Jack Howarth | 31 Oct 03:47 2014
Picon

libtool2 update needed for Yosemite

Max,
    We need an fixed libtool2 package for Yosemite. The current one has the libtool.m4 bug which confused 10.10 with 10.1 and results in shared library being linked with "-dynamiclib -flat_namespace" rather than the appropriate "-dynamiclib -undefined dynamic_lookup". While this is fixed in the new libtool 2.4.3 release, they appear to have broken --program-prefix=g in that release.
  Attached is a libtool2-2.4.2-4 packaging which uses the same back port of the fix as home-brew.


Index: libtool2.info

===================================================================

RCS file: /cvsroot/fink/dists/10.7/stable/main/finkinfo/devel/libtool2.info,v

retrieving revision 1.5

diff -r1.5 libtool2.info

19c19

< Revision: 3

---

> Revision: 4

26c26,28

< Source-MD5: d2f3b7d4627e69e13514a40e72a24d50 

---

> Source-MD5: d2f3b7d4627e69e13514a40e72a24d50

> PatchFile: %n.patch

> PatchFile-MD5: da6decbe2f0b7a3572db27c4bddcadb5

29a32

>   %{default_script}


This version passes 'fink -m' and also produces a glib tool which properly links
the files in cyrus-sasl2-shlibs on Yosemite.
              Jack
ps The current fink 0.38.2 release now treats the absence of the TWOLEVEL flag from the output of 'toool -hv' on a non-bundle shared library as a marker for the use of -flat_namespace and uses a fatal validation error. The inappropriate use of -dynamiclib -flat_namespace causes major runtime regressions for packages like gmp/mpfr/gmp and libgfortran from FSF gcc.
Attachment (libtool2.info): application/octet-stream, 5110 bytes
Attachment (libtool2.patch): application/octet-stream, 3294 bytes
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Hanspeter Niederstrasser | 29 Oct 12:49 2014

texi2html-1.82-1 fails tests on 10.10

On 10.10 (a VM), texi2html-1.82-1 fails test like so.  The full build 
log is available at http://snaggledworks.com/fink/logs/

