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Investigate CI/CD pipeline notes

CI/CD builds successfully, but buildcheck step returns some notes (eg, https://code.usgs.gov/water/peakfqr/-/jobs/1019396) that should be investigated/addressed, if possible:

  • checking if this is a source package ... NOTE Found the following apparent object files/libraries: ci/lib/extraDistr/libs/extraDistr.so ci/lib/trend/libs/trend.so Object files/libraries should not be included in a source package.

  • checking for hidden files and directories ... NOTE Found the following hidden files and directories: .gitlab-ci.yml These were most likely included in error. See section ‘Package structure’ in the ‘Writing R Extensions’ manual.

  • checking top-level files ... NOTE Non-standard file/directory found at top level: ‘app.R’ This will be fixed with #150 (closed)

  • checking R code for possible problems ... [40s/39s] NOTE write_log: no visible binding for '<<-' assignment to ‘track_log’ write_log: no visible binding for global variable ‘track_log’ Undefined global functions or variables: track_log

  • checking compilation flags used ... NOTE Compilation used the following non-portable flag(s): ‘-Wdate-time’ ‘-Werror=format-security’ ‘-Wformat’

  • checking compiled code ... NOTE File ‘peakfq/libs/peakfq.so’: Found ‘_gfortran_st_write’, possibly from ‘write’ (Fortran), ‘print’ (Fortran) Objects: ‘dcdflib1.o’, ‘emafit.o’, ‘imslfake.o’, ‘probfun.o’ Compiled code should not call entry points which might terminate R nor write to stdout/stderr instead of to the console, nor use Fortran I/O nor system RNGs. Seth is working on this.

  • checking installed package size ... NOTE installed size is 51.9Mb sub-directories of 1Mb or more: extdata 50.0Mb libs 1.1Mb

  • checking for executable files ... WARNING

  • checking package subdirectories ... NOTE

These notes do not appear to affect functionality.

We will need to get rid of as many build notes as possible to publish to CRAN.

Edited by Faunce, Kaycee Elizabeth