Add CMake build system #107

JohanMabille · 2019-03-06T16:50:29Z

Add CMake build system
Build dynamic libraries on Windows
Append new builds to the CI
Add tests
Make the CI run the test suite (should be done in a dedicated PR)

massich · 2019-03-06T17:06:05Z

To replicate the build in linux ubuntu/debian

SRC_DIR=/home/sik/repos/matio
BUILD_DIR=/home/sik/Workspace/matio/build_linux
INSTALL_DIR=$BUILD_DIR/simulate_install_dir

cd $BUILD_DIR
rm $BUILD_DIR/* -Rf
cmake $SRC_DIR \
      -DCMAKE_INSTALL_PREFIX=$INSTALL_DIR

cmake --build . -- -j 8
make install

It works when hdf5 is installed using apt-get: sudo apt-get install hdf5-tools libhdf5-dev hdf5-helpers and/or conda: conda install hdf5

To run it in windows @JohanMabille and I we tested only using gitbash and conda with the following lines:

cmake -G "NMake Makefiles" -DCMAKE_INSTALL_PREFIX=%MINICONDA%/Library -DCMAKE_PREFIX_PATH=%MINICONDA%/Library/cmake ..

nmake matdump

(be aware that the windows snipped might have some typo since I didn't copy paste it)

tbeu · 2019-03-06T17:34:01Z

I believe adding the tests is optional and agree that it is beyond the scope of this PR adding CMake support for the libmatio build.

Nelson-numerical-software · 2019-03-10T10:55:46Z

CMakeLists.txt

@@ -0,0 +1,25 @@
+# Autogenerated by auto2cmake on 2018-03-07 11:49:59
+cmake_minimum_required(VERSION 3.9)


please support 3.7.2 (available in debian stretch)
I tested with 3.7.2 and it works

Nelson-numerical-software · 2019-03-10T11:06:41Z

How to build a dynamic library ?
Current cmake configuration seems to generate only a static library

debian9:/tmp/matio$ sudo make install
[ 10%] Built target getopt
[ 70%] Built target matio
[ 80%] Built target matdump
[ 90%] Built target test_snprintf
[100%] Built target test_mat
Install the project...
-- Install configuration: "Release"
-- Up-to-date: /usr/local/lib/libmatio.a
-- Up-to-date: /usr/local/include/matio.h
-- Up-to-date: /usr/local/include/matio_pubconf.h
-- Up-to-date: /usr/local/include/matio_export.h

tbeu · 2019-03-10T11:43:24Z

There are typos in CheckHeaderSTDC.cmake: Cheking -> Checking

tbeu · 2019-03-10T11:50:30Z

Also works with CMake 3.6.2 on Cygwin:

laptop ~
$ cd /cygdrive/c/Projects/

laptop /cygdrive/c/Projects
$ git clone https://github.com/JohanMabille/matio --branch cmake matio-cmake-cygwin
Klone nach 'matio-cmake-cygwin' ...
remote: Enumerating objects: 37, done.
remote: Counting objects: 100% (37/37), done.
remote: Compressing objects: 100% (33/33), done.
remote: Total 6641 (delta 9), reused 28 (delta 4), pack-reused 6604
Empfange Objekte: 100% (6641/6641), 3.44 MiB | 686.00 KiB/s, Fertig.
Löse Unterschiede auf: 100% (4923/4923), Fertig.
Checke Dateien aus: 100% (490/490), Fertig.

laptop /cygdrive/c/Projects
$ cd matio-cmake-cygwin/

laptop /cygdrive/c/Projects/matio-cmake-cygwin
$ sed -i 's/ 3.9/ 3.6.2/' CMakeLists.txt

laptop /cygdrive/c/Projects/matio-cmake-cygwin
$ cmake --version
cmake version 3.6.2

CMake suite maintained and supported by Kitware (kitware.com/cmake).

