Your message dated Fri, 21 Aug 2015 09:55:27 +0000
with message-id <e1zsj2l-0001dn...@franck.debian.org>
and subject line Bug#795586: fixed in libfreecontact-perl 0.08-3
has caused the Debian Bug report #795586,
regarding libfreecontact-perl: FTBFS: Can't load 
'/tmp/buildd/libfreecontact-perl-0.08/blib/arch/auto/FreeContact/FreeContact.so
to be marked as done.

This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.

(NB: If you are a system administrator and have no idea what this
message is talking about, this may indicate a serious mail system
misconfiguration somewhere. Please contact ow...@bugs.debian.org
immediately.)


-- 
795586: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=795586
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems
--- Begin Message ---
Source: libfreecontact-perl
Version: 0.08-2
Severity: serious
Justification: fails to build from source

Dear Maintainer,

libfreecontact-perl fails to build from source on unstable/amd64:

  [..]
  Failed 3/3 subtests 
  
  #   Failed test 'use FreeContact;'
  #   at t/02test.t line 6.
  #     Tried to use 'FreeContact'.
  #     Error:  Can't load
  
'/tmp/buildd/libfreecontact-perl-0.08/blib/arch/auto/FreeContact/FreeContact.so'
  for module FreeContact:
  
/tmp/buildd/libfreecontact-perl-0.08/blib/arch/auto/FreeContact/FreeContact.so:
  undefined symbol:
  
_ZN11freecontact9predictor3runERKNS_5ali_tERKSt6vectorIdSaIdEEdddtddbdbbdilPSt3mapINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEdSt4lessISF_ESaISt4pairIKSF_dEEE
  at /usr/lib/x86_64-linux-gnu/perl/5.20/DynaLoader.pm line 187.
  #  at t/02test.t line 6.
  # Compilation failed in require at t/02test.t line 6.
  # BEGIN failed--compilation aborted at t/02test.t line 6.
  Can't locate object method "_new" via package "FreeContact::Predictor"
  at /tmp/buildd/libfreecontact-perl-0.08/blib/lib/FreeContact.pm line
  50.
  # Looks like you planned 10 tests but ran 1.

  [..]

The full build log is attached or can be viewed here:

  
https://reproducible.debian.net/rbuild/unstable/amd64/libfreecontact-perl_0.08-2.rbuild.log.gz


Regards,

-- 
      ,''`.
     : :'  :     Chris Lamb
     `. `'`      la...@debian.org / chris-lamb.co.uk
       `-
Starting to build libfreecontact-perl/unstable on 2015-08-10 19:26
The jenkins build log is/was available at 
https://jenkins.debian.net/job/reproducible_builder_zeta/25426/console
Reading package lists...
Building dependency tree...
Reading state information...
NOTICE: 'libfreecontact-perl' packaging is maintained in the 'Git' version 
control system at:
git://anonscm.debian.org/debian-med/libfreecontact-perl.git
Need to get 63.2 kB of source archives.
Get:1 http://ftp.de.debian.org/debian/ unstable/main libfreecontact-perl 0.08-2 
(dsc) [2079 B]
Get:2 http://ftp.de.debian.org/debian/ unstable/main libfreecontact-perl 0.08-2 
(tar) [58.7 kB]
Get:3 http://ftp.de.debian.org/debian/ unstable/main libfreecontact-perl 0.08-2 
(diff) [2477 B]
Fetched 63.2 kB in 0s (274 kB/s)
Download complete and in download only mode
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA1

