please unblock pdl 2.4.3-8
Moin,
could you please unblock pdl 2.4.3-8. I would really like to have that
version in lenny. Reasons:
- Problems with perl 5.10 transition (which was done by binary NMU,
apparently without any regression tests):
* OpenGL support ceased to work (upstream is working on it, but this will
not be ready in time for lenny; I disabled this module, which also
shortens the dependency list)
* Documentation 'apropos' search ceased to work, I backported the
respective changes from upstream cvs;
- All patches documented
- transition build-dep x-dev to x11proto-core-dev: no Lintian errors anymore
- fixes for annoying bugs leading to wrong results in some functions
(as not every user is hit by them, I did only classify them as normal)
Here is the debdiff:
-------------- debdiff between 2.4.3-6 and 2.4.3-8 -----------------
diff -u pdl-2.4.3/debian/changelog pdl-2.4.3/debian/changelog
--- pdl-2.4.3/debian/changelog
+++ pdl-2.4.3/debian/changelog
@@ -1,3 +1,31 @@
+pdl (1:2.4.3-8) unstable; urgency=low
+
+ * add proper description to the dpatch pathes (6 lintian warnings)
+ * backport documentation 'apropos' search function from upstream cvs
+ (closes: #499758)
+ * remove empty manpage /usr/share/man/man3/PDL::PP.3pm (lintian warning)
+ * update standarts version to 3.8.0 (lintian warning)
+ * build-depend on x11proto-core-dev instead of x-dev (lintian error)
+ * remove libgl1 from Suggests; there is no 3d support presently
+ * bump readline Suggests: to Recommends:, as users are lost in
+ interactive mode without it
+ * Fix doc-base entry (Science/Mathematics instead of Apps/Math)
+ * suggest doc-base
+
+ -- Henning Glawe <glaweh@debian.org> Mon, 22 Sep 2008 09:42:25 +0200
+
+pdl (1:2.4.3-7) unstable; urgency=low
+
+ * patch upstream IO/Makefile.PL to also install Dicom IO module
+ (closes: #474751)
+ * disable opengl based PDL::Graphics::TriD, it is not working
+ with perl 5.10. this considerably lowers PDL's dependencies,
+ upstream does not yet have a solution for this problem
+ (closes: #495379)
+ * apply upstream patch for the pct() problem (closes: #488092)
+
+ -- Henning Glawe <glaweh@debian.org> Sat, 20 Sep 2008 13:44:57 +0200
+
pdl (1:2.4.3-6) unstable; urgency=low
[ Rafael Laboissiere ]
diff -u pdl-2.4.3/debian/control pdl-2.4.3/debian/control
--- pdl-2.4.3/debian/control
+++ pdl-2.4.3/debian/control
@@ -2,13 +2,14 @@
Section: math
Priority: optional
Maintainer: Henning Glawe <glaweh@debian.org>
-Standards-Version: 3.7.2
-Build-Depends: gfortran, xlibmesa-gl-dev, libglu1-xorg-dev | xlibmesa-glu-dev, x-dev, libncurses-dev, perl (>= 5.8.0-3), debhelper (>= 4.0.0), libplplot-dev, libinline-perl (>= 0.43), libgsl0-dev, fftw-dev, dpatch, libxext-dev, libhdf4g-dev, proj, libgd2-xpm-dev, libastro-fits-header-perl
+Standards-Version: 3.8.0
+Build-Depends: gfortran, x11proto-core-dev, libncurses-dev, perl (>= 5.8.0-3), debhelper (>= 4.0.0), libplplot-dev, libinline-perl (>= 0.43), libgsl0-dev, fftw-dev, dpatch, libxext-dev, libhdf4g-dev, proj, libgd2-xpm-dev, libastro-fits-header-perl
Package: pdl
Architecture: any
Depends: ${perl:Depends}, libterm-readkey-perl, ${shlibs:Depends}
-Suggests: pgperl, libgl1, netpbm | imagemagick, libastro-fits-header-perl, libinline-perl, libterm-readline-gnu-perl | libterm-readline-perl-perl, libplplot-dev
+Recommends: libterm-readline-gnu-perl | libterm-readline-perl-perl
+Suggests: pgperl, netpbm | imagemagick, libastro-fits-header-perl, libinline-perl, libplplot-dev, doc-base
Conflicts: r-pdl
Replaces: r-pdl
Description: perl data language: Perl extensions for numerics
diff -u pdl-2.4.3/debian/patches/60_fix_gsl_versioncheck.dpatch pdl-2.4.3/debian/patches/60_fix_gsl_versioncheck.dpatch
--- pdl-2.4.3/debian/patches/60_fix_gsl_versioncheck.dpatch
+++ pdl-2.4.3/debian/patches/60_fix_gsl_versioncheck.dpatch
@@ -2,7 +2,7 @@
## 60_fix_gsl_versioncheck.dpatch by Henning Glawe <glaweh@physik.fu-berlin.de>
##
## All lines beginning with `## DP:' are a description of the patch.
-## DP: No description.
