CVS commit: pkgsrc/math/R-survey

["Makoto Fujiwara" <mef%netbsd.org@localhost>]

Module Name:    pkgsrc
Committed By:   mef
Date:           Wed Jun 10 22:00:47 UTC 2026

Modified Files:
        pkgsrc/math/R-survey: Makefile distinfo
Added Files:
        pkgsrc/math/R-survey/files: Makevars

Log Message:
(math/R-survey) Updated 4.4.2 to 4.5

(pkgsrc)
   - There is a file src/Makevars.makefile, but it does not seem to be used
     (changes on that file does not affect anything) so files/Makevars are
     added for PKG_LIBS+= -lexecinfo

(upstream)
4.5     start of first version of multiphase() for arbitrary multiphase sampling
        (experimental, may contain nuts)

        Wilson ('score test') confidence intervals in svyciprop (from Stas Kolenikov)

        svydesign() gives a clearer error message when there are more stages in
        fpc= than in id= (for Stephanie Zimmer)

        svrepdesign(type="ACS") now uses mse=TRUE unless mse=FALSE is explicitly
        given, in which case it warns (for Anthony Damico)

        svystat,svrepstat objects lose their variance attribute and class on
        math operations so the standard errors don't end up misleading. Use
        svycontrast() to get transformed versions with SEs
        (for Pavel Krivitsky)

        The $aic component of svyglm objects, which is undocumented and meaningless,
        is now set to NA. If this breaks your code, your code was already wrong.
        (for Michael Reiss)

        svyby(covmat=TRUE) now works for estimators where subset() doesn't actually
        drop rows

        svydesign(.., weights=1) now works, though it's still not recommended. Attempts
        to recycle a weights vector that isn't of length 1 get an error

        for replicate-weight designs with user-forced degrees of freedom, the
        degrees of freedom shouldn't change under subsetting
        (because that's computationally expensive).  For Joel Barnes, Isabelle Michaud

        clarify that calibrate() can take margins specified in either of the formats
        that rake() accepts

        rake() now handles much larger sets of margins (from Ben Schneider)
        The results may be different if too loose a tolerance was specified or if
        zeroes make the true optimum non-unique.

        confint(withReplicates()) assigns names when there aren't any,
        rather than failing (from Ben Schneider)

        degf<-.svyrep.design() to allow the user to modify the degrees of freedom
        if they specified it by hand

        a bit more detail on svyciprop(type="xlogit") (from Ben Schneider)

        Bell-McCaffrey standard errors (from Stas Kolenikov)

        remove spurious warning in svyvar for replicate-weights with mse=TRUE
        (Ben Schneider)

        change deprecated arma::is_finite to standard::isfinite

        Add option na_weights. If "allow" or "warn", svydesign will drop any
        records with NA weights before setting up the design.
        The default, "fail", will give an error.
        For database-backed designs it is currently only possible to have "fail"
        but this may change in the future (for Stephanie Zimmer and David Wilson)

4.4-3   options(survey.lonely.psu="adjust") needed strata to be a factor or numeric
        (for Richard Li, Durga Nagori)

        Initial version of multiframe() for dual-frame sampling and
        reweight() for optimising frame weights. Methods for svytotal,
        svymean, svyglm, svyvar, svychisq, update, subset

        Initial version of withCrossval() for cross-validation

        withPV with action=fun and rewrite=TRUE wasn't working

        add "pps_spec" virtual class for all the PPS sparse matrix things

        support calibration to the influence functions of a phase-1 model in calibrate.twophase and
        calibrate.twophase2 (currently only with simple random sampling at phase 1)

        added svychisq.twophase2 (for Yilin Zhang)

        twophase2 objects now print the call that created them better

        ?svystat and ?svrepstat now point to ?surveysummary, which describes the structure
        (for Terry Therneau)

        predict.svyglm will impute zero for NA coefficients (Terry Therneau).