Format: 3.0 (quilt)
Source: libfreecontact-perl
Binary: libfreecontact-perl
Architecture: any
Version: 0.08-2
Maintainer: Debian Med Packaging Team 
<debian-med-packag...@lists.alioth.debian.org>
Uploaders: Laszlo Kajan <lka...@rostlab.org>
Homepage: http://rostlab.org/
Standards-Version: 3.9.4
Vcs-Browser: 
http://anonscm.debian.org/gitweb/?p=debian-med/libfreecontact-perl.git
Vcs-Git: git://anonscm.debian.org/debian-med/libfreecontact-perl.git
Build-Depends: debhelper (>= 9.0.0), libextutils-xspp-perl, libfreecontact0-dev 
(>= 1.0.21-1~), perl
Package-List: 
 libfreecontact-perl deb perl extra
Checksums-Sha1: 
 dea098c8025b42e79227265dd74252ceedbfa007 58672 
libfreecontact-perl_0.08.orig.tar.gz
 acb37c09d3a6e3d667f12c7832761c0045b084a1 2477 
libfreecontact-perl_0.08-2.debian.tar.gz
Checksums-Sha256: 
 7386762985b9e36ec13379948528f1f18e49cf799ba5436a46aa60e9cb041911 58672 
libfreecontact-perl_0.08.orig.tar.gz
 d0ecf233da20d826c6e4efb465c3d837e1bbf48d7dbc59cb6117424d5969fe46 2477 
libfreecontact-perl_0.08-2.debian.tar.gz
Files: 
 798e25cfc3954e027d208f62dd3fe6ea 58672 libfreecontact-perl_0.08.orig.tar.gz
 93cde55bc0aa93b788d6a9e1c08efdcb 2477 libfreecontact-perl_0.08-2.debian.tar.gz

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+ sudo timeout -k 12.1h 12h /usr/bin/ionice -c 3 /usr/bin/nice 
/usr/sbin/pbuilder --build --configfile 
/srv/reproducible-results/tmp.jbuDJd2yb8/pbuilderrc_0kfa --debbuildopts -b 
--basetgz /var/cache/pbuilder/unstable-reproducible-base.tgz --buildresult b1 
--logfile b1/build.log libfreecontact-perl_0.08-2.dsc
W: /root/.pbuilderrc does not exist
I: Logging to b1/build.log
I: using fakeroot in build.
I: pbuilder: network access will be disabled during build
I: Current time: Mon Aug 10 07:26:09 GMT+12 2015
I: pbuilder-time-stamp: 1439234769
I: Building the build Environment
I: extracting base tarball [/var/cache/pbuilder/unstable-reproducible-base.tgz]
I: creating local configuration
I: copying local configuration
I: mounting /proc filesystem
I: mounting /run/shm filesystem
I: mounting /dev/pts filesystem
I: Mounting /dev/shm
I: Mounting /sys
I: policy-rc.d already exists
I: Installing the build-deps
 -> Attempting to satisfy build-dependencies
 -> Creating pbuilder-satisfydepends-dummy package
Package: pbuilder-satisfydepends-dummy
Version: 0.invalid.0
Architecture: amd64
Maintainer: Debian Pbuilder Team <pbuilder-ma...@lists.alioth.debian.org>
Description: Dummy package to satisfy dependencies with aptitude - created by 
pbuilder
 This package was created automatically by pbuilder to satisfy the
 build-dependencies of the package being currently built.
Depends: debhelper (>= 9.0.0), libextutils-xspp-perl, libfreecontact0-dev (>= 
1.0.21-1~), perl
dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in 
'/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'.
Selecting previously unselected package pbuilder-satisfydepends-dummy.
(Reading database ... 20247 files and directories currently installed.)
Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ...
Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ...
dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring 
anyway as you requested:
 pbuilder-satisfydepends-dummy depends on libextutils-xspp-perl; however:
  Package libextutils-xspp-perl is not installed.
 pbuilder-satisfydepends-dummy depends on libfreecontact0-dev (>= 1.0.21-1~); 
however:
  Package libfreecontact0-dev is not installed.

Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ...
Reading package lists...
Building dependency tree...
Reading state information...
Initializing package states...
Writing extended state information...
Building tag database...
The following NEW packages will be installed:
  libblas-common{a} libblas3{a} libextutils-xspp-perl{a} libfreecontact0{a} 
  libfreecontact0-dev{a} libgfortran3{a} liblapack3{a} 
0 packages upgraded, 7 newly installed, 0 to remove and 0 not upgraded.
Need to get 2648 kB of archives. After unpacking 9062 kB will be used.
Writing extended state information...
Get: 1 http://ftp.de.debian.org/debian/ unstable/main libgfortran3 amd64 
5.2.1-15 [253 kB]
Get: 2 http://ftp.de.debian.org/debian/ unstable/main libblas-common amd64 
1.2.20110419-10 [8496 B]
Get: 3 http://ftp.de.debian.org/debian/ unstable/main libblas3 amd64 
1.2.20110419-10 [167 kB]
Get: 4 http://ftp.de.debian.org/debian/ unstable/main liblapack3 amd64 3.5.0-4 
[1852 kB]
Get: 5 http://ftp.de.debian.org/debian/ unstable/main libfreecontact0 amd64 
1.0.21-3+b1 [85.9 kB]
Get: 6 http://ftp.de.debian.org/debian/ unstable/main libextutils-xspp-perl all 
0.1800-2 [191 kB]
Get: 7 http://ftp.de.debian.org/debian/ unstable/main libfreecontact0-dev amd64 
1.0.21-3+b1 [90.6 kB]
Fetched 2648 kB in 0s (12.2 MB/s)
debconf: delaying package configuration, since apt-utils is not installed
Selecting previously unselected package libgfortran3:amd64.
(Reading database ... 
(Reading database ... 5%
(Reading database ... 10%
(Reading database ... 15%
(Reading database ... 20%
(Reading database ... 25%
(Reading database ... 30%
(Reading database ... 35%
(Reading database ... 40%
(Reading database ... 45%
(Reading database ... 50%
(Reading database ... 55%
(Reading database ... 60%
(Reading database ... 65%
(Reading database ... 70%
(Reading database ... 75%
(Reading database ... 80%
(Reading database ... 85%
(Reading database ... 90%
(Reading database ... 95%
(Reading database ... 100%
(Reading database ... 20247 files and directories currently installed.)
Preparing to unpack .../libgfortran3_5.2.1-15_amd64.deb ...
Unpacking libgfortran3:amd64 (5.2.1-15) ...
Selecting previously unselected package libblas-common.
Preparing to unpack .../libblas-common_1.2.20110419-10_amd64.deb ...
Unpacking libblas-common (1.2.20110419-10) ...
Selecting previously unselected package libblas3.
Preparing to unpack .../libblas3_1.2.20110419-10_amd64.deb ...
Unpacking libblas3 (1.2.20110419-10) ...
Selecting previously unselected package liblapack3.
Preparing to unpack .../liblapack3_3.5.0-4_amd64.deb ...
Unpacking liblapack3 (3.5.0-4) ...
Selecting previously unselected package libfreecontact0.
Preparing to unpack .../libfreecontact0_1.0.21-3+b1_amd64.deb ...
Unpacking libfreecontact0 (1.0.21-3+b1) ...
Selecting previously unselected package libextutils-xspp-perl.
Preparing to unpack .../libextutils-xspp-perl_0.1800-2_all.deb ...
Unpacking libextutils-xspp-perl (0.1800-2) ...
Selecting previously unselected package libfreecontact0-dev.
Preparing to unpack .../libfreecontact0-dev_1.0.21-3+b1_amd64.deb ...
Unpacking libfreecontact0-dev (1.0.21-3+b1) ...
Processing triggers for man-db (2.7.0.2-5) ...
Setting up libgfortran3:amd64 (5.2.1-15) ...
Setting up libblas-common (1.2.20110419-10) ...
Setting up libblas3 (1.2.20110419-10) ...
update-alternatives: using /usr/lib/libblas/libblas.so.3 to provide 
/usr/lib/libblas.so.3 (libblas.so.3) in auto mode
Setting up liblapack3 (3.5.0-4) ...
update-alternatives: using /usr/lib/lapack/liblapack.so.3 to provide 
/usr/lib/liblapack.so.3 (liblapack.so.3) in auto mode
Setting up libfreecontact0 (1.0.21-3+b1) ...
Setting up libextutils-xspp-perl (0.1800-2) ...
Setting up libfreecontact0-dev (1.0.21-3+b1) ...
Processing triggers for libc-bin (2.19-19) ...
Reading package lists...
Building dependency tree...
Reading state information...
