CVS commit: pkgsrc/math/R

["Wen Heping" <wen%netbsd.org@localhost>]

Module Name:    pkgsrc
Committed By:   wen
Date:           Tue Jun 30 02:38:52 UTC 2015

Modified Files:
        pkgsrc/math/R: Makefile distinfo
        pkgsrc/math/R/patches: patch-src_main_character.c
Removed Files:
        pkgsrc/math/R/patches: patch-src_include_Rinterface.h

Log Message:
Update to 3.2.1

Upstream changes:
CHANGES IN R 3.2.1
NEW FEATURES

    utf8ToInt() now checks that its input is valid UTF-8 and returns NA if it is not.

    install.packages() now allows type = "both" with repos = NULL if it can infer the type of file.

    nchar(x, *) and nzchar(x) gain a new argument keepNA which governs how the result for NAs in x is determined. For the R 3.2.x series, the default remains FALSE which is fully back compatible. 
From R 3.3.0, the default will change to keepNA = NA and you are advised to consider this for code portability.

    news() more flexibly extracts dates from package ‘NEWS.Rd’ files.

    lengths(x) now also works (trivially) for atomic x and hence can be used more generally as an efficient replacement of sapply(x, length) and similar.

    The included version of PCRE has been updated to 8.37, a bug-fix release.

    diag() no longer duplicates a matrix when extracting its diagonal.

    as.character.srcref() gains an argument to allow characters corresponding to a range of source references to be extracted.

BUG FIXES

    acf() and ccf() now guarantee values strictly in [-1,1] (instead of sometimes very slightly outside). PR#15832.

    as.integer("111111111111") now gives NA (with a warning) as it does for the corresponding numeric or negative number coercions. Further, as.integer(M + 0.1) now gives M (instead of NA) when M is 
the maximal representable integer.

    On some platforms nchar(x, "c") and nchar(x, "w") would return values (possibly NA) for inputs which were declared to be UTF-8 but were not, or for invalid strings without a marked encoding in a 
multi-byte locale, rather than give an error. Additional checks have been added to mitigate this.

    apply(a, M, function(u) c(X = ., Y = .)) again has dimnames containing "X" and "Y" (as in R < 3.2.0).

    (Windows only) In some cases, the --clean option to R CMD INSTALL could fail. (PR#16178)

    (Windows only) choose.files() would occasionally include characters from the result of an earlier call in the result of a later one. (PR#16270)

    A change in RSiteSearch() in R 3.2.0 caused it to submit invalid URLs. (PR#16329)

    Rscript and command line R silently ignored incomplete statements at the end of a script; now they are reported as parse errors. (PR#16350)

    Parse data for very long strings was not stored. (PR#16354)

    plotNode(), the workhorse of the plot method for "dendrogram"s is no longer recursive, thanks to Suharto Anggono, and hence also works for deeply nested dendrograms. (PR#15215)

    The parser could overflow internally when given numbers in scientific format with extremely large exponents. (PR#16358)

    If the CRAN mirror was not set, install.packages(type = "both") and related functions could repeatedly query the user for it. (Part of PR#16362)

    The low-level functions .rowSums() etc. did not check the length of their argument, so could segfault. (PR#16367)

    The quietly argument of library() is now correctly propagated from .getRequiredPackages2().

    Under some circumstances using the internal PCRE when building R fron source would cause external libs such as -llzma to be omitted from the main link.

    The .Primitive default methods of the logic operators, i.e., !, & and |, now give correct error messages when appropriate, e.g., for `&`(TRUE) or `!`(). (PR#16385)

    cummax(x) now correctly propagates NAs also when x is of type integer and begins with an NA.

    summaryRprof() could fail when the profile contained only two records. (PR#16395)

    HTML vignettes opened using vignette() did not support links into the rest of the HTML help system. (Links worked properly when the vignette was opened using browseVignettes() or from within the 
help system.)

    arima(*, xreg = .) (for d >= 1) computes estimated variances based on a the number of effective observations as in R version 3.0.1 and earlier. (PR#16278)

    slotNames(.) is now correct for "signature" objects (mostly used internally in methods).

    On some systems, the first string comparison after a locale change would result in NA.


To generate a diff of this commit:
cvs rdiff -u -r1.159 -r1.160 pkgsrc/math/R/Makefile
cvs rdiff -u -r1.66 -r1.67 pkgsrc/math/R/distinfo
cvs rdiff -u -r1.1 -r0 pkgsrc/math/R/patches/patch-src_include_Rinterface.h
cvs rdiff -u -r1.1 -r1.2 pkgsrc/math/R/patches/patch-src_main_character.c

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