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List:       pkgsrc-changes
Subject:    CVS commit: pkgsrc/math/R
From:       "Wen Heping" <wen () netbsd ! org>
Date:       2018-05-31 10:23:02
Message-ID: 20180531102302.79D0DFBEC () cvs ! NetBSD ! org
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Module Name:	pkgsrc
Committed By:	wen
Date:		Thu May 31 10:23:02 UTC 2018

Modified Files:
	pkgsrc/math/R: Makefile PLIST distinfo
	pkgsrc/math/R/patches: patch-configure.ac
Removed Files:
	pkgsrc/math/R/patches: patch-src_include_GraphicsBase.h

Log Message:
Update to 3.5.0

Upstream changes:
CHANGES IN R 3.5.0
SIGNIFICANT USER-VISIBLE CHANGES
All packages are by default byte-compiled on installation. This makes the installed \
packages larger (usually marginally so) and may affect the format of messages and \
tracebacks (which often exclude .Call and similar).

NEW FEATURES
factor() now uses order() to sort its levels, rather than sort.list(). This allows \
factor() to support custom vector-like objects if methods for the appropriate \
generics are defined. It has the side effect of making factor() succeed on empty or \
length-one non-atomic vector(-like) types (e.g., "list"), where it failed before.

diag() gets an optional names argument: this may require updates to packages defining \
S4 methods for it.

chooseCRANmirror() and chooseBioCmirror() no longer have a useHTTPS argument, not \
needed now all R builds support https:// downloads.

New summary() method for warnings() with a (somewhat experimental) print() method.

(methods package.) .self is now automatically registered as a global variable when \
registering a reference class method.

tempdir(check = TRUE) recreates the tempdir() directory if it is no longer valid \
(e.g. because some other process has cleaned up the ‘/tmp' directory).

New askYesNo() function and "askYesNo" option to ask the user binary response \
questions in a customizable but consistent way. (Suggestion of PR#17242.)

New low level utilities ...elt(n) and ...length() for working with ... parts inside a \
function.

isTRUE() is more tolerant and now true in

   x <- rlnorm(99)
   isTRUE(median(x) == quantile(x)["50%"])
New function isFALSE() defined analogously to isTRUE().

The default symbol table size has been increased from 4119 to 49157; this may improve \
the performance of symbol resolution when many packages are loaded. (Suggested by Jim \
Hester.)

line() gets a new option iter = 1.

Reading from connections in text mode is buffered, significantly improving the \
performance of readLines(), as well as scan() and read.table(), at least when \
specifying colClasses.

order() is smarter about picking a default sort method when its arguments are \
objects.

available.packages() has two new arguments which control if the values from the \
per-session repository cache are used (default true, as before) and if so how old \
cached values can be to be used (default one hour).

These arguments can be passed from install.packages(), update.packages() and \
functions calling that: to enable this available.packages(), packageStatus() and \
download.file() gain a ... argument.

packageStatus()'s upgrade() method no longer ignores its ... argument but passes it \
to install.packages().

installed.packages() gains a ... argument to allow arguments (including noCache) to \
be passed from new.packages(), old.packages(), update.packages() and packageStatus().

factor(x, levels, labels) now allows duplicated labels (not duplicated levels!). \
Hence you can map different values of x to the same level directly.

Attempting to use names<-() on an S4 derivative of a basic type no longer emits a \
warning.

The list method of within() gains an option keepAttrs = FALSE for some speed-up.

system() and system2() now allow the specification of a maximum elapsed time \
(‘timeout').

debug() supports debugging of methods on any object of S4 class "genericFunction", \
including group generics.

Attempting to increase the length of a variable containing NULL using length()<- \
still has no effect on the target variable, but now triggers a warning.

type.convert() becomes a generic function, with additional methods that operate \
recursively over list and data.frame objects. Courtesy of Arni Magnusson (PR#17269).

lower.tri(x) and upper.tri(x) only needing dim(x) now work via new functions .row() \
and .col(), so no longer call as.matrix() by default in order to work efficiently for \
all kind of matrix-like objects.

print() methods for "xgettext" and "xngettext" now use encodeString() which keeps, \
e.g. "\n", visible. (Wish of PR#17298.)

package.skeleton() gains an optional encoding argument.

approx(), spline(), splinefun() and approxfun() also work for long vectors.

deparse() and dump() are more useful for S4 objects, dput() now using the same \
internal C code instead of its previous imperfect workaround R code. S4 objects now \
typically deparse perfectly, i.e., can be recreated identically from deparsed code.

dput(), deparse() and dump() now print the names() information only once, using the \
more readable (tag = value) syntax, notably for list()s, i.e., including data frames.

