NEWS.md
HOME folder was a subfolder directly under the drive, e.g. HOME=C:\msys64.use().help("parse.SmartComments").warnings() for Verbose, and the corresponding generic function, has been deprecated in favor of the printWarnings().Documented the limitation that withTimeout() may fail to detect the timeout error if the language is temporarily switched during evaluation.
Updated moved and broken URLs in help pages.
filePath() could produce Error in if (components[pos] == ".." && components[pos - 1L] != "..") { : missing value where TRUE/FALSE needed when there were too many .. components in the specified path, e.g. filePath("C:/foo/../bar/../.."). Now it returns the maximum pruned path, e.g. "C:/..".
withTimeout() did not return NULL on timeouts when onTimeout was "warning" or "silent".
parseRepos() would produce "Error in get(".read_repositories", envir = ns) : object '.read_repositories' not found" in R-devel (>= rev 83148).
tempvar().Remove defunct Asserts$inherits() and S3 generic inherits(). Use Asserts$inheritsFrom() instead.
Remove defunct argument substitute from withCapture(). Use argument replace instead.
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.
queryRCmdCheck() failed to identify when R CMD check was running test scripts located in a subfolder under tests/, e.g. tests/testthat/.
gcDLLs() produced a “In sprintf(…) : argument not used by format” warning when giving an error message on what DLLs it failed to unload.
Arguments$getVector() could produce an error on “argument is missing, with no default” while trying to signal an assertion error.
intToHex() and intToOct() would no longer pad with zero on recent R-devel (to become R 4.2.0) versions.
useRepos() to use HTTPS instead of HTTP.R.utils::commandArgs() recognizes new --no-echo option in R (>= 4.0.0).wrap() for arrays used a list - not a numeric vector - to assign dimensions. This would produce an error in R (>= 4.0.0).
withSeed(..., seed = NULL) did not work for R (< 3.0.0).
fileAccess(..., mode = 2) would update .Random.seed.
fileAccess(path, mode = 2) could end up in an endless loop if the path folder contained all files of a, b, ..., z, A, B, ... Z.
sourceDirectory() did not respect argument modifiedOnly. Thanks to Anton Krasikov for the report and the fix.
createLink() could produce a spurious warning on MS Windows.
Previously defunct arrayIndex(), evalWithTimeout(), and resetWarnings() have been removed.
Assert$inherits() is defunct - use Assert$inheritsFrom() instead.
Argument substitute of withCapture() is defunct - use replace instead.
createWindowsShortcut() gained argument mustWork.
When createLink() fails, the error message now also report on the methods attempted.
displayCode(), commandArgs() and toCamelCase() used && and || on logical vectors that might not necessarily be of length one.
createWindowsShortcut() and createLink(method="windows-shortcut") failed to create Windows Shortcut links because filePath(..., expandLinks = "any") did not expand Windows Shortcut links. This bug was introduced in R.utils 1.34.0 (2014-10-07) due to a cut’n’paste mistake.
nullcon() that returns a (binary) connection to the nullfile().readTable() no longer runs the garbage collector - was done so implicitly through an internal system.time() call without using gcFirst = FALSE.evalWithTimeout() is now defunct. Use withTimeout() instead.
arrayIndex() is now defunct. Use base::arrayInd() instead.
Assert$inherits() is deprecated - renamed to Assert$inheritsFrom().
Removed deprecated and ignored argument reset of warnings() for Verbose.
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.
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.
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.
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.
CLEANUP: Defunct %<-% in favor of %<-% in the future package.
CLEANUP: Deprecated arrayIndex(). arrayInd() in base (>= 2.11.0) provides the same functionality.
CODE REFACTORING:
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.
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.
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.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. $[tolower]{y}. Thanks to Andre Mikulec for reporting on this.
downloadFile() via https://<user>:<pwd>@<domain>/ gave an error.
Added compressPDF() to compress PDFs.
If, and only if, path is an existing directory, then copyFile(pathname, path) copies file pathname to the path directory (previously destination always had to be a file). Analogously, renameFile(pathname, path) moves file pathname (not a directory though) to destination directory path.
