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    Yossi Farjoun
    @yfarjoun
    if I understood the yml, I would!
    I don't understand the Query dependencies and Restore R package cache part....is there some reading I coudl do to understand it?
    Jim Hester
    @jimhester
    It is figuring out what dependencies your package needs and restoring the package cache, if you are not using an R package and installing any dependencies some other way I guess you don't need them
    Yossi Farjoun
    @yfarjoun
    :+1:
    ok...so lint_dir("scripts") completed, and gave a bunch of warnings. but it's difficult to understand which file is the culprit, and there are not comments added by the lintr-bot:
    Run lintr::lint_dir("scripts")
      lintr::lint_dir("scripts")
      shell: /usr/local/bin/Rscript {0}
      env:
        GITHUB_PAT: ***
        R_LIBS_USER: /Users/runner/work/_temp/Library
        TZ: UTC
        _R_CHECK_SYSTEM_CLOCK_: FALSE
        NOT_CRAN: true
    Warning messages:
    Warning: Variable and function name style should be snake_case.
    1: In readLines(filename) :
    Warning: Use <-, not =, for assignment.
      incomplete final line found on '/Users/runner/work/VitaminD_COVID_MR_reproduce/VitaminD_COVID_MR_reproduce/scripts/VD_extract_SNPs_test.R'
    Warning: Put spaces around all infix operators.
    2: In readLines(file) :
    Warning: Variable and function name style should be snake_case.
      incomplete final line found on
    Jim Hester
    @jimhester
    comments are not going to work on a private repository, there is no way for the bot to access it
    Yossi Farjoun
    @yfarjoun
    ah. right.
    makes sense!
    can I give it a TOKEN?
    Jim Hester
    @jimhester
    no
    Yossi Farjoun
    @yfarjoun
    OK. thanks for your help!
    another question: Since bot isn't working for me, is there a way to make the outputted comments more verbose? when I run lintr on my laptop it gives more detail than I see in the github action:
    Jim Hester
    @jimhester
    I think you might be looking at the wrong place in the GitHub Actions log
    Yossi Farjoun
    @yfarjoun
    ah. could be.
    Screen Shot 2021-03-10 at 3.16.28 PM.png
    Jim Hester
    @jimhester
    yes, that is the overview, click on the job itself
    Yossi Farjoun
    @yfarjoun
    Screen Shot 2021-03-10 at 3.17.13 PM.png
    > lintr::lint_dir(".")
    ..
    VD_extract_SNPs_test.R:10:1: style: Variable and function name style should be snake_case.
    PThreshold=5e-8
    ^~~~~~~~~~
    VD_extract_SNPs_test.R:10:11: style: Use <-, not =, for assignment.
    PThreshold=5e-8
              ^
    VD_extract_SNPs_test.R:10:11: style: Put spaces around all infix operators.
    PThreshold=5e-8
             ~^~
    VD_extract_SNPs_test.R:11:1: style: Variable and function name style should be snake_case.
    CommanThreshold=0.01
    ^~~~~~~~~~~~~~~
    VD_extract_SNPs_test.R:11:16: style: Use <-, not =, for assignment.
    CommanThreshold=0.01
    I was hoping to see somethink like what I get from my interactive session
    Jim Hester
    @jimhester
    Are they there in the raw log?
    Yossi Farjoun
    @yfarjoun
    no.
    2021-03-10T19:49:17.0980180Z ##[group]Run lintr::lint_dir("scripts")
    2021-03-10T19:49:17.0980830Z lintr::lint_dir("scripts")
    2021-03-10T19:49:17.1071490Z shell: /usr/local/bin/Rscript {0}
    2021-03-10T19:49:17.1071970Z env:
    2021-03-10T19:49:17.1073190Z   GITHUB_PAT: ***
    2021-03-10T19:49:17.1073720Z   R_LIBS_USER: /Users/runner/work/_temp/Library
    2021-03-10T19:49:17.1074510Z   TZ: UTC
    2021-03-10T19:49:17.1074920Z   _R_CHECK_SYSTEM_CLOCK_: FALSE
    2021-03-10T19:49:17.1075430Z   NOT_CRAN: true
    2021-03-10T19:49:17.1075830Z ##[endgroup]
    2021-03-10T19:49:19.7085930Z Warning messages:
    2021-03-10T19:49:19.7097410Z ##[warning]Variable and function name style should be snake_case.
    2021-03-10T19:49:19.7111540Z 1: In readLines(filename) :
    2021-03-10T19:49:19.7114290Z ##[warning]Use <-, not =, for assignment.
    2021-03-10T19:49:19.7144680Z   incomplete final line found on '/Users/runner/work/VitaminD_COVID_MR_reproduce/VitaminD_COVID_MR_reproduce/scripts/VD_extract_SNPs_test.R'
    2021-03-10T19:49:19.7146330Z ##[warning]Put spaces around all infix operators.
    2021-03-10T19:49:19.7198740Z 2: In readLines(file) :
    2021-03-10T19:49:19.7199950Z ##[warning]Variable and function name style should be snake_case.
    2021-03-10T19:49:19.7214860Z   incomplete final line found on '/Users/runner/work/VitaminD_COVID_MR_reproduce/VitaminD_COVID_MR_reproduce/scripts/VD_extract_SNPs_test.R'
    2021-03-10T19:49:19.7216990Z ##[warning]Use <-, not =, for assignment.
    2021-03-10T19:49:19.7224510Z 3: In readLines(filename) :
    2021-03-10T19:49:19.7240970Z ##[warning]Put spaces around all infix operators.
    2021-03-10T19:49:19.7251730Z   incomplete final line found on '/Users/runner/work/VitaminD_COVID_MR_reproduce/VitaminD_COVID_MR_reproduce/scripts/VD_extract_SNPs.R'
    2021-03-10T19:49:19.7253750Z ##[warning]Use <-, not =, for assignment.
    2021-03-10T19:49:19.7257760Z 4: In readLines(file) :
    2021-03-10T19:49:19.7258620Z ##[warning]Put spaces around all infix operators.
    2021-03-10T19:49:19.7265990Z   incomplete final line found on '/Users/runner/work/VitaminD_COVID_MR_reproduce/VitaminD_COVID_MR_reproduce/scripts/VD_extract_SNPs.R'
    2021-03-10T19:49:19.7267820Z ##[warning]Use <-, not =, for assignment.
    2021-03-10T19:49:19.7290290Z ##[warning]Put spaces around all infix operators.
    2021-03-10T19:49:19.7323400Z ##[warning]Use <-, not =, for assignment.
    2021-03-10T19:49:19.7365950Z ##[warning]Put spaces around all infix operators.
    2021-03-10T19:49:19.7443010Z ##[warning]Use <-, not =, for assignment.
    2021-03-10T19:49:19.7513160Z ##[warning]Put spaces around all infix operators.
    2021-03-10T19:49:19.7585420Z ##[warning]Commas should always have a space after.
    2021-03-10T19:49:19.7646970Z ##[warning]Lines should not be more than 80 characters.
    2021-03-10T19:49:19.7727540Z ##[warning]Use <-, not =, for assignment.
    2021-03-10T19:49:19.7775000Z ##[warning]Put spaces around all infix operators.
    2021-03-10T19:49:19.7873440Z ##[warning]Commas should always have a space after.
    Jim Hester
    @jimhester
    I think if you install the dev version of lintr it might work better for you, in particular it would give you the change in jimhester/lintr#587, which seems to address this situation
    Yossi Farjoun
    @yfarjoun
    OK. I'll do that! thanks @jimhester .