/rtracklayer RELEASE_3_14 2>/dev/null' had status 1`

I have also attempted downloading the R package and installing locally, and receive the same error message.

Any assistance would be appreciated!

thackl commented 2 years ago

I'm not sure what is going on here. The installations seems to crash while installing bioconductor dependencies (ggtree, rtracklayer). Did you install ggtree through bioconductor as shown in the install instructions before installing gggenomes? Did that work without errors?

awalling commented 2 years ago

Hi - yes, I have successfully installed and used ggtree in the past, and loaded the library prior to attempting to install gggenomes. I reinstalled ggtree and then attempted to install gggenomes using devtools again and ran into the same error.

iimog commented 2 years ago

I'm happy to have a look at this and help with the installation. In order to do so can you give some information on your setup:

What happens if you manually run: /usr/bin/git ls-remote https://git.bioconductor.org/packages/ggtree RELEASE_3_14 on the command line?

awalling commented 2 years ago

Hi @iimog , thanks so much for your assistance. For anyone else reading, I'm on a Mac Catalina that I recently updated the OS of, and I think when I did that I needed to update my Xcode developer tools.

When I ran

/usr/bin/git ls-remote https://git.bioconductor.org/packages/ggtree RELEASE_3_14

I got the following error message:

xcrun: error: invalid active developer path (/Library/Developer/CommandLineTools), missing xcrun at: /Library/Developer/CommandLineTools/usr/bin/xcrun

Googling brought me to this stack overflow answer

Updating Xcode allowed me to successfully install gggenomes using devtools.

Thank you!