[Rd] R 4.2.0 is released
peter dalgaard
pd@|gd @end|ng |rom gm@||@com
Fri Apr 22 10:19:36 CEST 2022
The build system rolled up R-4.2.0.tar.gz (codename "Vigorous Calisthenics") this morning.
This is a major update, notably containing extensive rework on the Windows port and its toolchain, including UTF-8 support.
The list below details the changes in this release.
You can get the source code from
https://cran.r-project.org/src/base/R-4/R-4.2.0.tar.gz
or wait for it to be mirrored at a CRAN site nearer to you.
Binaries for various platforms will appear in due course.
For the R Core Team,
Peter Dalgaard
These are the checksums (md5 and SHA-256) for the freshly created files, in case you wish
to check that they are uncorrupted:
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This is the relevant part of the NEWS file
CHANGES IN R 4.2.0:
SIGNIFICANT USER-VISIBLE CHANGES:
* The formula method of aggregate() now matches the generic in
naming its first argument x (resolving PR#18299 by Thomas
Soeiro).
This means that calling aggregate() with a formula as a named
first argument requires name formula in earlier versions of R and
name x now, so portable code should not name the argument (code
in many packages did).
* Calling && or || with either argument of length greater than one
now gives a warning (which it is intended will become an error).
* Calling if() or while() with a condition of length greater than
one gives an error rather than a warning. Consequently,
environment variable _R_CHECK_LENGTH_1_CONDITION_ no longer has
any effect.
* Windows users should consult the WINDOWS section below for some
profound changes including
* Support for 32-bit builds has been dropped.
* UTF-8 locales are used where available.
* The default locations for the R installation and personal
library folder have been changed.
Thanks to Tomas Kalibera for months of work on the Windows port
for this release.
NEW FEATURES:
* matrix(x, n, m) now warns in more cases where length(x) differs
from n * m, as suggested by Abby Spurdle and Wolfgang Huber in
Feb 2021 on the R-devel mailing list.
This warning can be turned into an error by setting environment
variable _R_CHECK_MATRIX_DATA_ to TRUE: R CMD check --as-cran
does so unless it is already set.
* Function file_test() in package utils gains tests for symlinks,
readability and writability.
* capabilities("libxml") is now false.
The description of capabilities("http/ftp") now reflects that it
refers to the default method, no longer the internal one.
* simplify2array() gains an except argument for controlling the
exceptions used by sapply().
* Environment variables R_LIBS_USER and R_LIBS_SITE are both now
set to the R system default if unset or empty, and can be set to
NULL to indicate an empty list of user or site library
directories.
* The warning for axis()(-like) calls in cases of relatively small
ranges (typically in log-scale situations) is slightly improved
_and_ suppressed from explicit calls to .axisPars() as has always
been the intention.
* The contrasts setter function `contrasts<-` gains an explicit
default how.many = NULL rather than just using missing(how.many).
* grid.pretty() gains a new optional argument n = 5.
* There is a new function .pretty() with option bounds as a
technical-utility version of pretty(). It and pretty() gain a
new argument f.min with a better than back-compatible default.
* Function grDevices::axisTicks() and related functions such as
graphics::axis() work better, notably for the log scale; partly
because of the pretty() improvements, but also because care is
taken e.g., when ylim is finite but diff(ylim) is infinite.
* nclass.FD() gains a digits option.
* The R Mathlib internal C function bd0() (called indirectly from a
dozen probability density and distribution functions such as
dpois(), dbinom(), dgamma(), pgamma() _etc_) has been
complemented by a more sophisticated and (mostly) more accurate C
function ebd0(), currently called only by internal dpois_raw()
improving accuracy for R level dpois() and potentially others
calling it such as dnbinom(), dgamma() or pgamma(). (Thanks to
Morten Welinder's PR#15628.)
* write.ftable() gains sep = " " argument as suggested by Thomas
Soeiro.
* The names of the locale categories supported by R's
Sys.getlocale() and Sys.setlocale() are now provided by variable
.LC.categories in the base namespace.
* The Date and POSIXt methods for hist() and the histogram method
for plot() now also use the new default col = "lightgray" in
consistency with the corresponding change to hist()'s default for
R 4.0.0.
* hist.default() gains new fuzz argument, and the histogram plot
method no longer uses fractional axis ticks when displaying
counts ("Frequency").
