NEWS in package ‘R.utils’

---

Changes in version 2.11.0 (2021-09-25)

NEW FEATURES

• Now insert() support duplicates in 'ats', which then results in the corresponding 'values' being inserted in order at those duplicated indices.
• Relaxed insert() to accept a 'values' argument that is a list but not necessarily a formal vector.
• Now queryRCmdCheck() sets environment variable R_CMD_CHECK=true if it detects 'R CMD check' is running.
• Added format() for 'binmode'.
• hpaste() gained argument 'empty', which can be used to control what to return in case the output is of length zero.

BUG FIXES

• gcDLLs() produced a "In sprintf(...) : argument not used by format" warning when giving an error message on what DLLs it failed to unload.
• Arguments$getVector() could produce an error on "argument is missing, with no default" while trying to signal an assertion error.
• intToHex() and intToOct() would no longer pad with zero on recent R-devel (to become R 4.2.0) versions.

Changes in version 2.10.1 (2020-08-25)

NEW FEATURES

• Updated legacy function useRepos() to use HTTPS instead of HTTP.

DOCUMENTATION

• Update URLs with 301 redirects. Most of them were HTTP to HTTPS redirects.

Changes in version 2.10.0 (2020-08-24)

NEW FEATURES

• R.utils::commandArgs() recognizes new '--no-echo' option in R (>= 4.0.0).

BUG FIXES

• R.utils::getAbsolutePath("~/../Documents", expandTilde = TRUE) would adjust for '..' before adjusting for '~' resulting in an incorrect path. Thanks to Dean Attali for reporting on this.

Changes in version 2.9.2 (2019-12-07)

• CRAN POLICY CRAN: The help example for FileProgressBar and its package tests wrote to the user's home directory. They are now writing to a temporary directory instead.

Changes in version 2.9.1 (2019-12-05)

BUG FIXES

• wrap() for arrays used a list - not a numeric vector - to assign dimensions. This would produce an error in R (>= 4.0.0).
• withSeed(..., seed = NULL) did not work for R (< 3.0.0).
• fileAccess(..., mode = 2) would update .Random.seed.
• fileAccess(path, mode = 2) could end up in an end less loop if the 'path' folder contained all files of 'a, b, ..., z, A, B, ... Z'.

Changes in version 2.9.0 (2019-06-11)

BUG FIXES

• sourceDirectory() did not respect argument 'modifiedOnly'. Thanks to Anton Krasikov for the report and the fix.
• createLink() could produce a spurious warning on MS Windows.

DEPRECATE AND DEFUNCT

• Previously defunct arrayIndex(), evalWithTimeout(), and resetWarnings() have been removed.
• Assert$inherits() is defunct - use Assert$inheritsFrom() instead.
• Argument 'substitute' of withCapture() is defunct - use 'replace' instead.

Changes in version 2.8.0 (2019-02-13)

NEW FEATURES

• createWindowsShortcut() gained argument 'mustWork'.
• When createLink() fails, the error message now also report on the methods attempted.

BUG FIXES

• displayCode(), commandArgs() and toCamelCase() used && and || on logical vectors that might not necessarily be of length one.
• createWindowsShortcut() and createLink(method="windows-shortcut") failed to create Windows Shortcut links because filePath(..., expandLinks = "any") did not expand Windows Shortcut links. This bug was introduced in R.utils 1.34.0 (2014-10-07) due to a cut'n'paste mistake.

Changes in version 2.7.0 (2018-08-26)

NEW FEATURES

• Added nullcon() that returns a (binary) connection to the nullfile().

PERFORMANCE

• readTable() no longer runs the garbage collector - was done so implicitly through an internal system.time() call without using gcFirst = FALSE.

BUG FIXES

• Rscript -e "R.utils::cmdArg(a=42L)" -a:=1:3 would set 'a' to NA_integer_.

DEPRECATE AND DEFUNCT

• evalWithTimeout() is now defunct. Use withTimeout() instead.
• arrayIndex() is now defunct. Use base::arrayInd() instead.
• Assert$inherits() is deprecated - renamed to Assert$inheritsFrom().
• Removed deprecated and ignored argument 'reset' of warnings() for Verbose.

Changes in version 2.6.0 (2017-11-05)

NEW FEATURES

• Argument 'install' of use() now defaults to option 'R.utils.use.install', which in turn defaults to environment variable 'R_R_UTILS_USE_INSTALL'. If neither is set, the default is TRUE.
• ROBUSTNESS: Now gcDLLs() runs the garbage collector before removing stray DLLs in order for any finalizers who rely on the DLL to be called before the DLL is removed.
• loadObject() and loadToEnv() give more informative error message if an error occurs while reading from a file / connection.
• All withNnn() functions gained argument 'substitute' making it possible to pass an expression object, e.g. withTimeout(expr, subsitute = FALSE, ...). The exception is withCapture(), where, the now deprecated (see below), argument 'substitute' means something else for legacy reasons.

BUG FIXES

• withTimeout() would produce a regular error but not a TimeoutException for timeouts reaching the _total_ CPU time limit while it would work for those reaching the _elapsed_ CPU time limit. Thanks to Alexej Gossmann at Tulane University for troubleshooting and provide a fix.
• findSourceTraceback() could fail and give an obscure error when for instance the 'XML' package was attached. It now tries a bit harder to locate the internal 'srcfile' object.
• Forgot to register S3 method '['() for GenericSummary.
• intToOct() would convert to hexadecimals.
• intToBin() would output garbage for negative values.

DEPRECATE AND DEFUNCT

• Argument 'substitute' of withCapture() has been renamed to 'replace'. Code that calls withCapture(..., substitute = ...) will still work, but the use of 'substitute' is deprecated and will later become defunct. The purpose of this change of argument name is so that the meaning of 'substitute' can be harmonized with the other withNnn() functions.
• Deprecated evalWithTimeout(); use withTimeout() - the preferred name.

Changes in version 2.5.0 (2016-11-07)

BUG FIXES

• withCapture(x <- 1L) would drop integer suffix 'L' from the output when run in non-interactive mode.

DEPRECATE AND DEFUNCT

• CLEANUP: Removed operator '%<-%' which was defunct since 2.4.0. An alternative is to use ditto of the future package.
• CLEANUP: Made resetWarnings() defunct.

Changes in version 2.4.0 (2016-09-13)

NEW FEATURES

• Added strayDLLs() and gcDLLs() to identify and unload stray DLLs that was left behind by packages that have already been unloaded.
• Added nullfile().
• Now setThreshold() for Verbose accepts also logical values.
• Argument 'absolutePath' for Arguments$getReadablePathname() was renamed to 'absolute'. For backward compatibililty, the old name will still work for some time.

DEPRECATE AND DEFUNCT

• CLEANUP: Defunct '%<-%' in favor of '%<-%' in the future package.
• CLEANUP: Deprecated arrayIndex(). arrayInd() in base (>= 2.11.0) provides the same functionality.

CODE REFACTORING

• Package now formally requires R (>= 2.14.0) released October 2011.

Changes in version 2.3.0 (2016-04-13)

NEW FEATURES

• Added hsize().
• Added tmpfile() for creating temporary files with content that is deleted automatically by the garbage collector unless there is a reference to it.
• ROBUSTNESS: Now compressFile() and decompressFile(), and therefore also functions such as gzip() and gunzip(), output atomically by writing to a temporary file which is only renamed when completed.

DEPRECATE AND DEFUNCT

• CLEANUP: Deprecated '%<-%' in favor of '%<-%' in the future package.

CODE REFACTORING

• Package now formally requires R (>= 2.14.0) released Oct 2011.

Changes in version 2.2.0 (2015-12-09)

NEW FEATURES

• loadObject() and saveObject() gained argument 'format' in order to support also RDS files (in addition to XDR files). File formats XDR and RDS are supported. The default format is inferred from the filename extension. If this is not possible, then the XDR format is assumed (default; backward compatible).
• mkdirs() gained arguments 'mustWork' and 'maxTries'.
• seqToHumanReadable() gained argument 'tau'.
• R.utils::commandArgs() now also ackowledges 'argv' set by the littler executable.
• R.utils::commandArgs() recognizes more reserved command-line arguments, e.g. --debugger-args=N, --min-vsize=N and --min-nsize=N.
• ROBUSTNESS: Now writeDataFrame(..., sep, quote = FALSE) asserts that none of the columns contains the field separator 'sep', because then the written file would be corrupt/invalid.
• ROBUSTNESS: Explicit import of all 'graphics', 'grDevices', 'stats' and 'utils' functions.

DOCUMENTATION

• Clarified in help for compressFile() et al. that these functions remove the input file by default after the output file is generated. Thanks to Ben Bond-Lamberty (Pacific Northwest National Laboratory) for pointing out this potential pitfall.

BUG FIXES

• seqToHumanReadable(c(1:2, 4:5)) gave "1-2, 4, 5".
• withTimeout() did not work in non-English locales. Thanks to Arnaud Malapert at University Nice Sophia Antipolis for reporting on this.
• GString ignored "simple" attributes, e.g. $[tolower]{y}. Thanks to Andre Mikulec for reporting on this.
• downloadFile() via https://user:pwd@domain/ gave an error.

DEPRECATE AND DEFUNCT

• CLEANUP: Deprecated resetWarnings().

Changes in version 2.1.0 (2015-05-27)

NEW FEATURES

• Added compressPDF() to compress PDFs.
• If, and only if, 'path' is an existing directory, then copyFile(pathname, path) copies file 'pathname' to the 'path' directory (previously destination always had to be a file). Analogously, renameFile(pathname, path) moves file 'pathname' (not a directory though) to destination directory 'path'.
• CLEANUP: createLink(..., skip = TRUE) would give a false warning if a proper link already existed and the target was elsewhere than the current directory.
• INCONSISTENCY: captureOutput(..., collapse = "\n") did not drop newline of the last line as captureOutput(..., collapse = "\r") and any other collapse != "\n" strings. Added package tests.

BUG FIXES

• captureOutput(..., file = "foo.txt") gave an error.

Changes in version 2.0.2 (2015-04-27)

BUG FIXES

• Arguments$getReadablePathname(NA, mustExist = FALSE) no longer gives an error with recent R devel (>= 2015-04-23) related to an update on how nchar() handles missing values. This bug affected only Windows.

CODE REFACTORING

• ROBUSTNESS: Now nchar(..., type = "chars") is used internally for all file and directory names.

