version 7.3-57

DESCRIPTION

@@ -1,8 +1,8 @@
 Package: MASS
 Priority: recommended
-Version: 7.3-56
-Date: 2022-03-23
-Revision: $Rev: 3561 $
+Version: 7.3-57
+Date: 2022-04-05
+Revision: $Rev: 3564 $
 Depends: R (>= 3.3.0), grDevices, graphics, stats, utils
 Imports: methods
 Suggests: lattice, nlme, nnet, survival
@@ -24,7 +24,7 @@ License: GPL-2 | GPL-3
 URL: http://www.stats.ox.ac.uk/pub/MASS4/
 Contact: <MASS@stats.ox.ac.uk>
 NeedsCompilation: yes
-Packaged: 2022-03-23 07:38:58 UTC; ripley
+Packaged: 2022-04-19 04:13:16 UTC; ripley
 Author: Brian Ripley [aut, cre, cph],
   Bill Venables [ctb],
   Douglas M. Bates [ctb],
@@ -33,4 +33,4 @@ Author: Brian Ripley [aut, cre, cph],
   David Firth [ctb]
 Maintainer: Brian Ripley <ripley@stats.ox.ac.uk>
 Repository: CRAN
-Date/Publication: 2022-03-23 07:51:46 UTC
+Date/Publication: 2022-04-22 11:45:27 UTC

