_) in Rd
files.Added package tests (from examples).
Importing suggested functions using ::.
Declaring all S3 methods.
Bumped package dependencies.
Now celToApd() throws a more informative error
message if it fails to located an APD map file.
Now the aroma.apd Package object is
also available when the package is only loaded (but not
attached).
Now writeApd() is atomic, which is achieved by first
writing to a temporary file which is then renamed upon
completion.
celToApd() assumed that affxparser was
already attached.Removed unnecessary import statements from NAMESPACE.
Some of the examples assumed that the suggested affxparser was installed and attached.
Bumped up package version requirements.
cdfToApdMap() did not validate and assign argument
verbose.
Forgot to import trim() from
R.oo.
Removed fallback attachments of R.utils and R.huge as these are no longer needed with R.oo (>= 1.15.1).
Package no longer utilizes import(), only
importFrom():s.
Now only using Authors@R in DESCRIPTION, which is
possible since R (>= 2.14.0).
Dropped obsolete R (< 2.0.0) code that was never used.
Package no longer attaches/loads R.utils and R.huge (only imports them). However, they will be attached dynamically, when certain methods are called.
Utilizing new startupMessage() of
R.oo.
rm() calls with NULL
assignments.\usage{} lines are at most 90
characters long.R CMD check NOTE that
.onAttach() tries to load the affxparser
package.packageStartupMessage() instead of
cat().{read|update|write}Apd() to coerce argument
writeMap to integer indices. readApd() also
coerce argument indices to the same. Before it used to
coerce to doubles, if using R.utils v1.1.4 or before.
These updates should make no difference to anyone. The main purpose is
just to use Arguments$getIndices() instead of
Arguments$getNumerics() where ever possible.autoload("setMethodS3", package="R.oo"),
etc. Package would not install on Linux.Added updateApdUnits().
Now all probe indices are not longer zero-based but one-based.
However, there is still an option to change this to zero-based indices
again by using argument indexOffset = 0. This option might
be remove in the future, because zero-based indices are really confusing
in R.
There is now a quite large set of methods to process APD files.
All of the methods to re-arrange CDF structures and to create cell-index maps have been moved to the affxparser package.