Hanspeter
****

make check || exit 2
Making check in .
make[1]: Nothing to be done for `check-am'.
Making check in doc
/Applications/Xcode.app/Contents/Developer/usr/bin/make  check-local
TEXINPUTS=.::$TEXINPUTS \
        ../texi2html -V ./texi2html.texi
# Expanded: ifclear html verbatim ifset titlepage documentdescription 
menu ifnottex ifnotdocbook ifnotinfo ifnotxml ifnotplaintext ifhtml copying
# USE_UNICODE 1, USE_UNIDECODE 1
# putting result files into current directory
# Files and directories:
# rdir() path_to_working_dir()
# doc(texi2html.html) top(texi2html.html) toc(texi2html.html) 
stoc(texi2html.html)
# foot(texi2html.html) about(texi2html.html) frame(texi2html.html) 
toc_frame(texi2html_toc_frame.html)
# using 'en' as document language
# reading from ./texi2html.texi
# including ./version.texi
# end of pass texi
# Encodings: doc UNDEF, in UNDEF out UNDEF, name utf-8
# using 'en' as document language
# end of pass structure
# Encodings: doc UNDEF, in UNDEF out UNDEF, name utf-8
# using 'en' as document language
# Writing elements:
# Writing to texi2html.html 
.[Top].......................................................................................................
# writing Footnotes in texi2html.html
# writing Footnotes in current file
# writing Contents in texi2html.html
# writing Contents in current file
# writing Overview in texi2html.html
# writing Overview in current file
# writing About in texi2html.html
# writing About in current file
# File (0) ./texi2html.texi processed
# that's all folks
Making check in Tests
make[1]: Nothing to be done for `check'.
Making check in test
Making check in .
for dir in htmlxref htmlxref-only_mono htmlxref-only_split; do \
         .././install-sh -c -d $dir/.texinfo/ ; \
         if [ -f $dir/.texinfo/htmlxref.cnf ]; then : ; \
         else cp ./$dir/htmlxref.cnf $dir/.texinfo/ ; \
         fi ; \
     done
/Applications/Xcode.app/Contents/Developer/usr/bin/make  check-TESTS
macros: 0
D: diffs/equivalent_nodes.diff
D: diffs/equivalent_nodes_no_node.diff
sectionning: 1
D: diffs/formatting.diff
coverage: 1
D: diffs/ref_in_anchor.diff
D: diffs/formatting_weird_quotes.diff
S: (no tex4ht) simplest_httex
formatting: 1
D: diffs/nodetest.diff
D: diffs/nodetest_chapter.diff
D: diffs/nodetest_no_unicode.diff
D: diffs/nodetest_utf8.diff
D: diffs/nodetest_utf8_no_unicode.diff
D: diffs/nodetest_latin1.diff
D: diffs/nodetest_latin1_no_unicode.diff
D: diffs/formatting_fr.diff
D: diffs/formatting_fr_icons.diff
D: diffs/formatting_converted_to_utf8.diff
encodings: 1
indices: 0
D: diffs/formatting_regions.diff
D: diffs/formatting_exotic.diff
D: diffs/formatting_makeinfo.diff
D: diffs/formatting_chm.diff
layout: 1
D: diffs/nested_group.diff
D: diffs/nested_itemize.diff
D: diffs/nested_menu.diff
D: diffs/nested_table.diff
D: diffs/nested_flushright.diff
D: diffs/nested_multitable.diff
D: diffs/nested_cartouche.diff
D: diffs/nested_enumerate.diff
D: diffs/nested_deffn.diff
D: diffs/nested_example.diff
D: diffs/nested_quotation.diff
nested_formats: 1
D: diffs/contents_in_middle_section.diff
D: diffs/contents_in_middle_section_inline.diff
contents: 1
htmlxref: 0
htmlxref-only_mono: 0
htmlxref-only_split: 0
D: diffs/formats_not_closed.diff
invalid: 1
FAIL: base_tests
=========================================
1 of 1 tests failed
Please report to texi2html-bug <at> nongnu.org
=========================================

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Jack Howarth | 29 Oct 03:09 2014
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Fwd: validation test for Puma-linked shared libraries on darwin14 and later


---------- Forwarded message ----------
From: Jack Howarth <howarth.at.fink <at> gmail.com>
Date: Tue, Oct 28, 2014 at 9:38 PM
Subject: Re: [Fink-devel] validation test for Puma-linked shared libraries on darwin14 and later
To: Alexander Hansen <alexanderk.hansen <at> gmail.com>


As I mentioned to Alexander on fink irc, it appears that we can use...

# /Library/Developer/CommandLineTools/usr/bin/dyldinfo -bind .libs/libgdbm.3.0.0.dylib

bind information:

segment section          address        type    addend dylib            symbol

__DATA  __got            0x00004000    pointer      0 libSystem        ___stack_chk_guard

__DATA  __nl_symbol_ptr  0x00004008    pointer      0 libSystem        dyld_stub_binder


vs

# /Library/Developer/CommandLineTools/usr/bin/dyldinfo -bind .libs/libgdbm.3.0.0.dylib | grep flat

__DATA  __got            0x00004000    pointer      0 flat-namespace   ___stack_chk_guard

__DATA  __got            0x00004008    pointer      0 flat-namespace   _gdbm_errno

__DATA  __nl_symbol_ptr  0x00004010    pointer      0 flat-namespace   dyld_stub_binder


and just grep the output for flat-namespace.
              Jack

On Tue, Oct 28, 2014 at 9:14 PM, Alexander Hansen <alexanderk.hansen <at> gmail.com> wrote:
On 10/28/14, 6:05 PM, Jack Howarth wrote:
      As I mentioned to Alexander on fink irc, I think we can add a
fatal fink validation error for the dynamic shared libraries on darwin14
and later that are erroneously linked with -flat_namespace rather than
-undefined dynamic_lookup due to the buggy libtool. We can use the
following approach...