CLEANUP: createLink(..., skip = TRUE) would give a false warning if a proper link already existed and the target was elsewhere than the current directory.
INCONSISTENCY: captureOutput(..., collapse = "\n") did not drop newline of the last line as captureOutput(..., collapse = "\r") and any other collapse != "\n" strings. Added package tests.
Arguments$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.toCamelCase() with missing values would give an error in R devel (>= 2015-04-23) due to an update how nchar() handles missing values.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.
help("captureOutput"). Thanks to Mikko Korpela (Issue #4) for reporting on this.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.
ROBUSTNESS: Forgot to declare “default” warnings() as an S3 method.
R.utils::use() without arguments attaches R.utils.
ROBUSTNESS: Package test coverage is 66%.
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.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.
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.
writeDataFrame() - argument col.names = !append. Also, if append = TRUE, header comments are only written if specified. Added package system test for writeDataFrame().getAbsolutePath("/tmp", expandTilde = TRUE) returned "//tmp". This would in turn have implications on getRelativePath(), e.g. getRelativePath("/tmp/a", relativeTo = "/tmp") returned "../../tmp/a".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) }).
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.mkdirs() could return “object ‘res’ not found” error.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.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.
commandArgs() would drop command-line arguments with periods, hyphens, or underscores in their names, e.g. --src_file=x.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.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.egsub() also works with functions, in case it substitutes on the body of the function.help("withTimeout") on the limitations of the function and when it is/is not possible to interrupt a function via timeouts.R_USER to a Cygwin-flavored directory, which causes normalizePath("~") to return a non-existing directory. Thanks Uwe Ligges (CRAN) for reporting on this.filePath("./././././") now returns "." (was ""). Added package system tests for filePath().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.
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).
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 Bioconductor) 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.
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.
newline to evalCapture().substitute to evalCapture() for substituting symbols “on the fly” in the expression before it is evaluated.modifiedOnly to sourceDirectory(), which was previously passed via ... to sourceTo(), and it now defaults to TRUE.use() would not install package dependencies.max.deparse.length to evalCapture().evalCapture() utilizes deparse() to get the source code and acknowledges options deparse.cutoff to control the code wrapping. Previously capture.output(print()) was used.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.detachPackage(), getAbsolutePath(), getRelativePath(), isAbsolutePath(), isDirectory(), isFile(), isOpen(), isPackageInstalled(), touchFile() and toUrl(). Added package system tests for several of them.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.createLink() to work."Error: SET_VECTOR_ELT() can only be applied to alist, not ainteger") 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.cmdArgsCall() for easy calling of functions from the command line, e.g. Rscript -e R.utils::cmdArgsCall(rnorm) n=4.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").
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().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.createLink().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).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").
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.Now argument asGString for Arguments$getCharacters() defaults to getOption("Arguments$getCharacters/args/asGString", TRUE). This makes it possible to disable this feature, even when it is not possible to directly pass that argument. This will also make it possible to set the default to FALSE in the future (instead of TRUE as today).
Added argument inherits to evaluate() for GString. Default is TRUE for backward compatibility.
c() for GenericSummary.Arguments$getNumerics(NA, range = c(0,1)) no longer gives warnings on “no non-missing arguments to min()” etc.System$getMappedDrivesOnWindows() failed to return the proper path for net use mounted drives, iff the path contained spaces.CLEANUP: Removed a few non-used internal objects.
Forgot to declare enterf() for Verbose as an S3 method.
CLEANUP: Some methods had to attach R.utils in the past in order to work properly. These are no longer attaching R.utils: copyDirectory(), createLink(), createWindowsShortcut(), downloadFile(), installPackages(), removeDirectory(), and sourceDirectory().
Bumped up package dependencies.
CLEANUP: Now explicitly importing only what is needed in NAMESPACE.
CLEANUP: Dropped obsolete autoload():s.
ROBUSTNESS: The overriding of getOption() to become a generic function does now call base::getOption() in the default, instead of copy the latter.
Bumped up package dependencies.
Now argument recursive of listDirectory() can also specify the maximum recursive depth, e.g listDirectory(..., recursive = 5L).