Changes in version 2.0.1 (2015-04-24)

NEW FEATURES

• R.utils no longer generates a warning if the R session is saved when R exits. Thanks to Jose Alquicira Hernandez for reporting on this.

BUG FIXES

• toCamelCase() with missing values would give an error in R devel (>= 2015-04-23) due to an update how nchar() handles missing values.

Changes in version 2.0.0 (2015-02-28)

NEW FEATURES

• ROBUSTNESS: Now %<-% evaluates the expression in a local() environment, and it assign to environments, e.g. env$a %<-% 1.
• Added compressFile(), decompressFile() and isCompressedFile() methods, which gzip()/gunzip() and the new bzip2()/bunzip2() now use. Thanks to Peter Hickey for pushing for this.
• Now eget() uses inherits = FALSE (was TRUE) and mode = "default" (was "any"), where "default" corresponds to the mode of argument 'default', unless it's NULL when mode = "any" is used.
• Now commandArgs(asValues = TRUE, adhoc = TRUE) interprets 'x:=1:10' such that 'x' become the integer vector 1:10. Likewise, you can do 'x:=seq(1,3, by = 0.1)' and 'x:=pi'. To get the string "pi", use quotation marks, i.e. 'x:="pi"', or just 'x=pi'.
• Added cmsg(), cout(), ccat(), cprintf(), cprint(), cstr(), cshow() for outputting to "console", which is neither R stdout nor stderr and can therefor not be intercepted via capture.output(), sink() or similar. These functions are useful for outputting messages that requires user's attention and are often followed by a prompt via readline(), which also cannot be captured.
• Added mpager() which is a "pager" function compatible with file.show() that will display file contents on standard error.
• Just like for listDirectory(), argument 'recursive' of findFiles() can in addition to be FALSE (depth = 0) and TRUE (depth = +Inf), be any non-negative numeric number specifying how deeply the recursive search should be done.
• On Windows, Arguments$getReadablePathname() now gives an informative warning if a pathname of length 256 or longer is used/generated, which are not supported on Windows.

DOCUMENTATION

• Fixed mistake in help("captureOutput"). Thanks to Mikko Korpela (Issue #4) for reporting on this.

BUG FIXES

• use(..., quietly = FALSE) no longer captures/buffers the output, which prevented it from displaying full prompt messages that required a user response. use(..., quietly = TRUE), which is the default, no longer tries to ask user of Windows and OS X if they wish to install from source if the binary is older.
• Now the returned value of all withNnn() functions preserves the "visibility" of the eval():uated expression. Added package tests.
• withCapture({}) no longer generates a warning.
• Now isUrl(NA) returns FALSE (instead of NA).
• seqToIntervals(integer(0)) gave error "object 'res' not found".
• attachLocally() on an environment would remove the attached fields/variables from that environment.

CODE REFACTORING

• ROBUSTNESS: Forgot to declare "default" warnings() as an S3 method.
• R.utils::use() without arguments attaches 'R.utils'.
• ROBUSTNESS: Package test coverage is 66%.

Changes in version 1.34.0 (2014-10-07)

CODE REFACTORING

• Added URL and BugReports fields to DESCRIPTION.
• Submitted to CRAN.

Changes in version 1.33.10 (2014-10-03)

NEW FEATURES

• Added shell.exec2(), which does a better job than shell.exec() in opening pathnames with forward slashes and files on mapped drives, which may or may not open depending software, e.g. Google Chrome fails to open the latter. Add options(browser = function(...) R.utils::shell.exec2(...)) to your ~/.Rprofile file to make browseURL() use this function instead of shell.exec(). This function is only useful on Windows.

BUG FIXES

• Now Arguments$getReadablePathname(file, path) ignores 'path' if 'file' specifies an absolute pathname.

Changes in version 1.33.9 (2014-10-03)

NEW FEATURES

• Now countLines() automatically supports gzipped files as well. Thanks to Sarah Nelson at Dept of Biostatistics at University of Washington for the suggestion.
• Now downloadFile("https://...") will use 'curl', and if not available 'wget', to download the file over the HTTPS protocol. Previously only 'wget' was used. The 'curl' software is available on more operating systems, include OS X, whereas 'wget' sometimes needs a separate installation.

Changes in version 1.33.8 (2014-10-02)

NEW FEATURES

• Added argument 'unmap' to filePath() for "following" paths that are on mapped Windows drives.
• CLEANUP: use() would try temporarily set package repository options even when not needed. This could trigger unnecessary warnings for users who haven't set a default CRAN mirror and using use() to load/attach an already installed package.

Changes in version 1.33.7 (2014-09-18)

NEW FEATURES

• New default for writeDataFrame() - argument 'col.names = !append'. Also, if append = TRUE, header comments are only written if specified. Added package system test for writeDataFrame().

Changes in version 1.33.6 (2014-09-16)

BUG FIXES

• getAbsolutePath("/tmp", expandTilde = TRUE) returned "//tmp". This would in turn have implications on getRelativePath(), e.g. getRelativePath("/tmp/a", relativeTo = "/tmp") returned "../../tmp/a".

Changes in version 1.33.5 (2014-09-15)

NEW FEATURES

• Added withSeed() and withSink().
• ROBUSTNESS: Now withOptions() also resets all the options available upon entry even if no explicit options were specified. This covers the case when 'expr' changes the options and/or adds new options, e.g. withOptions({ options(width = 10, foo = "new"); str(letter) }).

Changes in version 1.33.4 (2014-09-05)

BUG FIXES

• ROBUSTNESS: Arguments$getWritablePathname() could sometimes generate warning "file.remove(pathnameT) : cannot remove file 'file...', reason 'Permission denied'. Now it tries to remove that files several times before giving up.

Changes in version 1.33.3 (2014-09-04)

NEW FEATURES

• ROBUSTNESS: Now copyDirectory(), just as copyFile() already did, silently drops arguments 'copy.mode' and 'copy.date' for older R versions where base::file.copy() does not support them.

Changes in version 1.33.2 (2014-09-01)

BUG FIXES

• mkdirs() could return "object 'res' not found" error.

Changes in version 1.33.1 (2014-08-25)

BUG FIXES

• countLines() would not count the last line if it did not contain a newline. It would also give an error if the newline characters were only CR. This despite it was documented that both cases were supported. Added package system tests for them.

Changes in version 1.33.0 (2014-08-24)

NEW FEATURES

• Added mprint(), mcat(), mstr(), mshow() and mprintf() that work like the corresponding print(), cat(), etc., but output using message(), which in turn sends to standard error (instead of standard output). See also mout().
• Added withLocale().
• Now the test for target discrepancies by createLink(..., skip = TRUE) is more forgiving on Windows (by assuming a case-insensitive file system) before generating a warning.
• Now useRepos(..., fallback = TRUE), and hence use(), will fallback to known/predefined CRAN repositories in case '@CRAN@' is not set. If done, it will give an informative warning message.

BUG FIXES

• commandArgs() would drop command-line arguments with periods, hyphens, or underscores in their names, e.g. --src_file=x.

Changes in version 1.32.6 (2014-08-12)

BUG FIXES

• withCapture({ if (T) 1 else 2 }) would give a parse error on "unexpected 'else'", because the internal deparsing puts the 'else' statement on a new line whenever an if-else statement is enclosed in an { ... } expression. This problem is also described in R help thread "deparse() and the 'else' statement" by Yihui Xie on 2009-11-09 [http://tolstoy.newcastle.edu.au/R/e8/help/09/11/4204.html]. The workaround is to detect standalone 'else' statements and merge them with the previous line. Added package system test for this case.

Changes in version 1.32.5 (2014-05-15)

BUG FIXES

• egsub() would return an invalid expression if the input had definitions of functions without arguments, e.g. egsub("x", "x", substitute(y <- function() 0)) which would throw "Error: badly formed function expression" if deparsed/printed. Added package test for this.

Changes in version 1.32.4 (2014-05-14)

NEW FEATURES

• Now egsub() also works with functions, in case it substitutes on the body of the function.

DOCUMENTATION

• Added clarification to help("withTimeout") on the limitations of the function and when it is/is not possible to interrupt a function via timeouts.

SOFTWARE QUALITY

• Made the package test on absolute and relative paths less conservative, because it gave an error on Windows systems that have set R_USER to a Cygwin-flavored directory, which causes normalizePath("~") to return a non-existing directory. Thanks Uwe Ligges (CRAN) for reporting on this.

Changes in version 1.32.3 (2014-05-08)

BUG FIXES

• filePath("./././././") now returns "." (was ""). Added package system tests for filePath().

Changes in version 1.32.2 (2014-05-07)

NEW FEATURES

• Added support for substitution of expressions in withCapture() based on regular expressions utilizing new egsub().
• Added egsub(), which is gsub() for expressions with some bells and whistles.

Changes in version 1.32.1 (2014-05-04)

NEW FEATURES

• Now downloadFile() "adjusts" the output filename by decoding URL encoded characters, e.g. 'Hello%20world.txt' becomes 'Hello world.txt'. Also, unsafe filename characters (':', '*', '\') are encoded, e.g. 'How_to:_RSP.txt' becomes 'How_to%3A_RSP.txt'.
• Added argument 'adjust' to Arguments$getReadablePathname(). When adjust = "url" it decodes and encodes the filename the same way as downloadFile() now adjusts it (see above).

Changes in version 1.32.0 (2014-05-01)

NEW FEATURES

• Added captureOutput() which is much faster than capture.output() for large outputs. withCapture() utilizes this now. Added package system tests for both functions.
• use() now installs missing packages from all set repositories (as before) and uses the mainstream (CRAN and BioC) ones as fall backs.
• Added withRepos() for installing/updating packages using a set of temporarily set repositories. It is possible to specify repositories by names, which are then selected from a set of known repositories, e.g. withRepos(install.packages("edgeR"), repos = "[[BioC]]").
• Added withOptions() for evaluating an expression with a set of options temporarily set.
• Renamed evalCapture() to withCapture() and evalWithTimeout() and withTimeout(). The old name is kept for backward compatibility, but will eventually be deprecated.

Changes in version 1.31.1 (2014-04-29)

NEW FEATURES

• Now use("repos::pkg") will detect when a repository is unknown and give an informative error message on how to update option 'repos'.

Changes in version 1.31.0 (2014-04-26)

NEW FEATURES

• Added assignment operator %<-% for delayed assignments.
• Added option "evalCapture/newline".