MD5

@@ -1,7 +1,7 @@
-5406299e9b97fecdfbdf44be87b06072 *DESCRIPTION
+37e8e45658ca2512e47990c80e3fe867 *DESCRIPTION
 35aff05a505ecf7e81e0473767794ca9 *INDEX
 c7acdc0fa828f781a0a5586ab9d4fa1b *LICENCE.note
-0ac7b30ad35a4c19ea69d76a6a366b02 *NAMESPACE
+3c2dfc5f75d8a5a108ce9a1948aaf8dc *NAMESPACE
 aed71ed40bb9bfdd7d19edfdbd163087 *R/add.R
 667178114b2cc60142fed7fc16c00f90 *R/area.R
 2b449dd3fde83489799ef5f72bc8ead0 *R/boxcox.R
@@ -15,7 +15,7 @@ bca9a041d73f25376018c9e4cca65922 *R/cov.trob.R
 81f2b80d082acd4bf2cdcdf581277cc1 *R/fitdistr.R
 deb0581428073be21384b2fea27457cc *R/fractions.R
 fdd720ed0d234e62ec46ad80ffc5c3f6 *R/gamma.shape.R
-33245613e19889f159059b2955e34bff *R/glmmPQL.R
+51280f00f8f92b878f6c29bf9d2d9854 *R/glmmPQL.R
 f6c250dc2c0287a0d9a7e577352bc3f1 *R/hist.scott.R
 66ee029442522726306cd7d4a869b725 *R/huber.R
 feed05160fcb53f8d07c559e1afa9873 *R/hubers.R
@@ -46,7 +46,7 @@ f1db7f02de9bae7087fc01a7ffe4748e *R/truehist.R
 bbde4307b98d968e9b85d55f46a0cbe6 *R/ucv.R
 29fdbf836b6ebffc562ce7d2b54ab5eb *R/write.matrix.R
 4f74ab00a8fd8a8eaf56957b1e13aa52 *R/zzz.R
-32d54847e7474d04ae8b386217f45fea *build/partial.rdb
+1961639f6f4f7f9efffa91b624b3d060 *build/partial.rdb
 e4aa969dc4062a5dfa605a141bf32f29 *data/Aids2.rda
 3c5a57a9f86ee32ac10f6114826a762b *data/Animals.rda
 689cd33a62093be4f53a38cc8405e083 *data/Boston.rda
@@ -160,8 +160,8 @@ caebd3270cdb7268117f8a5a0cddd7be *inst/scripts/ch15.R
 3a3a57e6adb876a749a48669092ee37b *inst/scripts/ch16.R
 1b78ed518f4fbf6ed3704b0a8463715b *man/Aids2.Rd
 d5b9cf75996ccdc90872d49b2f87cae5 *man/Animals.Rd
-6a7a598f4cb667af6b8dc886b520696a *man/Boston.Rd
-917c6645bb1cee53e03f4155fc6f8599 *man/Cars93.Rd
+e0715295dbeae3214279d07bd1d89116 *man/Boston.Rd
+0ac21fa2c81d16c1e1efdb6b2ca5aea7 *man/Cars93.Rd
 e1cc4debb9ba4982b2a78864d03bf5d7 *man/Cushings.Rd
 5e497af7fdc9b4d6b7e771f3839a0c4e *man/DDT.Rd
 fc4ebf60ca33228804e86cd08ee7b990 *man/GAGurine.Rd
@@ -196,15 +196,15 @@ e79ea25d60ba827b71a57f7458f733d2 *man/bcv.Rd
 2f6ba17e14d2daa4afc541d3445190ad *man/birthwt.Rd
 bebc2ad312668d479d67adbb5fd3777d *man/boxcox.Rd
 2ca64d5540ffa5e91f3c8461e6e3124b *man/cabbages.Rd
-dc0c0d7f1beb93b31c7df02fa2c691ae *man/caith.Rd
+9a9a2f5323a13a701a74a514785cd771 *man/caith.Rd
 726868057d0e31cad05e01c7b379573c *man/cats.Rd
 017ddc74606e2e08885a718313f9ea6b *man/cement.Rd
 1ce122787e058327f52bd789e3a12dc9 *man/chem.Rd
 00995ff596440aa4a397749326348872 *man/con2tr.Rd
 e35fa2f6ee37f213648c7ec087ce8b83 *man/confint.Rd
 4480f1a975763e68c264a8fdbe30cf7b *man/contr.sdif.Rd
 88bb557bbfe7f9a6889f4f01ef7f490f *man/coop.Rd
-3cca451869361d60a11f741ee676136a *man/corresp.Rd
+4b5232b75977adcc4eafa9823e8d3912 *man/corresp.Rd
 7c046b9650055e52296467fbe378309a *man/cov.rob.Rd
 b1a92f03d6905de2e74059df3a93f334 *man/cov.trob.Rd
 795a3a88f04d699ea466dbefb30adfcf *man/cpus.Rd
@@ -262,7 +262,7 @@ f8a1e349fbe9051ba75a935ba2803149 *man/minn38.Rd
 fbf5b11e7ed253d29500bac780e2e794 *man/negative.binomial.Rd
 c73e2dbd1f3749c2a85df1c993699d9f *man/newcomb.Rd
 0d589532d9330eedf9abb57688afdab6 *man/nlschools.Rd
-d7fa0f842323e2546a258c19eb1566c1 *man/npk.Rd
+9e1448db88f35cf2fe22a0b358514a3c *man/npk.Rd
 919de166373a81866c8f6152e64dc418 *man/npr1.Rd
 0fb65b5e6d3e0ceaf209f50d14caf636 *man/oats.Rd
 00698a2eb415969b83999b0ff995cced *man/painters.Rd
@@ -321,16 +321,16 @@ ceefe8e558dfa70a28f54fcae1ca3df0 *man/whiteside.Rd
 1191b3abb0caad62ecd5e4ad544361c4 *po/R-ko.po
 b6e225a125d6368318896f92ffd91e0f *po/R-pl.po
 020be0ec5305b41949da681312f305cb *src/MASS.c
-1d9128cf14bc66205891d2dbeed67ff4 *src/lqs.c
+c4ed0a42234771cb07d140e375edc23f *src/lqs.c
 7b1360150b8598b576e82534b12345a2 *tests/BankWages.rda
-1360a62ffb03bbf29abbb192009dfcf4 *tests/Examples/MASS-Ex.Rout.save
+31c485d8c85fdda93c7248b83e0f1bbb *tests/Examples/MASS-Ex.Rout.save
 d87553db40364fdc9c337fa31c009b17 *tests/confint.R
-1f8da7753dd46912a4839450ee3d7f44 *tests/cov.mcd.R
+e059b0451b55d1e8cb8ebf51ecce76ea *tests/cov.mcd.R
 a0854fee9b36691ca1d0880da31d6f79 *tests/fitdistr.R
 55c6f4de353b9479359459d2718a017e *tests/fitdistr.Rout.save
 afd4f607cba7fda8ec4d22bffd88fc50 *tests/glm.nb.R
 7fea2161b12d01c8940107342815dd0e *tests/hubers.R
-80c50d5c299f0d0a4dbbb457a235faba *tests/lme.R
+7f6efdd17aea2750feda4db0abd46d48 *tests/lme.R
 edee76adc2d27e4ba90f1ff79360148b *tests/polr.R
 f4e6b3ffb6521ea7625515e2f0ae7f98 *tests/profile.R
 a23ddf89e02a02ed030e4ed5538d3430 *tests/regression.R