+## DP: fix error in GSL version detection code
@DPATCH@
diff -urNad pdl-2.4.3~/Lib/GSL/Makefile.PL pdl-2.4.3/Lib/GSL/Makefile.PL
diff -u pdl-2.4.3/debian/patches/10_upstream_testsuite_64bit.dpatch pdl-2.4.3/debian/patches/10_upstream_testsuite_64bit.dpatch
--- pdl-2.4.3/debian/patches/10_upstream_testsuite_64bit.dpatch
+++ pdl-2.4.3/debian/patches/10_upstream_testsuite_64bit.dpatch
@@ -2,7 +2,7 @@
## 10_upstream_testsuite_64bit.dpatch by Henning Glawe <glaweh@physik.fu-berlin.de>
##
## All lines beginning with `## DP:' are a description of the patch.
-## DP: No description.
+## DP: classify also ia64 as a 64 bit architecture
@DPATCH@
diff -urNad pdl-2.4.3/t/flexraw.t /tmp/dpep.iGuX3h/pdl-2.4.3/t/flexraw.t
diff -u pdl-2.4.3/debian/patches/70_testsuite.dpatch pdl-2.4.3/debian/patches/70_testsuite.dpatch
--- pdl-2.4.3/debian/patches/70_testsuite.dpatch
+++ pdl-2.4.3/debian/patches/70_testsuite.dpatch
@@ -2,7 +2,7 @@
## 70_testsuite.dpatch by Henning Glawe <glaweh@physik.fu-berlin.de>
##
## All lines beginning with `## DP:' are a description of the patch.
-## DP: No description.
+## DP: avoid dump() in test suite, as it causes false positives
@DPATCH@
diff -urNad pdl-2.4.3~/t/xvals.t pdl-2.4.3/t/xvals.t
diff -u pdl-2.4.3/debian/patches/30_gaussian_fit_synopsis.dpatch pdl-2.4.3/debian/patches/30_gaussian_fit_synopsis.dpatch
--- pdl-2.4.3/debian/patches/30_gaussian_fit_synopsis.dpatch
+++ pdl-2.4.3/debian/patches/30_gaussian_fit_synopsis.dpatch
@@ -2,7 +2,7 @@
## 30_gaussian_fit_synopsis.dpatch by Henning Glawe <glaweh@physik.fu-berlin.de>
##
## All lines beginning with `## DP:' are a description of the patch.
-## DP: No description.
+## DP: documentation fix for the gaussian fit module
@DPATCH@
diff -urNad pdl-2.4.3~/Lib/Fit/Gaussian/gaussian.pd pdl-2.4.3/Lib/Fit/Gaussian/gaussian.pd
diff -u pdl-2.4.3/debian/patches/20_OpenGL_GLvoid_workaround.dpatch pdl-2.4.3/debian/patches/20_OpenGL_GLvoid_workaround.dpatch
--- pdl-2.4.3/debian/patches/20_OpenGL_GLvoid_workaround.dpatch
+++ pdl-2.4.3/debian/patches/20_OpenGL_GLvoid_workaround.dpatch
@@ -2,7 +2,8 @@
## 20_OpenGL_GLvoid_workaround.dpatch by Henning Glawe <glaweh@physik.fu-berlin.de>
##
## All lines beginning with `## DP:' are a description of the patch.
-## DP: No description.