laptop /cygdrive/c/Projects/matio-cmake-cygwin
$ cmake -G "Unix Makefiles" ./
-- The C compiler identification is GNU 7.4.0
-- The CXX compiler identification is GNU 7.4.0
-- Check for working C compiler: /usr/bin/cc
-- Check for working C compiler: /usr/bin/cc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Detecting C compile features
-- Detecting C compile features - done
-- Check for working CXX compiler: /usr/bin/c++.exe
-- Check for working CXX compiler: /usr/bin/c++.exe -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
 DEBUG Enabled
 EXTENDED_SPARSE Enabled
 MAT73 Enabled
 PROFILE Enabled
-- Looking for pthread.h
-- Looking for pthread.h - found
-- Looking for pthread_create
-- Looking for pthread_create - found
-- Found Threads: TRUE
-- Found HDF5: /usr/lib/libhdf5_cpp.dll.a;/usr/lib/libhdf5.dll.a (found version "1.8.20")
-- Found ZLIB: /usr/lib/libz.dll.a (found version "1.2.11")
-- Looking for sys/types.h
-- Looking for sys/types.h - found
-- Looking for stdint.h
-- Looking for stdint.h - found
-- Looking for stddef.h
-- Looking for stddef.h - found
-- Check size of char
-- Check size of char - done
-- Check size of double
-- Check size of double - done
-- Check size of float
-- Check size of float - done
-- Check size of int
-- Check size of int - done
-- Check size of long
-- Check size of long - done
-- Check size of long long
-- Check size of long long - done
-- Check size of short
-- Check size of short - done
-- Check size of size_t
-- Check size of size_t - done
-- Looking for vsnprintf
-- Looking for vsnprintf - found
-- Looking for snprintf
-- Looking for snprintf - found
-- Looking for vasprintf
-- Looking for vasprintf - found
-- Looking for asprintf
-- Looking for asprintf - found
-- Looking for strcasecmp
-- Looking for strcasecmp - found
-- Looking for getopt
-- Looking for getopt - found
-- Looking for inttypes.h
-- Looking for inttypes.h - found
-- Looking for strings.h
-- Looking for strings.h - found
-- Looking for ctype.h
-- Looking for ctype.h - found
-- Looking for stdlib.h
-- Looking for stdlib.h - found
-- Looking for string.h
-- Looking for string.h - found
-- Looking for stdarg.h
-- Looking for stdarg.h - found
-- Cheking for ANSI C header files
-- Cheking for ANSI C header files - found
-- Check size of uint8_t
-- Check size of uint8_t - done
-- Check size of uint16_t
-- Check size of uint16_t - done
-- Check size of uint32_t
-- Check size of uint32_t - done
-- Check size of uint64_t
-- Check size of uint64_t - done
-- Check size of int8_t
-- Check size of int8_t - done
-- Check size of int16_t
-- Check size of int16_t - done
-- Check size of int32_t
-- Check size of int32_t - done
-- Check size of int64_t
-- Check size of int64_t - done
-- Performing Test COMPILER_HAS_DEPRECATED_ATTR
-- Performing Test COMPILER_HAS_DEPRECATED_ATTR - Success
-- Configuring done
-- Generating done
-- Build files have been written to: /cygdrive/c/Projects/matio-cmake-cygwin