These functions gain a new control option "niceNames" (see .deparseOpts()), which \
when set (as by default) also uses the (tag = value) syntax for atomic vectors. On \
the other hand, without deparse options "showAttributes" and "niceNames", names are \
no longer shown also for lists. as.character(list( c (one = 1))) now includes the \
name, as as.character(list(list(one = 1))) has always done.

m:n now also deparses nicely when m > n.

The "quoteExpressions" option, also part of "all", no longer quote()s formulas as \
that may not re-parse identically. (PR#17378)

If the option setWidthOnResize is set and TRUE, R run in a terminal using a recent \
readline library will set the width option when the terminal is resized. Suggested by \
Ralf Goertz.

If multiple on.exit() expressions are set using add = TRUE then all expressions will \
now be run even if one signals an error.

mclapply() gets an option affinity.list which allows more efficient execution with \
heterogeneous processors, thanks to Helena Kotthaus.

The character methods for as.Date() and as.POSIXlt() are more flexible via new \
arguments tryFormats and optional: see their help pages.

on.exit() gains an optional argument after with default TRUE. Using after = FALSE \
with add = TRUE adds an exit expression before any existing ones. This way the \
expressions are run in a first-in last-out fashion. (From Lionel Henry.)

On Windows, file.rename() internally retries the operation in case of error to \
attempt to recover from possible anti-virus interference.

Command line completion on :: now also includes lazy-loaded data.

If the TZ environment variable is set when date-time functions are first used, it is \
recorded as the session default and so will be used rather than the default deduced \
from the OS if TZ is subsequently unset.

There is now a [ method for class "DLLInfoList".

glm() and glm.fit get the same singular.ok = TRUE argument that lm() has had forever. \
As a consequence, in glm(*, method = <your_own>), user specified methods need to \
accept a singular.ok argument as well.

aspell() gains a filter for Markdown (‘.md' and ‘.Rmd') files.

intToUtf8(multiple = FALSE) gains an argument to allow surrogate pairs to be \
interpreted.

The maximum number of DLLs that can be loaded into R e.g. via dyn.load() has been \
increased up to 614 when the OS limit on the number of open files allows.

Sys.timezone() on a Unix-alike caches the value at first use in a session: inter alia \
this means that setting TZ later in the session affects only the current time zone \
and not the system one.

Sys.timezone() is now used to find the system timezone to pass to the code used when \
R is configured with --with-internal-tzcode.

When tar() is used with an external command which is detected to be GNU tar or \
libarchive tar (aka bsdtar), a different command-line is generated to circumvent \
line-length limits in the shell.

system(*, intern = FALSE), system2() (when not capturing output), file.edit() and \
file.show() now issue a warning when the external command cannot be executed.

The "default" ("lm" etc) methods of vcov() have gained new optional argument complete \
= TRUE which makes the vcov() methods more consistent with the coef() methods in the \
case of singular designs. The former (back-compatible) behavior is given by vcov(*, \
complete = FALSE).

coef() methods (for lm etc) also gain a complete = TRUE optional argument for \
consistency with vcov(). For "aov", both coef() and vcov() methods remain \
back-compatibly consistent, using the other default, complete = FALSE.

attach(*, pos = 1) is now an error instead of a warning.

New function getDefaultCluster() in package parallel to get the default cluster set \
via setDefaultCluster().

str(x) for atomic objects x now treats both cases of is.vector(x) similarly, and \
hence much less often prints "atomic". This is a slight non-back-compatible change \
producing typically both more informative and shorter output.

write.dcf() gets optional argument useBytes.

New, partly experimental packageDate() which tries to get a valid "Date" object from \
a package ‘DESCRIPTION' file, thanks to suggestions in PR#17324.

tools::resaveRdaFiles() gains a version argument, for use when packages should remain \
compatible with earlier versions of R.

ar.yw(x) and hence by default ar(x) now work when x has NAs, mostly thanks to a patch \
by Pavel Krivitsky in PR#17366. The ar.yw.default()'s AIC computations have become \
more efficient by using determinant().

New warnErrList() utility (from package nlme, improved).

By default the (arbitrary) signs of the loadings from princomp() are chosen so the \
first element is non-negative.