* mapply() and hence Map() now also obey the "max-or-0-if-any"
recycling rule, such that, e.g., Map(`+`, 1:3, 1[0]) is valid
now.
* as.character(<obj>) for "hexmode" or "octmode" objects now
fulfils the important basic rule as.character(x)[j] ===
as.character(x[j]).
* The set utility functions, notably intersect() have been tweaked
to be more consistent and symmetric in their two set arguments,
also preserving a common mode.
* substr(ch, start,end) <- new now e.g., preserves names(ch); ditto
for substring(), thanks to a patch from Brodie Gaslam.
* plot(<lm>) gains a extend.ylim.f argument, in partial response to
PR#15285; further PR#17784 is fixed thanks to several
contributors and a patch by Elin Waring. The Cook's dist
contours get customizable via cook.col and cook.lty with a
different default color and their legend is nicer by default and
customizable via cook.legendChanges.
* Attempting to subset an object that is not subsettable now
signals an error of class notSubsettableError. The
non-subsettable object is contained in the object field of the
error condition.
* Subscript-out-of-bounds errors are now signaled as errors of
class subscriptOutOfBoundsError.
* Stack-overflow errors are now signaled as errors inheriting from
class stackOverflowError. See ?stackOverflowError for more
details.
* New partly experimental Sys.setLanguage() utility, solving the
main problem of PR#18055.
* gettext() and gettextf() get a new option trim = TRUE which when
set to false allows translations for strings such as "Execution
halted\n" typical for C code.
* An experimental implementation of hash tables is now available.
See ?hashtab for more details.
* identical() gains a extptr.as.ref argument for requesting that
external pointer objects be compared as reference objects.
* reorder() gets an argument decreasing which it passes to sort()
for level creation; based on the wish and patch by Thomas Soeiro
in PR#18243.
* as.vector() gains a data.frame method which returns a simple
named list, also clearing a long standing 'FIXME' to enable
as.vector(<data.frame>, mode="list"). This breaks code relying
on as.vector(<data.frame>) to return the unchanged data frame.
* legend() is now vectorized for arguments cex, x.intersp, and
text.width. The latter can now also be specified as a vector
(one element for each column of the legend) or as NA for
computing a proper column wise maximum value of strwidth(legend).
The argument y.intersp can be specified as a vector with one
entry for each row of the legend.
legend() also gains new arguments title.cex and title.font.
Thanks to Swetlana Herbrandt.
* Deparsing no longer remaps attribute names dim, dimnames, levels,
names and tsp to historical S-compatible names (which structure()
maps back).
* sample() and sample.int() have additional sanity checks on their
size and n arguments.
all.equal.numeric() gains a sanity check on its tolerance
argument - calling all.equal(a, b, c) for three numeric vectors
is a surprisingly common error.
mean(na.rm =), rank(na.last =), barplot(legend.text =),
boxplot(), contour(drawlabels =), polygon(border =) and
methods::is(class2 =) have more robust sanity checks on their
arguments.
R CMD Rd2pdf (used by R CMD check) has a more robust sanity check
on the format of \alias{} commands.
* psigamma(x, deriv) for negative x now also works for deriv = 4
and 5; their underlying C level dpsifn() is documented in
'Writing R Extensions'.
* The HTML help system now uses HTML5 (wish of PR#18149).
* ks.test() now provides exact p-values also with ties and MC
p-values in the two-sample (Smirnov) case. By Torsten Hothorn.
* ks.test() gains a formula interface, with y ~ 1 for the
one-sample (Kolmogorov) test and y ~ group for the two-sample
(Smirnov) test. Contributed by Torsten Hothorn.
* The return value from ks.test() now has class c("ks.test",
"htest") - packages using try() need to take care to use
inherits() and not == on the class.
* New functions psmirnov(), qsmirnov() and rsmirnov() in package
stats implementing the asymptotic and exact distributions of the
two-sample Smirnov statistic.
* iconv() now allows sub = "c99" to use C99-style escapes for UTF-8
inputs which cannot be converted to encoding to.
* In a forward pipe |> expression it is now possible to use a named
argument with the placeholder _ in the rhs call to specify where
the lhs is to be inserted. The placeholder can only appear once
on the rhs.