Now the R.utils Package object is also available when the package is only loaded (but not attached).
R.methodsS3::appendVarArgs().commandArgs(asValues = TRUE) failed to set the value of the very last argument to TRUE if it was a flag, e.g. R --args --bar. Thanks to Stijn van Dongen at EMBL-EBI in Cambridge/Hinxton, UK for reporting on this.Added use() for easy attaching/loading and automatic installation of packages.
Now isPackageInstalled() suppresses warnings.
CLEANUP: Arguments$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.
inherits() as an S3 method.System$findGhostscript() could still give errors. Completely rewrote how Ghostscripts is searched. On Windows, environment variable GSC is now also searched. Thanks to Brian Ripley for the feedback.System$findGhostscript() would give Error in pathname [sapply(pathname, FUN = isFile)]: invalid subscript type 'list' if no device was found.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:/".
BUG FIX: gunzip() would ignore argument overwrite.
BUG FIX: filePath("C:/foo/..") returned "C:", which should be "C:/".
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.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.
UPDATE: Now gzip()/gunzip() returns the output file (was number of output bytes processed which are now returned as an attribute).
Added isGzipped() for testing whether a file is gzipped or not.
dims of extract() can also be dimension names.Minor speedups by replacing rm() calls with NULL assignments.
SPEEDUP: readTable() no longer calls gc().
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.
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).addFinalizerToLast(), filePath(), patchCode(), readWindowsShellLink(), readWindowsShortcut(), and loadAnywhere() for Settings.capitalize()/decapitalize() would return "NANA" for missing values. Reported by Liviu Andronic.commandArgs(..., adhoc = TRUE) to coerce T and F to logicals TRUE and FALSE. They are now preserved as character string.commandArgs(..., adhoc = TRUE) utilizes utils::type.convert().cmdArg() for retrieving a single command line argument with a default value and type, e.g. n <- cmdArg("n", 42).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().eps for isZero() may also be a character string specifying either "double.eps" or "single.eps".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.
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$unmapDriveOnWindows() did not handle paths with a lower case Windows drive letter. Oddly, it is only now that we have received an single report (on a Windows 7 system) that such getwd() may return such drive letters, e.g. c:/path/ instead of C:/path/.
BUG FIX: evaluate(..., where = "parent") for GString would result in an endless loop.
BUG FIX: displayCode(code) incorrectly processed code as GString:s.
version to isPackageLoaded() would give “Error: ’manglePackageName` is defunct.” in recent versions of
R CMD check for R devel no longer gives a NOTE on attach().CLEANUP: R CMD check no longer warns on global assignments.
BUG FIX: Arguments$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.
queryRCmdCheck() did not detect “tests” evidences when R CMD check was testing multiple architectures.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 correspondingelement inheader` argument to NULL if they were NULL.
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.
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.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.
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$getReadablePathname().
mkdirs(path) could generate a warning if the path was created by another process as a race condition. Now it always checks to see if the directory already exists just before trying to create the directory.Moved Arguments$getFilename() from R.filesets to R.utils. Added Rd help.
ROBUSTNESS: Bumped up package dependencies.
evalWithTimeout() would not reset the time limits after returning. Thanks to Gregory Ryslik at Yale University for reporting on this.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.
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().
moveInSearchPath() no longer calls .Internal(detach(...)) but instead base::detach() in such a way that neither detach hooks nor .Last.lib() are called.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.
CLEANUP: Dropped the graphics device related functions that were moved to R.devices.
System$findGraphicsDevice() no longer tries to create a PNG device using png2(), because that has now moved to R.devices.
Updated package dependencies.
Added systemR() for launching an external R process.
Package no longer loads (via a DESCRIPTION Depends) the R.devices package, because that would cause a circular package dependency. Instead, we’re keeping the graphical device functions here until all reverse dependent packages have been set to explicitly use R.devices.
findFiles(), which orginates from the affxparser package.Now it is possible to have devEval() rename incompletely generated image files, by using argument onIncomplete = "rename". This will simplify troubleshooting. The default is still to remove incomplete files.
ROBUSTNESS: Updated package dependencies.