1) test with the 'file' command to make sure the shared library isn't
really a bundle
2) if not a bundle, use 'otool -H <filename> | grep Hint' to look for...

Two-level namespace hints table (0 hints)


which shared libraries created with -flat_namespace should be missing.


If this test fails on darwin14 or later, this should be treated as a
fatal validation error with the appropriate error message.

                Jack




The good news is that Validation.pm already has a loop over the installed dylibs in a .deb, excluding bundles, so adding an extra test won't be too difficult.

The bad news is that my test case (libtcd-shlibs on 10.10 with and without the PatchScript) didn't seem to give different "otool -H " output whether or not -flat_namespace was used.
--
Alexander Hansen, Ph.D.
Fink User Liaison
My package updates: http://finkakh.wordpress.com/


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Jack Howarth | 29 Oct 03:09 2014
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Fwd: validation test for Puma-linked shared libraries on darwin14 and later


---------- Forwarded message ----------
From: Jack Howarth <howarth.at.fink <at> gmail.com>
Date: Tue, Oct 28, 2014 at 10:08 PM
Subject: Re: [Fink-devel] validation test for Puma-linked shared libraries on darwin14 and later
To: Alexander Hansen <alexanderk.hansen <at> gmail.com>


Alternatively, the Apple linker developer pointed out, we can use...

# otool -hv libgdbm.3.0.0.dylib

libgdbm.3.0.0.dylib:

Mach header

      magic cputype cpusubtype  caps    filetype ncmds sizeofcmds      flags

MH_MAGIC_64  X86_64        ALL  0x00       DYLIB    14       1536   NOUNDEFS DYLDLINK TWOLEVEL NO_REEXPORTED_DYLIBS


vs

# otool -hv libgdbm.3.0.0.dylib

libgdbm.3.0.0.dylib:

Mach header

      magic cputype cpusubtype  caps    filetype ncmds sizeofcmds      flags

MH_MAGIC_64  X86_64        ALL  0x00       DYLIB    14       1536 DYLDLINK NO_REEXPORTED_DYLIBS


and look for the presence of TWOLEVEL.

On Tue, Oct 28, 2014 at 9:38 PM, Jack Howarth <howarth.at.fink <at> gmail.com> wrote:
As I mentioned to Alexander on fink irc, it appears that we can use...

# /Library/Developer/CommandLineTools/usr/bin/dyldinfo -bind .libs/libgdbm.3.0.0.dylib

bind information:

segment section          address        type    addend dylib            symbol

__DATA  __got            0x00004000    pointer      0 libSystem        ___stack_chk_guard

__DATA  __nl_symbol_ptr  0x00004008    pointer      0 libSystem        dyld_stub_binder


vs

# /Library/Developer/CommandLineTools/usr/bin/dyldinfo -bind .libs/libgdbm.3.0.0.dylib | grep flat

__DATA  __got            0x00004000    pointer      0 flat-namespace   ___stack_chk_guard

__DATA  __got            0x00004008    pointer      0 flat-namespace   _gdbm_errno

__DATA  __nl_symbol_ptr  0x00004010    pointer      0 flat-namespace   dyld_stub_binder


and just grep the output for flat-namespace.
              Jack

On Tue, Oct 28, 2014 at 9:14 PM, Alexander Hansen <alexanderk.hansen <at> gmail.com> wrote:
On 10/28/14, 6:05 PM, Jack Howarth wrote:
      As I mentioned to Alexander on fink irc, I think we can add a
fatal fink validation error for the dynamic shared libraries on darwin14
and later that are erroneously linked with -flat_namespace rather than
-undefined dynamic_lookup due to the buggy libtool. We can use the
following approach...

1) test with the 'file' command to make sure the shared library isn't
really a bundle
2) if not a bundle, use 'otool -H <filename> | grep Hint' to look for...

Two-level namespace hints table (0 hints)


which shared libraries created with -flat_namespace should be missing.


If this test fails on darwin14 or later, this should be treated as a
fatal validation error with the appropriate error message.