* The included LAPACK sources have been updated to version 3.10.0,
except for the four Fortran 77 routines which 3.10.0 has
re-implemented in Fortran 90 (where the older versions have been
retained as the R build process does not support Fortran 90).
* path.expand() and most other uses of tilde expansion now warn if
a path would be too long if expanded. (An exception is
file.exists(), which silently returns false.)
* trunc(<Date>, *) now supports units = "months" or "years" for
consistency with the POSIXt method, thanks to Dirk Eddelbuettel's
proposal in PR#18099.
* list2DF() now checks that its arguments are of the same length,
rather than use recycling.
* The HTML help system has several new features: LaTeX-like math
can be typeset using either KaTeX or MathJax, usage and example
code is highlighted using Prism, and for dynamic help the output
of examples and demos can be shown within the browser if the
knitr package is installed. These features can be disabled by
setting the environment variable _R_HELP_ENABLE_ENHANCED_HTML_ to
a false value.
GRAPHICS:
* The graphics engine version, R_GE_version, has been bumped to 15
and so packages that provide graphics devices should be
reinstalled.
* The grid package now allows the user to specify a "vector" of
pattern fills. The fill argument to gpar() accepts a list of
gradients and/or patterns and the functions linearGradient(),
radialGradient(), and pattern() have a new group argument.
Points grobs (data symbols) can now also have a pattern fill.
The grobCoords() function now returns a more informative and
complex result.
* The grid package has new functions for drawing isolated groups:
grid.group(), grid.define(), and grid.use(). These functions add
compositing operators and affine transformations to R's graphics
capabilities.
The grid package also has new functions for stroking and filling
paths: grid.stroke(), grid.fill(), and grid.fillStroke().
A new function as.path() allows the user to specify the fill rule
for a path that is to be used for clipping, stroking, or filling;
available options are "winding" and "evenodd". A new function
as.mask() allows the user to specify the type of a mask;
available options are "alpha" and "luminance".
These new features are only supported so far (at most) on the
Cairo-based graphics devices and on the pdf() device.
* dev.capabilities() reports on device support for the new
features.
* par() now warns about unnamed non-character arguments to prevent
misuse such as {usr <- par("usr"); par(usr)}.
WINDOWS:
* R uses UTF-8 as the native encoding on recent Windows systems (at
least Windows 10 version 1903, Windows Server 2022 or Windows
Server 1903). As a part of this change, R uses UCRT as the C
runtime. UCRT should be installed manually on systems older than
Windows 10 or Windows Server 2016 before installing R.
* The default personal library on Windows, folder R\win-library\x.y
where x.y stands for R release x.y.z, is now a subdirectory of
Local Application Data directory (usually a hidden directory
C:\Users\username\AppData\Local). Use shell.exec(.libPaths()[1])
from R to open the personal library in Explorer when it is first
in the list (PR#17842).
* R uses a new 64-bit Tcl/Tk bundle. The previous 32-bit/64-bit
bundle had a different layout and can no longer be used.
* Make files and installer scripts for Windows have been tailored
to Rtools42, the newly recommended 64-bit gcc 10.3 MinGW-W64 UCRT
toolchain.
* Rtools42 by default uses the Windows security features ASLR and
DEP; hence CRAN builds of R and packages also do.
* R now supports files Makevars.ucrt, Makefile.ucrt, configure.ucrt
and cleanup.ucrt in packages, which are used in preference to the
.win variants. This allows keeping the .win files around to
support older versions of R. This feature will be removed in the
future once support for older versions of R would no longer be
needed.
* R.version gains a new field crt (only on Windows) to denote the C
runtime. The value is "ucrt".
* On Windows, download.file(method = "auto") and url(method =
"default") now follow Unix in using "libcurl" for all except
file:// URIs.
* Rtools42 includes an unpatched Msys2 build of GNU tar. Paths
including drive letters can be made to work by adding
--force-local to environment variable TAR_OPTIONS. (Rtools40 and
earlier included a patched version which defaulted to this
option.)
* Installer builds of R automatically find the Rtools42 software
collection as well as the compiler toolchain. No PATH setting is
required from the user.
* The default installation directory of R for a user-only
installation has been changed to the User Program Files directory
(usually a hidden directory
C:\Users\username\AppData\Local\Programs) to follow Windows
conventions. Use shell.exec(R.home()) from R to open the R
installation directory in Explorer (PR#17842).