Changes in version 1.30.7 (2014-04-26)

NEW FEATURES

• Added argument 'xtrim' to draw() for density object.
• CLEANUP: createLink(..., skip = TRUE) no longer warns if the link file was skipped. Now it only warns if the skipped link file links to a different file than the intended target file.

CODE REFACTORING

• CLEANUP: Dropping '::' in calls where possible.

Changes in version 1.30.6 (2014-04-24)

NEW FEATURES

• Added argument 'newline' to evalCapture().

Changes in version 1.30.5 (2014-04-22)

NEW FEATURES

• Added argument 'substitute' to evalCapture() for substituting symbols "on the fly" in the expression before it is evaluated.

Changes in version 1.30.4 (2014-04-18)

NEW FEATURES

• Added argument 'modifiedOnly' to sourceDirectory(), which was previously passed via '...' to sourceTo(), and it now defaults to TRUE.

Changes in version 1.30.3 (2014-04-15)

BUG FIXES

• use() would not install package dependencies.

Changes in version 1.30.2 (2014-04-08)

NEW FEATURES

• Added argument 'max.deparse.length' to evalCapture().

Changes in version 1.30.1 (2014-04-06)

NEW FEATURES

• Now evalCapture() utilizes deparse() to get the source code and acknowledges options 'deparse.cutoff' to control the code wrapping. Previously capture.output(print()) was used.

BUG FIXES

• WORKAROUND: moveInSearchPath() redirects any messages to stderr that base::attach() sent to stdout. UPDATE: This attach() issue has been fixed in R 3.1.0 patched.

Changes in version 1.30.0 (2014-04-06)

NEW FEATURES

• Vectorized detachPackage(), getAbsolutePath(), getRelativePath(), isAbsolutePath(), isDirectory(), isFile(), isOpen(), isPackageInstalled(), touchFile() and toUrl(). Added package system tests for several of them. For backward compatibility, getAbsolutePath(), getRelativePath(), isAbsolutePath(), isFile(), and isDirectory() treats an empty vector of path/pathnames equal to ".". However, in a future version, empty results will returned by these too.

BUG FIXES

• toCamelCase(character(0L)) gave an error.

Changes in version 1.29.11 (2014-04-02)

BUG FIXES

• str() and summary() for Verbose did not acknowledge argument 'level'.

Changes in version 1.29.10 (2014-02-28)

DOCUMENTATION

• Added a help section on privileges required on Windows in order for createLink() to work.

Changes in version 1.29.9 (2014-02-24)

NEW FEATURES

• ROBUSTNESS: Added a package redundancy test for a bug occurring in R.oo (< 1.18.0) causing R to core dump (with "Error: SET_VECTOR_ELT() can only be applied to a 'list', not a 'integer'") or gives an error (with "Error: not a weak reference") under certain conditions when a registered finalizer tried to reload R.oo if it was unloaded. This occurred only on R prior to R 3.0.2 patched (2014-02-21 r65057). Also, the 'methods' package needs to be attached, so it is still not clear what is the true cause of the bug. In R.oo (>= 1.18.0) this bug is avoided.

Changes in version 1.29.8 (2014-01-27)

BUG FIXES

• Although eget(K = 2, cmdArgs = TRUE) would use command-line argument 'K=1' as the default (instead of K=2), calling eget("K", 2, cmdArgs = TRUE) would not.
• commandArgs(excludeReserved = TRUE) failed to drop reserved arguments of type --key=value, e.g. --encoding=ASCII.

Changes in version 1.29.7 (2014-01-27)

NEW FEATURES

• Added trial version of the CmdArgsFunction class.

Changes in version 1.29.6 (2014-01-27)

NEW FEATURES

• Added cmdArgsCall() for easy calling of functions from the command line, e.g. Rscript -e R.utils::cmdArgsCall(rnorm) n=4.

Changes in version 1.29.5 (2014-01-27)

NEW FEATURES

• doCall() gained argument 'envir', which also means that the new behavior is to evaluate the call within the calling frame. Also, doCall() now accepts call a function object in addition to a name of a function.

Changes in version 1.29.4 (2014-01-26)

NEW FEATURES

• Added argument 'unique' to cmdArgs().
• Now commandArgs(asValues = TRUE) returns no-named arguments as a list element with the argument as the value and with a "" name. For instance, in the past one would get list(R = NA, a = "1", noname = NA) whereas now one gets list("R", a = "1", "noname").

BUG FIXES

• Now attachLocally() no longer tries to attach elements with an empty name, e.g. list(a = 1, 2). Previously it gave an error. Added a package system test for attachLocally().

Changes in version 1.29.3 (2014-01-19)

NEW FEATURES

• CONSISTENCY: Now createLink(..., method = "windows-shortcut") returns the path/pathname to the link (and not the target) just like it does for the other types of file links. By link we here mean the path/pathname without the *.lnk extension.

SOFTWARE QUALITY

• ROBUSTNESS: Added package system tests for createLink().

Changes in version 1.29.2 (2014-01-12)

NEW FEATURES

• Now Arguments$getCharacters() preserves attributes. Also, made argument 'useNames' defaults to TRUE.
• Added [() for GenericSummary.

Changes in version 1.29.1 (2014-01-10)

NEW FEATURES

• Added argument 'what' to Sys.readlink2(), where what = "corrected" makes sure to return the proper target path (not just the one relative to where the link lives).

Changes in version 1.29.0 (2014-01-07)

• The following file I/O methods follows symbolic links (also on Windows) and returns information based on the target file/directory (rather than the link itself): fileAccess(), file.info2(), isDirectory(), isFile() and lastModified().
• Added file.info2() for retrieving file information such that symbolic file links are also acknowledged on Windows.
• Added Sys.readlink2() for reading symbolic file links also on Windows.
• removeDirectory() can now be used to remove symbolic directory links (also on Windows where neither file.remove() nor unlink() work). The target directory will never be removed.
• BUG FIX: renameFile() would give an error on directories.
• Added package system tests for copyFile() and renameFile().
• ROBUSTNESS: createLink() will no longer try to create Windows file links on non-Windows platforms.
• ROBUSTNESS: Updated a shell() calls that assume the Windows command interpreter to explicitly specify shell = Sys.getenv("COMSPEC").

Changes in version 1.28.6 (2014-01-06)

• Added argument 'skip' (in addition to existing 'overwrite') to copyFile() to allow for better control on how to handle existing destination files. For backward compatibilities, it defaults to FALSE, but may be changed to skip = !overwrite in a future version. Furthermore, copyFile() now passes (known) arguments '...' to base::file.copy() making it possible to copy with or without file permissions etc. Thanks Taku Tokuyasu (UCSF) for reporting on this.

Changes in version 1.28.5 (2013-12-15)

• Now argument 'asGString' for Arguments$getCharacters() defaults to getOption("Arguments$getCharacters/args/asGString", TRUE). This makes it possible to disable this feature, even when it is not possible to directly pass that argument. This will also make it possible to set the default to FALSE in the future (instead of TRUE as today).
• Added argument 'inherits' to evaluate() for GString. Default is TRUE for backward compatibility.

Changes in version 1.28.4 (2013-11-20)

• Minor updates to NAMESPACE file.

Changes in version 1.28.3 (2013-11-15)

• Added method c() for GenericSummary.

Changes in version 1.28.2 (2013-11-15)

• CLEANUP: Arguments$getNumerics(NA, range = c(0,1)) no longer gives warnings on "no non-missing arguments to min()" etc.

Changes in version 1.28.1 (2013-10-30)

• BUG FIX: System$getMappedDrivesOnWindows() failed to return the proper path for 'net use' mounted drives, iff the path contained spaces.

Changes in version 1.28.0 (2013-10-20)

• CLEANUP: Removed a few non-used internal objects.
• Forgot to declare enterf() for Verbose as an S3 method.

Changes in version 1.27.6 (2013-10-13)

• CLEANUP: Some methods had to attach 'R.utils' in the past in order to work properly. These are no longer attaching 'R.utils': copyDirectory(), createLink(), createWindowsShortcut(), downloadFile(), installPackages(), removeDirectory(), and sourceDirectory().
• Bumped up package dependencies.

Changes in version 1.27.5 (2013-10-07)

• CLEANUP: Now explicitly importing only what is needed in NAMESPACE.
• CLEANUP: Dropped obsolete autoload():s.
• ROBUSTNESS: The overriding of getOption() to become a generic function does now call base::getOption() in the default, instead of copy the latter.
• Bumped up package dependencies.

Changes in version 1.27.4 (2013-09-28)

• Now argument 'recursive' of listDirectory() can also specify the maximum recursive depth, e.g listDirectory(..., recursive = 5L).
• Now the 'R.utils' Package object is also available when the package is only loaded (but not attached).

Changes in version 1.27.3 (2013-09-20)

• ROBUSTNESS: Forgot to import R.methodsS3::appendVarArgs().

Changes in version 1.27.2 (2013-09-15)

• TYPO: An error message of dimNA<-() was referring to 'files' rather than to 'elements'.

Changes in version 1.27.1 (2013-09-10)

• BUG FIX: commandArgs(asValues = TRUE) failed to set the value of the very last argument to TRUE if it was a flag, e.g. 'R --args --bar'. Thanks to Stijn van Dongen at EMBL-EBI in Cambridge/Hinxton, UK for reporting on this.

Changes in version 1.27.0 (2013-08-30)

• Added use() for easy attaching/loading and automatic installation of packages.
• Now isPackageInstalled() suppresses warnings.

Changes in version 1.26.4 (2013-08-27)

• CLEANUP: Arguments$getReadablePathnames(files, paths = NULL) no longer warns about "rep(paths, length.out = nbrOfFiles) : 'x' is NULL so the result will be NULL" if length(files) > 0.
• CLEANUP: Package no longer utilizes ':::'.
• DOCUMENTATION: Help for installPackages() was missing. Thanks Gabor Grothendieck for reporting on this.

Changes in version 1.26.3 (2013-08-20)

• Forgot to declare default inherits() as an S3 method.

Changes in version 1.26.2 (2013-07-30)

• ROBUSTNESS/BUG FIX: System$findGhostscript() could still give errors. Completely rewrote how Ghostscripts is searched. On Windows, environment variable 'GSC' is now also searched. Thanks to Brian Ripley for the feedback.

Changes in version 1.26.1 (2013-07-29)

• BUG FIX: System$findGhostscript() would give "Error in pathname [sapply(pathname, FUN = isFile)]: invalid subscript type 'list'" if no device was found.