If --default-packages is not used, then Rscript now checks the environment variable \
R_SCRIPT_DEFAULT_PACKAGES. If this is set, then it takes precedence over \
R_DEFAULT_PACKAGES. If default packages are not specified on the command line or by \
one of these environment variables, then Rscript now uses the same default packages \
as R. For now, the previous behavior of not including methods can be restored by \
setting the environment variable R_SCRIPT_LEGACY to yes.

When a package is found more than once, the warning from find.package(*, \
verbose=TRUE) lists all library locations.

POSIXt objects can now also be rounded or truncated to month or year.

stopifnot() can be used alternatively via new argument exprs which is nicer and \
useful when testing several expressions in one call.

The environment variable R_MAX_VSIZE can now be used to specify the maximal vector \
heap size. On macOS, unless specified by this environment variable, the maximal \
vector heap size is set to the maximum of 16GB and the available physical memory. \
This is to avoid having the R process killed when macOS over-commits memory.

sum(x) and sum(x1,x2,..,x<N>) with many or long logical or integer vectors no longer \
overflows (and returns NA with a warning), but returns double numbers in such cases.

Single components of "POSIXlt" objects can now be extracted and replaced via [ \
indexing with 2 indices.

S3 method lookup now searches the namespace registry after the top level environment \
of the calling environment.

Arithmetic sequences created by 1:n, seq_along, and the like now use compact internal \
representations via the ALTREP framework. Coercing integer and numeric vectors to \
character also now uses the ALTREP framework to defer the actual conversion until \
first use.

Finalizers are now run with interrupts suspended.

merge() gains new option no.dups and by default suffixes the second of two duplicated \
column names, thanks to a proposal by Scott Ritchie (and Gabe Becker).

scale.default(x, center, scale) now also allows center or scale to be \
"numeric-alike", i.e., such that as.numeric(.) coerces them correctly. This also \
eliminates a wrong error message in such cases.

par*apply and par*applyLB gain an optional argument chunk.size which allows to \
specify the granularity of scheduling.

Some as.data.frame() methods, notably the matrix one, are now more careful in not \
accepting duplicated or NA row names, and by default produce unique non-NA row names. \
This is based on new function .rowNamesDF(x, make.names = *) <- rNms where the \
logical argument make.names allows to specify how invalid row names rNms are handled. \
.rowNamesDF() is a "workaround" compatible default.

R has new serialization format (version 3) which supports custom serialization of \
ALTREP framework objects. These objects can still be serialized in format 2, but less \
efficiently. Serialization format 3 also records the current native encoding of \
unflagged strings and converts them when de-serialized in R running under different \
native encoding. Format 3 comes with new serialization magic numbers (RDA3, RDB3, \
RDX3). Format 3 can be selected by version = 3 in save(), serialize() and saveRDS(), \
but format 2 remains the default for all serialization and saving of the workspace. \
Serialized data in format 3 cannot be read by versions of R prior to version 3.5.0.

The "Date" and "date-time" classes "POSIXlt" and "POSIXct" now have a working \
`length<-` method, as wished in PR#17387.

optim(*, control = list(warn.1d.NelderMead = FALSE)) allows to turn off the warning \
when applying the default "Nelder-Mead" method to 1-dimensional problems.

matplot(.., panel.first = .) etc now work, as log becomes explicit argument and ... \
is passed to plot() unevaluated, as suggested by Sebastian Meyer in PR#17386.

Interrupts can be suspended while evaluating an expression using suspendInterrupts. \
Subexpression can be evaluated with interrupts enabled using allowInterrupts. These \
functions can be used to make sure cleanup handlers cannot be interrupted.

R 3.5.0 includes a framework that allows packages to provide alternate \
representations of basic R objects (ALTREP). The framework is still experimental and \
may undergo changes in future R releases as more experience is gained. For now, \
documentation is provided in https://svn.r-project.org/R/branches/ALTREP/ALTREP.html.

UTILITIES
install.packages() for source packages now has the possibility to set a ‘timeout' \
(elapsed-time limit). For serial installs this uses the timeout argument of \
system2(): for parallel installs it requires the timeout utility command from GNU \
coreutils.

It is now possible to set ‘timeouts' (elapsed-time limits) for most parts of R CMD \
check via environment variables documented in the ‘R Internals' manual.

The ‘BioC extra' repository which was dropped from Bioconductor 3.6 and later has \
been removed from setRepositories(). This changes the mapping for 6–8 used by \
setRepositories(ind=).

R CMD check now also applies the settings of environment variables \
_R_CHECK_SUGGESTS_ONLY_ and _R_CHECK_DEPENDS_ONLY_ to the re-building of vignettes.