* R now supports installation-time patching of packages. Patches
may be installed from a supplied URL or a local directory or
disabled. Patches are included into the installed packages for
reference. This experimental feature may be removed in the
future.
* libcurl is now required for building from source.
* The clipboard connection now works also with text in other than
the current native encoding (PR#18267, with Hiroaki Yutani).
Text is always pasted to the clipboard in UTF16-LE and the
encoding argument is ignored.
* The internal case-changing functions are now used by default on
Windows - this circumvents problems (for example with E acute) of
the UCRT Windows' runtime.
* R on Windows now uses the system memory allocator. Doug Lea's
allocator was used since R 1.2.0 to mitigate performance
limitations seen with system allocators on earlier versions of
Windows.
* memory.limit() and memory.size() are now stubs on Windows (as on
Unix-alikes).
* Applications embedding R on Windows can now use additional
callbacks, which have so far only been available only on Unix
(PR#18286).
INSTALLATION:
* Facilities for accessing ftp:// sites are no longer tested
(except _pro tem_ for curlGetHeaders()) as modern browsers have
removed support.
* R can now be built with DEFS = -DSTRICT_R_HEADERS .
PACKAGE INSTALLATION:
* R CMD INSTALL no longer tangles vignettes. This completes an R
CMD build change in R 3.0.0 and affects packages built before R
3.0.2. Such packages should be re-made with R CMD build to have
the tangled R code of vignettes shipped with the tarball.
* USE_FC_LEN_T will become the default: this uses the correct
prototypes for Fortran BLAS/LAPACK routines called from C/C++,
and requires adjustment of most such calls - see 'Writing R
Extensions' SS6.6.2. (This has been supported since R 3.6.2.)
* Package installation speed for packages installed with
keep.source has been improved. This resolve the issue reported by
Ofek Shilon in PR#18236.
UTILITIES:
* R CMD check can optionally report files/directories left behind
in home, /tmp (even though TMPDIR is set) and other directories.
See the "R Internals" manual for details.
* R CMD check now reports byte-compilation errors during
installation. These are not usually fatal but may result in
parts of the package not being byte-compiled.
* _R_CHECK_DEPENDS_ONLY_ can be applied selectively to examples,
tests and/or vignettes in R CMD check: see the "R Internals"
manual.
* _R_CHECK_SRC_MINUS_W_IMPLICIT_ now defaults to true: recent
versions of Apple clang on macOS have made implicit function
declarations in C into a compilation error.
* R CMD check --as-cran makes use of the environment variable
AUTORECONF. See the "R Internals" manual SS8 for further details.
* R CMD check --use-valgrind also uses valgrind when re-building
vignettes as some non-Sweave vignettes unhelpfully comment out
all their code when R CMD check runs vignettes.
* Errors in re-building vignettes (unless there are LaTeX errors)
are reported by R CMD check as ERROR rather than WARNING when
running vignettes has been skipped (as it frequently is in CRAN
checks and by --as-cran).
* R CMD Rd2pdf gains a --quiet option that is used by R CMD build
when building the PDF package manual.
* R CMD Rd2pdf now always runs LaTeX in batch mode, consistent with
Texinfo >= 6.7. The --batch option is ignored.
* R CMD build and R CMD check now include the Rd file name and line
numbers in the error message of an \Sexpr evaluation failure.
* For packages using the \doi Rd macro (now an install-time \Sexpr)
but no other dynamic Rd content, R CMD build now produces a
smaller tarball and is considerably faster - skipping temporary
package installation.
C-LEVEL FACILITIES:
* The non-API header R_ext/R-ftp-http.h is no longer provided, as
the entry points it covered are now all defunct.
* A number of non-API declarations and macro definitions have been
moved from the installed header Rinternals.h to the internal
header Defn.h. Packages that only use entry points and
definitions documented to be part of the API as specified in
'Writing R Extensions' SS6 should not be affected.
* The macro USE_RINTERNALS no longer has any effect when compiling
package code. Packages which also use R_NO_REMAP will need to
ensure that the remapped names are used for calls to API
functions that were formerly also made available as macros.