                Jack




The good news is that Validation.pm already has a loop over the installed dylibs in a .deb, excluding bundles, so adding an extra test won't be too difficult.

The bad news is that my test case (libtcd-shlibs on 10.10 with and without the PatchScript) didn't seem to give different "otool -H " output whether or not -flat_namespace was used.
--
Alexander Hansen, Ph.D.
Fink User Liaison
My package updates: http://finkakh.wordpress.com/



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Jack Howarth | 29 Oct 02:05 2014
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validation test for Puma-linked shared libraries on darwin14 and later

     As I mentioned to Alexander on fink irc, I think we can add a fatal fink validation error for the dynamic shared libraries on darwin14 and later that are erroneously linked with -flat_namespace rather than -undefined dynamic_lookup due to the buggy libtool. We can use the following approach...

1) test with the 'file' command to make sure the shared library isn't really a bundle
2) if not a bundle, use 'otool -H <filename> | grep Hint' to look for...

Two-level namespace hints table (0 hints)


which shared libraries created with -flat_namespace should be missing.


If this test fails on darwin14 or later, this should be treated as a fatal validation error with the appropriate error message.

               Jack

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Jack Howarth | 28 Oct 01:12 2014
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Puma linkages on Yosemite

Hanspeter,
      I assume you are aware that the current libtool releases have a bug which causes the shared library linkages on 10.10 to be erroneously treated as linkages on 10.1 (Puma) such that 

${wl}-flat_namespace ${wl}-undefined ${wl}suppress


is used instead of the appropriate


${wl}-undefined ${wl}dynamic_lookup


This can produce some really nasty breakage like...


https://gcc.gnu.org/bugzilla/show_bug.cgi?id=63610


The approach that I have taken is to start from a clean bootstrap and 

collect complete fink build logs for a large fink build such as


fink install relax-py27


The log can then be used with...


grep flat_namespace fink_build.log | grep -v bundle | grep dynamic


to produce a list of linkages which are incorrectly done as if the Yosemite machine were on Puma.

    The configure files in these programs can be perl edited to be correct with...


# Patch configure to not link like Puma on Yosemite

perl -pi.bak -e 's|10\.\[012\]\*\)|10\.\[012\]\[\,\.\]\*\)|g' configure


with all of the configure files in the package listed at the end of the line.

This will produce a change of the form...


diff -uNr gmp-6.0.0.orig/configure gmp-6.0.0/configure

--- gmp-6.0.0.orig/configure    2014-03-25 10:38:04.000000000 -0400

+++ gmp-6.0.0/configure 2014-10-26 01:08:59.000000000 -0400

<at> <at> -14809,7 +14809,7 <at> <at>

       case ${MACOSX_DEPLOYMENT_TARGET-10.0},$host in

        10.0,*86*-darwin8*|10.0,*-darwin[91]*)

          _lt_dar_allow_undefined='${wl}-undefined ${wl}dynamic_lookup' ;;

-       10.[012]*)

+       10.[012][,.]*)

          _lt_dar_allow_undefined='${wl}-flat_namespace ${wl}-undefined ${wl}suppress' ;;

        10.*)

          _lt_dar_allow_undefined='${wl}-undefined ${wl}dynamic_lookup' ;;


I then normally just do test build of each fixed package in a new window and search the contents for '-flat_namespace' to confirm it isn't being used with -dynamiclib.
               Jack
ps I can help work through the qt packages after mid-week if your are short on time.
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Jack Howarth | 27 Oct 14:19 2014
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octave-3.6.4-13 and octave-3.8.2-4

Alexander,

     The linkage problems on Yosemite can be solved in the octave-3.6.4 and octave-3.8.2 packages with the following perl edit lines to adjust configure rather than appending to the respective patches. Can you commit this to 10.7 tree?

       Thanks in advance.