laptop /cygdrive/c/Projects/matio-cmake-cygwin
$ make
Scanning dependencies of target getopt
[  5%] Building C object CMakeFiles/getopt.dir/getopt/getopt_long.c.o
[ 10%] Linking C static library libgetopt.a
[ 10%] Built target getopt
Scanning dependencies of target matio
[ 15%] Building C object CMakeFiles/matio.dir/src/endian.c.o
[ 20%] Building C object CMakeFiles/matio.dir/src/mat.c.o
/cygdrive/c/Projects/matio-cmake-cygwin/src/mat.c: In Funktion »Mat_VarDelete«:
/cygdrive/c/Projects/matio-cmake-cygwin/src/mat.c:1032:5: Warnung: »mktemp« ist veraltet: the use of `mktemp' is dangerous; use `mkstemp' instead [-Wdeprecated-declarations]
     if ( (tmp_name = mktemp(temp)) != NULL ) {
     ^~
In file included from /cygdrive/c/Projects/matio-cmake-cygwin/src/mat.c:32:0:
/usr/include/stdlib.h:134:8: Anmerkung: hier deklariert
 char * mktemp (char *) _ATTRIBUTE ((__deprecated__("the use of `mktemp' is dangerous; use `mkstemp' instead")));
        ^~~~~~
[ 25%] Building C object CMakeFiles/matio.dir/src/io.c.o
[ 30%] Building C object CMakeFiles/matio.dir/src/inflate.c.o
[ 35%] Building C object CMakeFiles/matio.dir/src/mat73.c.o
[ 40%] Building C object CMakeFiles/matio.dir/src/matvar_cell.c.o
[ 45%] Building C object CMakeFiles/matio.dir/src/matvar_struct.c.o
[ 50%] Building C object CMakeFiles/matio.dir/src/mat4.c.o
[ 55%] Building C object CMakeFiles/matio.dir/src/mat5.c.o
[ 60%] Building C object CMakeFiles/matio.dir/src/snprintf.c.o
[ 65%] Building C object CMakeFiles/matio.dir/src/read_data.c.o
[ 70%] Linking C static library libmatio.a
[ 70%] Built target matio
Scanning dependencies of target matdump
[ 75%] Building C object CMakeFiles/matdump.dir/tools/matdump.c.o
[ 80%] Linking C executable matdump.exe
[ 80%] Built target matdump
Scanning dependencies of target test_mat
[ 85%] Building C object CMakeFiles/test_mat.dir/test/test_mat.c.o
[ 90%] Linking C executable test_mat.exe
[ 90%] Built target test_mat
Scanning dependencies of target test_snprintf
[ 95%] Building C object CMakeFiles/test_snprintf.dir/test/test_snprintf.c.o
[100%] Linking C executable test_snprintf.exe
[100%] Built target test_snprintf

laptop /cygdrive/c/Projects/matio-cmake-cygwin
$

tbeu · 2019-03-10T12:43:18Z

Any chance to use matio.rc for Win builds?

tbeu · 2019-03-10T12:47:38Z

Please do add yourself the Acknowledgements section of both README and README.md.

massich · 2019-03-12T08:36:29Z

Any chance to use matio.rc for Win builds?

Ok I see what the .rc file does. Is there any chance to have all this metadata in the same manner for windows/linux/osx ?

tbeu · 2019-03-12T10:17:35Z

Is there any chance to have all this metadata in the same manner for windows/linux/osx ?

https://stackoverflow.com/q/6693100/8520615 might give some clues.

massich · 2019-03-12T12:01:24Z

What I meant was: sure that we can generate the `.rc` from Cmake (which is what the stackoverflow link illustrates) or use the `.rc` to populate the Cmake. But the question is can we agree in a manner that we use to populate autoconf, Cmake and visual? All at once?

…

On Tue, Mar 12, 2019, 11:17 tbeu ***@***.***> wrote: Is there any chance to have all this metadata in the same manner for windows/linux/osx ? https://stackoverflow.com/q/6693100/8520615 might give some clues. — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#107 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AGt-4-ZKz9PSeYCSil62eQHINBwWhM_4ks5vV37AgaJpZM4bhWG9> .

tbeu · 2019-03-13T10:09:34Z

Even today, autoconf and VS version information are independent.

massich · 2019-03-20T14:05:53Z

@tbeu travis seems to not run in the PRs. Can you trigger it?

tbeu · 2019-03-20T14:12:52Z

Usually it did. Could it be that this is a draft PR?

tbeu · 2019-03-20T14:16:12Z

tbeu · 2019-03-20T18:05:13Z

It says: Could not parse tbeu/matio/.travis.yml@844e9935

Syntax error?

tbeu · 2019-03-23T19:30:50Z

Travis now runs, but still some command error, see https://travis-ci.org/tbeu/matio/builds/510386199 for https://github.com/tbeu/matio/tree/cmake

tbeu · 2019-04-02T21:18:29Z

If it says "Could NOT find HDF5" (as in https://travis-ci.org/tbeu/matio/jobs/514751765#L1658) then HAVE_HDF5 must not be defined (if MAT73 is defined).

massich · 2019-04-03T21:29:32Z

it builds, now what it does not do is test properly.

tbeu · 2019-04-04T06:02:55Z

it builds, now what it does not do is test properly.