.onAttach() would try to call getMessage(ex) on an error if there was a problem adding a finalizer, resulting in “no applicable method for ‘getMessage’ applied to an object of class”c(‘simpleError’, ‘error’, ‘condition’)“. Now using ex$message instead.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.
capture() for Verbose uses withVisible() instead of an .Internal(eval.with.vis()) call.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.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(...)$width if neither argument width nor height was given.
System$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).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.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.evalWithTimeout(readline()) does not throw a timeout exception until after readline() returns.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.
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().ROBUSTNESS: Now parse() and as.character() handles “empty” GString:s.
ROBUSTNESS: Now GString() asserts that it only holds one string.
SPEEDUP: Now Arguments$getCharacters(s, asGString = TRUE) is much faster for elements of s that are non-GStrings. For long character vectors the speedup is 100-200x times.
SPEEDUP: Now as.character() and parse() for GString return faster if the string is a plain string without markup etc. This made as.character() about 10-15 times faster.
Added quarts to the list of (possible) devices for devOptions().
BUG FIX: devOptions() assumed that all devices exist on all platforms, causing it to give an error on some.
evalCapture() for evaluating an expression and capturing its deparsed code and/or output.Added toEPS(), toPDF(), toPNG(), and toSVG().
Added devOptions().
Added default width and height values to eps().
Turned png2() and jpeg2() into plain functions without a generic. This is consistent with how eps() is defined.
GENERALIZATION: Now the default width is inferred from devOptions() if needed.
DOCUMENTATION: Added an example to help(devEval).
queryRCmdCheck(), which retrieves the status of R CMD check, iff it is running.dims to extract() for arrays. Also, argument drop was moved to the end.Arguments$getNumerics(c(Inf), disallow = "Inf") would report that it contains NA instead of Inf values.methods of createLink() can be set via option createLink/args/methods.installPackages() for installing R packages by names or URLs. This method was previously in the hbLite.R script of braju.com.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.
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.
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.
.conflicts.OK in order to avoid several warnings when loading package..conflicts.OK is no longer exported, because it would cause other “downstream” packages to generate a WARNING in R CMD check.isReplicated() and replicates() for identifying entries in a vector that are non-unique. Corresponding isSingle() and singles() identifies entries that exists only once.hpaste(..., sep = " ", maxHead = Inf) corresponds to paste(..., sep = " ", collapse = ", "). Added to example.Added hpaste() for human-readable pasting, e.g. "1, 2, 3, ..., 10".
Now argument force of devEval() defaults to getOption("devEval/args/force", TRUE).
Now argument path of devEval() defaults to getOption("devEval/args/path", "figures/").
Now devEval() does a better job of “cleaning up” name and tags.
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.
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.
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.
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.
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.
fixed (not fix) in regexpr() calls.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.
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.
resample(), which contrary to sample() also works when drawing from a single element.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).link argument of createLink() is inferred from the target argument if it is "." (or NULL).Added an example to help(findSourceTraceback).
BUG FIX: Each entry identified by findSourceTraceback() would be duplicated.
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()$exe if it is a file and on Windows, otherwise it relies on file.access().
DOCUMENTATION: Added an example to help(fileAccess).
MISC: Added support for readRdHelp(..., format = "text") in R < 2.10.0.
Added readRdHelp() for locating and reading installed Rd help pages in various formats.
Now downloadFile() supports authentication, if wget is available on the system.
stext(), which previously was in the aroma.core package.Now arrayIndex() returns an integer matrix.
DOCUMENTATION: Now the help of arrayIndex() links to the new arrayInd() in the base package.
getAbsolutePath("//server/dir/") would incorrectly drop the initial double-slashes (//) and return "/server/dir/". Thanks Richard Cotton at Health and Safety Laboratory (HSL), UK, for reporting this.printf(), as a convenient wrapper for cat(sprintf(...)).downloadFile() for safer and more convenient downloads.Now R.utils requires R v2.5.0 (circa 2007) or newer. This is because there was a change in base::parse() from R v2.4.1 and R v2.5.0. See news for R.utils v0.9.3.
