CVS commit: pkgsrc/misc/R-Hmisc

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

Module Name:    pkgsrc
Committed By:   mef
Date:           Wed Jan 29 11:49:15 UTC 2025

Modified Files:
        pkgsrc/misc/R-Hmisc: Makefile distinfo

Log Message:
(misc/R-Hmisc) Updated 5.1.1 to 5.2.2

Changes in version 5.2-2 (2025-01-10)

   * cutGn: new function to group a numeric variable into interals
     guaranteeing a minimum group size; uses new Fortran subroutine
     cutgn
   * ordGroupBoot: new function to group a numeric variable minimally
     so that bootstrap samples will cover all the original distinct
     data values
   * plsmo, xy.group.s: use cutGn instead of cut2
   * num.intercepts: look at fit$info.matrix if fit$var is empty

Changes in version 5.2-1 (2024-11-30)

   * re-wrote rcorr Fortran subroutine using vectorization and
     improved numerical algorithm
   * added function qrxcenter
   * fixed llist so that label is not applied at the end if
     labels=FALSE, and labels are not applied to NULLs
   * added type to returned value for rcorr

Changes in version 5.2-0 (2024-10-19)
   * added requireNamespace for safer in qcrypt
   * require R 4.2.0 or later, to handle pipes
   * new function pMedian for pseudomedian (Hodges-Lehmann one-sample
     estimator)
   * added pMedian to describe function
   * Converted all Ratfor code to Fortran 2018

Changes in version 5.1-3 (2024-05-18)

   * areg.boot: intercepted use of xlim when y is categorical; need to
     improve logic on xout=
   * redun: stored scores matrix in returned object, suitable for
     r2describe
   * r2describe: new function to list strongest predictors of each
     variable in a matrix, from all the other columns
   * movStats: added lrm_args argument
   * logrank (in spower.s): removed non-working non-executed code for
     stratified log rank, change hazard ratio estimate to Pike's
     estimator.  Previous hazard ratio calculation was incorrect.

   * qcrypt: added service=NA to bypass keyring
   * runParallel: changed progress directory explicitly to /tmp for Mac
   * printL: new function
   * redun: got around model.frame problem so that negated variables
     are omitted from analysis; also fixed printing of missing values

Changes in version 5.1-2 (2024-03-09)

   * dotchartpl: remove length(ugroup) criterion (unsure what this was
     doing and made lower and upper be not plotted)

   * dotchartpl: got around new bug in plotly when numeric vectors
     were given to axis ticktext; changed to character via format()

   * cut2: fixed to handle large g values (Thanks Cole Beck
     https://github.com/harrelfe/Hmisc/pull/170)

   * Added dependency on R 4.1.0 or later because of use of new pipe
     operator in describe etc.

   * GiniMd: got around bug in sum(empty vector) = 0 by returning NA
     if na.rm=FALSE and there were any NAs

   * testCharDateTime: correctly handle case where all values are NA
     or '' and convert=TRUE

   * hdquantile: allowed for scalar probs (see
     https://github.com/harrelfe/Hmisc/pull/180; thanks Cole Beck)

   * movStats: added nignore argument, defaults to 10 (the previous
     behavior)

   * history.data.frame, ecdf: fixed dev issue
     https://github.com/harrelfe/Hmisc/issues/181

   * spikecomp: for tresult='segments' removed attributes from vectors
     to make data.table compliant

   * xless: adapted for MacOS using open system command


To generate a diff of this commit:
cvs rdiff -u -r1.8 -r1.9 pkgsrc/misc/R-Hmisc/Makefile
cvs rdiff -u -r1.7 -r1.8 pkgsrc/misc/R-Hmisc/distinfo

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

Modified files:

Index: pkgsrc/misc/R-Hmisc/Makefile
diff -u pkgsrc/misc/R-Hmisc/Makefile:1.8 pkgsrc/misc/R-Hmisc/Makefile:1.9
--- pkgsrc/misc/R-Hmisc/Makefile:1.8    Wed Jan 24 14:05:07 2024
+++ pkgsrc/misc/R-Hmisc/Makefile        Wed Jan 29 11:49:14 2025
@@ -1,7 +1,7 @@
-# $NetBSD: Makefile,v 1.8 2024/01/24 14:05:07 mef Exp $
+# $NetBSD: Makefile,v 1.9 2025/01/29 11:49:14 mef Exp $
 