See your 5 point plan above and my #107 (comment).

coveralls · 2019-04-08T21:26:49Z

Coverage decreased (-82.8%) to 0.0% when pulling 9a3b7da on JohanMabille:cmake into 596cb3c on tbeu:master.

massich · 2019-04-10T07:47:22Z

If CIs turn green, this should be ready to merge. We can take whatever is left out for subsequent PRs.

@tbeu feel free to push any changes in the travis.yml

tbeu · 2019-04-12T14:35:25Z

There are typos in CheckHeaderSTDC.cmake: Cheking -> Checking

Still not fixed.

tbeu · 2019-04-12T14:47:02Z

On Win, with HDF5 installed and properly detected, I always get using cmake-gui

Configuring done
CMake Error at cmake/tools.cmake:1 (add_executable):
  Target "matdump" links to target "hdf5::hdf5-static" but the target was not
  found.  Perhaps a find_package() call is missing for an IMPORTED target, or
  an ALIAS target is missing?
Call Stack (most recent call first):
  CMakeLists.txt:29 (include)


CMake Error at cmake/tools.cmake:1 (add_executable):
  Target "matdump" links to target "hdf5::hdf5-static" but the target was not
  found.  Perhaps a find_package() call is missing for an IMPORTED target, or
  an ALIAS target is missing?
Call Stack (most recent call first):
  CMakeLists.txt:29 (include)


CMake Error at cmake/tools.cmake:1 (add_executable):
  Target "matdump" links to target "hdf5::hdf5-static" but the target was not
  found.  Perhaps a find_package() call is missing for an IMPORTED target, or
  an ALIAS target is missing?
Call Stack (most recent call first):
  CMakeLists.txt:29 (include)


CMake Error at cmake/tools.cmake:1 (add_executable):
  Target "matdump" links to target "hdf5::hdf5-static" but the target was not
  found.  Perhaps a find_package() call is missing for an IMPORTED target, or
  an ALIAS target is missing?
Call Stack (most recent call first):
  CMakeLists.txt:29 (include)


CMake Error at cmake/src.cmake:32 (add_library):
  Target "matio" links to target "hdf5::hdf5-static" but the target was not
  found.  Perhaps a find_package() call is missing for an IMPORTED target, or
  an ALIAS target is missing?
Call Stack (most recent call first):
  CMakeLists.txt:27 (include)


CMake Error at cmake/src.cmake:32 (add_library):
  Target "matio" links to target "hdf5::hdf5-static" but the target was not
  found.  Perhaps a find_package() call is missing for an IMPORTED target, or
  an ALIAS target is missing?
Call Stack (most recent call first):
  CMakeLists.txt:27 (include)


CMake Error at cmake/src.cmake:32 (add_library):
  Target "matio" links to target "hdf5::hdf5-static" but the target was not
  found.  Perhaps a find_package() call is missing for an IMPORTED target, or
  an ALIAS target is missing?
Call Stack (most recent call first):
  CMakeLists.txt:27 (include)


CMake Error at cmake/src.cmake:32 (add_library):
  Target "matio" links to target "hdf5::hdf5-static" but the target was not
  found.  Perhaps a find_package() call is missing for an IMPORTED target, or
  an ALIAS target is missing?
Call Stack (most recent call first):
  CMakeLists.txt:27 (include)


CMake Error at cmake/test.cmake:6 (add_executable):
  Target "test_snprintf" links to target "hdf5::hdf5-static" but the target
  was not found.  Perhaps a find_package() call is missing for an IMPORTED
  target, or an ALIAS target is missing?
Call Stack (most recent call first):
  CMakeLists.txt:30 (include)


CMake Error at cmake/test.cmake:6 (add_executable):
  Target "test_snprintf" links to target "hdf5::hdf5-static" but the target
  was not found.  Perhaps a find_package() call is missing for an IMPORTED
  target, or an ALIAS target is missing?
Call Stack (most recent call first):
  CMakeLists.txt:30 (include)


CMake Error at cmake/test.cmake:6 (add_executable):
  Target "test_snprintf" links to target "hdf5::hdf5-static" but the target
  was not found.  Perhaps a find_package() call is missing for an IMPORTED
  target, or an ALIAS target is missing?
Call Stack (most recent call first):
  CMakeLists.txt:30 (include)


