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$getVector()
could produce an error on "argument is
missing, with no default" while trying to signal an assertion
error.
intToHex()
and intToOct()
would no longer pad with zero on
recent R-devel (to become R 4.2.0) versions.
useRepos()
to use HTTPS instead of HTTP.R.utils::commandArgs()
recognizes new --no-echo
option in R (>=
4.0.0).R.utils::getAbsolutePath("~/../Documents", expandTilde = TRUE)
would adjust for ..
before adjusting for ~
resulting in an
incorrect path. Thanks to Dean Attali for reporting on this.wrap()
for arrays used a list - not a numeric vector - to assign
dimensions. This would produce an error in R (>= 4.0.0).
withSeed(..., seed = NULL)
did not work for R (< 3.0.0).
fileAccess(..., mode = 2)
would update .Random.seed
.
fileAccess(path, mode = 2)
could end up in an endless loop if the
path
folder contained all files of a, b, ..., z, A, B, ... Z
.
sourceDirectory()
did not respect argument modifiedOnly
.
Thanks to Anton Krasikov for the report and the fix.
createLink()
could produce a spurious warning on MS Windows.
Previously defunct arrayIndex()
, evalWithTimeout()
, and
resetWarnings()
have been removed.
Assert$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.
For backward compatibility, getAbsolutePath()
,
getRelativePath()
, isAbsolutePath()
, isFile()
, and
isDirectory()
treats an empty vector of path/pathnames equal to
"."
. However, in a future version, empty results will returned
by these too.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 a
list, not a
integer"
) or gives an error (with "Error: not a weak reference")
under certain conditions when a registered finalizer tried to
reload R.oo if it was unloaded. This occurred only on R prior to R
3.0.2 patched (2014-02-21 r65057). Also, the methods package
needs to be attached, so it is still not clear what is the true
cause of the bug. In R.oo (>= 1.18.0) this bug is avoided.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$unmapDriveOnWindows()
did
not handle paths with a lower case Windows drive letter. Oddly, it
is only now that we have received an single report (on a Windows 7
system) that such getwd()
may return such drive letters,
e.g. c:/path/
instead of C:/path/
.
BUG FIX: evaluate(..., where = "parent")
for GString would result
in an endless loop.
BUG FIX: displayCode(code)
incorrectly processed code
as
GString:s.
version
to isPackageLoaded()
would
give "Error: 'manglePackageName` is defunct." in recent versions of
R. Thanks to Brian Ripley (R core) for reporting on this.Now .Last.lib
is exported.
Bumped up package dependencies.
startupMessage()
of R.oo.R CMD check
for R devel no longer gives a NOTE on attach()
.CLEANUP: R CMD check
no longer warns on global assignments.
BUG FIX: Arguments$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 in
header` 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.
Any scripts or data that you put into this service are public.
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.