Reading extended state information...
Initializing package states...
Writing extended state information...
Building tag database...
 -> Finished parsing the build-deps
Reading package lists...
Building dependency tree...
Reading state information...
fakeroot is already the newest version.
0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded.
I: Copying source file
I: copying [libfreecontact-perl_0.08-2.dsc]
I: copying [./libfreecontact-perl_0.08.orig.tar.gz]
I: copying [./libfreecontact-perl_0.08-2.debian.tar.gz]
I: Extracting source
gpgv: keyblock resource `/tmp/buildd/.gnupg/trustedkeys.gpg': file open error
gpgv: Signature made Sat Sep 28 08:55:17 2013 GMT+12 using RSA key ID 9A0C52FA
gpgv: Can't check signature: public key not found
dpkg-source: warning: failed to verify signature on 
./libfreecontact-perl_0.08-2.dsc
dpkg-source: info: extracting libfreecontact-perl in libfreecontact-perl-0.08
dpkg-source: info: unpacking libfreecontact-perl_0.08.orig.tar.gz
dpkg-source: info: unpacking libfreecontact-perl_0.08-2.debian.tar.gz
I: Building the package
I: Running cd tmp/buildd/*/ && env 
PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" dpkg-buildpackage -us -uc  -b 
-rfakeroot
dpkg-buildpackage: source package libfreecontact-perl
dpkg-buildpackage: source version 0.08-2
dpkg-buildpackage: source distribution unstable
dpkg-buildpackage: source changed by Laszlo Kajan <lka...@rostlab.org>
 dpkg-source --before-build libfreecontact-perl-0.08
dpkg-buildpackage: host architecture amd64
 fakeroot debian/rules clean
dh clean --parallel
   dh_testdir -O--parallel
   debian/rules override_dh_auto_clean
make[1]: Entering directory '/tmp/buildd/libfreecontact-perl-0.08'
rm -f Makefile.old
dh_auto_clean
make[1]: Leaving directory '/tmp/buildd/libfreecontact-perl-0.08'
   dh_clean -O--parallel
 debian/rules build
dh build --parallel
   dh_testdir -O--parallel
   debian/rules override_dh_auto_configure
make[1]: Entering directory '/tmp/buildd/libfreecontact-perl-0.08'
dh_auto_configure -- OPTIMIZE="-Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 
-fstack-protector-strong -Wformat -Werror=format-security" LD="'cc'  
-Wl,-z,relro"
        perl Makefile.PL INSTALLDIRS=vendor "OPTIMIZE=-g -O2 
-fstack-protector-strong -Wformat -Werror=format-security -Wdate-time 
-D_FORTIFY_SOURCE=2" "LD=cc -g -O2 -fstack-protector-strong -Wformat 
-Werror=format-security -Wl,-z,relro" "OPTIMIZE=-Wdate-time -D_FORTIFY_SOURCE=2 
-g -O2 -fstack-protector-strong -Wformat -Werror=format-security" "LD='cc'  
-Wl,-z,relro"
Checking if your kit is complete...
Looks good
Generating a Unix-style Makefile
Writing Makefile for FreeContact
Writing MYMETA.yml and MYMETA.json
make[1]: Leaving directory '/tmp/buildd/libfreecontact-perl-0.08'
   dh_auto_build -O--parallel
        make -j23
make[1]: Entering directory '/tmp/buildd/libfreecontact-perl-0.08'
/usr/bin/perl /usr/share/perl/5.20/ExtUtils/xsubpp  -C++ -hiertype 
-noprototypes -typemap /usr/share/perl/5.20/ExtUtils/typemap -typemap 
perlobject.map -typemap typemap -typemap typemap  FreeContact.xs > 
FreeContact.xsc && mv FreeContact.xsc FreeContact.c
Running Mkbootstrap for FreeContact ()
chmod 644 FreeContact.bs
cp lib/FreeContact.pm blib/lib/FreeContact.pm
AutoSplitting blib/lib/FreeContact.pm (blib/lib/auto/FreeContact)
g++ -c  -I. -D_REENTRANT -D_GNU_SOURCE -DDEBIAN -fwrapv -fno-strict-aliasing 
-pipe -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 
-Wdate-time -D_FORTIFY_SOURCE=2 -g -O2 -fstack-protector-strong -Wformat 
-Werror=format-security   -DVERSION=\"0.08\" -DXS_VERSION=\"0.08\" -fPIC 
"-I/usr/lib/x86_64-linux-gnu/perl/5.20/CORE"   FreeContact.c
rm -f blib/arch/auto/FreeContact/FreeContact.so
'cc'  -Wl,-z,relro  -shared -L/usr/local/lib -fstack-protector FreeContact.o  
-o blib/arch/auto/FreeContact/FreeContact.so      \
   -lfreecontact        \
  