NAMESPACE

@@ -104,6 +104,7 @@ S3method(extractAIC, loglm)
 S3method(extractAIC, polr)
 S3method(family, negbin)
 S3method(fitted, loglm)
+S3method(formula, glmmPQL)
 S3method(gamma.shape, glm)
 S3method(lda, data.frame)
 S3method(lda, default)

R/glmmPQL.R

@@ -1,5 +1,5 @@
 # file MASS/R/glmmPQL.R
-# copyright (C) 2002-2015 W. N. Venables and B. D. Ripley
+# copyright (C) 2002-2022 W. N. Venables and B. D. Ripley
 #
 #  This program is free software; you can redistribute it and/or modify
 #  it under the terms of the GNU General Public License as published by
@@ -138,3 +138,7 @@ logLik.glmmPQL <- function (object, ...)
 
 anova.glmmPQL <- function (object, ...)
     stop("'anova' is not available for PQL fits")
+
+## Suggested by Sebastian Meyer 2022-03
+
+formula.glmmPQL <- function(x, ...) eval(x$call$fixed)

man/Boston.Rd

@@ -1,5 +1,5 @@
 % file MASS/man/Boston.Rd
-% copyright (C) 1994-9 W. N. Venables and B. D. Ripley
+% copyright (C) 1994-2022 W. N. Venables and B. D. Ripley
 %
 \name{Boston}
 \alias{Boston}
@@ -43,7 +43,7 @@ Boston
       index of accessibility to radial highways.
     }
     \item{\code{tax}}{
-      full-value property-tax rate per \$10,000.
+      full-value property-tax rate per $10,000.
     }
     \item{\code{ptratio}}{
       pupil-teacher ratio by town.
@@ -56,7 +56,7 @@ Boston
       lower status of the population (percent).
     }
     \item{\code{medv}}{
-      median value of owner-occupied homes in \$1000s.
+      median value of owner-occupied homes in $1000s.
     }
   }
 }

man/Cars93.Rd

@@ -1,5 +1,5 @@
 % file MASS/man/Cars93.Rd
-% copyright (C) 1994-2018 W. N. Venables and B. D. Ripley
+% copyright (C) 1994-2022 W. N. Venables and B. D. Ripley
 %
 \name{Cars93}
 \alias{Cars93}
@@ -26,14 +26,14 @@ Cars93
       \code{"Compact"}, \code{"Midsize"}, \code{"Large"} and \code{"Van"}.
     }
     \item{\code{Min.Price}}{
-      Minimum Price (in \$1,000): price for a basic version.
+      Minimum Price (in $1,000): price for a basic version.
     }
     \item{\code{Price}}{
-      Midrange Price (in \$1,000): average of \code{Min.Price} and
+      Midrange Price (in $1,000): average of \code{Min.Price} and
       \code{Max.Price}.
     }
     \item{\code{Max.Price}}{
-      Maximum Price (in \$1,000): price for \dQuote{a premium version}.
+      Maximum Price (in $1,000): price for \dQuote{a premium version}.
     }
     \item{\code{MPG.city}}{
       City MPG (miles per US gallon by EPA rating).