R CMD check with environment variable _R_CHECK_DEPENDS_ONLY_ set to a true value \
makes test-suite-management packages available and (for the time being) works around \
a common omission of rmarkdown from the VignetteBuilder field.

INSTALLATION on a UNIX-ALIKE
Support for a system Java on macOS has been removed — install a fairly recent \
Oracle Java (see ‘R Installation and Administration'  §C.3.2).

configure works harder to set additional flags in SAFE_FFLAGS only where necessary, \
and to use flags which have little or no effect on performance.

In rare circumstances it may be necessary to override the setting of SAFE_FFLAGS.

C99 functions expm1, hypot, log1p and nearbyint are now required.

configure sets a -std flag for the C++ compiler for all supported C++ standards \
(e.g., -std=gnu++11 for the C++11 compiler). Previously this was not done in a few \
cases where the default standard passed the tests made (e.g. clang 6.0.0 for C++11).

C-LEVEL FACILITIES
‘Writing R Extensions' documents macros MAYBE_REFERENCED, MAYBE_SHARED and \
MARK_NOT_MUTABLE that should be used by package C code instead NAMED or SET_NAMED.

The object header layout has been changed to support merging the ALTREP branch. This \
requires re-installing packages that use compiled code.

‘Writing R Extensions' now documents the R_tryCatch, R_tryCatchError, and \
R_UnwindProtect functions.

NAMEDMAX has been raised to 3 to allow protection of intermediate results from \
(usually ill-advised) assignments in arguments to BUILTIN functions. Package C code \
using SET_NAMED may need to be revised.

DEPRECATED AND DEFUNCT
Sys.timezone(location = FALSE) is defunct, and is ignored (with a warning).

methods:::bind_activation() is defunct now; it typically has been unneeded for years.

The undocumented ‘hidden' objects .__H__.cbind and .__H__.rbind in package base are \
deprecated (in favour of cbind and rbind).

The declaration of pythag() in ‘Rmath.h' has been removed — the entry point has \
not been provided since R 2.14.0.

BUG FIXES
printCoefmat() now also works without column names.

The S4 methods on Ops() for the "structure" class no longer cause infinite recursion \
when the structure is not an S4 object.

nlm(f, ..) for the case where f() has a "hessian" attribute now computes LL' = H +  \
µI correctly. (PR#17249).

An S4 method that "rematches" to its generic and overrides the default value of a \
generic formal argument to NULL no longer drops the argument from its formals.

Rscript can now accept more than one argument given on the #! line of a script. \
Previously, one could only pass a single argument on the #! line in Linux.

Connections are now written correctly with encoding "UTF-16LE". (PR#16737).

Evaluation of ..0 now signals an error. When ..1 is used and ... is empty, the error \
message is more appropriate.

(Windows mainly.) Unicode code points which require surrogate pairs in UTF-16 are now \
handled. All systems should properly handle surrogate pairs, even those systems that \
do not need to make use of them. (PR#16098)

stopifnot(e, e2, ...) now evaluates the expressions sequentially and in case of an \
error or warning shows the relevant expression instead of the full stopifnot(..) \
call.

path.expand() on Windows now accepts paths specified as UTF-8-encoded character \
strings even if not representable in the current locale. (PR#17120)

line(x, y) now correctly computes the medians of the left and right group's x-values \
and in all cases reproduces straight lines.

Extending S4 classes with slots corresponding to special attributes like dim and \
dimnames now works.

Fix for legend() when fill has multiple values the first of which is NA (all colours \
used to default to par(fg)). (PR#17288)

installed.packages() did not remove the cached value for a library tree that had been \
emptied (but would not use the old value, just waste time checking it).

The documentation for installed.packages(noCache = TRUE) incorrectly claimed it would \
refresh the cache.

aggregate(<data.frame>) no longer uses spurious names in some cases. (PR#17283)

object.size() now also works for long vectors.

packageDescription() tries harder to solve re-encoding issues, notably seen in some \
Windows locales. This fixes the citation() issue in PR#17291.

poly(<matrix>, 3) now works, thanks to prompting by Marc Schwartz.

readLines() no longer segfaults on very large files with embedded '\0' (aka ‘nul') \
characters. (PR#17311)

ns() (package splines) now also works for a single observation. interpSpline() gives \
a more friendly error message when the number of points is less than four.

dist(x, method = "canberra") now uses the correct definition; the result may only \
differ when x contains values of differing signs, e.g. not for 0-1 data.

methods:::cbind() and methods:::rbind() avoid deep recursion, thanks to Suharto \
Anggono via PR#17300.

