CVS commit: pkgsrc/math/R-SparseM

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

Module Name:    pkgsrc
Committed By:   mef
Date:           Sat Oct 26 12:16:54 UTC 2024

Modified Files:
        pkgsrc/math/R-SparseM: Makefile distinfo

Log Message:
(math/R-SparseM) Updated 1.81 to 1.84.2

(inst/ChangeLog, chronological order)
The version 1.82

1.  Modernized the cholesky.f to remove arithmetic ifs, suggested by BDR.
2.  Repaired some syntax errors in lsq.Rd.
3.  Commented out S3Method lines at the end of NAMESPACE file, at suggestion
of Ivan Krylov, see mail of May 27, 2024.
4.  This version was accepted by Uwe for CRAN, despite generating an error
with balanceTest() in the RItools package.
5.  After some chaos involving namespace issues that were due to extraneous
conditions, the package passed R CMD check after adding a setGeneric(image)
command in SparseM.R.  (This allowed me to restore the vignette in its Rnw
form.
6.  This left things in the status quo ante with the problem in RItools, which
I'm hoping Jake Bowers and his collaborators can help debug.
7.  Meanwhile there is a broken 1.82 on CRAN that I've asked Uwe to remove.
8.  The problem with the RItools example turned out to be that chol was being
applied to a singular matrix. I've added a warning in the documentation that
is no pre-checking for PD matrices.
9.  I also found that determinant wasn't acknowledged to be generic, so this
has been repaired, however there is still a problem with accessing the
documentation of this.

The version 1.84
                 (much by Martin Maechler who also adds himself to the Authors 'ctb')

1.  chol(<matrix.csr)     gets new argument `warn.only = FALSE` in order to
        still return in case of errors (as this has happened in older
        versions, at least coincidentally).  Further new arguments for
        previously hardwired "tuning" constants are
        'tiny = 1e-30',
        'Large = 1e128',
        'cacheKb = 1024L',
        'level = 8L'.
        Note that `cacheKb` was hardwired to 64, clearly too small a
        default for today's hardware.
        Further, the chol() method is well documented ( ../man/SparseM.solve.Rd ).
        An example has been added where _decreasing_ `tiny` was beneficial.

2.  determinant(<matrix.csr>) allows to pass optional arguments for chol().
3.  det() now works, automagically calling _our_ determinant().
4.  Fix backsolve() and forwardsolve() methods documentation, adding an
    `drop=TRUE` argument in one case.
4b. These tweaks have also eliminated the unpleasant message when SparseM is attached:

        The following object is masked from ‘package:base’:  \cr   backsolve

5.  A nice simple show() method now (auto-)prints our sparse matrices with
    structural zeros shown as  " . "
6.  norm(<matrix.csr>, "I") now gives an error (instead of invisible(NULL)).
7.  demo(LeastSquares)  and  demo(Solve)  work now.

The version 1.84-1

- src/SparseM.h : use 'int_least32_t' instead of 'int'  for Fortran 'logical', in two cases (fixing 'LTO').
- src/csr.f (etc): drop first *unused* argument 'ra' from nzero().
- src/cholesky.f:  replace computed goto's in code by  select case(.) case() ...


To generate a diff of this commit:
cvs rdiff -u -r1.7 -r1.8 pkgsrc/math/R-SparseM/Makefile
cvs rdiff -u -r1.6 -r1.7 pkgsrc/math/R-SparseM/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-SparseM/Makefile
diff -u pkgsrc/math/R-SparseM/Makefile:1.7 pkgsrc/math/R-SparseM/Makefile:1.8
--- pkgsrc/math/R-SparseM/Makefile:1.7  Sat Sep 11 10:09:17 2021
+++ pkgsrc/math/R-SparseM/Makefile      Sat Oct 26 12:16:54 2024
@@ -1,13 +1,19 @@
-# $NetBSD: Makefile,v 1.7 2021/09/11 10:09:17 mef Exp $
+# $NetBSD: Makefile,v 1.8 2024/10/26 12:16:54 mef Exp $
 
 R_PKGNAME=     SparseM
-R_PKGVER=      1.81
+R_PKGVER=      1.84-2
 
 MAINTAINER=    pkgsrc-users%NetBSD.org@localhost
 COMMENT=       Sparse linear algebra
 LICENSE=       gnu-gpl-v2 OR gnu-gpl-v3
 
+TEST_DEPENDS+= R-knitr-[0-9]*:../../print/R-knitr
+
+# !pdfTeX error: pdflatex (file ecti1000): Font ecti1000 at 600 not found
 TEST_DEPENDS+= tex-ec-[0-9]*:../../fonts/tex-ec
+TEST_DEPENDS+= tex-inconsolata-[0-9]*:../../fonts/tex-inconsolata
+TEST_DEPENDS+= tex-latex-bin-[0-9]*:../../print/tex-latex-bin
+TEST_DEPENDS+= tex-url-[0-9]*:../../print/tex-url
 
 USE_LANGUAGES= c fortran
 

Index: pkgsrc/math/R-SparseM/distinfo
diff -u pkgsrc/math/R-SparseM/distinfo:1.6 pkgsrc/math/R-SparseM/distinfo:1.7
--- pkgsrc/math/R-SparseM/distinfo:1.6  Tue Oct 26 10:55:23 2021
+++ pkgsrc/math/R-SparseM/distinfo      Sat Oct 26 12:16:54 2024
@@ -1,5 +1,5 @@
-$NetBSD: distinfo,v 1.6 2021/10/26 10:55:23 nia Exp $
+$NetBSD: distinfo,v 1.7 2024/10/26 12:16:54 mef Exp $
 
-BLAKE2s (R/SparseM_1.81.tar.gz) = 767e9f31161e0a2996b0830340f7aef319fc75a7e11b76ee73fa41a390b587f5
-SHA512 (R/SparseM_1.81.tar.gz) = 3fba6796a48a32059e9b7a7a22302c251a57abaca3c8a90dd531a9f7d201cb1156b65382b00b3d9e4dc919031d7adbe9c7744304401974c81063ef23d98fe126
-Size (R/SparseM_1.81.tar.gz) = 735100 bytes
+BLAKE2s (R/SparseM_1.84-2.tar.gz) = 821610aa1ad4d4e7a7b1ea57a5455e6f83b5e55f50a3fb8084c54fc9f3aeec74
+SHA512 (R/SparseM_1.84-2.tar.gz) = b8b0d54a9b18aea11103d000d308eea6cfc0f90c0edc90f7a1652bf69becb809801f0ce2e2fda5ff2296d30bfa8ce7aea7f9e2ed4b5c77911ef94fe08c7d9e50
+Size (R/SparseM_1.84-2.tar.gz) = 553080 bytes