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Bioconductor / BiocCheck

http://bioconductor.org/packages/BiocCheck
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Properly check pkg installation calls in vignettes #170

Closed almeidasilvaf closed 2 years ago

almeidasilvaf commented 2 years ago

Hi, @lshep and @LiNk-NY

I extended the changes in my previous pull request from earlier today (#169) to include installation functions from {remotes} and {devtools} (install_github, install_gitlab, install_bioc, etc)

Now, BiocCheck::BiocCheck() will flag package installation calls in evaluated vignette code (including install_* functions from {remotes}/{devtools} and install() from {BiocManager} and {devtools}), but it will not misidentify logical functions <tool>_is_installed() as problematic, because they do not end in "install".

Best, Fabricio

LiNk-NY commented 2 years ago

Hi Fabricio, Thank you for reporting. I separated the two methods for checking the code (fixed and pattern matching). Pattern matching includes any functions that match the .*install[^ed].* pattern. Best regards, Marcel

almeidasilvaf commented 2 years ago

Thanks a million, @LiNk-NY!

Best, Fabricio