Arithmetic with zero-column data frames now works more consistently; issue raised by \
Bill Dunlap.

Arithmetic with data frames gives a data frame for ^ (which previously gave a numeric \
matrix).

pretty(x, n) for large n or large diff(range(x)) now works better (though it was \
never meant for large n); internally it uses the same rounding fuzz (1e-10) as \
seq.default() — as it did up to 2010-02-03 when both were 1e-7.

Internal C-level R_check_class_and_super() and hence R_check_class_etc() now also \
consider non-direct super classes and hence return a match in more cases. This e.g., \
fixes behaviour of derived classes in package Matrix.

Reverted unintended change in behavior of return calls in on.exit expressions \
introduced by stack unwinding changes in R 3.3.0.

Attributes on symbols are now detected and prevented; attempt to add an attribute to \
a symbol results in an error.

fisher.test(*, workspace = <n>) now may also increase the internal stack size which \
allows larger problem to be solved, fixing PR#1662.

The methods package no longer directly copies slots (attributes) into a prototype \
that is of an "abnormal" (reference) type, like a symbol.

The methods package no longer attempts to call length<-() on NULL (during the \
bootstrap process).

The methods package correctly shows methods when there are multiple methods with the \
same signature for the same generic (still not fully supported, but at least the user \
can see them).

sys.on.exit() is now always evaluated in the right frame. (From Lionel Henry.)

seq.POSIXt(*, by = "<n> DSTdays") now should work correctly in all cases and is \
faster. (PR#17342)

.C() when returning a logical vector now always maps values other than FALSE and NA \
to TRUE (as documented).

Subassignment with zero length vectors now coerces as documented (PR#17344).
Further, x <- numeric(); x[1] <- character() now signals an error ‘replacement has \
length zero' (or a translation of that) instead of doing nothing.

(Package parallel.) mclapply(), pvec() and mcparallel() (when mccollect() is used to \
collect results) no longer leave zombie processes behind.

R CMD INSTALL <pkg> now produces the intended error message when, e.g., the LazyData \
field is invalid.

as.matrix(dd) now works when the data frame dd contains a column which is a data \
frame or matrix, including a 0-column matrix/d.f. .

mclapply(X, mc.cores) now follows its documentation and calls lapply() in case \
mc.cores = 1 also in the case mc.preschedule is false. (PR#17373)

aggregate(<data.frame>, drop=FALSE) no longer calls the function on <empty> parts but \
sets corresponding results to NA. (Thanks to Suharto Anggono's patches in PR#17280).

The duplicated() method for data frames is now based on the list method (instead of \
string coercion). Consequently unique() is better distinguishing data frame rows, \
fixing PR#17369 and PR#17381. The methods for matrices and arrays are changed \
accordingly.

Calling names() on an S4 object derived from "environment" behaves (by default) like \
calling names() on an ordinary environment.

read.table() with a non-default separator now supports quotes following a \
non-whitespace character, matching the behavior of scan().

parLapplyLB and parSapplyLB have been fixed to do load balancing (dynamic \
scheduling). This also means that results of computations depending on random number \
generators will now really be non-reproducible, as documented.

Indexing a list using dollar and empty string (l$"") returns NULL.

Using \usage{ data(<name>, package="<pkg>") } no longer produces R CMD check \
warnings.

match.arg() more carefully chooses the environment for constructing default choices, \
fixing PR#17401 as proposed by Duncan Murdoch.

Deparsing of consecutive ! calls is now consistent with deparsing unary - and + calls \
and creates code that can be reparsed exactly; thanks to a patch by Lionel Henry in \
PR#17397. (As a side effect, this uses fewer parentheses in some other deparsing \
involving ! calls.)

[R logo] CHANGES IN R 3.4.4
NEW FEATURES
Sys.timezone() tries more heuristics on Unix-alikes and so is more likely to succeed \
(especially on Linux). For the slowest method, a warning is given recommending that \
TZ is set to avoid the search.

The version of LAPACK included in the sources has been updated to 3.8.0 (for the \
routines used by R, a very minor bug-fix change).

parallel::detectCores(logical = FALSE) is ignored on Linux systems, since the \
information is not available with virtualized OSes.