Added a NAMESPACE.
Added alpha version of an onGarbageCollect() method.
BUG FIX: findSourceTraceback() stopped working; probably due to some recent updates in base::source().
sourceTo(..., modifiedOnly = FALSE) followed by a sourceTo(..., modifiedOnly = TRUE) will now work as expected. Before you had to do at least one modifiedOnly = TRUE call before for it to work.
sourceTo() no longer gives a warning if there is a missing EOL.
System$mapDriveOnWindows(), System$unmapDriveOnWindows(), and System$getMappedDrivesOnWindows() for associating drive letters with paths on Windows.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$getCharacters(s) would return a logical instead of a character vector if s contained all NAs.
BUG FIX: Now isFile(NA) and isDirectory(NA) return FALSE. Before it gave an unexpected error.
envir = new.env() to loadToEnv().x is a logical vector, Arguments$getIndices(x) will now return the same as if x <- which(x).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$getWritablePathname(path) validates that there is enough file permissions so that a file can be created in the path directory.
CLEAN UP: On Windows Vista, createLink() produced a stderr message “You do not have sufficient privilege to perform this operation”, when trying to use Windows mklink command. Those message are now silenced.
findSourceTraceback(), which finds the pathnames of all files currently being source():ed.Added createLink().
Added createWindowsShortcut(). Currently it only works on Windows and version of Windows that runs VB scripts.
Added argument useNames = FALSE to getCharacters() of Arguments. For forgotten reasons, before (the default now) names attributes were always dropped. Now they can be kept, if wanted.
Added dimNA<-().
getParent(..., depth = 0) gave an error, instead of returning the input path.dThreshold of less() for Verbose had to be named in order to be mapped.UPDATE: Now getEnvironment(), getRegularExpression(), and getReadablePathname() give clearer error messages if more the input contains more than one element.
Now Arguments$getWritablePathname() better explains why a file cannot be opened for creation/modification due to wrong file permissions.
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.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.
Added isPackageInstalled().
FIXUP: There were some Rd warnings with the new R v2.9.0.
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.
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".
sourceDirectory() also searches for source files with extensions *.r, *.q, *.s, and *.S, cf. R manual ‘Writing R Extensions’.commandArgs() gave “Error in !attr(args,”isEnvVars”) : invalid argument type” if both arguments excludeReserved = TRUE and excludeEnvVars = TRUE were used.Now devDone(which = 1) does nothing. Before it gave an error.
BUG FIX: Argument type of devNew() did not take function:s.
mapToIntervals(), inAnyInterval(), and mergeIntervals().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.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.
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().
x in insert(x, ...) had zero length, an “Error in from:to : NA/NaN argument” was thrown.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.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.
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).
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.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 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.
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.
readTable() tried to access base::read.table() but that was moved to utils as of R v2.5.0.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.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.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.require(R.io) in openBrowser() for System.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.
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.
.Last() function saved in .RData from previous R sessions will be updated with the new modifactions according to R.utils v0.8.5.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().
System$findGhostscript() searches all Program Files directories too, if on Windows.arrayIndex() to get the multi-dimensional index of an array from a one-dimensional index.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.
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.
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.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.
png2() and jpeg2() devices are in this package, the eps() device from R.graphics has been moved here for consistency.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.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.
extract() for arrays, matrices, and vectors.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.
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.
overwrite in getWritablePathname() in Arguments to mustNotExist. Renamed all mustExists to mustExist in all methods of class Arguments.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".
readWindowsShortcut() failed on some Network-only links.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$openBrowser() was broken, because startsWith() and endsWith() were missing.
Added trial version of jpeg2() and png2().
findGraphicsDevice() to System. The methods search for a working device among a list of potential ones. This is for instance useful if it is known in advance that the PNG device is available (then the bitmap() device is an option).Added argument asGString = TRUE to the Verbose constructor.
Added remove() to FileProgressBar.
Replace argument gString of getCharacters() to asGString, cf. Verbose class.
Now Arguments$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.
filePath() returns NULL, if no arguments or only NULL arguments are passed to it.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.
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.
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.
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.
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.
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.
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.