+## DP: work-around for type mismatches in the opengl code in combination
+## DP: with new versions of Mesa
@DPATCH@
diff -urNad pdl-2.4.3/Graphics/TriD/OpenGL/opengl.pd /tmp/dpep.Y9hWHj/pdl-2.4.3/Graphics/TriD/OpenGL/opengl.pd
diff -u pdl-2.4.3/debian/patches/00list pdl-2.4.3/debian/patches/00list
--- pdl-2.4.3/debian/patches/00list
+++ pdl-2.4.3/debian/patches/00list
@@ -2,5 +2,8 @@
-20_OpenGL_GLvoid_workaround
+# 20_OpenGL_GLvoid_workaround
30_gaussian_fit_synopsis
40_upstream_uniqsortvec
60_fix_gsl_versioncheck
70_testsuite
+70_install_pdl_io_dicom
+70_upstream_pct
+70_upstream_pdldoc_apropos
only in patch2:
unchanged:
--- pdl-2.4.3.orig/debian/pdl.remove
+++ pdl-2.4.3/debian/pdl.remove
@@ -2,3 +2,4 @@
usr/share/man/man3/PDL::BAD2_demo.3pm
usr/share/man/man3/PDL::Config.3pm
usr/share/man/man3/PDL::Doc::Config.3pm
+usr/share/man/man3/PDL::PP.3pm
only in patch2:
unchanged:
--- pdl-2.4.3.orig/debian/pdl.doc-base
+++ pdl-2.4.3/debian/pdl.doc-base
@@ -6,10 +6,9 @@
and includes bindings to a lot of external libraries for data
processing and representation (plotting). This manual includes
both introductory documents and a command reference.
-Section: Apps/Math
+Section: Science/Mathematics
Format: HTML
Index: /usr/share/doc/pdl/html/Index.html
Files: /usr/share/doc/pdl/html/*.html
-
only in patch2:
unchanged:
--- pdl-2.4.3.orig/debian/perldl.conf
+++ pdl-2.4.3/debian/perldl.conf
@@ -91,7 +91,7 @@
# There are problems with the build on OS-X, so we turn it off by default
# for such systems
#
- WITH_3D => 1,
+ WITH_3D => 0,
#
# For Mesa 3.2
only in patch2:
unchanged:
--- pdl-2.4.3.orig/debian/patches/70_upstream_pdldoc_apropos.dpatch
+++ pdl-2.4.3/debian/patches/70_upstream_pdldoc_apropos.dpatch
@@ -0,0 +1,136 @@
+#! /bin/sh /usr/share/dpatch/dpatch-run
+## 70_upstream_pdldoc_apropos.dpatch by Henning Glawe <glaweh@debian.org>
+##
+## All lines beginning with `## DP:' are a description of the patch.
+## DP: Backport from upstream cvs: make apropos function in pdldoc work with perl 5.10
+
+@DPATCH@
+diff -urNad pdl-2.4.3~/Doc/Doc/Perldl.pm pdl-2.4.3/Doc/Doc/Perldl.pm
+--- pdl-2.4.3~/Doc/Doc/Perldl.pm 2004-03-18 07:49:04.000000000 +0100
++++ pdl-2.4.3/Doc/Doc/Perldl.pm 2008-09-22 00:17:40.235509207 +0200
+@@ -40,7 +40,7 @@
+
+ use PDL::Doc;
+ use IO::File;
+-use Pod::Text;
++use Pod::PlainText;
+
+ $PDL::onlinedoc = undef;
+ $PDL::onlinedoc = new PDL::Doc (FindStdFile());
+@@ -48,23 +48,6 @@
+ use PDL::Config;
+ my $bvalflag = $PDL::Config{WITH_BADVAL} || 0;
+
+-# pod commands are stripped from the ref string before printing.
+-# How we do this depends on the version of Pod::Text installed.
+-#
+-# I'm guessing the difference in behaviour is between versions
+-# 1 and 2 of Pod::Text (it's certainly true for
+-# version 1.0203 (perl5.005_03) and 2.03 (perl 5.6.0))
+-#
+-# version 1:
+-# we use a private routine from Pod::Text
+-# (prepare_for_output) in printmatch() in order
+-# to strip away pod directives from the ref
+-# string
+-#
+-# version 2: (Thanks to Tim Jenness)
+-# create an object and use the interpol() method
+-#
+-
+ # Find std file
+
+ sub FindStdFile {
+@@ -97,9 +80,6 @@
+ || 72;
+ }
+
+-# the $^W assignment stops Pod::Text::fill() from
+-# generating "Use of uninitialised values" errors
+-#
+ sub printmatch {
+ my @match = @_;
+ if (@match) {
+@@ -113,58 +93,34 @@
+ # for the given matches
+ #
+ sub format_ref {
+- my @match = @_;
+- my @text = ();
++ my @match = @_;
++ my @text = ();
+
+- # XXX this is NASTY
+- my $width = screen_width()-17;
+- if ( $Pod::Text::VERSION < 2 ) {
+- $Pod::Text::indent = 0;
+- $Pod::Text::SCREEN = $width;
+- local $^W = 0;
+- for my $m (@match) {
+- $_ = $m->[1]{Ref} ||
+- ( (defined $m->[1]{CustomFile})
+- ? "[No ref avail. for `".$m->[1]{CustomFile}."']"