Changes in version 1.26.0 (2013-07-27)

• Added tempvar() for creating non-existing temporary variables.
• Added enterf() to Verbose, which is an sprintf-like enter().
• Now System$findGhostscript() returns system variable 'R_GSCMD' if set and it refers to an existing executable (and unless force = TRUE). It then checks with Sys.which(). On Windows, it finally searches for 'gswin64c.exe' and 'gswin32c.exe' on known locations. Added arguments 'firstOnly' and 'force'.
• Now getAbsolutePath() shortens paths if possible, e.g. "C:/foo/.." becomes "C:/".
• Added argument 'skip' to gzip() and gunzip().
• BUG FIX: gunzip() would ignore argument 'overwrite'.
• BUG FIX: filePath("C:/foo/..") returned "C:", which should be "C:/".

Changes in version 1.25.3 (2013-07-27)

• BUG FIX: findSourceTraceback() would give an error "Unknown class of 'srcfile': character" for source(..., keep.source = FALSE) in recent R devel and R v3.0.1 patched. Thanks Duncan Murdoch for the report.

Changes in version 1.25.2 (2013-07-03)

• Now installPackages() may also install from https URLs.
• Now more methods can be used without attaching ("loading") the package: copyFile(), copyDirectory(), removeDirectory(), createLink(), createWindowsShortcut(), downloadFile(), sourceDirectory(), and installPackages(), e.g. R.utils::downloadFile().
• Now touchFile() utilizes base::Sys.setFileTime(), iff available.

Changes in version 1.25.1 (2013-07-01)

• Bumped up package dependencies.

Changes in version 1.25.0 (2013-06-27)

• UPDATE: Now gzip()/gunzip() returns the output file (was number of output bytes processed which are now returned as an attribute).
• Added argument 'temporary' to gzip()/gunzip().
• Added isGzipped() for testing whether a file is gzipped or not.

Changes in version 1.24.4 (2013-06-17)

• Now argument 'dims' of extract() can also be dimension names.

Changes in version 1.24.3 (2013-05-25)

• Minor speedups by replacing rm() calls with NULL assignments.
• SPEEDUP: readTable() no longer calls gc().

Changes in version 1.24.2 (2013-05-20)

• CRAN POLICY: Now all Rd \usage{} lines are at most 90 characters long.
• CRAN POLICY: Now all Rd example lines are at most 100 characters long.

Changes in version 1.24.1 (2013-05-13)

• The workaround needed by isDirectory() due to a bug in file.info() is now applied only for R (< 3.0.2), since the bug was been fixed in R 3.0.1 patched (PR#15302).

Changes in version 1.24.0 (2013-04-18)

• Several methods now output messages and verbose output to standard error (instead of standard output), including addFinalizerToLast(), filePath(), patchCode(), readWindowsShellLink(), readWindowsShortcut(), and loadAnywhere() for Settings.

Changes in version 1.23.4 (2013-04-15)

• BUG FIX: capitalize()/decapitalize() would return "NANA" for missing values. Reported by Liviu Andronic.

Changes in version 1.23.3 (2013-03-29)

• BUG FIX: downloadFile('https://...') did not work if 'username' or 'password' was NULL.

Changes in version 1.23.2 (2013-03-22)

• BUG FIX: Previous update caused commandArgs(..., adhoc = TRUE) to coerce 'T' and 'F' to logicals TRUE and FALSE. They are now preserved as character string.

Changes in version 1.23.1 (2013-03-21)

• Now commandArgs(..., adhoc = TRUE) utilizes utils::type.convert().

Changes in version 1.23.0 (2013-03-20)

• Added ecget() which is like eget() with the default value corresponding to the command-line argument.
• Added eget() for retrieving a single variable, with a fallback to a default value, e.g. n <- eget(n = 42).
• Added support for cmdArg(n = 42) as an alias to cmdArg("n", 42).

Changes in version 1.22.0 (2013-03-14)

• Added cmdArg() for retrieving a single command line argument with a default value and type, e.g. n <- cmdArg("n", 42).

Changes in version 1.21.2 (2013-03-11)

• Bumped up package dependencies.

Changes in version 1.21.1 (2013-03-08)

• Added an Authors@R field to the DESCRIPTION.

Changes in version 1.21.0 (2013-03-07)

• Major improvement of commandArgs(). For instance, now it never consider arguments after '--args' to be reserved or environment variable arguments; they are always user arguments. It is also doing a better job on interpreting -*key=value arguments; previously it could happen that it would split the value. Added systems test for commandArgs() and cmdArgs().

Changes in version 1.20.2 (2013-03-07)

• Now argument 'eps' for isZero() may also be a character string specifying either "double.eps" or "single.eps".

Changes in version 1.20.1 (2013-03-04)

• DOCUMENTATION: Updated the help usage section for all static methods.

Changes in version 1.20.0 (2013-02-24)

• Added cmdArgs() which is short for R.utils::commandArgs(asValues = TRUE, adhoc = TRUE, unique = TRUE, excludeReserved = TRUE, ...)[-1L].
• Now it is possible to specify default arguments in commandArgs(). In addition, if asValues = TRUE, then the values of the parsed command-line arguments will be coerced to the data type of the default ones if they share names. If adhoc = TRUE, arguments will be coerced to numerics unless the result is NA.
• For conveniency, getAbsolutePath() and getRelativePath() returns the same pathname if it is a URL.
• Added gstring() and gcat().
• Now it is possible to escape the sed-like search replace format for GString:s via quoting, e.g. ${'R.rsp/HttpDaemon/RspVersion'} .
• BUG FIX: getParent() and filePath() as well as System$mapDriveOnWindows() and System$unmapDriveOnWindows() did not handle paths with a lower case Windows drive letter. Oddly, it is only now that we have received an single report (on a Windows 7 system) that such getwd() may return such drive letters, e.g. 'c:/path/' instead of 'C:/path/'.
• BUG FIX: evaluate(..., where = "parent") for GString would result in an endless loop.
• BUG FIX: displayCode(code) incorrectly processed 'code' as GString:s.

Changes in version 1.19.5 (2013-01-11)

• BUG FIX: Specifying argument 'version' to isPackageLoaded() would give "Error: 'manglePackageName' is defunct." in recent versions of R. Thanks to Brian Ripley (R core) for reporting on this.

Changes in version 1.19.4 (2013-01-07)

• Now '.Last.lib' is exported.
• Bumped up package dependencies.

Changes in version 1.19.3 (2012-12-19)

• Utilizing new startupMessage() of R.oo.

Changes in version 1.19.2 (2012-12-18)

• R CMD check for R devel no longer gives a NOTE on attach().

Changes in version 1.19.1 (2012-12-02)

• CLEANUP: R CMD check no longer warns on global assignments.
• BUG FIX: Arguments$getIndices(x, max = 0, disallow = "NaN") where 'x' contains only NA_integer_, would give "Exception: Argument 'x' is of length 1 although the range ([0,0]) implies that is should be empty." although it should return 'x' as is.

Changes in version 1.19.0 (2012-11-29)

• CLEANUP: Dropped lapply() for MultiVerbose.
• Added as.list() to MultiVerbose.

Changes in version 1.18.4 (2012-11-21)

• Now declaring all S3 methods in the namespace.

Changes in version 1.18.3 (2012-11-06)

• BUG FIX: queryRCmdCheck() did not detect "tests" evidences when 'R CMD check' was testing multiple architectures.

Changes in version 1.18.2 (2012-11-04)

• CLEANUP: Replaced all whichVector() with which(), because the latter is now the fastest again.
• CLEANUP: Dropped pre-R 2.3.0 patch of as.character.hexmode().
• CLEANUP: Dropped pre-R 2.5.0 patch of Sys.setenv().
• BUG FIX: The 'columnClasses' header field created by writeDataFrame() would contain "integer" for "factor":s. Now using class(x)[1] instead of storage.mode(x) to infer column classes.
• BUG FIX: Despite documented header fields 'createdBy' and 'createdOn' to be ignored if NULL, they did set the corresponding' element in 'header' argument to NULL if they were NULL.

Changes in version 1.18.1 (2012-10-31)

• Now gzip()/gunzip()/bunzip2() creates the directory of destination pathname 'destfile', iff missing.

Changes in version 1.18.0 (2012-10-29)

• Added trial version of readWindowsShellLink(), which eventually will replace readWindowsShortcut().
• GENERALIZATION: Now filePath() does a better job reading Windows Shell Links/Windows Shortcut (*.lnk) files.
• ROBUSTNESS: Now createWindowsShortcut() uses an improved validation strategy of the created *.lnk file.

Changes in version 1.17.4 (2012-10-26)

• BUG FIX: example(createWindowsShortcut) could throw an error on some systems. The exact reason for this is unknown, so for now it's instead generating a warning rather that an error.

Changes in version 1.17.3 (2012-10-26)

• RECOMMENDATION: Since R v2.11.0, you should use base::which() instead of whichVector(), which now help("whichVector") also explains. Also, whichVector() was removed from the help index of the package.
• CRAN POLICY: Made the examples run faster for R CMD check.

Changes in version 1.17.2 (2012-10-21)

• ROBUSTNESS: Added argument 'maxTries' to Arguments$getWritablePathname() to have the method try to create missing directories multiple times before giving up. This also means that it will take a longer for this method to fail creating a directory.
• Now Arguments$getWritablePathname() gives a more informative error if failed, analogously to Arguments$getReadablePathname().

Changes in version 1.17.1 (2012-10-19)

• mkdirs(path) could generate a warning if the path was created by another process as a race condition. Now it always checks to see if the directory already exists just before trying to create the directory.

Changes in version 1.17.0 (2012-10-16)

• Moved Arguments$getFilename() from R.filesets to R.utils. Added Rd help.
• ROBUSTNESS: Bumped up package dependencies.

Changes in version 1.16.6 (2012-10-09)

• BUG FIX: evalWithTimeout() would not reset the time limits after returning. Thanks to Gregory Ryslik at Yale University for reporting on this.

Changes in version 1.16.5 (2012-09-26)

• Added argument 'skip' to createLink().
• ROBUSTNESS: Now createLink(..., overwrite = TRUE) will try to undo the overwrite, iff it failed to create the new link.
• BUG FIX: createLink(..., overwrite = TRUE) would give an error saying "file already exists" (iff that is true) when it tries to create a "unix-symlink" link. Thanks Taku Tokuyasu at UCSF for the report.