man/caith.Rd

@@ -1,5 +1,5 @@
 % file MASS/man/caith.Rd
-% copyright (C) 1999 W. N. Venables and B. D. Ripley
+% copyright (C) 1999-2022 W. N. Venables and B. D. Ripley
 %
 \name{caith}
 \alias{caith}
@@ -27,7 +27,10 @@ caith
   \emph{Modern Applied Statistics with S.} Fourth edition.  Springer.
 }
 \examples{
+## IGNORE_RDIFF_BEGIN
+## The signs can vary by platform
 corresp(caith)
+## IGNORE_RDIFF_END
 dimnames(caith)[[2]] <- c("F", "R", "M", "D", "B")
 par(mfcol=c(1,3))
 plot(corresp(caith, nf=2)); title("symmetric")

man/corresp.Rd

@@ -1,5 +1,5 @@
 % file MASS/man/corresp.Rd
-% copyright (C) 1994-2020 W. N. Venables and B. D. Ripley
+% copyright (C) 1994-2022 W. N. Venables and B. D. Ripley
 %
 \name{corresp}
 \alias{corresp}
@@ -86,11 +86,14 @@ corresp(x, \dots)
   \code{\link{svd}}, \code{\link{princomp}}.
 }
 \examples{
+## IGNORE_RDIFF_BEGIN
+## The signs can vary by platform
 (ct <- corresp(~ Age + Eth, data = quine))
 plot(ct)
 
 corresp(caith)
 biplot(corresp(caith, nf = 2))
+## IGNORE_RDIFF_END
 }
 \keyword{category}
 \keyword{multivariate}

man/npk.Rd

@@ -48,6 +48,7 @@ npk
 \examples{
 options(contrasts = c("contr.sum", "contr.poly"))
 npk.aov <- aov(yield ~ block + N*P*K, npk)
+## IGNORE_RDIFF_BEGIN
 npk.aov
 summary(npk.aov)
 alias(npk.aov)
@@ -56,7 +57,6 @@ options(contrasts = c("contr.treatment", "contr.poly"))
 npk.aov1 <- aov(yield ~ block + N + K, data = npk)
 summary.lm(npk.aov1)
 se.contrast(npk.aov1, list(N=="0", N=="1"), data = npk)
-## IGNORE_RDIFF_BEGIN
 model.tables(npk.aov1, type = "means", se = TRUE)
 ## IGNORE_RDIFF_END}
 \keyword{datasets}

src/lqs.c

@@ -70,18 +70,25 @@ static void sample_noreplace(int *x, int n, int k)
 }
 
 /*
-   Find all subsets of size k in order: this gets a new one each call
+   Find all subsets of size k of n in order: this gets a new one each call
  */
+// mis-compiled by GCC 11.[012] at -O3, so avoid it.
+// also GCC pre-12 at -O2 only up to Apr 2022 so releases should be OK.
+#if defined __GNUC__ && __GNUC__ == 12 && __GNUC_MINOR__ < 1
+#pragma GCC optimize "-O1"
+#elif defined __GNUC__ && __GNUC__ == 11 && __GNUC_MINOR__ <= 2
+#pragma GCC optimize "-O2"
+#endif
 static void next_set(int *x, int n, int k)
 {
-    int i, j, tmp;
-
-    j = k - 1;
-    tmp = x[j]++;
+    int j = k - 1;
+    int tmp = x[j]++;
     while(j > 0 && x[j] >= n - (k - 1 -j)) tmp = ++x[--j];
-    for(i = j+1; i < k; i++)  x[i] =  ++tmp;
+    for(int i = j + 1; i < k; i++)  x[i] = ++tmp;
 }
-
+#if defined __GNUC__
+#pragma GCC reset_options
+#endif
 
 /*
    Adjust the constant for an LMS fit. This is the midpoint of the
@@ -356,8 +363,8 @@ mve_fitlots(double *x, int *n, int *p, int *qn, int *mcd,
 	if(!(*sample)) {if(trial > 0) next_set(which, nn, nnew);}
 	else sample_noreplace(which, nn, nnew);
 
-	/* for(i = 0; i < nnew; i++) printf("%d ", which[i]); printf("\n");
-	   fflush(stdout);*/
+	/* for(i = 0; i < nnew; i++) printf("%d ", 1+which[i]);
+	   printf("\n"); fflush(stdout); */
 
 
 	/* Find the mean and covariance matrix of the sample. Check if singular.
@@ -396,7 +403,7 @@ mve_fitlots(double *x, int *n, int *p, int *qn, int *mcd,
 	    }
 
 	}
-	/*   printf("this %f\n", thiscrit);*/
+	/* printf("this %f\n", thiscrit); */
 
 
 	if(thiscrit < best) { /* warning: first might be singular */