addFile: Add a file to a data repo.
In jefferys/DataRepo: Manage a large data file repository

Description Usage Arguments Value Examples

Copies the specified file= into the repo=, or to the current directory if no repository is specified. It will be renamed if asFile= is specified, and will be put into a subdirectory of the repo if entry= is specified, possibly as a multi-directory path. This will be created if needed. Assuming all optional elements are specified, the path of the file created in the repository will be <repo>\< entry>\<asFile>. To validate the file before copy, expected fileSize= and checksum= can be given. If inspection of file= does not match, an error-containing validation vector will be returned. Regardless of initial validation, the copy will be validated using the actual file size and file checksum after copy. Successful copy is reported as a vector of empty strings. Problems are reported with one or more non-empty elements.

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addFile(file, repo = getwd(), entry = NULL, asFile = basename(file),
  writeGroup = NULL, fileSize = NULL, checksum = NULL,
  checksumFunc = "tools::md5sum")

`file`	The file to copy into the repo. May be relative or absolute, but may not be a symlink or a directory. File copies will be created with permissions "664" (read by all, write by group and owner, execute by none) and with group `writeGroup` if that was specified.
`repo`	The base directory for the repo. Must exist on the file system and should have a restrictive set of ownerships and permissions that includes restrictions on parent directories. By default will use the current directory if not specified.
`entry`	A subdirectory or subdirectory tree in the repo where the file should be put. These will be created (recursively) if they don't exist with the specified group owner and permissions 2775. This translates to sticky directories with full permissions except other-write. Due to the way `repoDir` is expected to be set up, this is NOT world readable. Leading and trailing path separators are ignored.
`asFile`	The new name for the file in the repository. Must be a plain base name, not a directory (extensions are fine.) By default this is the base name of `file`.
`writeGroup`	The file system group that all created directories and the file copy will be assigned, if set. The default group is used if this if left `NULL` (the default).
`fileSize`	The expected size of the source file, in bytes. By default this is `NULL`, meaning file size will not be checked. If a positive value is supplied it will be checked against the size of the source file on the file system. If it does not match then failure is reported and the checksum is not checked.
`checksum`	The expected checksum of the source file. By default this is `NULL`, meaning no checksum is generated. If given it will be checked agains the value provided by the `checksumFunc`.
`checksumFunc`	The function or function name (as a string) that will be used when calculating checksums. The calculated source file checksum will be verified against any provided checksums before copying and against a recalculated checksum after copying. String function names may be qualified with a `SomePackage::` prefix as the function named is retrieved using `getSomewhere`. By default the function used is '`'tools::md5sum'`. The specified function should have one parameter, a file path. The returned checksum value should be an (atomic) vector type but can not be `NULL` or a missing value. When `checksumFunc` is called, `path` has already been verified and is known to exist on the file system as a real file (not a directory or link).

A named vector of validation results. Each element is named for a check performed, and will be the empty string if the check succeeded, a failure string if the check failed, and a missing value if the check was not performed (i.e. was not wanted or previous checks failed making further checking irrelevant.)

## Not run: 
checks <- addFile( sourcefile, repoDir, entry= 'proj_3/set_A', asFile= 's1.dat'
   writeGroup= 'repoWrite', fileSize= 1234567890, checksum= sourceFileMd5 )

report <- checkSummary(checks)
if (report != '') { stop(report) }

## End(Not run)