Changes in version 1.16.4 (2012-09-24)

• BUG FIX: Arguments$getReadablePath(..., mustExist = FALSE) did not work.

Changes in version 1.16.3 (2012-09-21)

• Now insert() silently expands 'values' to be of the same length as 'ats', iff length(values) == 1.
• toCamelCase(..., preserveSameCase = TRUE) makes all-upper-case words into same-case words, e.g. toCamelCase("HTML View", preserveSameCase = TRUE) outputs "htmlView" (not "hTMLView"). Added system tests for toCamelCase().

Changes in version 1.16.2 (2012-09-12)

• ROBUSTNESS/CRAN POLICY: moveInSearchPath() no longer calls .Internal(detach(...)) but instead base::detach() in such a way that neither detach hooks nor .Last.lib() are called.

Changes in version 1.16.1 (2012-09-07)

• Now createLink() also supports targets with '~' in the path.
• ROBUSTNESS: createLink(target = "C:/") would try to create a link with name "C:", which is not valid resulting is the somewhat confusing error on "cannot symlink 'S:' to 'S:', reason 'Access is denied'". Now it instead throws "Cannot infer a valid link name from argument 'target': C:/".
• ROBUSTNESS/BUG FIX: On Windows, it could happen that createLink() would generate a zero-size link file that did not link to the target as a result of a failed file.symlink(). This is now tested for such that if an invalid link file was created, it is removed again.

Changes in version 1.16.0 (2012-07-11)

• CLEANUP: Dropped the graphics device related functions that were moved to R.devices.
• System$findGraphicsDevice() no longer tries to create a PNG device using png2(), because that has now moved to R.devices.
• Updated package dependencies.

Changes in version 1.15.1 (2012-06-16)

• Now package only imports/no longer depends on the 'utils' package. This means that all packages that depends on 'R.utils' for loading 'utils' for them need to explicitly load it themselves.

Changes in version 1.15.0 (2012-05-22)

• Added systemR() for launching an external R process.
• Package no longer loads (via a DESCRIPTION Depends) the R.devices package, because that would cause a circular package dependency. Instead, we're keeping the graphical device functions here until all reverse dependent packages have been set to explicitly use R.devices.

Changes in version 1.14.0 (2012-05-01)

• Copied all functions related to graphics devices to new package R.devices (v2.1.1), which is now on CRAN. For backward compatibility, the R.utils package will for now depend and hence load the R.devices package.

Changes in version 1.13.1 (2012-04-16)

• Added findFiles(), which orginates from the affxparser package.

Changes in version 1.13.0 (2012-04-07)

• Added toBMP() and toTIFF().

Changes in version 1.12.2 (2012-04-05)

• Now it is possible to have devEval() rename incompletely generated image files, by using argument onIncomplete = "rename". This will simplify troubleshooting. The default is still to remove incomplete files.
• ROBUSTNESS: Updated package dependencies.

Changes in version 1.12.1 (2012-03-20)

• BUG FIX: .onAttach() would try to call getMessage(ex) on an 'error' if there was a problem adding a finalizer, resulting in "no applicable method for 'getMessage' applied to an object of class "c('simpleError', 'error', 'condition')". Now using 'ex$message' instead.

Changes in version 1.12.0 (2012-03-08)

• CRAN POLICY: Renamed remove() for FileProgressBar to cleanup(), because otherwise it would be inevitable to create an internal copy of base::remove() which contains an .Internal() call. This move may break existing code that calls remove() on an FileProgressBar object.
• CRAN POLICY: Removed all internal copies of 'base' and 'utils' functions that have .Internal() calls.
• CLEANUP: Removed relibrary() function, because it has not worked properly since R introduced namespaces, which is several years.

Changes in version 1.11.2 (2012-02-29)

• CRAN POLICY: Now capture() for Verbose uses withVisible() instead of an .Internal(eval.with.vis()) call.

Changes in version 1.11.1 (2012-02-28)

• ROBUSTNESS: The creation of image files by devEval() is now close to being "atomic". That is, if the code for plotting the figure is interrupted (e.g. by a user interrupt or an error), then any created image file is removed. This avoids leaving incomplete/blank image files behind.

Changes in version 1.11.0 (2012-02-26)

• GENERALIZATION: Now devOptions() accepts passing a device function in addition a string, e.g. devOptions(png) and devOptions("png").
• Added argument 'scale' to devNew().
• BUG FIX: Before devNew(..., aspectRatio = 1) would ignore devOptions(...)$width if neither argument 'width' nor 'height' was given.

Changes in version 1.10.0 (2012-02-23)

• Added swapXY() and draw() for 'density' objects. Used to be in the aroma.core package.
• ROBUSTNESS: Package now explicitly depends on 'utils' and 'R.methodsS3'. Before it relied on 'R.oo' to load those.

Changes in version 1.9.11 (2012-01-17)

• ROBUSTNESS: Now System$findGraphicsDevice() not only assert that an image file is generated, but also that its filesize is non-zero. This avoids returning a device that generates empty image files. Also updated the time out to 10 secs (was 30 secs).

Changes in version 1.9.10 (2012-01-12)

• CLEANUP: reassignInPackage() calls function that are considered "unsafe" by the new CRAN policies, i.e. unlockBinding() and assignInNamespace(). However, we still wish to keep this method available to advanced users. In order to avoid getting NOTEs from R CMD check, we have "hidden" those unsafe function calls.

Changes in version 1.9.9 (2012-01-11)

• BUG FIX: writeRaw() for Verbose would throw error "Trying to coerce more than one character string to a GString, which is not supported." iff passing a vector of strings.

Changes in version 1.9.8 (2011-12-30)

• DOCUMENTATION: The help now explains that evalWithTimeout(readline()) does not throw a timeout exception until after readline() returns.

Changes in version 1.9.7 (2011-12-16)

• BUG FIX: evalWithTimeout() would not detect timeouts in R sessions that use a non-English locale.
• BUG FIX: Now evalWithTimeout(..., onTimeout = "silent") works. Thanks Nicholas Beeton (Univ. of Tasmania, Australia) for reporting on this.

Changes in version 1.9.6 (2011-11-23)

• BUG FIX: evalCapture() with argument 'envir' defaulting to parent.frame() would not be evaluated in the parent frame as it should. It appears that the internal capture.output() prevents this from happening, unless argument 'envir' is explictly evaluated within evalCapture().

Changes in version 1.9.5 (2011-11-19)

• ROBUSTNESS: Now parse() and as.character() handles "empty" GString:s.
• ROBUSTNESS: Now GString() asserts that it only holds one string.

Changes in version 1.9.4 (2011-11-15)

• SPEEDUP: Now Arguments$getCharacters(s, asGString = TRUE) is much faster for elements of 's' that are non-GStrings. For long character vectors the speedup is 100-200x times.
• SPEEDUP: Now as.character() and parse() for GString return faster if the string is a plain string without markup etc. This made as.character() about 10-15 times faster.

Changes in version 1.9.3 (2011-11-07)

• Added 'quarts' to the list of (possible) devices for devOptions().
• BUG FIX: devOptions() assumed that all devices exist on all platforms, causing it to give an error on some.

Changes in version 1.9.2 (2011-11-06)

• Added evalCapture() for evaluating an expression and capturing its deparsed code and/or output.

Changes in version 1.9.1 (2011-11-05)

• Added toEPS(), toPDF(), toPNG() and toSVG().
• Added devOptions().
• Added default 'width' and 'height' values to eps().
• Turned png2() and jpeg2() into plain functions without a generic. This is consistent with how eps() is defined.
• GENERALIZATION: Now the default 'width' is inferred from devOptions() if needed.
• DOCUMENTATION: Added an example to help(devEval).

Changes in version 1.9.0 (2011-11-03)

• Added queryRCmdCheck(), which retrieves the status of 'R CMD check', iff it is running.

Changes in version 1.8.8 (2011-11-01)

• Added argument 'dims' to extract() for arrays. Also, argument 'drop' was moved to the end.

Changes in version 1.8.7 (2011-11-01)

• CLEANUP: Fixed a R CMD check NOTE that would show up in R v2.15.0 devel.

Changes in version 1.8.6 (2011-10-31)

• Added argument 'field' to devEval().

Changes in version 1.8.5 (2011-10-16)

• CORRECTION: Arguments$getNumerics(c(Inf), disallow = "Inf") would report that it contains "NA" instead of "Inf" values.

Changes in version 1.8.4 (2011-10-08)

• Now the default for argument 'methods' of createLink() can be set via option "createLink/args/methods".

Changes in version 1.8.3 (2011-09-30)

• Added installPackages() for installing R packages by names or URLs. This method was previously in the hbLite.R script of braju.com.

Changes in version 1.8.2 (2011-09-24)

• devNew() no longer gives a warning about argument 'aspectRatio' is specified when both or neither of 'width' and 'height' are given, and 'aspectRatio' is 1.
• Internal readDWord() and readQWord() of readWindowsShortcut() would try read 4- and 8-byte integers as non-signed, which is not supported by base::readBin() and hence instead read as signed integers. Starting with R v2.13.1 this would generate a lot of warnings.

Changes in version 1.8.1 (2011-09-19)

• Now System$mapDriveOnWindows(), System$unmapDriveOnWindows(), and System$getMappedDrivesOnWindows() also handles Windows UNC paths (i.e. network resource). This was triggered by a discussion with Keith Jewell at Campden BRI Group, UK.
• WORKAROUND: isDirectory("C:/") would not return TRUE due to a bug in file.info("C:/") causing it to return NAs.
• Now attachLocally() returns a character vector also of length zero. Before NULL was returned.

Changes in version 1.8.0 (2011-09-14)

• Added writeDataFrame().
• ROBUSTNESS: Added sanity checks to example(capitalize).
• DOCUMENTATION: Improved example(commandArgs).
• BUG FIX: commandArgs() would not handle '-key value' and '--key value' properly in all cases.

Changes in version 1.7.8 (2011-07-24)

• Undoing v1.7.7 to again exports '.conflicts.OK' in order to avoid several warnings when loading package.

Changes in version 1.7.7 (2011-07-23)

• '.conflicts.OK' is no longer exported, because it would cause other "downstream" packages to generate a WARNING in R CMD check.

Changes in version 1.7.6 (2011-04-30)

• Added isReplicated() and replicates() for identifying entries in a vector that are non-unique. Corresponding isSingle() and singles() identifies entries that exists only once.