               Jack


--- octave-3.6.4.info.orig 2014-10-25 23:13:45.000000000 -0400

+++ octave-3.6.4.info 2014-10-27 01:17:15.000000000 -0400

<at> <at> -2,7 +2,7 <at> <at>

 Package: octave%type_pkg[-blas]%type_pkg[-x11]

 Type: -blas (. -atlas -ref), oct (3.6.4), gcc (4.9), -x11 (boolean), lapack (3.5.0)

 Version: 3.6.4

-Revision: 12

+Revision: 13

 Maintainer: Alexander Hansen <alexkhansen <at> users.sourceforge.net>

 

 BuildDepends: <<

<at> <at> -178,6 +178,9 <at> <at>

 

  # instead of using flag-sort, ensure that the right sysdep.h is used

  grep -lr '#include "sysdep.h"' * | xargs perl -pi.orig -e 's,sysdep.h,%b/src/sysdep.h,'

+

+ # Patch configure to not link like Puma on Yosemite

+ perl -pi.bak -e 's|10\.\[012\]\*\)|10\.\[012\]\[\,\.\]\*\)|g' configure

 <<

 

 GCC: 4.0




--- octave-3.8.2.info.orig 2014-10-26 11:58:44.000000000 -0400

+++ octave-3.8.2.info 2014-10-27 01:18:27.000000000 -0400

<at> <at> -2,7 +2,7 <at> <at>

 Package: octave%type_pkg[-blas]%type_pkg[-x11]%type_pkg[-qtui]

 Type: -blas (. -atlas -ref), oct (3.8.2), gcc (4.9), -x11 (boolean), lapack (3.5.0), java (1.6), -qtui (. -qtmac -qtx11)

 Version: 3.8.2

-Revision: 3

+Revision: 4

 

 Description: MATLAB-like language for computations

 Maintainer: Alexander Hansen <alexkhansen <at> users.sourceforge.net>

<at> <at> -147,6 +147,9 <at> <at>

  if [ $osversion -ge 13 ] ; then

  patch -p1 < %{PatchFile3}

  fi

+

+ # Patch configure to not link like Puma on Yosemite

+ perl -pi.bak -e 's|10\.\[012\]\*\)|10\.\[012\]\[\,\.\]\*\)|g' configure

 <<

 

 GCC: 4.0


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Jack Howarth | 26 Oct 18:04 2014
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minor glitch in path-prefix on 10.10

Alexander,
       While debugging the test suite regressions in gcc49 on Yosemite (which were due to the erroneous Puma-like shared library linkage), I noticed a glitch in the PATH set in fink builds for the path-prefix on 10.10. We end up with the expected /sw/var/lib/fink/path-prefix-libcxx on PATH followed by bogus /sw/var/lib/fink/path-prefix-g++-4.0 as well. I assume the conditional...


# FIXME: (No)SetPATH is undocumented

        unless ($self->has_param('NoSetPATH')) {

                # use path-prefix-* to give magic to 'gcc' and related commands

                my $pathprefix;

                if  ($config->param("Distribution") lt "10.6") {

                        # Enforce g++-4.0 even for uncooperative packages, by making it the

                        # first 'g++' in the path (symbol-munging binary compatibility)

                        $pathprefix = ensure_gpp_prefix('4.0');

                }


in /sw/lib/perl5/Fink/PkgVersion.pm is incorrectly seeing 10.10 as 10.1.
             Jack
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Jack Howarth | 26 Oct 17:33 2014
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Don't be a Puma on Yosemite

Alexander,
      I appears that both octave 3.6.4 and 3.8.2 will need configure patched to prevent 
the shared libraries being linked with

-Wl,-flat_namespace -Wl,-undefined -Wl,suppress


instead of


-Wl,-undefined -Wl,dynamic_lookup


when MACOSX_DEPLOYMENT_TARGET is set to 10.10 as fink does by default.


The fixes should be of the form...