* The deprecated legacy S-compatibility macros PROBLEM, MESSAGE,
ERROR, WARN, WARNING, RECOVER, ... are no longer defined in
R_exts/RS.h (included by R.h). Replace these by calls to
Rf_error and Rf_warning (defined in header R_ext/Error.h included
by R.h).
Header R_ext/RS.h no longer includes R_ext/Error.h.
* Header R_ext/Constants.h (included by R.h) when included from C++
now includes the C++ header cfloat rather than the C header
float.h (now possible as C++11 is required).
* The legacy S-compatibility macros DOUBLE_* in R_ext/Constants.h
(included by R.h) are deprecated.
* The deprecated S-compatibility macros SINGLE_* in
R_ext/Constants.h (included by R.h) have been removed.
* R_Calloc, R_Free and R_Realloc are preferred to their unprefixed
forms and error messages now use the prefix. These forms were
introduced in R 3.4.0 and are available even when
STRICT_R_HEADERS is defined.
* rmultinom has been documented in 'Writing R Extensions' SS6 so is
now part of the R API.
* Similarly, Rtanpi, called from R level tanpi() is now part of the
R API.
* The long-deprecated, undocumented and non-API entry point call_R
is no longer declared in R_ext/RS.h (included by R.h).
* The header S.h which has been unsupported since Jan 2016 has been
removed. Use R.h instead.
DEPRECATED AND DEFUNCT:
* The (non-default and deprecated) method = "internal" for
download.file() and url() no longer supports http:// nor ftp://
URIs. (It is used only for file:// URIs.)
On Windows, download.file(method = "wininet") no longer supports
ftp:// URIs. (It is no longer the default method, which is
"libcurl" and does.)
On Windows, the deprecated method = "wininet" now gives a warning
for http:// and https:// URIs for both download.file() and url().
(It is no longer the default method.)
* On Windows, the command-line option --max-mem-size and
environment variable R_MAX_MEM_SIZE are defunct. The memory
allocation limit was important for 32-bit builds, but these are
no longer supported.
* default.stringsAsFactors() is now formally deprecated, where that
was only mentioned on its regular help page, previously. So it
now gives a warning if called.
* unix.time() is defunct now; it had been deprecated since R 3.4.0.
BUG FIXES:
* Setting digits = 0 in format(), print.default() (and hence
typically print()) or options() is again invalid. Its behaviour
was platform-dependent, and it is unclear what "zero significant
digits" should mean (PR#18098).
* Messages from C code in the cairo section of package grDevices
are now also offered for translation, thanks to Michael Chirico's
PR#18123.
* mean(x) with finite x now is finite also without "long.double"
capability.
* R CMD Rd2pdf no longer leaves an empty build directory behind
when it aborts due to an already existing output file. (Thanks
to Sebastian Meyer's PR#18141.)
* density(x, weights = w, na.rm = TRUE) when anyNA(x) is true, now
removes weights "in parallel" to x, fixing PR#18151, reported by
Matthias Gondan. Additionally, it gets a subdensity option.
* Conversion of \Sexpr[]{<expR>} to LaTeX or HTML no longer
produces long blocks of empty lines when <expR> itself contains
several lines all producing empty output. Thanks to a report and
patch by Ivan Krylov posted to R-devel.
* R CMD build no longer fails if a package vignette uses child
documents and inst/doc exists. (Thanks to Sebastian Meyer's
PR#18156.)
* When an R documentation ('help' source) file man/foo.Rd in a
package has \donttest{..} examples with a syntax error, it is now
signalled as ERROR and with correct line numbers relating to the
*-Ex.R file, thanks to Duncan Murdoch and Sebastian Meyer's
reports and patch proposals in PR#17501.
* Improved determination of the correct translation domain in
non-base packages, addressing the combination of PR#18092 and
PR#17998 (#c6) with reports and _augmented_ patch #2904 by
Suharto Anggono.
Note that "R-base" is no longer the default domain e.g., for
top-level calls to gettext(); rather translation needs explicit
domain = * specification in such cases.
* identical(attrib.as.set=FALSE) now works correctly with data
frames with default row names (Thanks to Charlie Gao's PR#18179).
* txtProgressBar() now enforces a non-zero width for argument char,
without which no progress can be visible.
* dimnames(table(d)) is more consistent in the case where d is a
list with a single component, thanks to Thomas Soeiro's report to
R-devel.