Changes in version 1.7.5 (2011-04-12)

• Now devEval("jpg", ...) is recognized as devEval("jpeg", ...).

Changes in version 1.7.4 (2011-04-03)

• Now hpaste(..., sep = " ", maxHead = Inf) corresponds to paste(..., sep = " ", collapse = ", "). Added to example.

Changes in version 1.7.3 (2011-04-02)

• Added hpaste() for human-readable pasting, e.g. "1, 2, 3, ..., 10".
• Now argument 'force' of devEval() defaults to getOption("devEval/args/force", TRUE).

Changes in version 1.7.2 (2011-03-18)

• Now argument 'path' of devEval() defaults to getOption("devEval/args/path", "figures/").
• Now devEval() does a better job of "cleaning up" 'name' and 'tags'.

Changes in version 1.7.1 (2011-03-18)

• devNew() gained option 'devNew/args/par', which can be used to specify the default graphical parameters for devNew(). Any additional parameters passed via argument 'par' will override such default ones, if both specifies the same parameter.
• The automatic archiving of devEval() is not considered unless the R.archive package is loaded, regardless of option settings.
• DOCUMENTATION: The title of help(devDone) was incorrect.

Changes in version 1.7.0 (2011-03-10)

• Now argument 'aspectRatio' of devNew() defaults to 1 (not NULL).
• Added setOption(), the "set version" of getOption().
• Added env() for creating an environment and evaluating an expression inside of it in one go.
• Added argument 'path' to sourceTo().
• REPRODUCIBLE RESEARCH: Now devEval() archives any generated image files if R.archive option 'devEval' is TRUE.
• BUG FIX: sourceTo() would not work for URLs.

Changes in version 1.6.6 (2011-03-08)

• Now Arguments$getWritablePath(NULL) returns NULL without asserting write permission, which is analogue to how it is done with Arguments$getReadablePath(NULL).
• Added argument 'timestamp' to printf() for Verbose so that the timestamp can be turned off/on explicitly as for cat().

Changes in version 1.6.5 (2011-03-03)

• Added trial version of createFileAtomically() for creating files atomically, by writing to a temporary file which is then renamed.
• Added trial versions of push-, popBackupFile() for backing up and restoring a file.
• Added trial versions of push-, popTemporaryFile() for working toward a temporary file.
• Added trial version of renameFile(), which to additional validation afterward.

Changes in version 1.6.4 (2011-02-28)

• (Incomplete revision submitted to CRAN by mistake)

Changes in version 1.6.3 (2011-02-20)

• Added argument 'par' to devNew() for applying graphical parameters at the same time as the device is opened, which is especially useful when using devEval().
• Changed argument 'force' of devEval() to default to TRUE.

Changes in version 1.6.2 (2011-02-14)

• Added trial version of devEval() for simple creation of images.
• Added argument 'aspectRatio' to devNew(), which updates/sets the 'height' or the 'width', if the one of the other is not given.

Changes in version 1.6.1 (2011-02-01)

• ROBUSTNESS: Now using argument 'fixed' (not 'fix') in regexpr() calls.

Changes in version 1.6.0 (2010-12-07)

• Added evalWithTimeout().

Changes in version 1.5.8 (2010-11-21)

• ROBUSTNESS: Now loadObject() asserts that the file exists. If file doesn't exist, an informative error message is thrown.
• ROBUSTNESS: Now System$mapDriveOnWindows() does not give an error if trying to map the same drive letter to the same path multiple times.
• TYPO: Static methods getVector() and getRegularExpression() of Arguments would report the incorrect argument name.
• BUG FIX: System$mapDriveOnWindows() and System$unmapDriveOnWindows() did not work if the path contained a space. Now the path is quoted.
• BUG FIX: Now removeDirectory() also works for paths starting with a tilde (~). The reason was/is that base::unlink() used internally does not support that. We now use base::path.expand() first.

Changes in version 1.5.7 (2010-11-07)

• ROBUSTNESS: Now read/writeBinFragments() assert that argument 'idxs' contains only non-negative indices.
• Added support to readBinFragments() to start reading from either the current file position (default; as previously) or from the start of the connection. For backward compatibility, we keep the default to be relative to the current position, but this may change in the future.

Changes in version 1.5.6 (2010-11-03)

• Added resample(), which contrary to sample() also works when drawing from a single element.

Changes in version 1.5.5 (2010-10-26)

• Now argument 'which' to devSet() can be any object. If not a single numeric or a single character string, then a checksum character string is generated using digest::digest(which).

Changes in version 1.5.4 (2010-10-13)

• Now the 'link' argument of createLink() is inferred from the 'target' argument if it is "." (or NULL).

Changes in version 1.5.3 (2010-09-29)

• Added an example to help(findSourceTraceback).
• BUG FIX: Each entry identified by findSourceTraceback() would be duplicated.

Changes in version 1.5.2 (2010-09-15)

• fileAccess() no longer returns a named value if file.access() is used.
• ROBUSTNESS: Added a more robust test for fileAccess(path, mode = 2) when 'path' is a directory. Thanks Chao Chen at University of Chicago for reporting issues with this.
• BUG FIX: Now fileAccess(..., mode = 1) only utilizes file.info()$exe if it is a file and on Windows, otherwise it relies on file.access().
• DOCUMENTATION: Added an example to help(fileAccess).
• MISC: Added support for readRdHelp(..., format = "text") in R < 2.10.0.

Changes in version 1.5.1 (2010-08-28)

• Added readRdHelp() for locating and reading installed Rd help pages in various formats.
• Now downloadFile() supports authentication, if 'wget' is available on the system.

Changes in version 1.5.0 (2010-08-04)

• Added stext(), which previously was in the aroma.core package.

Changes in version 1.4.4 (2010-07-05)

• Now arrayIndex() returns an @integer @matrix.
• DOCUMENTATION: Now the help of arrayIndex() links to the new arrayInd() in the base package.

Changes in version 1.4.3 (2010-06-23)

• BUG FIX: getAbsolutePath("//server/dir/") would incorrectly drop the initial double-slashes ('//') and return "/server/dir/". Thanks Richard Cotton at Health and Safety Laboratory (HSL), UK, for reporting this.

Changes in version 1.4.2 (2010-06-09)

• Added printf(), as a convenient wrapper for cat(sprintf(...)).

Changes in version 1.4.1 (2010-05-26)

• Added downloadFile() for safer and more convenient downloads.

Changes in version 1.4.0 (2010-03-24)

• Now R.utils requires R v2.5.0 (circa 2007) or newer. This is because there was a change in base::parse() from R v2.4.1 and R v2.5.0. See news for R.utils v0.9.3.
• Added a NAMESPACE.

Changes in version 1.3.4 (2010-03-02)

• Added alpha version of an onGarbageCollect() method.
• BUG FIX: findSourceTraceback() stopped working; probably due to some recent updates in base::source().

Changes in version 1.3.3 (2010-01-25)

• ROBUSTNESS: Added validation of argument 'range' in Arguments methods.

Changes in version 1.3.2 (2010-01-09)

• sourceTo(..., modifiedOnly = FALSE) followed by a sourceTo(..., modifiedOnly = TRUE) will now work as expected. Before you had to do at least one modifiedOnly = TRUE call before for it to work.
• sourceTo() no longer gives a warning if there is a missing EOL.

Changes in version 1.3.1 (2010-01-08)

• Added System$mapDriveOnWindows(), System$unmapDriveOnWindows(), and System$getMappedDrivesOnWindows() for associating drive letters with paths on Windows.

Changes in version 1.3.0 (2010-01-02)

• Added argument 'max' to Arguments$getIndices().
• Added Arguments$getInstanceOf(...).
• Now Arguments$getWritablePath() and Arguments$getWritablePathname() throws an error is an NA file/directory is specified.
• Now Arguments$getReadablePath() and Arguments$getReadablePathname() throws an error is an NA file/directory is specified, unless 'mustExist' is FALSE.
• Moved private GenericSummary from aroma.core to R.utils.
• ROBUSTNESS: Now getParent(), getAbsolutePath() and getRelativePath() returns a (character) NA if the input is NA.
• ROBUSTNESS: Any NA arguments in '...' to filePath(...) would be parsed as "NA" resulting in paths such as "NA/foo/NA" (just as file.path() does it). Now a (character) NA is returned.
• BUG FIX: The example(GString) code escaped a backslash incorrectly.
• BUG FIX: Arguments$getCharacters(s) would return a *logical* instead of a *character* vector if 's' contained all NAs.
• BUG FIX: Now isFile(NA) and isDirectory(NA) return FALSE. Before it gave an unexpected error.

Changes in version 1.2.6 (2009-12-19)

• Added argument envir = new.env() to loadToEnv().

Changes in version 1.2.5 (2009-11-20)

• If 'x' is a logical vector, Arguments$getIndices(x) will now return the same as if x <- which(x).

Changes in version 1.2.4 (2009-10-30)

• ROBUSTIFICATION: Lowered the risk for saveObject() to leave an incomplete file due to say power failures etc. This is done by first writing to a temporary file, which is then renamed. If the temporary file already exists, an exception is thrown.
• ROBUSTIFICATION: Now Arguments$getWritablePathname(path) validates that there is enough file permissions so that a file can be created in the 'path' directory.
• CLEAN UP: On Windows Vista, createLink() produced a stderr message "You do not have sufficient privilege to perform this operation", when trying to use Windows 'mklink' command. Those message are now silenced.

Changes in version 1.2.3 (2009-10-20)

• Added findSourceTraceback(), which finds the pathnames of all files currently being source():ed.

Changes in version 1.2.2 (2009-10-16)

• Some cleanup of Rd files to meet the stricter requirements.

Changes in version 1.2.1 (2009-10-03)

• Added createLink().
• Added createWindowsShortcut(). Currently it only works on Windows and version of Windows that runs VB scripts.

Changes in version 1.2.0 (2009-09-09)

• Fixed broken/missing Rd links.

Changes in version 1.1.9 (2009-06-29)

• Added argument 'useNames = FALSE' to getCharacters() of Arguments. For forgotten reasons, before (the default now) 'names' attributes were always dropped. Now they can be kept, if wanted.
• Added dimNA<-().

Changes in version 1.1.8 (2009-06-07)

• BUG FIX: getParent(..., depth = 0) gave an error, instead of returning the input path.

Changes in version 1.1.7 (2009-05-30)

• BUG FIX: Argument 'dThreshold' of less() for Verbose had to be named in order to be mapped.