CMake Error at cmake/test.cmake:6 (add_executable):
  Target "test_snprintf" links to target "hdf5::hdf5-static" but the target
  was not found.  Perhaps a find_package() call is missing for an IMPORTED
  target, or an ALIAS target is missing?
Call Stack (most recent call first):
  CMakeLists.txt:30 (include)


CMake Error at cmake/test.cmake:3 (add_executable):
  Target "test_mat" links to target "hdf5::hdf5-static" but the target was
  not found.  Perhaps a find_package() call is missing for an IMPORTED
  target, or an ALIAS target is missing?
Call Stack (most recent call first):
  CMakeLists.txt:30 (include)


CMake Error at cmake/test.cmake:3 (add_executable):
  Target "test_mat" links to target "hdf5::hdf5-static" but the target was
  not found.  Perhaps a find_package() call is missing for an IMPORTED
  target, or an ALIAS target is missing?
Call Stack (most recent call first):
  CMakeLists.txt:30 (include)


CMake Error at cmake/test.cmake:3 (add_executable):
  Target "test_mat" links to target "hdf5::hdf5-static" but the target was
  not found.  Perhaps a find_package() call is missing for an IMPORTED
  target, or an ALIAS target is missing?
Call Stack (most recent call first):
  CMakeLists.txt:30 (include)


CMake Error at cmake/test.cmake:3 (add_executable):
  Target "test_mat" links to target "hdf5::hdf5-static" but the target was
  not found.  Perhaps a find_package() call is missing for an IMPORTED
  target, or an ALIAS target is missing?
Call Stack (most recent call first):
  CMakeLists.txt:30 (include)


CMake Error at cmake/src.cmake:32 (add_library):
  Target "matio" links to target "hdf5::hdf5-static" but the target was not
  found.  Perhaps a find_package() call is missing for an IMPORTED target, or
  an ALIAS target is missing?
Call Stack (most recent call first):
  CMakeLists.txt:27 (include)


CMake Error at cmake/tools.cmake:1 (add_executable):
  Target "matdump" links to target "hdf5::hdf5-static" but the target was not
  found.  Perhaps a find_package() call is missing for an IMPORTED target, or
  an ALIAS target is missing?
Call Stack (most recent call first):
  CMakeLists.txt:29 (include)


CMake Error at cmake/test.cmake:6 (add_executable):
  Target "test_snprintf" links to target "hdf5::hdf5-static" but the target
  was not found.  Perhaps a find_package() call is missing for an IMPORTED
  target, or an ALIAS target is missing?
Call Stack (most recent call first):
  CMakeLists.txt:30 (include)


CMake Error at cmake/test.cmake:3 (add_executable):
  Target "test_mat" links to target "hdf5::hdf5-static" but the target was
  not found.  Perhaps a find_package() call is missing for an IMPORTED
  target, or an ALIAS target is missing?
Call Stack (most recent call first):
  CMakeLists.txt:30 (include)


Generating done

Even if I deselect MAT73 (which means HDF5 dependency is not necessary) I get the above errors.

tbeu · 2019-04-12T14:54:44Z

On Cygwin, with HDF5 not installed, and MAT73 enabled (default), it fails to compile, since HAVE_HDF5 is set, but hdf5.h cannot be found. I would prefer if the default cmake config succeeds to configure and build.

tbeu · 2019-04-12T14:56:17Z

Please do add yourself the Acknowledgements section of both README and README.md.

Still open.

tbeu · 2020-03-06T18:53:51Z

Happy anniversary, #107! How to move on? I can think of the following alternatives.

Move on: Some volunteer fixes the review comments from @thejohnfreeman and me, and finalizes the remaining two relevant tasks. I can happily merge it,
Status quo: I can have this PR open one more year without much progress.
Back: I can close with unmerged commits.