INSTALLATION on a UNIX-ALIKE
configure will use pkg-config to find the flags to link to jpeg if available (as it \
should be for the recently-released jpeg-9c and libjpeg-turbo). (This amends the code \
added in R 3.3.0 as the module name in jpeg-9c is not what that tested for.)

DEPRECATED AND DEFUNCT
Sys.timezone(location = FALSE) (which was a stop-gap measure for Windows long ago) is \
deprecated. It no longer returns the value of environment variable TZ (usually a \
location).

Legacy support of make macros such as CXX1X is formally deprecated: use the CXX11 \
forms instead.

BUG FIXES
power.prop.test() now warns when it cannot solve the problem, typically because of \
impossible constraints. (PR#17345)

removeSource() no longer erroneously removes NULL in certain cases, thanks to Dénes \
Tóth.

nls(`NO [mol/l]` ~ f(t)) and nls(y ~ a) now work. (Partly from PR#17367)

R CMD build checks for GNU cp rather than assuming Linux has it. (PR#17370 says \
‘Alpine Linux' does not.)

Non-UTF-8 multibyte character handling fixed more permanently (PR#16732).

sum(<large ints>, <stuff>) is more consistent. (PR#17372)

rf() and rbeta() now also work correctly when ncp is not scalar, notably when \
(partly) NA. (PR#17375)

is.na(NULL) no longer warns. (PR#16107)

R CMD INSTALL now correctly sets C++ compiler flags when all source files are in \
sub-directories of ‘src'.


To generate a diff of this commit:
cvs rdiff -u -r1.184 -r1.185 pkgsrc/math/R/Makefile
cvs rdiff -u -r1.28 -r1.29 pkgsrc/math/R/PLIST
cvs rdiff -u -r1.79 -r1.80 pkgsrc/math/R/distinfo
cvs rdiff -u -r1.2 -r1.3 pkgsrc/math/R/patches/patch-configure.ac
cvs rdiff -u -r1.2 -r0 pkgsrc/math/R/patches/patch-src_include_GraphicsBase.h

Please note that diffs are not public domain; they are subject to the
copyright notices on the relevant files.


--_----------=_1527762182246100
Content-Disposition: inline
Content-Length: 6943
Content-Transfer-Encoding: binary
Content-Type: text/x-diff; charset=us-ascii

Modified files:

Index: pkgsrc/math/R/Makefile
diff -u pkgsrc/math/R/Makefile:1.184 pkgsrc/math/R/Makefile:1.185
--- pkgsrc/math/R/Makefile:1.184	Sun Apr 29 21:31:52 2018
+++ pkgsrc/math/R/Makefile	Thu May 31 10:23:02 2018
@@ -1,7 +1,6 @@
-# $NetBSD: Makefile,v 1.184 2018/04/29 21:31:52 adam Exp $
+# $NetBSD: Makefile,v 1.185 2018/05/31 10:23:02 wen Exp $
 
-DISTNAME=	R-3.4.3
-PKGREVISION=	5
+DISTNAME=	R-3.5.0
 CATEGORIES=	math
 MASTER_SITES=	${MASTER_SITE_R_CRAN:=base/R-3/}
 

Index: pkgsrc/math/R/PLIST
diff -u pkgsrc/math/R/PLIST:1.28 pkgsrc/math/R/PLIST:1.29
--- pkgsrc/math/R/PLIST:1.28	Sat Oct 21 02:40:56 2017
+++ pkgsrc/math/R/PLIST	Thu May 31 10:23:02 2018
@@ -1,4 +1,4 @@
-@comment $NetBSD: PLIST,v 1.28 2017/10/21 02:40:56 markd Exp $
+@comment $NetBSD: PLIST,v 1.29 2018/05/31 10:23:02 wen Exp $
 bin/R
 bin/Rscript
 info/R-FAQ.info.gz
@@ -86,6 +86,7 @@ lib/R/etc/javaconf
 lib/R/etc/ldpaths
 lib/R/etc/repositories
 lib/R/include/R.h
+lib/R/include/R_ext/Altrep.h
 lib/R/include/R_ext/Applic.h
 lib/R/include/R_ext/Arith.h
 lib/R/include/R_ext/BLAS.h
@@ -395,6 +396,7 @@ lib/R/library/cluster/po/fr/LC_MESSAGES/
 lib/R/library/cluster/po/ko/LC_MESSAGES/R-cluster.mo
 lib/R/library/cluster/po/ko/LC_MESSAGES/cluster.mo
 lib/R/library/cluster/po/pl/LC_MESSAGES/R-cluster.mo
+lib/R/library/cluster/test-tools.R
 lib/R/library/codetools/DESCRIPTION
 lib/R/library/codetools/INDEX
 lib/R/library/codetools/Meta/Rd.rds