Changes in version 1.1.6 (2009-05-19)

• UPDATE: Now getEnvironment(), getRegularExpression(), and getReadablePathname() give clearer error messages if more the input contains more than one element.
• Now Arguments$getWritablePathname() better explains why a file cannot be opened for creation/modification due to wrong file permissions.

Changes in version 1.1.5 (2009-05-16)

• Changed argument 'asMode' for Arguments$getNumerics() to default to NULL instead of "numeric". This will case the method to return integer if the input is integer, and double if the input is double. The previous default was alway returning doubles, cf. notes on common misconception of how as.numeric() works. In the case when the input is neither integer or double, the default is to coerce to doubles.

Changes in version 1.1.4 (2009-04-04)

• Now getReadablePathname(..., mustExist = TRUE) of Arguments reports also the working directory if the a relative pathname is missing.
• BUG FIX: getReadablePathname(..., mustExist = TRUE) of Arguments gave an internal error if the pathname was in the current directory and did not exist.

Changes in version 1.1.3 (2009-01-12)

• Added isPackageInstalled().
• FIXUP: There were some Rd warnings with the new R v2.9.0.

Changes in version 1.1.2 (2008-12-27)

• Now getReadablePathname(..., mustExist = TRUE) and getWritablePathname(..., mkdirs = FALSE) of Arguments report which of the parent directories exists when the requested pathname is not found. This will help troubleshooting missing pathnames.
• Added removeDirectory() for a convenient and safe way to remove directories.
• Added argument 'useNames' to insert(), which is now aware of names of the input object.
• Added subplots() originating from (obsolete) R.graphics.

Changes in version 1.1.1 (2008-12-03)

• Now getReadablePathname() and getWritablePathname() of Arguments, and sourceTo() use the more trusted fileAccess() instead of file.access() of 'base'. This will hopefully solve some problems where these methods incorrectly gives an error reporting lack of file permissions; this could happen when some OSs mounted to other external file systems.
• Added fileAccess() which is intended to give tries harder than file.access() to infer file permissions.
• STABILITY: Added balance and sanity checks for exit() of Verbose.
• Now gzip() and gunzip() removes the partially written output file if the process is interrupted.
• BUG FIX: readWindowsShortcut() would not work with some Windows shortcut files linking to a Windows network file system and generated on Windows Vista. Their "flags" in the file headers had more than the 8 known bits, which was reported as a file format error. Although we don't know what these unknown bits are for, we now accept them quitely accepted so at least the known part of the file format is returned.
• BUG FIX: filePath("\\\\shared/foo") would return "\\shared/foo".

Changes in version 1.1.0 (2008-10-24)

• Now sourceDirectory() also searches for source files with extensions *.r, *.q, *.s, and *.S, cf. R manual 'Writing R Extensions'.

Changes in version 1.0.9 (2008-10-17)

• BUG FIX: commandArgs() would 'Error in !attr(args, "isEnvVars") : invalid argument type' if both arguments excludeReserved = TRUE and excludeEnvVars = TRUE were used.

Changes in version 1.0.8 (2008-10-16)

• Now devDone(which = 1) does nothing. Before it gave an error.
• BUG FIX: Argument 'type' of devNew() did not take function:s.

Changes in version 1.0.7 (2008-09-20)

• Added mapToIntervals(), inAnyInterval(), and mergeIntervals().

Changes in version 1.0.6 (2008-09-08)

• Now devNew() filters out arguments 'file' and 'filename' if the device is interactive.

Changes in version 1.0.5 (2008-08-04)

• Now commandArgs(...) pass '...' to base::commandArgs() making it fully backward compatible. It is also updated to recognize all R command line options as of R v2.7.1 and R v2.8.0 devel.

Changes in version 1.0.4 (2008-08-01)

• Now sourceDirectory() is guaranteed to source directories and files in lexicographic order.
• Added countLines() for counting number of lines in a text file.
• Added several functions for extending the current functions dealing with devices. All added functions can address a device by a label in addition to the standard device index. The devGetLabel() and devSetLabel() gets and sets the label of a give device. devList() lists the indices of existing device named by their labels, cf. dev.list(). The functions devSet() and devOff() work like dev.set() and dev.off() but accept labels as well. Furthermore, devSet(idx) will open a device with index 'idx' if it does not exists, and devSet(label) a device with that label if not already opened. The devIsOpen() checks if a device is open or not. The devDone() function calls devOff() except for screen devices.

Changes in version 1.0.3 (2008-07-10)

• Added readBinFragments() and writeBinFragments() to read and write binary data scattered across a connection or a file. These methods moved from the R.huge package.
• Added intervalsToSeq(), which is bijective to seqToIntervals().
• Added whichVector(), which is almost twice as fast which() for logical vectors, especially when there are no missing values.
• IMPROVEMENT: Major speed up of seqToIntervals().
• Added gzip().
• Renamed inst/HISTORY to inst/NEWS according to new R standards.
• CLEAN UP: as.character() for 'hexmode' is only added if missing.
• BETA: Added (for now internal) toAsciiRegExprPattern().

Changes in version 1.0.2 (2008-03-31)

• BUG FIX: If 'x' in insert(x, ...) had zero length, an "Error in from:to : NA/NaN argument" was thrown.

Changes in version 1.0.1 (2008-03-06)

• BUG FIX: Regular expression pattern 'a-Z' is illegal on (at least) some locale, e.g. 'C' (where 'A-z' works). The only way to specify the ASCII alphabet is to list all characters explicitly, which we now do in all methods of the package. See the r-devel thread "invalid regular expression '[a-Z]'" on 2008-03-05 for details.

Changes in version 1.0.0 (2008-02-26)

• Added touchFile() for updating the timestamp of a file.
• Added colClasses() for creating "colClasses" vectors.
• Added isPackageLoaded().
• The default filename for eps() had extension *.ps not *.eps.
• Cleaned out empty sections from the Rd help pages.
• Now the '...' arguments to Arguments$getVerbose() are passed to the constructor of Verbose. This allows constructs such as Arguments$getVerbose(-10, timestamp = TRUE).
• BUG FIX: When argument 'values' of insert() was a non-list its values were placed in a single-element list even when 'ats' contained more than one element. Should have been as.list() in those cases.

Changes in version 0.9.8 (2007-11-26)

• Added copyFile() which safely copies a file by copying to a temporary file, which is then renamed.
• Added isEof() for connections to test for "End of File".
• Added reassignInPackage().
• Added dataFrame(), which allocated a data frame of given size and column classes.
• BUG FIX: writeRaw() of MultiVerbose returned a list of logicals. Now it returns TRUE (invisibly).

Changes in version 0.9.7 (2007-09-17)

• BUG FIX/WORKAROUND: moveInSearchPath() would make the package environment loose the 'path' attribute, which is for instance is needed by packageDescription(). This would in turn cause sessionInfo() to throw an error. Now moveInSearchPath() makes sure to set all attributes on a moved package environment to what it used to be.

Changes in version 0.9.6 (2007-08-29)

• Made documentation for saveObject() and loadObject() public.
• Now the startup message when loading the package is generated with packageStartupMessage() so that it can be suppressed.
• Added flush() to TextStatusBar. Added flush() to example(TextStatusBar) so it displays correctly on Rgui on Windows.
• Added bunzip2(), cf. gunzip().
• Added argument 'remove' to gunzip().
• BUG FIX: There was a typo in readWindowsShortcut() causing field 'iconFilename' to potentially be invalid. Thanks Tony Plate for reporting this.

Changes in version 0.9.5 (2007-06-09)

• Updated code to pass the more strict R CMD check R v2.6.0.
• BUG FIX: Used omit.na() instead of na.omit() in static method parseDebian() of System.

Changes in version 0.9.4 (2007-05-10)

• BUG FIX: readTable() tried to access base::read.table() but that was moved to 'utils' as of R v2.5.0.

Changes in version 0.9.3 (2007-05-09)

• BUG FIX: Using the R v2.4.x build of R.utils in R v2.5.0 gives "Error in parse.default(text = src) : 4 arguments passed to 'parse' which requires 6". This is because the internal call in base::parse() use different sets of arguments in R v2.4.1 and R v2.5.0. The fix was to dynamically assign patch.default() when the package is loaded.

Changes in version 0.9.2 (2007-04-26)

• Added trial version of a MultiVerbose class. With this class it is possible to write verbose output via multiple Verbose objects through one MultiVerbose object, e.g. writing to standard output and to log file at the same time.

Changes in version 0.9.1 (2007-04-12)

• BUG FIX: findGhostscript() would give error "paste(path0, collapse = ", ") : object "path0" not found" on Windows if Ghostscript was not found. This error was caught by CRAN. These problems have not been detected locally where Ghostscript is installed.

Changes in version 0.9.0 (2007-04-11)

• BUG FIX: findGhostscript() of System would give error on "invalid subscript type" if non of the paths to be searched exist. This error was caught by CRAN.

Changes in version 0.8.9 (2007-04-07)

• Removed never needed require(R.io) in openBrowser() for System.

Changes in version 0.8.8 (2007-04-03)

• Added saveObject() and loadObject().
• Removed the warning in getRelativePath() about "Cannot infer relative pathname, because the two pathnames are not refering to the same root/device". The warning was more confusing than helpful.
• BUG FIX: getAbsolutePath("C:/foo/", expandTilde = TRUE) would return "C://foo" and not "C:/foo". Now the method also replace all multiple occurances of slashes with a single one. This bug cause getRelativePath("C:/foo", "C:/") to return the wrong thing.
• BUG FIX: toCamelCase(toCamelCase(s)) would not be equal to toCamelCase(s), but instead result in all lower case letters.
• BUG FIX: Default value of argument 'format' of timestamp() was invalid.

Changes in version 0.8.7 (2007-03-24)

• Added moveInSearchPath() to reshuffle the search path. Useful to change the order of packages after they have loaded.
• Added toCamelCase() to convert strings.
• Added loadToEnv() for loading saved data to a new environment.
• The warning message on "cannot refer relative pathname" for getRelativePath() didn't paste the path resulting in a funny looking warning.

Changes in version 0.8.6 (2007-02-27)

• An R.utils (v0.8.4) modified .Last() function saved in .RData from previous R sessions will be updated with the new modifactions according to R.utils v0.8.5.

