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**To**:**pkgsrc-changes%NetBSD.org@localhost****Subject**:**CVS commit: pkgsrc/math/R****From**:**"Wen Heping" <wen%netbsd.org@localhost>**- Date: Fri, 21 Dec 2018 02:55:06 +0000

Module Name: pkgsrc Committed By: wen Date: Fri Dec 21 02:55:06 UTC 2018 Modified Files: pkgsrc/math/R: Makefile PLIST distinfo Log Message: Update to 3.5.2 Upstream changes: CHANGES IN R 3.5.2: PACKAGE INSTALLATION: * New macro CXX_VISIBILITY analogous to C_VISIBILITY (which several packages have been misusing for C++ code) for the default C++ compiler (but not necessarily one used for non-default C++ dialects like C++14). TESTING: * The random number generator tests in tests/p-r-random-tests.R no longer fail occasionally as they now randomly sample from "certified" random seeds. BUG FIXES: * The "glm" method of drop1() miscalculated the score test (test="Rao") when the model contained an offset. * Linear multiple empty models such as lm(y ~ 0) now have a correctly dimensioned empty coefficient matrix; reported by Brett Presnell. * vcov(<empty mlm>) and hence confint() now work (via a consistency change in summary.lm()). * confint(<multiple lm()>) now works correctly; reported on R-devel by Steven Pav. * quade.test() now also works correctly when its arguments are not yet sorted along groups, fixing PR#15842. * Installation on a Unix-alike tries harder to link to the pthread library where required (rather than relying on OpenMP to provide it: configuring with --disable-openmp was failing on some Linux systems). * The data.frame method for print(x) is fast now also for large data frames x and got an optional argument max, thanks to suggestions by Juan Telleria. * hist() no longer integer overflows in very rare cases, fixing PR#17450. * untar() ignored a character compressed argument: however many external tar programs ignore the flags which should have been set and automagically choose the compression type, and if appropriate gzip or bzip2 compression would have been chosen from the magic header of the tarball. * zapsmall(x) now works for more "number-like" objects. * The tools-internal function called from R CMD INSTALL now gets a warnOption = 1 argument and only sets options(warn = warnOption) when that increases the warning level (PR#17453). * Analogously, the tools-internal function called from R CMD check gets a warnOption = 1 argument and uses the larger of that and getOption("warn"), also allowing to be run with increased warning level. * Parse data now have deterministic parent nodes (PR#16041). * Calling match() with length one x and POSIXlt table gave a segfault (PR#17459). * Fork clusters could hang due to a race condition in cluster initialization (makeCluster()). * nextn(n) now also works for larger n and no longer loops infinitely for e.g, n <- 214e7. * cooks.distance() and rstandard() now work correctly for multiple linear models ("mlm"). * polym() and corresponding lm() prediction now also work for a boundary "vector" case fixing PR#17474, reported by Alexandre Courtiol. * With a very large number of variables terms() could segfault (PR#17480). * cut(rep(0, 7)) now works, thanks to Joey Reid and Benjamin Tyner (PR#16802). * download.file(*, method = "curl", cacheOK = FALSE) should work now on Windows, thanks to Kevin Ushey's patch in PR#17323. * duplicated(<dataframe with 'f'>) now works, too, thanks to Andreas Kersting's PR#17485; ditto for anyDuplicated(). * legend(*, cex = 1:2) now works less badly. * The print() method for POSIXct and POSIXlt now correctly obeys getOption("max.print"), fixing a long-standing typo, and it also gets a corresponding optional max argument. * Unserialization of raw vectors serialized in ASCII representation now works correctly. * <data frame>[TRUE, <new>] <- list(c1, c2) now works correctly, thanks to Suharto Anggono's PR#15362 and Emil Bode's patch in PR#17504. * seq.int(*, by=by, length=n) no longer wrongly "drops fractional parts" when by is integer, thanks to Suharto Anggono's report PR#17506. * Buffering is disabled for file() connections to non-regular files (like sockets), as well as fifo() and pipe() connections. Fixes PR#17470, reported by Chris Culnane. To generate a diff of this commit: cvs rdiff -u -r1.193 -r1.194 pkgsrc/math/R/Makefile cvs rdiff -u -r1.30 -r1.31 pkgsrc/math/R/PLIST cvs rdiff -u -r1.81 -r1.82 pkgsrc/math/R/distinfo Please note that diffs are not public domain; they are subject to the copyright notices on the relevant files.

