I am trying to run ExperimentHubData::makeExperimentHubMetadata(".") on a package (begin in the working directory).

Platform Windows 10. These are the errors I am getting:

[1] Creating log directory C:\\Users\\wewol\\OneDrive\\Documents/.AnnotationHubData

Attaching package: ‘futile.logger’

The following object is masked _by_ ‘.GlobalEnv’:

    DEBUG

Failed to copy the script/BiocCheck.bat or
script/BiocCheckGitClone.bat script to
C:/PROGRA~1/R/R-40~1.3/bin. If you want to be able to run 'R
CMD BiocCheck' you'll need to copy it yourself to a
directory on your PATH, making sure it is executable. See
the BiocCheck vignette for more information.
missing or NA values for 'Coordinate_1_based set to TRUE'
Loading valid species information.
Error: invalid version specification ‘NA’

Question 1. is this my windows system misconfigured, causing the Failure to copy these files or is adding script/BiocCheck.bat, script/BiocCheckGitClone.bat standard procedure? Question 2. What is the realpath to these files (should be possible to print in the error message). For the moment, the info in which package they are would be helpful?

What version of R are you running? If you are trying to submit a new package you should be running under 4.1 as the current devel of Bioconductor under which the package would be released is running R devel. In Bioconductor devel 3.13 BiocCheck no longer is supported from running on the command line, only from within R and the installation steps are no longer needed. If you install BiocCheck >= 1.27.7 you should hopefully not get this ERROR anymore, BiocCheck should install, and you should be able to run BiocCheck(<pathTopackage>) .
If you are running an older version of R, you could force install the latest version of BiocCheck from github by doing BiocManager::install('Bioconductor/BiocCheck')