Build failing due to skipped (but available) dependencies

[vivekbhr]

Hi

Here's my build report

The error:

* checking package dependencies ... ERROR
Package required but not available: 'TxDb.Dmelanogaster.UCSC.dm6.ensGene'

which is due to line 180 :

Rscript -e 'if (!("remotes" %in% rownames(installed.packages()))) q(status=1)'
+ Rscript -e 'options(repos=c(CRAN="https://cran.rstudio.com")); remotes::install_deps(dependencies = TRUE, type="both")'
Skipping 3 packages not available: GenomeInfoDbData, Rsubread, TxDb.Dmelanogaster.UCSC.dm6.ensGene

My build fails as the required dependency GenomeInfoDbData and TxDb.Dmelanogaster.UCSC.dm6.ensGene are apparently not available. But I can install them on my windows desktop with the same architecture. I don't know whether it's an issue with remotes (ping @gaborcsardi ).

Any help appreciated. Thanks

[gaborcsardi]

This was fixed in remotes. To enable falling back to source packages, you need to set the R_COMPILE_AND_INSTALL_PACKAGES environment variable to always.

@krlmlr maybe it would make sense to set it by default?

References: https://github.com/r-lib/remotes/issues/128 https://github.com/r-lib/remotes/commit/d3a6766c0bcb456b82a0b06608f6149fe4f5d83e

[krlmlr]

Thanks for pointing me to this env var. For now I'd rather document it in the README of this repo. PR welcome!

[vivekbhr]

@gaborcsardi This change from remotes is not yet in the cran release so my build is still failing. Is there a way to point r-appveyor to use remotes from github?

[krlmlr]

You might be able to install it manually from your appveyor.yml.

[vivekbhr]

@krlmlr @gaborcsardi I tried installing it manually but failed with this message

Downloading GitHub repo gaborcsardi/remotes@master
185 Error in utils::download.file(url, path, method = download_method(), quiet = quiet,  : 
186  cannot open URL 'https://api.github.com/repos/gaborcsardi/remotes/zipball/master'

My appveyor.yml My build report

Is that an issue with my config?

[gaborcsardi]

My guess is a GitHub rate limiting problem. Here is another way to install it, from R:

source("https://install-github.me/r-lib/remotes")

[vivekbhr]

I got :

137 'source' is not recognized as an internal or external command,
138 operable program or batch file.
139 Command exited with code 1

[gaborcsardi]

This is how to run an R script from the command line:

Rscript -e 'source(...)'

[vivekbhr]

sorry i figured this one .. never mind

[vivekbhr]

Thank you @gaborcsardi and @krlmlr . my build is passing now