+- : "[No reference available]"
+- );
+- Pod::Text::prepare_for_output(); # adds a '\n' to $_
+- $_ = Pod::Text::fill $_; # try and get `nice' wrapping
+- s/\n*$//; # remove last new lines (so substitution doesn't append spaces at end of text)
+- s/\n/\n /g;
+- my $name = $m->[0];
+- if ( length($name) > 15 ) {
+- push @text, sprintf "%s ...\n %s\n", $name, $_;
+- } else {
+- push @text, sprintf "%-15s %s\n", $name, $_;
+- }
+- }
+- } else {
+- my $parser = new Pod::Text( width => $width, indent => 0, sentence => 0 );
+-
+- for my $m (@match) {
+- my $ref = $m->[1]{Ref} ||
+- ( (defined $m->[1]{CustomFile})
+- ? "[No ref avail. for `".$m->[1]{CustomFile}."']"
+- : "[No reference available]"
+- );
++ my $width = screen_width()-17;
++ my $parser = new Pod::PlainText( width => $width, indent => 0, sentence => 0 );
+
+- $ref = $parser->interpolate( $ref );
+- $ref = $parser->reformat( $ref );
+-
+- # remove last new lines (so substitution doesn't append spaces at end of text)
+- $ref =~ s/\n*$//;
+- $ref =~ s/\n/\n /g;
++ for my $m (@match) {
++ my $ref = $m->[1]{Ref} ||
++ ( (defined $m->[1]{CustomFile})
++ ? "[No ref avail. for `".$m->[1]{CustomFile}."']"
++ : "[No reference available]"
++ );
+
+- my $name = $m->[0];
+- if ( length($name) > 15 ) {
+- push @text, sprintf "%s ...\n %s\n", $name, $ref;
+- } else {
+- push @text, sprintf "%-15s %s\n", $name, $ref;
+- }
+- }
++ $ref = $parser->interpolate( $ref );
++ $ref = $parser->reformat( $ref );
++
++ # remove last new lines (so substitution doesn't append spaces at end of text)
++ $ref =~ s/\n*$//;
++ $ref =~ s/\n/\n /g;
++
++ my $name = $m->[0];
++ if ( length($name) > 15 ) {
++ push @text, sprintf "%s ...\n %s\n", $name, $ref;
++ } else {
++ push @text, sprintf "%-15s %s\n", $name, $ref;
+ }
+- return wantarray ? @text : $text[0];
++ }
++ return wantarray ? @text : $text[0];
+
+ } # sub: format_ref()
+
only in patch2:
unchanged:
--- pdl-2.4.3.orig/debian/patches/70_install_pdl_io_dicom.dpatch
+++ pdl-2.4.3/debian/patches/70_install_pdl_io_dicom.dpatch
@@ -0,0 +1,19 @@
+#! /bin/sh /usr/share/dpatch/dpatch-run
+## 70_install_pdl_io_dicom.dpatch by Henning Glawe <glaweh@physik.fu-berlin.de>
+##
+## All lines beginning with `## DP:' are a description of the patch.
+## DP: install the dicom io module
+
+@DPATCH@
+diff -urNad pdl-2.4.3~/IO/Makefile.PL pdl-2.4.3/IO/Makefile.PL
+--- pdl-2.4.3~/IO/Makefile.PL 2006-04-13 00:02:37.000000000 +0200
++++ pdl-2.4.3/IO/Makefile.PL 2008-04-08 11:54:06.097561103 +0200
+@@ -3,7 +3,7 @@
+
+ # do we build PDL::IO::Browser ?
+ #
+-my @dirs = qw( FastRaw Misc FlexRaw Pnm NDF Storable FITS HDF GD );
++my @dirs = qw( FastRaw Misc FlexRaw Pnm NDF Storable FITS HDF GD Dicom );
+ my $build_browser = $PDL::Config{WITH_IO_BROWSER} || 0;
+ if ( $build_browser ) {
+ # PDL::IO::Browser isn't (yet?) supported for win32 systems
only in patch2:
unchanged:
--- pdl-2.4.3.orig/debian/patches/70_upstream_pct.dpatch
+++ pdl-2.4.3/debian/patches/70_upstream_pct.dpatch
@@ -0,0 +1,98 @@
+#! /bin/sh /usr/share/dpatch/dpatch-run
+## 70_upstream_pct.dpatch by Henning Glawe <glaweh@physik.fu-berlin.de>
+##
+## All lines beginning with `## DP:' are a description of the patch.