--- octave-3.6.4/configure.orig 2014-10-26 12:26:48.000000000 -0400

+++ octave-3.6.4/configure 2014-10-26 12:28:00.000000000 -0400

<at> <at> -40142,7 +40142,7 <at> <at>

       case ${MACOSX_DEPLOYMENT_TARGET-10.0},$host in

  10.0,*86*-darwin8*|10.0,*-darwin[91]*)

    _lt_dar_allow_undefined='${wl}-undefined ${wl}dynamic_lookup' ;;

- 10.[012]*)

+ 10.[012][,.]*)

    _lt_dar_allow_undefined='${wl}-flat_namespace ${wl}-undefined ${wl}suppress' ;;

  10.*)

    _lt_dar_allow_undefined='${wl}-undefined ${wl}dynamic_lookup' ;;


assuming you don't autoreconf.
               Jack
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Jack Howarth | 26 Oct 16:47 2014
Picon

hot fixes for yosemite

      We need to push out some hot fixes to repair breakage on Yosemite. MacPorts is using patches to configure to address the inappropriate linkage of shared libraries with...

-Wl,-flat_namespace -Wl,-undefined -Wl,suppress


instead of


-Wl,-undefined -Wl,dynamic_lookup


when MACOSX_DEPLOYMENT_TARGET is set to 10.10 as fink does by default.

The fix is always of the form...


diff -uNr mpfr-3.1.2.orig/configure mpfr-3.1.2/configure

--- mpfr-3.1.2.orig/configure   2013-03-13 11:38:20.000000000 -0400

+++ mpfr-3.1.2/configure        2014-10-26 01:00:37.000000000 -0400

<at> <at> -10401,7 +10401,7 <at> <at>

       case ${MACOSX_DEPLOYMENT_TARGET-10.0},$host in

        10.0,*86*-darwin8*|10.0,*-darwin[91]*)

          _lt_dar_allow_undefined='${wl}-undefined ${wl}dynamic_lookup' ;;

-       10.[012]*)

+       10.[012][,.]*)

          _lt_dar_allow_undefined='${wl}-flat_namespace ${wl}-undefined ${wl}suppress' ;;

        10.*)

          _lt_dar_allow_undefined='${wl}-undefined ${wl}dynamic_lookup' ;;

diff -uNr mpfr-3.1.2.orig/m4/libtool.m4 mpfr-3.1.2/m4/libtool.m4

--- mpfr-3.1.2.orig/m4/libtool.m4       2013-03-13 11:38:16.000000000 -0400

+++ mpfr-3.1.2/m4/libtool.m4    2014-10-26 01:00:37.000000000 -0400

<at> <at> -1052,7 +1052,7 <at> <at>

       case ${MACOSX_DEPLOYMENT_TARGET-10.0},$host in

        10.0,*86*-darwin8*|10.0,*-darwin[[91]]*)

          _lt_dar_allow_undefined='${wl}-undefined ${wl}dynamic_lookup' ;;

-       10.[[012]]*)

+       10.[[012]][[,.]]*)

          _lt_dar_allow_undefined='${wl}-flat_namespace ${wl}-undefined ${wl}suppress' ;;

        10.*)

          _lt_dar_allow_undefined='${wl}-undefined ${wl}dynamic_lookup' ;;


     Without this hot-fix shared libraries are being linked as if the target were Puma instead

of Yosemite. The issue is very wide spread as libtool needs to be updated in all the

packages using it. It also can cause nasty side-effects as witnessed by the large number

of gcc49 test suite regressions when linked in this way. I will push a fix to gcc49-4.9.1 later

today.

            Jack

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Jack Howarth | 26 Oct 07:19 2014
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Yosemite linking like Puma

   I puzzled out the regressions in gcc49's fortran test suite on Yosemite. It is due to the libtool bug that causes  -Wl-flat_namespace -undefined suppress to be erroneously used on Yosemite as if it were on Puma. Applying the MacPorts fix of...


to gcc49 is the fix. We have many packages that will require this fix including gmp5, mpfr4, cloog-org2, libiconv, etc.
          Jack
ps While doing the original clean bootstrap under Yosemite with 'fink -m' during the builds, I noticed a number of packages with inexplicable test suite regressions. These may well be solve by rebuilding with the libtool error to configure being patched.
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