Modified files: Index: pkgsrc/math/R/Makefile diff -u pkgsrc/math/R/Makefile:1.193 pkgsrc/math/R/Makefile:1.194 --- pkgsrc/math/R/Makefile:1.193 Thu Dec 13 19:52:08 2018 +++ pkgsrc/math/R/Makefile Fri Dec 21 02:55:06 2018 @@ -1,7 +1,6 @@ -# $NetBSD: Makefile,v 1.193 2018/12/13 19:52:08 adam Exp $ +# $NetBSD: Makefile,v 1.194 2018/12/21 02:55:06 wen Exp $ -DISTNAME= R-3.5.1 -PKGREVISION= 5 +DISTNAME= R-3.5.2 CATEGORIES= math MASTER_SITES= ${MASTER_SITE_R_CRAN:=base/R-3/} Index: pkgsrc/math/R/PLIST diff -u pkgsrc/math/R/PLIST:1.30 pkgsrc/math/R/PLIST:1.31 --- pkgsrc/math/R/PLIST:1.30 Wed Jul 4 07:27:13 2018 +++ pkgsrc/math/R/PLIST Fri Dec 21 02:55:06 2018 @@ -1,4 +1,4 @@ -@comment $NetBSD: PLIST,v 1.30 2018/07/04 07:27:13 wen Exp $ +@comment $NetBSD: PLIST,v 1.31 2018/12/21 02:55:06 wen Exp $ bin/R bin/Rscript info/R-FAQ.info.gz @@ -1071,6 +1071,9 @@ lib/R/library/survival/doc/adjcurve.pdf lib/R/library/survival/doc/compete.R lib/R/library/survival/doc/compete.Rnw lib/R/library/survival/doc/compete.pdf +lib/R/library/survival/doc/concordance.R +lib/R/library/survival/doc/concordance.Rnw +lib/R/library/survival/doc/concordance.pdf lib/R/library/survival/doc/index.html lib/R/library/survival/doc/multi.R lib/R/library/survival/doc/multi.Rnw Index: pkgsrc/math/R/distinfo diff -u pkgsrc/math/R/distinfo:1.81 pkgsrc/math/R/distinfo:1.82 --- pkgsrc/math/R/distinfo:1.81 Wed Jul 4 07:27:13 2018 +++ pkgsrc/math/R/distinfo Fri Dec 21 02:55:06 2018 @@ -1,9 +1,9 @@ -$NetBSD: distinfo,v 1.81 2018/07/04 07:27:13 wen Exp $ +$NetBSD: distinfo,v 1.82 2018/12/21 02:55:06 wen Exp $ -SHA1 (R-3.5.1.tar.gz) = 9314d3d372b05546a33791fbc8dd579c92ebd16b -RMD160 (R-3.5.1.tar.gz) = 394b122f4477b0c8e87c48fcc8cf4a1f8282a9bc -SHA512 (R-3.5.1.tar.gz) = 382cc6e200469dd168799948edcf3a0b869d7ef3b3176fdfc60752f3f37e6ba356323c47d8815a4d9ab6ad3a21cd045d26ef5e75107c8685328e0ffcfd172f7f -Size (R-3.5.1.tar.gz) = 29812849 bytes +SHA1 (R-3.5.2.tar.gz) = 057ea91daed3e68a12b2a473ee1283cf26f360e2 +RMD160 (R-3.5.2.tar.gz) = c1cee244f1ae0cf7466b2af69a70bb7eee1321ed +SHA512 (R-3.5.2.tar.gz) = 53e94f01ecee6c90cecfa07ee9950d62130a331010c0b23baaf88ab5009007856c9352ce97916404ff35d19632495902d41cb655a5fd116a7d2f5d6767d7b447 +Size (R-3.5.2.tar.gz) = 30186438 bytes SHA1 (patch-ad) = a43b4875a2ee4677b5f762abf3f9a623fd12cbb5 SHA1 (patch-configure.ac) = f4829c37304e81485e13b4ed8beaeac7edd16189 SHA1 (patch-m4_R.m4) = 704d5514e10adf0b5217bb71b06f44a612eca6e0

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