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$getVector() could produce an error on
“argument is missing, with no default” while trying to signal an
assertion error.
intToHex() and intToOct() would no
longer pad with zero on recent R-devel (to become R 4.2.0)
versions.
useRepos() to use HTTPS instead
of HTTP.R.utils::commandArgs() recognizes new
--no-echo option in R (>= 4.0.0).R.utils::getAbsolutePath("~/../Documents", expandTilde = TRUE)
would adjust for .. before adjusting for ~
resulting in an incorrect path. Thanks to Dean Attali for reporting on
this.wrap() for arrays used a list - not a numeric vector
- to assign dimensions. This would produce an error in R (>=
4.0.0).
withSeed(..., seed = NULL) did not work for R (<
3.0.0).
fileAccess(..., mode = 2) would update
.Random.seed.
fileAccess(path, mode = 2) could end up in an
endless loop if the path folder contained all files of
a, b, ..., z, A, B, ... Z.
sourceDirectory() did not respect argument
modifiedOnly. Thanks to Anton Krasikov for the report and
the fix.
createLink() could produce a spurious warning on MS
Windows.
Previously defunct arrayIndex(),
evalWithTimeout(), and resetWarnings() have
been removed.
Assert$inherits() is defunct - use
Assert$inheritsFrom() instead.
Argument substitute of withCapture() is
defunct - use replace instead.
createWindowsShortcut() gained argument
mustWork.
When createLink() fails, the error message now also
report on the methods attempted.
displayCode(), commandArgs() and
toCamelCase() used && and
|| on logical vectors that might not necessarily be of
length one.
createWindowsShortcut() and
createLink(method="windows-shortcut") failed to create
Windows Shortcut links because
filePath(..., expandLinks = "any") did not expand Windows
Shortcut links. This bug was introduced in R.utils
1.34.0 (2014-10-07) due to a cut’n’paste mistake.
nullcon() that returns a (binary) connection to
the nullfile().readTable() no longer runs the garbage collector - was
done so implicitly through an internal system.time() call
without using gcFirst = FALSE.Rscript -e "R.utils::cmdArg(a=42L)" -a:=1:3 would set
a to NA_integer_.evalWithTimeout() is now defunct. Use
withTimeout() instead.
arrayIndex() is now defunct. Use
base::arrayInd() instead.
Assert$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.
withCapture(x <- 1L) would drop integer suffix
L from the output when run in non-interactive mode.CLEANUP: Removed operator %<-% which was defunct
since 2.4.0. An alternative is to use ditto of the
future package.
CLEANUP: Made resetWarnings() defunct.
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.
%<-% in favor of
%<-% in the future package.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. $[tolower]{y}. Thanks to Andre Mikulec for reporting
on this.
downloadFile() via
https://<user>:<pwd>@<domain>/ gave an
error.
resetWarnings().Added compressPDF() to compress PDFs.
If, and only if, path is an existing directory, then
copyFile(pathname, path) copies file pathname
to the path directory (previously destination always had to
be a file). Analogously, renameFile(pathname, path) moves
file pathname (not a directory though) to destination
directory path.
CLEANUP: createLink(..., skip = TRUE) would give a
false warning if a proper link already existed and the target was
elsewhere than the current directory.
INCONSISTENCY: captureOutput(..., collapse = "\n")
did not drop newline of the last line as
captureOutput(..., collapse = "\r") and any other
collapse != "\n" strings. Added package tests.
captureOutput(..., file = "foo.txt") gave an
error.Arguments$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.nchar(..., type = "chars") is used
internally for all file and directory names.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%.
Added URL and BugReports fields to DESCRIPTION.
Submitted to CRAN.
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.path if file specifies an absolute
pathname.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) }).
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.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.
use("<repos>::<pkg>") will detect when
a repository is unknown and give an informative error message on how to
update option repos.Added assignment operator %<-% for delayed
assignments.
Added option evalCapture/newline.
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.
:: in calls where possible.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.toCamelCase(character(0L)) gave an error.str() and summary() for Verbose did not
acknowledge argument level.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.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.
cmdArgsCall() for easy calling of functions from
the command line,
e.g. Rscript -e R.utils::cmdArgsCall(rnorm) n=4.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.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().Now Arguments$getCharacters() preserves attributes.
Also, made argument useNames defaults to TRUE.
Added [() for GenericSummary.
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().dimNA<-() was referring to
files rather than to elements.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:/".
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:/".
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 argument temporary to
gzip()/gunzip().
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.downloadFile("https://...") did not work if
username or password was NULL.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().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).
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.
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$unmapDriveOnWindows() did not handle paths with a
lower case Windows drive letter. Oddly, it is only now that we have
received an single report (on a Windows 7 system) that such
getwd() may return such drive letters,
e.g. c:/path/ instead of C:/path/.
BUG FIX: evaluate(..., where = "parent") for GString
would result in an endless loop.
BUG FIX: displayCode(code) incorrectly processed
code as GString:s.
version to
isPackageLoaded() would give “Error: ’manglePackageName` is
defunct.” in recent versions of
Now .Last.lib is exported.
Bumped up package dependencies.
startupMessage() of
R.oo.R CMD check for R devel no longer gives a NOTE on
attach().CLEANUP: R CMD check no longer warns on global
assignments.
BUG FIX:
Arguments$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.
CLEANUP: Dropped lapply() for MultiVerbose.
Added as.list() to MultiVerbose.
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.
gzip()/gunzip()/bunzip2()
creates the directory of destination pathname destfile, iff
missing.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.
Arguments$getReadablePath(..., mustExist = FALSE) did not
work.Now insert() silently expands values to
be of the same length as ats, iff
length(values) == 1.
toCamelCase(..., preserveSameCase = TRUE) makes
all-upper-case words into same-case words,
e.g. toCamelCase("HTML View", preserveSameCase = TRUE)
outputs "htmlView" (not "hTMLView"). Added
system tests for toCamelCase().
moveInSearchPath() no longer
calls .Internal(detach(...)) but instead
base::detach() in such a way that neither detach hooks nor
.Last.lib() are called.Now createLink() also supports targets with
~ in the path.
ROBUSTNESS: createLink(target = "C:/") would try to
create a link with name C:, which is not valid resulting is
the somewhat confusing error on “cannot symlink ‘S:’ to ‘S:’, reason
‘Access is denied’”. Now it instead throws “Cannot infer a valid link
name from argument ‘target’: C:/”.
ROBUSTNESS/BUG FIX: On Windows, it could happen that
createLink() would generate a zero-size link file that did
not link to the target as a result of a failed
file.symlink(). This is now tested for such that if an
invalid link file was created, it is removed again.
CLEANUP: Dropped the graphics device related functions that were moved to R.devices.
System$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.toBMP() and toTIFF().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.
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.
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.R CMD check NOTE that would show up in
R v2.15.0 devel.field to devEval().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.devEval("jpg", ...) is recognized as
devEval("jpeg", ...).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.
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().
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.evalWithTimeout().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().
range in
Arguments methods.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().devNew() filters out arguments file
and filename, if the device is interactive.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 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.
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.
BUG FIX: sourceDirectory(..., onError = "error")
would quietly ignore errors in source().
Added methods more() and less() to the
Verbose class.
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.
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.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.