chmod 755 blib/arch/auto/FreeContact/FreeContact.so
/usr/bin/perl -MExtUtils::Command::MM -e 'cp_nonempty' -- FreeContact.bs 
blib/arch/auto/FreeContact/FreeContact.bs 644
Manifying blib/man3/FreeContact.3pm
make[1]: Leaving directory '/tmp/buildd/libfreecontact-perl-0.08'
   dh_auto_test -O--parallel
        make -j23 test TEST_VERBOSE=1
make[1]: Entering directory '/tmp/buildd/libfreecontact-perl-0.08'
Running Mkbootstrap for FreeContact ()
chmod 644 FreeContact.bs
PERL_DL_NONLAZY=1 /usr/bin/perl "-MExtUtils::Command::MM" "-MTest::Harness" 
"-e" "undef *Test::Harness::Switches; test_harness(1, 'blib/lib', 'blib/arch')" 
t/*.t

#   Failed test 'use FreeContact;'
#   at t/01FreeContact.t line 9.
#     Tried to use 'FreeContact'.
#     Error:  Can't load 
'/tmp/buildd/libfreecontact-perl-0.08/blib/arch/auto/FreeContact/FreeContact.so'
 for module FreeContact: 
/tmp/buildd/libfreecontact-perl-0.08/blib/arch/auto/FreeContact/FreeContact.so: 
undefined symbol: 
_ZN11freecontact9predictor3runERKNS_5ali_tERKSt6vectorIdSaIdEEdddtddbdbbdilPSt3mapINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEdSt4lessISF_ESaISt4pairIKSF_dEEE
 at /usr/lib/x86_64-linux-gnu/perl/5.20/DynaLoader.pm line 187.
#  at t/01FreeContact.t line 9.
# Compilation failed in require at t/01FreeContact.t line 9.
# BEGIN failed--compilation aborted at t/01FreeContact.t line 9.

#   Failed test 'FreeContact->can(...)'
#   at t/01FreeContact.t line 17.
#     FreeContact->can('get_ps_evfold') failed
#     FreeContact->can('get_ps_psicov') failed
#     FreeContact->can('get_ps_psicov_sd') failed

#   Failed test 'FreeContact::Predictor->can(...)'
#   at t/01FreeContact.t line 18.
#     FreeContact::Predictor->can('_get_seq_weights') failed
#     FreeContact::Predictor->can('_run') failed
# Looks like you failed 3 tests of 3.
t/01FreeContact.t .. 
1..3
not ok 1 - use FreeContact;
not ok 2 - FreeContact->can(...)
not ok 3 - FreeContact::Predictor->can(...)
Dubious, test returned 3 (wstat 768, 0x300)
Failed 3/3 subtests 