Changes in version 0.8.5 (2007-02-26)

• Added argument 'depth' to getParent().
• BUG FIX: Added tryCatch() and explicit check for finalizeSession(). Otherwise if, under special circumstance, one might get the error 'Error in .Last() : could not find function "finalizeSession"' when trying to quit R with quit(). Thanks Elizabeth Purdum at UC Berkeley for reporting this.
• When running R v2.5.0, Sys.getenv() is used instead of deprecated Sys.putenv().

Changes in version 0.8.4 (2007-01-10)

• Now System$findGhostscript() searches all 'Program Files' directories too, if on Windows.

Changes in version 0.8.3 (2006-11-10)

• Added arrayIndex() to get the multi-dimensional index of an array from a one-dimensional index.

Changes in version 0.8.2 (2006-10-05)

• Added popMessage() to TextStatusBar. See example().
• Added argument 'modifiedOnly' to sourceTo() so that a file is only sourced if it has been modified since the last call. Note that this argument is passed on by sourceDirectory() too.

Changes in version 0.8.1 (2006-09-16)

• BUG FIX: sourceDirectory(..., onError = "error") would quietly ignore errors in source().
• Added methods more() and less() to the Verbose class.

Changes in version 0.8.0 (2006-08-21)

• Added isOpen() to check if there is another connection opened to a specific file.
• pushState() of Verbose generated an unnecessary warning due to a typo.

Changes in version 0.7.9 (2006-07-17)

• The capture() method in Verbose modified a text connection while it was still open; from R v2.4.0 this is not allowed. Thanks Brian Ripley for pointing this out.

Changes in version 0.7.8 (2006-05-22)

• Added the TextStatusBar class.

Changes in version 0.7.7 (2006-03-30)

• The method list in the class-overview help page was missing for several classes.
• Added as.double() to Verbose.
• saveAnywhere() of Settings now returns (invisibly) the pathname where the settings were saved.

Changes in version 0.7.6 (2006-02-15)

• Since the png2() and jpeg2() devices are in this package, the eps() device from R.graphics has been moved here for consistency.

Changes in version 0.7.5 (2006-02-09)

• as.character.hexmode() is available in R v2.3.0 and forward. Thus, the method is only added by this package for pre-R v2.3.0.

Changes in version 0.7.4 (2005-12-23)

• Updated getHostname() and getUsername() in System to first try to find the details using Sys.info(). After that system environment variable and so on are checked.
• Added argument 'expandTilde = FALSE' to getAbsolutePath() so that tildes (~) are expanded to there corresponding path.
• Now relative paths handle tildes too.
• Added optional automatic timestamping for the Verbose class. This is useful for Verbose objects writing to log files.
• BUG FIX: Added protection against infinite loops in isFile(), where relative path is the same as the absolute path.

Changes in version 0.7.3 (2005-11-24)

• Added extract() for arrays, amtrices and vectors.

Changes in version 0.7.2 (2005-11-22)

• BUG FIX: filePath(..., expandLinks = "any") would return the relative link instead of the network pathname, even if there were no local pathname.
• BUG FIX: Now using scan() instead of readLines() to parse header. This way the header can now also be quoted.
• BUG FIX: Missing object 'ndim' in wrap(); should be 'ndims'.
• BUG FIX: Sequences of length one was given as intervals by seqToHumanReadable(), e.g. 10-10.
• Static Arguments class: Added getReadablePathnames(). Now getCharacter() accepts vectors of length zero or one only.

Changes in version 0.7.1 (2005-11-12)

• Added functions wrap() and unwrap() to reshape arrays (and matrices) by joining and splitting dimensions, respectively, and optionally by permuting dimensions too. This is for instance useful when storing multidimensional arrays in tabular formats.

Changes in version 0.7.0 (2005-11-10)

• Added trial version of readTable(). It extends the read.table() in two major ways. First it allows you to specify colClasses as a column name to column class map. Second, it allows you you to read any subset of rows, which substantially improves speed and decrease memory usage. Use readTableIndex() to create a look-up index for rows of interest.
• Added seqToIntervals(), which finds all contigous (integer) regions in a set of integers, cf. seqToHumanReadable().
• BUG FIX: isDirectory() on a file would result in an infinite recursive loop to itself.
• Added inifite recursive call detection to listDirectory().
• Now sourceDirectory() returns the source files invisibly.
• Gathered files recursively in sourceDirectory(), but it was not needed since sourceDirectory() itself is recursive.

Changes in version 0.6.3 (2005-10-26)

• Renamed argument 'overwrite' in getWritablePathname() in Arguments to 'mustNotExist'. Renamed all 'mustExists' to 'mustExist' in all methods of class Arguments.

Changes in version 0.6.2 (2005-10-20)

• Update loadAnywhere() for the Settings clas so that it works on objects too for which the default basename is the static basename.
• BUG FIX: getLeaves() would give an error for empty Options objects.
• BUG FIX: filePath(".") would return "".
• BUG FIX: filePath("//shared/foo") would return "/shared/foo".

Changes in version 0.6.1 (2005-10-17)

• BUG FIX: readWindowsShortcut() failed on some Network-only links.

Changes in version 0.6.0 (2005-09-24)

• Now filePath() removes repeated '/' and '\\', except for network files such as \\server\foo\bar.
• BUG FIX: Argument 'pager' of displayCode() did not support functions.
• Updated Options class to make it easier for subclasses to retrieve options more easy. This was needed for the future ROptions class to map to options().
• BUG FIX: System$openBrowser() was broken, because startsWith() and endsWith() were missing.
• Added trial version of jpeg2() and png2().

Changes in version 0.5.9 (2005-09-18)

• Added static function findGraphicsDevice() to System. The methods search for a working device among a list of potential ones. This is for instance useful if it is known in advance that the PNG device is available (then the bitmap() device is an option).

Changes in version 0.5.8 (2005-09-06)

• Added argument asGString = TRUE to the Verbose constructor.
• Added remove() to FileProgressBar.
• Replace argument 'gString' of getCharacters() to 'asGString', cf. Verbose class.
• Now Arguments$getReadablePathname() follows Windows shortcut files.
• BUG FIX: displayCode() was interpreting the code as GString:s.
• Now making use of relative pathnames internally in copyDirectory(). Sometimes relative pathnames will work when the absolute ones does not (because of missing file access rights).
• BUG FIX: copyDirectory() would not return copied files if recursive == TRUE.
• BUG FIX: Smart comments preceeded by TABs would not be recognized.
• GString's parse() could return warning because it was incorrectly assumed that regexpr() did not return more than one value.

Changes in version 0.5.7 (2005-08-12)

• Function filePath() returns NULL, if no arguments or only NULL arguments are passed to it.

Changes in version 0.5.6 (2005-08-02)

• BUG FIX: splitByPattern() tried to access non-existing class Argument.
• Arguments' getReadablePathname() no longer returns the absolute pathname by default. This is because on some systems the relative pathname can be queried wheras the absolute one may not be access due to missing file permissions.
• isFile() and isDirectory() is now comparing to current working directory if no file information is available (due to missing file permissions); assumes that the current working directory always exists.
• getParent() now returns NULL instead of "".
• Added argument 'caseSensitive' to getRelativePath().
• isAbsolutePath(NULL) returns FALSE.
• mkdirs() tries to create directory with relative path if absolute path fails. This sometimes works when the file permission are missing.
• Added argument 'code' to displayCode(). The function now also used file.show() to display the code.
• Added isUrl() and hasUrlProtocol().
• Added copyDirectory().
• Added getEnvironment() and getRegularExpression() to Arguments.

Changes in version 0.5.5 (2005-07-21)

• BUG FIX: Example illustrating Windows Shortcut methods tried to access 'HISTORY.lnk' and not 'HISTORY.LNK', which would fail on Unix.
• BUG FIX: getCharacters() would not coerce Object:s correctly.
• Now sourceDirectory() does 'chdir = FALSE' instead of 'chdir = FALSE'.
• Now mkdirs() has an internal check for infinit-recursive calls.

Changes in version 0.5.4 (2005-07-19)

• BUG FIX: If there are no files to source in a directory, and verbose is active, basefile() on NULL was called generating an error.
• BUG FIX: sourceTo(..., chdir = TRUE) would generate an error. This would for instance make sourceDirectory() useless.

Changes in version 0.5.3 (2005-07-18)

• Added resetWarnings() and splitByPattern().
• Added summary() to class Verbose and a corresponding VComments tag.
• Arguments$getCharacters() returned attribute 'names' too. Removed.
• sourceDirectory() is no longer catching warnings in tryCatch(), because otherwise it will interrupt the call as if the warnings were errors.

Changes in version 0.5.2 (2005-06-27)

• Added getRelativePath().
• Added LComments which is a VComments class with different defaults.
• Made SmartComments classes and methods non-static.
• Escaping double quotes in VComments messages.

Changes in version 0.5.1 (2005-06-23)

• Package passes R CMD check for R v2.1.0.
• Added trial version of SmartComments and subclass VComments where the latter are R comments with a special format generating verbose output if source is first pre-processed by compile() method. If not preprocessed, they are just regular comments, adding no overhead in processing speed. I can imagine to add, say, AComments that Asserts conditions at given test points in code; when code works, just source code without pre-processing them!
• Now it is possible to set the default verbose level used by all Verbose methods if not explicitly given.
• Now all Verbose messages are GString:ed. This makes VComments slim.

Changes in version 0.5.0 (2005-06-19)

• Package passes R CMD check for R v2.1.0.
• Now commandArgs() recognizes environment variables.
• Added attachLocally().
• When package is loaded, .Last() is modified so that 'onSessionExit' hooks are called when R finishes.
• Added onSessionExit(), finalizeSession() and addFinalizerToLast().
• Added callHooks().
• Added the NullVerbose() class.
• Moved (de-)capitalize() and seqToHumanReadable() from R.basic to here.
• Added new GString class.
• Added the Assert class.
• Moved the System class from R.lang to this package. System was also cleaned out from several never used methods and fields.
• Added filePath() together with file methods isFile(), isDirectory(), isAbsolutePath(), mkdirs(), lastModified(), and toUrl().
• Moved sourceTo() from R.io to this package.
• Moved doCall() from R.basic to this package.
• Created the Options class.
• Added several methods to the Verbose class. Also added support for indentation by enter() and exit() of Verbose.
• Moved the Java and Verbose class from R.matlab to this package. This requires that this package is on CRAN before R.matlab is updated.
• Moved the ProgressBar and FileProgressBar from the R.ui package, which then becomes more or less empty.
• Created.