+## DP: Backport from upstream cvs: fix pct() projection
+
+@DPATCH@
+diff -urNad pdl-2.4.3~/Basic/Ufunc/ufunc.pd pdl-2.4.3/Basic/Ufunc/ufunc.pd
+--- pdl-2.4.3~/Basic/Ufunc/ufunc.pd 2006-06-21 17:46:51.000000000 +0200
++++ pdl-2.4.3/Basic/Ufunc/ufunc.pd 2008-08-14 08:36:48.420212035 +0200
+@@ -612,52 +612,67 @@
+
+ pp_def('pctover',
+ Pars => 'a(n); p(); [o]b(); [t]tmp(n);',
+- Doc => '
++ Doc => '
+
+ Project via percentile to N-1 dimensions
+
+ This function reduces the dimensionality of a piddle by one by finding
+ the specified percentile (p) along the 1st dimension. The specified
+ percentile must be between 0.0 and 1.0. When the specified percentile
+-falls between data points, the result is interpolated.
++falls between data points, the result is interpolated. Values outside
++the allowed range are clipped to 0.0 or 1.0 respectively. The algorithm
++implemented here is based on the interpolation variant described at
++L< http://en.wikipedia.org/wiki/Percentile>.
+
+ By using L<xchg|PDL::Slices/xchg> etc. it is possible to use
+ I<any> dimension.
+
+ =for usage
+
+- $a = pctover($b, $p);
++$a = pctover($b, $p);
+
+ =for example
+
+- $spectrum = pctover $image->xchg(0,1) $p
++$spectrum = pctover $image->xchg(0,1) $p
+
+ =cut
+ ',
+ Code => '
+ int nn, nn1, nn2;
+- double pp1, pp2;
+- loop(n) %{ $tmp() = $a(); %}
+- nn = $COMP(__n_size)-1;
++ double np, pp1, pp2;
++ loop(n) %{ $tmp() = $a(); %}
++ nn = $COMP(__n_size);
+ $TBSULQFD(pdl_qsort_B,pdl_qsort_S,pdl_qsort_U,
+- pdl_qsort_L,pdl_qsort_Q,pdl_qsort_F,pdl_qsort_D) ($P(tmp), 0, nn);
+-
+- nn1 = (nn + 1)*$p() - 1 + 0.5; nn2 = nn1+1;
+- if (nn2 > nn) nn2 = nn;
+- if (nn1 > nn) nn1 = nn;
+- pp1 = (double)nn1/(double)nn;
++ pdl_qsort_L,pdl_qsort_Q,pdl_qsort_F,pdl_qsort_D) ($P(tmp), 0, nn-1);
++
++ np = nn*$p()-0.5;
++ nn1 = np;
++ nn2 = nn1+1;
++
++ nn1 = (nn1 < 0) ? 0 : nn1;
++ nn2 = (nn2 < 0) ? 0 : nn2;
++
++ nn1 = (nn1 > nn - 1) ? nn - 1 : nn1;
++ nn2 = (nn2 > nn - 1) ? nn - 1 : nn2;
++
++ pp1 = (double)nn1/(double)nn;
+ pp2 = (double)nn2/(double)nn;
+- if ($tmp(n => nn2) == $tmp(n => nn1)) {
+- $b() = $tmp(n => nn1);
++
++ if ( np < 0.5 ) {
++ $b() = $tmp(n => 0);
++ } else if ( np > nn - 0.5 ) {
++ $b() = $tmp(n => nn-1);
++ } else if ($tmp(n => nn2) == $tmp(n => nn1)) {
++ $b() = $tmp(n => nn1);
+ } else if ($p() == pp1) {
+- $b() = $tmp(n => nn1);
++ $b() = $tmp(n => nn1);
+ } else if ($p() == pp2) {
+- $b() = $tmp(n => nn2);
++ $b() = $tmp(n => nn2);
+ } else {
+- $b() = ($p() - pp1)/(pp2 - pp1)*
+- ( $tmp(n => nn2) - $tmp(n => nn1) ) + $tmp(n => nn1);
++ $b() = (np - nn1)*($tmp(n => nn2) - $tmp(n => nn1)) + $tmp(n => nn1);
+ }
+-');
++');
++
+
+ pp_def('oddpctover',
+ Pars => 'a(n); p(); [o]b(); [t]tmp(n);',
-------------------------------------------------------------------------------------------
--
c u
henning
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