While 1. is very unlikely to happen, it would be my preferred option.

papadop · 2020-03-06T23:14:15Z

I have (at least a partial one) an update with the "cheking' correction and most of the cmake changes. Plus a merge from origin/master (I hope). But I cannot push it here and my own fork refuses it too....
Not too sure what is the best solution.

tbeu · 2020-03-21T19:20:18Z

@papadop Thanks for your offer. I tried to look for the branch in your fork but did not see any recent commits. You can simply push to your repo and I will cherry-pick your commits afterwards.

added missing definitions to matio_pubconf Add getopt=1 as target_compile_definition fixed getopt build and added MATIO_VERSION_STR definition Expose HAVE_HDF5 Fixed link with HDF5

tbeu · 2020-03-22T11:30:18Z

I resolved the merge conflict with the Travis CI configuration and applied it again. Now the CMake build is running at Travis CI somehow, but I noticed other strange stings:

It does not build with zlib support, though I explicitly set ZLB_LIBRARY and ZLIB_INCLUDE_DIR.
make install does not install matdump

tbeu · 2020-06-22T15:08:12Z

Closing now, since there is no more progress to expect.

emmenlau · 2020-06-22T15:12:14Z

:-(

agramfort · 2020-06-22T20:29:31Z

:-(

Febbe · 2020-07-16T12:24:21Z

Closing now, since there is no more progress to expect.

It's sad to hear that the development is stopped. Autotools and vs-projects are really a pain. :-(
May I ask, why there is no progress and what prevented a merge?

emmenlau · 2020-07-16T12:55:27Z

Closing now, since there is no more progress to expect.

It's sad to hear that the development is stopped. Autotools and vs-projects are really a pain. :-(
May I ask, why there is no progress and what prevented a merge?

Well, basically you just need to scroll up to see the details...

Nelson-numerical-software reviewed Mar 10, 2019

View reviewed changes

tbeu added the enhancement label Mar 10, 2019

JohanMabille marked this pull request as ready for review March 20, 2019 13:43

massich mentioned this pull request Apr 2, 2019

Several cmake improvements #75

Closed

massich force-pushed the cmake branch from 0083072 to 197976f Compare April 3, 2019 16:26

tbeu force-pushed the master branch from d3f29f6 to 7fa1ef0 Compare January 4, 2020 08:27

tbeu mentioned this pull request Jan 21, 2020

Release? #133

Closed

diegoferigo mentioned this pull request Feb 6, 2020

Add logger for the Human-Dynamics-Estimation devices robotology/human-dynamics-estimation#151

Closed

Test HDF5 1.12.0

596cb3c

JohanMabille and others added 7 commits March 21, 2020 21:49

Add CMake build system

a9dda36

added missing definitions to matio_pubconf Add getopt=1 as target_compile_definition fixed getopt build and added MATIO_VERSION_STR definition Expose HAVE_HDF5 Fixed link with HDF5

Use Debian's CMake version

9f635cf

[skip ci] this works in linux

bd2c15a

refactor the cmake

63e9bfa

Fixed HAVE_GETOPT

781c520

Fix: comment typo in CMake is # not //

9ab4815

Bump version

4667af0

tbeu force-pushed the cmake branch from 2b7d540 to 66ce399 Compare March 22, 2020 11:26

Update Travis CI [skip appveyor]

9a3b7da

tbeu force-pushed the cmake branch from 66ce399 to 9a3b7da Compare March 23, 2020 19:12

tbeu force-pushed the master branch 2 times, most recently from d4d4d70 to 212bde3 Compare May 16, 2020 14:45

tbeu mentioned this pull request May 25, 2020

CMake tool #139

Closed

tbeu closed this Jun 22, 2020

tbeu removed the help wanted label Jun 22, 2020

S-Dafarra mentioned this pull request Jul 10, 2020

Create a logging tool using matio ami-iit/bipedal-locomotion-framework#69

Closed

MaartenBent mentioned this pull request Aug 30, 2020

CMake revived #150

Merged

		@@ -0,0 +1,25 @@
		# Autogenerated by auto2cmake on 2018-03-07 11:49:59
		cmake_minimum_required(VERSION 3.9)

Add CMake build system #107

Add CMake build system #107

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JohanMabille commented Mar 6, 2019 •

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tbeu commented Mar 20, 2019 •

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coveralls commented Apr 8, 2019 •

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tbeu commented Mar 22, 2020 •

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