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GLEON / GLMr

R package for basic GLM model running
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Package cleanup #113

Closed jsta closed 7 years ago

jsta commented 7 years ago

I ran the goodpractice package checks here with the following results:

It is good practice to

✖ omit "Date" in DESCRIPTION. It is not required and it gets invalid quite often. A build date will be added to the package when you perform R CMD build on it. ✖ add a "URL" field to DESCRIPTION. It helps users find information about your package online. If your package does not have a homepage, add an URL to GitHub, or the CRAN package package page. ✖ add a "BugReports" field to DESCRIPTION, and point it to a bug tracker. Many online code hosting services provide bug trackers for free, https://github.com, https://gitlab.com, etc. ✖ use '<-' for assignment instead of '='. '<-' is the standard, and R users and developers are used it and it is easier to read your code for them if you use '<-'.

R/run_glm.R:109:12

✖ avoid long code lines, it is bad for readability. Also, many people prefer editor windows that are about 80 characters wide. Try make your lines shorter than 80 characters

R/run_glm.R:39:1
R/run_glm.R:70:1
R/run_glm.R:97:1
R/run_glm.R:113:1
R/run_glm.R:119:1

✖ avoid calling setwd(), it changes the global environment. If you need it, consider using on.exit() to restore the working directory.

R/run_glm.R:64:9
R/run_glm.R:72:17
R/run_glm.R:76:17
R/run_glm.R:90:3
R/run_glm.R:100:5
... and 4 more lines

✖ fix this R CMD check NOTE: Malformed Description field: should contain one or more complete sentences. ✖ fix this R CMD check NOTE: nml_template_path: no visible global function definition for ‘packageName’ run_glmNIX: no visible global function definition for ‘packageName’ run_glmOSx: no visible global function definition for ‘packageName’ run_glmWin: no visible global function definition for ‘packageName’ Undefined global functions or variables: packageName Consider adding importFrom("utils", "packageName") to your NAMESPACE file. ✖ avoid 'T' and 'F', as they are just variables which are set to the logicals 'TRUE' and 'FALSE' by default, but are not reserved words and hence can be overwritten by the user. Hence, one should always use 'TRUE' and 'FALSE' for the logicals.

R/run_glm.R:NA:NA

I plan to submit a PR shortly addressing some of them.