#   Failed test 'use FreeContact;'
#   at t/02test.t line 6.
#     Tried to use 'FreeContact'.
#     Error:  Can't load 
'/tmp/buildd/libfreecontact-perl-0.08/blib/arch/auto/FreeContact/FreeContact.so'
 for module FreeContact: 
/tmp/buildd/libfreecontact-perl-0.08/blib/arch/auto/FreeContact/FreeContact.so: 
undefined symbol: 
_ZN11freecontact9predictor3runERKNS_5ali_tERKSt6vectorIdSaIdEEdddtddbdbbdilPSt3mapINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEdSt4lessISF_ESaISt4pairIKSF_dEEE
 at /usr/lib/x86_64-linux-gnu/perl/5.20/DynaLoader.pm line 187.
#  at t/02test.t line 6.
# Compilation failed in require at t/02test.t line 6.
# BEGIN failed--compilation aborted at t/02test.t line 6.
Can't locate object method "_new" via package "FreeContact::Predictor" at 
/tmp/buildd/libfreecontact-perl-0.08/blib/lib/FreeContact.pm line 50.
# Looks like you planned 10 tests but ran 1.
# Looks like you failed 1 test of 1 run.
# Looks like your test exited with 255 just after 1.
t/02test.t ......... 
1..10
not ok 1 - use FreeContact;
Dubious, test returned 255 (wstat 65280, 0xff00)
Failed 10/10 subtests 

Test Summary Report
-------------------
t/01FreeContact.t (Wstat: 768 Tests: 3 Failed: 3)
  Failed tests:  1-3
  Non-zero exit status: 3
t/02test.t       (Wstat: 65280 Tests: 1 Failed: 1)
  Failed test:  1
  Non-zero exit status: 255
  Parse errors: Bad plan.  You planned 10 tests but ran 1.
Files=2, Tests=4,  0 wallclock secs ( 0.04 usr  0.01 sys +  0.11 cusr  0.03 
csys =  0.19 CPU)
Result: FAIL
Failed 2/2 test programs. 4/4 subtests failed.
Makefile:992: recipe for target 'test_dynamic' failed
make[1]: *** [test_dynamic] Error 255
make[1]: Leaving directory '/tmp/buildd/libfreecontact-perl-0.08'
dh_auto_test: make -j23 test TEST_VERBOSE=1 returned exit code 2
debian/rules:30: recipe for target 'build' failed
make: *** [build] Error 2
dpkg-buildpackage: error: debian/rules build gave error exit status 2
E: Failed autobuilding of package
I: unmounting /sys filesystem
I: unmounting /dev/shm filesystem
I: unmounting dev/pts filesystem
I: unmounting run/shm filesystem
I: unmounting proc filesystem
I: cleaning the build env 
I: removing directory /var/cache/pbuilder/build//15954 and its subdirectories
Warning: No second build log

--- End Message ---
--- Begin Message ---
Source: libfreecontact-perl
Source-Version: 0.08-3

We believe that the bug you reported is fixed in the latest version of
libfreecontact-perl, which is due to be installed in the Debian FTP archive.

A summary of the changes between this version and the previous one is
attached.

Thank you for reporting the bug, which will now be closed.  If you
have further comments please address them to 795...@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.

Debian distribution maintenance software
pp.
Andreas Tille <ti...@debian.org> (supplier of updated libfreecontact-perl 
package)

(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing ftpmas...@ftp-master.debian.org)


-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA256

Format: 1.8
Date: Fri, 21 Aug 2015 11:42:20 +0200
Source: libfreecontact-perl
Binary: libfreecontact-perl
Architecture: source amd64
Version: 0.08-3
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team 
<debian-med-packag...@lists.alioth.debian.org>
Changed-By: Andreas Tille <ti...@debian.org>
Description:
 libfreecontact-perl - fast protein contact predictor - binding for Perl
Closes: 795586
Changes:
 libfreecontact-perl (0.08-3) unstable; urgency=medium
 .
   * cme fix dpkg-control
   * add myself to Uploaders
   * Priority: optional
   * Rebuild against gcc-5 transitioned libfreecontact-dev
     Closes: #795586
   * simplify debian/rules
   * DEP5 fix
Checksums-Sha1:
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