        With se.fit=FALSE, predict.svyglm returns a numeric vector rather than a
        svystat object


To generate a diff of this commit:
cvs rdiff -u -r1.5 -r1.6 pkgsrc/math/R-survey/Makefile
cvs rdiff -u -r1.6 -r1.7 pkgsrc/math/R-survey/distinfo
cvs rdiff -u -r0 -r1.1 pkgsrc/math/R-survey/files/Makevars

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-survey/Makefile
diff -u pkgsrc/math/R-survey/Makefile:1.5 pkgsrc/math/R-survey/Makefile:1.6
--- pkgsrc/math/R-survey/Makefile:1.5   Sun Nov 24 05:23:25 2024
+++ pkgsrc/math/R-survey/Makefile       Wed Jun 10 22:00:47 2026
@@ -1,7 +1,7 @@
-# $NetBSD: Makefile,v 1.5 2024/11/24 05:23:25 mef Exp $
+# $NetBSD: Makefile,v 1.6 2026/06/10 22:00:47 mef Exp $
 
 R_PKGNAME=     survey
-R_PKGVER=      4.4-2
+R_PKGVER=      4.5
 
 MAINTAINER=    pkgsrc-users%NetBSD.org@localhost
 COMMENT=       Analysis of complex survey samples
@@ -19,7 +19,13 @@ TEST_DEPENDS+=       R-RSQLite-[0-9]*:../../da
 TEST_DEPENDS+= R-quantreg-[0-9]*:../../math/R-quantreg
 
 USE_LANGUAGES= c++
+GCC_REQD+=     8
 
+.include "../../mk/bsd.prefs.mk"
+pre-patch:
+.if ${OPSYS} != SunOS && ${OPSYS} != Linux
+       ${CP} ${FILESDIR}/Makevars ${WRKSRC}/src/
+.endif
 .include "../../math/R-RcppArmadillo/buildlink3.mk"
 .include "../../math/R/Makefile.extension"
 .include "../../mk/bsd.pkg.mk"

Index: pkgsrc/math/R-survey/distinfo
diff -u pkgsrc/math/R-survey/distinfo:1.6 pkgsrc/math/R-survey/distinfo:1.7
--- pkgsrc/math/R-survey/distinfo:1.6   Sun Nov 24 05:23:25 2024
+++ pkgsrc/math/R-survey/distinfo       Wed Jun 10 22:00:47 2026
@@ -1,5 +1,5 @@
-$NetBSD: distinfo,v 1.6 2024/11/24 05:23:25 mef Exp $
+$NetBSD: distinfo,v 1.7 2026/06/10 22:00:47 mef Exp $
 
-BLAKE2s (R/survey_4.4-2.tar.gz) = 62fae78306d03f9a1c0d4d05a556f63f6760bd6369631d612984dbb43db7e83c
-SHA512 (R/survey_4.4-2.tar.gz) = e9648cb482e2b5a8edefd609c5faa0305a43a5a9d91dcd0dd27e8275252486126320cc60ed2f899c016fa2aced8682bb75649a3386a936f0981256a5d8f41746
-Size (R/survey_4.4-2.tar.gz) = 2341313 bytes
+BLAKE2s (R/survey_4.5.tar.gz) = 82a428f632ab86b146b9755471adce78ea6b3ea37cb5fd1a58414a1edb93cf82
+SHA512 (R/survey_4.5.tar.gz) = 82c7bf193b89fe30e1801865842a715c8420c5b1aeb7977932770257f9ae3f650edf74111cfd1b5e7443e773a67fed80629741298dce0b062971cd8c3a4a8508
+Size (R/survey_4.5.tar.gz) = 2417046 bytes

Added files:

Index: pkgsrc/math/R-survey/files/Makevars
diff -u /dev/null pkgsrc/math/R-survey/files/Makevars:1.1
--- /dev/null   Wed Jun 10 22:00:47 2026
+++ pkgsrc/math/R-survey/files/Makevars Wed Jun 10 22:00:47 2026
@@ -0,0 +1 @@
+PKG_LIBS+=     -lexecinfo