 R_PKGNAME=     Hmisc
-R_PKGVER=      5.1-1
+R_PKGVER=      5.2-2
 CATEGORIES=    misc
 
 MAINTAINER=    pkgsrc-users%NetBSD.org@localhost
@@ -20,10 +20,10 @@ DEPENDS+=   R-htmlTable>=1.11.0:../../text
 DEPENDS+=      R-htmltools>=0.3.6:../../textproc/R-htmltools
 
 # Packages suggested but not available:
-#   'qreport', 'rms', 'mice', 'tables', 'plotly', 'leaps', 'pcaPP',
-#   'polspline', 'abind', 'kableExtra', 'rio', 'gt', 'sparkline', 'qs',
-#   'getPass', 'keyring', 'safer'
+#   'qreport', 'rms', 'mice', 'tables', 'plotly', 'leaps', 'polspline',
+#   'kableExtra', 'gt', 'sparkline', 'qs', 'keyring', 'safer', 'htm2txt'
 
+TEST_DEPENDS+= R-abind-[0-9]*:../../math/R-abind
 TEST_DEPENDS+= R-base64enc-[0-9]*:../../converters/R-base64enc
 TEST_DEPENDS+= R-chron-[0-9]*:../../math/R-chron
 TEST_DEPENDS+= R-Formula-[0-9]*:../../math/R-Formula
@@ -31,8 +31,11 @@ TEST_DEPENDS+=       R-gridExtra-[0-9]*:../../
 TEST_DEPENDS+= R-htmlTable-[0-9]*:../../textproc/R-htmlTable
 TEST_DEPENDS+= R-htmltools-[0-9]*:../../textproc/R-htmltools
 TEST_DEPENDS+= R-latticeExtra-[0-9]*:../../graphics/R-latticeExtra
+TEST_DEPENDS+= R-pcaPP-[0-9]*:../../math/R-pcaPP
+TEST_DEPENDS+= R-rio-[0-9]*:../../devel/R-rio
 TEST_DEPENDS+= R-VGAM-[0-9]*:../../math/R-VGAM
 TEST_DEPENDS+= R-viridis-[0-9]*:../../graphics/R-viridis
+TEST_DEPENDS+= R-getPass-[0-9]*:../../security/R-getPass
 #EST_DEPENDS+= R-rms-[0-9]*:
 #EST_DEPENDS+= R-mice-[0-9]*:
 #EST_DEPENDS+= R-tables-[0-9]*:

Index: pkgsrc/misc/R-Hmisc/distinfo
diff -u pkgsrc/misc/R-Hmisc/distinfo:1.7 pkgsrc/misc/R-Hmisc/distinfo:1.8
--- pkgsrc/misc/R-Hmisc/distinfo:1.7    Wed Jan 24 14:05:07 2024
+++ pkgsrc/misc/R-Hmisc/distinfo        Wed Jan 29 11:49:14 2025
@@ -1,5 +1,5 @@
-$NetBSD: distinfo,v 1.7 2024/01/24 14:05:07 mef Exp $
+$NetBSD: distinfo,v 1.8 2025/01/29 11:49:14 mef Exp $
 
-BLAKE2s (R/Hmisc_5.1-1.tar.gz) = a12785556ddabb0e85bc842f9183f58e57c705ab562a0cb07528e7f028911c48
-SHA512 (R/Hmisc_5.1-1.tar.gz) = 4589d5c9a574edff959f0d12da8312cf54a78df4c36231a7df4416e7359aa90c639c654aa3b2d20c4708bbbd776ba9cb1a623985e8bb45fc65b51fe96e056165
-Size (R/Hmisc_5.1-1.tar.gz) = 875858 bytes
+BLAKE2s (R/Hmisc_5.2-2.tar.gz) = efe630f95935726fcdc4010415e47a3f5e03a475f0c8b27d30a398c6b60490c0
+SHA512 (R/Hmisc_5.2-2.tar.gz) = 9ed72cd84866ccf5f8fa0af62e348c0d91aef203045bf60b1a6b7c361d2c268f0bfe500bb5ed8a623dd8045c18c52b79db50714b6ddf737217f0ecf7fab0483e
+Size (R/Hmisc_5.2-2.tar.gz) = 894979 bytes