Index: pkgsrc/math/R/distinfo
diff -u pkgsrc/math/R/distinfo:1.79 pkgsrc/math/R/distinfo:1.80
--- pkgsrc/math/R/distinfo:1.79	Fri Dec  1 03:19:30 2017
+++ pkgsrc/math/R/distinfo	Thu May 31 10:23:02 2018
@@ -1,13 +1,12 @@
-$NetBSD: distinfo,v 1.79 2017/12/01 03:19:30 wen Exp $
+$NetBSD: distinfo,v 1.80 2018/05/31 10:23:02 wen Exp $
 
-SHA1 (R-3.4.3.tar.gz) = 537d481888f20d385b3039f2f2b0c49b7b0fb5de
-RMD160 (R-3.4.3.tar.gz) = e7c7f17f8c39a8ea7ce253e32d248e9779b62227
-SHA512 (R-3.4.3.tar.gz) = \
d4b89daac5060c6d32b2287192c47fc7e8f71f8c2f70f133799bb279c6e486239cb7f298779a59a124eb4228d728ffdaf6bb138c4fd64653bbce0cdf5b0b3412
                
-Size (R-3.4.3.tar.gz) = 30249655 bytes
+SHA1 (R-3.5.0.tar.gz) = 69f9ff4ecc78057095aedc145eb33f66f48b27ed
+RMD160 (R-3.5.0.tar.gz) = 404a2795ddeb2539422b636a95670d31a54ee0a6
+SHA512 (R-3.5.0.tar.gz) = \
c2703e892eb6f12ec7b536540b823d4ef011dddcbdca06c12d438bc1f07debae9dbd0f72abb6f0d4c577a3c74b155452ef527489cf023ed892109dd86c23bc37
 +Size (R-3.5.0.tar.gz) = 30675040 bytes
 SHA1 (patch-ad) = a43b4875a2ee4677b5f762abf3f9a623fd12cbb5
-SHA1 (patch-configure.ac) = 64c7af42c2e0eadefdac6aa105e8f8c4a59e3958
+SHA1 (patch-configure.ac) = f4829c37304e81485e13b4ed8beaeac7edd16189
 SHA1 (patch-m4_R.m4) = 704d5514e10adf0b5217bb71b06f44a612eca6e0
 SHA1 (patch-m4_cairo.m4) = a0c4ec68d7d6d3a73a2a24481d0dee8c192bf154
-SHA1 (patch-src_include_GraphicsBase.h) = eed25eaca982ca76bf75d199dd8bf48be2a99ac5
 SHA1 (patch-src_library_stats_src_Makefile.in) = \
4eb93292858392792c37a706399e2cef91821bbe  SHA1 (patch-src_main_character.c) = \
1271cbd68ec57e28cf6a394398d21d6a18b6760b

Index: pkgsrc/math/R/patches/patch-configure.ac
diff -u pkgsrc/math/R/patches/patch-configure.ac:1.2 \
                pkgsrc/math/R/patches/patch-configure.ac:1.3
--- pkgsrc/math/R/patches/patch-configure.ac:1.2	Sat Oct 21 02:40:56 2017
+++ pkgsrc/math/R/patches/patch-configure.ac	Thu May 31 10:23:02 2018
@@ -1,9 +1,9 @@
-$NetBSD: patch-configure.ac,v 1.2 2017/10/21 02:40:56 markd Exp $
+$NetBSD: patch-configure.ac,v 1.3 2018/05/31 10:23:02 wen Exp $
 
 Do not include system paths in R_LD_LIBRARY_PATH.
 NetBSD, FreeBSD, DragonFly, Darwin and Solaris fixes
 
---- configure.ac.orig	2017-08-04 22:15:02.000000000 +0000
+--- configure.ac.orig	2018-04-23 13:57:20.000000000 +0000
 +++ configure.ac
 @@ -33,6 +33,7 @@ m4_define([R_VERSION],
  AC_INIT([R],[R_VERSION],[https://bugs.r-project.org],[R],[https://www.r-project.org])
 @@ -17,12 +17,12 @@ NetBSD, FreeBSD, DragonFly, Darwin and S
  
