Now importing throw() from R.oo instead of R.methodsS3, because the latter is deprecated and will soon be removed.
Coerced NEWS file to NEWS.md.
Update outdated or broken URLs in the documentation.
finalize() is called on any deleted AbstractFileArray objects.R.huge Package object is also available when the package is only loaded (but not attached).Package no longer utilizes import(), only importFrom():s.
Removed fallback attachments of R.utils as these are no longer needed with R.oo (>= 1.15.1).
Cleaned out unnecessary appendVarArgs().
Added another package system test.
For now, package attaches the R.oo package. This is needed due to what appears to be a bug in how R.oo finalizes Object:s assuming R.oo is/can be attached. Until that is resolved, we make sure R.oo is attached.
startupMessage() of R.oo.rm() calls with NULL assignments.\usage{} lines are at most 90 characters long.... to NextMethod(), cf. R-devel thread ‘Do not pass’…’ to NextMethod() - it’ll do it for you; missing documentation, a bug or just me?’ on Oct 16, 2012.Updated package requirements.
Package no longer call .Internal() functions. This will cause a slowdown, because we now have to deal with overhead in functions such as seek(), readBin() and writeBin().
Package no longer creates new generic functions for as.vector() and as.matrix() such that R CMD check no longer complaints.
cat().nchars (not nchar) when calling readChar().[() for FileMatrix explicitly specifies origin="current" in the call to readBinFragment(), which is an argument added in R.utils 1.5.7.writeValues() of AbstractFileArray would give “Error: 4 arguments passed to .Internal(writeBin) which requires 5”. Updated so it works with all versions of R.Now open() of AbstractFileArray first tries to open the file for reading and updating (as before). If that fails, then it tries to open the file for reading only. It might be that the file is only used for reading, so if the permission allows for that but not updating, then open it.
EXCEPTION HANDLING: Methods that creates/modifies files will give a clear error message if the file permissions does not allow it.
Moved internal readBinFragments() and writeBinFragments() to R.utils.
No bug fixes was made in this version.
packageStartupMessage() so that it can be suppressed.Argument dimOrder of the AbstractFileArray constructor was not recognized causing weird results if it was intended to be in a non-increasing order, e.g. FileMatrix(..., byrow=TRUE).
Reading/writing data from and to a FileMatrix via [() / [<-() was broken. Thanks Jens Oehlschlägel for troubleshooting and reporting this.
Added private readBinFragments() and writeBinFragments().
Added tests/ scripts.
Committed to CRAN.
Package passed R CMD check on R v2.5.0 and R v2.6.0 devel.
Package passed R CMD check on R v2.5.0.
Added more Rdoc comments.
Added getComments() and setComments() to AbstractFileArray.
Added a default buffer of free bytes after the header comments. This will make it easier to update the comments. Had to change the file format.
FileVector and abstract superclass AbstractFileArray. The FileVector class is now used by the APS methods in the affxparser.extras package.