Further, table(d1, d2) now gives an error when d1 and d2 are data
frames as suggested by Thomas in PR#18224.
* Fix for drawing semi-transparent lines and fills on the native
Windows graphics device (PR#18219 and PR#16694). Thanks to Nick
Ray for helpful diagnosis on Bugzilla.
* The deparser now wraps sub-expressions such as if(A) .. with
parentheses when needed; thanks to Duncan Murdoch's PR#18232 and
Lionel Henry's patches there.
* remove.packages() no longer tries to uninstall Priority: base
packages, thanks to a report and suggestions by Colin Fay in
PR#18227.
* win.metafile() now has xpinch and ypinch arguments so that the
user can override Windows' (potentially wrong) guess at device
dimensions.
* x[i] and x[[i]] for non-integer i should now behave in all cases
as always documented: the index used is equivalent to
as.integer(i) unless that would overflow where trunc(i) is used
instead; thanks to Suharto Anggono's report and patch proposals
in PR#17977.
* asOneSidedFormula() now associates the resulting formula with the
global environment rather than the evaluation environment created
for the call.
* <bibentry>$name now matches the field name case-insensitively,
consistent with bibentry() creation and the replacement method.
* cbind() failed to detect some length mismatches with a mixture of
time-series and non-time-series inputs.
* The default LaTeX style file Sweave.sty used by the RweaveLatex
driver no longer loads the obsolete ae package; thanks to a
report by Thomas Soeiro in PR#18271. Furthermore, it now skips
\usepackage[T1]{fontenc} for engines other than pdfTeX (if
detected) or if the new [nofontenc] option is used.
* smooth.spline() now stores its logical cv argument more safely,
fixing a rare bug when printing, and also stores n.
* smooth.spline(x,y,*) now computes the cv.crit statistic
correctly, also when is.unsorted(x), fixing PR#18294.
* The data.frame method of rbind() now warns when binding
not-wholly-recycling vectors, by analogy to the default method
(for matrices).
* setAs() finds the correct class for name to when multiple
packages define a class with that name. Thanks to Gabor Csardi
for the report.
* Fix for detaching a package when two classes of the same name are
present in method signatures for the same generic. Thanks to
Gabor Csardi for the report.
* match.arg("", c("", "a", "B")) gives a better error message, in
part from PR#17959, thanks to Elin Waring.
* R CMD Sweave --clean no longer removes pre-existing files or
subdirectories (PR#18242).
* The quartz() device no longer splits polylines into subpaths.
That has caused narrowly-spaced lines with many points to always
look solid even when dashed line type was used due to dash phase
restarts.
* Deparsing constructs such as quote(1 + `!`(2) + 3) works again as
before R 3.5.0, thanks to the report and patch in PR#18284 by
Suharto Anggono.
* as.list(f) for a factor f now keeps names(f), fixing PR#18309.
* qbeta(.001, .9, .009) and analogous qf() calls now return a
correct value instead of NaN or wrongly 1, all with a warning;
thanks to the report by Ludger Goeminne in PR#18302.
* plot.lm() failed to produce the plot of residuals vs. factor
levels (i.e., which=5 when leverages are constant) for models
with character predictors (PR#17840).
* interaction.plot(..., xtick = TRUE) misplaced the x-axis line
(PR#18305).
* Not strictly fixing a bug, format()ing and print()ing of
non-finite Date and POSIXt values NaN and +/-Inf no longer show
as NA but the respective string, e.g., Inf, for consistency with
numeric vector's behaviour, fulfilling the wish of PR#18308.
* R CMD check no longer runs test scripts generated from
corresponding .Rin files twice and now signals an ERROR if
processing an .Rin script fails.
* tools::Rd2txt() used for plain-text help pages now renders \hrefs
(if tools::Rd2txt_options(showURLs = TRUE)) and \urls with
percent-encoding and standards-compliant delimiting style (angle
brackets and no URL: prefix). \email is now rendered with a
mailto: prefix.
--
Peter Dalgaard, Professor,
Center for Statistics, Copenhagen Business School
Solbjerg Plads 3, 2000 Frederiksberg, Denmark
Phone: (+45)38153501
Office: A 4.23
Email: pd.mes using cbs.dk Priv: PDalgd using gmail.com
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