  ## As from R 3.2.0 split up -L... and -lR
  if test "${want_R_shlib}" = yes; then
--  LIBR0="-L\$(R_HOME)/lib\$(R_ARCH)"
-+  LIBR0="-Wl,-R${prefix}/lib/R/lib\$(R_ARCH) -L\$(R_HOME)/lib\$(R_ARCH)"
+-  LIBR0="-L\"\$(R_HOME)/lib\$(R_ARCH)\""
++  LIBR0="-Wl,-R${prefix}/lib/R/lib\$(R_ARCH) -L\"\$(R_HOME)/lib\$(R_ARCH)\""
    LIBR1=-lR
  else
    LIBR0=
-@@ -702,7 +703,7 @@ case "${host_os}" in
+@@ -713,7 +714,7 @@ case "${host_os}" in
      ## Not so bad in later versions of Darwin, 
      ## where DYLD_FALLBACK_LIBRARY_PATH is used (see below).
      ;;
@@ -31,7 +31,7 @@ NetBSD, FreeBSD, DragonFly, Darwin and S
      for arg in ${LDFLAGS}; do
        case "${arg}" in
          -L*)
-@@ -1339,7 +1340,7 @@ rm -f libconftest${DYLIB_EXT} conftest.c
+@@ -1367,7 +1368,7 @@ rm -f libconftest${DYLIB_EXT} conftest.c
      fpicflags="${darwin_pic}"
      shlib_cxxldflags="${shlib_ldflags}"
      ;;
@@ -40,7 +40,7 @@ NetBSD, FreeBSD, DragonFly, Darwin and S
      ## maybe this needs to depend on the compiler:
      ## -export-dynamic used to work, but does not with clang.
      ## Seems FreeBSD has used the GNU linker since at least 3.0 (Oct 1998)
-@@ -1428,6 +1429,12 @@ rm -f libconftest${DYLIB_EXT} conftest.c
+@@ -1456,6 +1457,12 @@ rm -f libconftest${DYLIB_EXT} conftest.c
      ;;
    netbsd*)
      ## See the comments about FreeBSD
@@ -53,7 +53,7 @@ NetBSD, FreeBSD, DragonFly, Darwin and S
      if ${CPP} - -dM < /dev/null | grep __ELF__ >/dev/null ; then
        main_ldflags="-Wl,--export-dynamic"
        shlib_ldflags="-shared"
-@@ -1464,22 +1471,22 @@ rm -f libconftest${DYLIB_EXT} conftest.c
+@@ -1493,22 +1500,22 @@ rm -f libconftest${DYLIB_EXT} conftest.c
    solaris*)
  ## SPARC has only an 8k global object table, 1024 entries on 64-bit,
  ## so need PIC not pic.  They are the same on other Solaris platforms.
@@ -80,16 +80,16 @@ NetBSD, FreeBSD, DragonFly, Darwin and S
        cpicflags="-KPIC"
        if test "`basename ${CXX}`" = "CC" ; then
          ## Forte version 7 needs -lCstd: Forte 6 does not.	
-@@ -1534,7 +1541,7 @@ R_SH_VAR_ADD(MAIN_LDFLAGS, [${main_ldfla
- : ${CPICFLAGS="${cpicflags}"}
- if test -z "${CPICFLAGS}"; then
+@@ -1587,7 +1594,7 @@ fi
+ : ${CXXPICFLAGS="${cxxpicflags}"}
+ if test -n "${CXX}" -a -z "${CXXPICFLAGS}"; then
    case "${host_os}" in
 -    aix*|mingw*)
 +    aix*|mingw*|darwin*)
        ;;
      *)
-       AC_MSG_WARN([I could not determine CPICFLAGS.])
-@@ -1616,10 +1623,10 @@ case "${host_os}" in
+       warn_cxxpicflags="I could not determine CXXPICFLAGS."
+@@ -1645,10 +1652,10 @@ case "${host_os}" in
      DYLIB_EXT=".dylib"
      dylib_ldflags="${darwin_dylib_ldflags}"
      MAJR_VERSION=`echo "${PACKAGE_VERSION}" | sed  -e "s/[[\.]][[1-9]]$/.0/"` 
@@ -103,7 +103,7 @@ NetBSD, FreeBSD, DragonFly, Darwin and S
      ;;
    hpux*)
      ## Needs to avoid embedding a relative path ../../../bin.
-@@ -2558,7 +2565,7 @@ case "${host_os}" in
+@@ -2615,7 +2622,7 @@ case "${host_os}" in
      r_ld_library_defaults="/usr/lib64:/lib64:/usr/lib:/lib"
      ;;
    solaris*)


--_----------=_1527762182246100--


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