Comments (7)
lima1
commented on June 1, 2024
Probably not super helpful me posting this since it's not supported yet, but compilation on arm64 fails for me here (both master and develop).
#0 4052.2 [ 61%] Creating directories for 'crc32-build'
#0 4052.2 [ 61%] Performing download step (download, verify and extract) for 'crc32-build'
#0 4052.2 -- Downloading...
#0 4052.2 dst='/root/gcssdk-install/v1.24.0/src/1.1.0.tar.gz'
#0 4052.2 timeout='none'
#0 4052.2 inactivity timeout='none'
#0 4052.2 -- Using src='https://github.com/google/crc32c/archive/1.1.0.tar.gz'
#0 4052.9 -- Downloading... done
#0 4053.0 -- extracting...
#0 4053.0 src='/root/gcssdk-install/v1.24.0/src/1.1.0.tar.gz'
#0 4053.0 dst='/root/gcssdk-install/v1.24.0/src/crc32-build'
#0 4053.0 -- extracting... [tar xfz]
#0 4053.0 -- extracting... [analysis]
#0 4053.0 -- extracting... [rename]
#0 4053.0 -- extracting... [clean up]
#0 4053.0 -- extracting... done
#0 4053.0 [ 61%] No update step for 'crc32-build'
#0 4053.0 [ 61%] No patch step for 'crc32-build'
#0 4053.1 [ 61%] Performing configure step for 'crc32-build'
#0 4053.1 -- The C compiler identification is GNU 11.3.0
#0 4053.2 -- The CXX compiler identification is GNU 11.3.0
#0 4053.2 -- Detecting C compiler ABI info
#0 4053.2 -- Detecting C compiler ABI info - done
#0 4053.2 -- Check for working C compiler: /usr/bin/cc - skipped
#0 4053.2 -- Detecting C compile features
#0 4053.2 -- Detecting C compile features - done
#0 4053.2 -- Detecting CXX compiler ABI info
#0 4053.3 -- Detecting CXX compiler ABI info - done
#0 4053.3 -- Check for working CXX compiler: /usr/bin/c++ - skipped
#0 4053.3 -- Detecting CXX compile features
#0 4053.3 -- Detecting CXX compile features - done
#0 4053.3 -- Performing Test CRC32C_HAVE_NO_DEPRECATED
#0 4053.3 -- Performing Test CRC32C_HAVE_NO_DEPRECATED - Success
#0 4053.3 -- Performing Test CRC32C_HAVE_NO_SIGN_COMPARE
#0 4053.4 -- Performing Test CRC32C_HAVE_NO_SIGN_COMPARE - Success
#0 4053.4 -- Performing Test CRC32C_HAVE_NO_UNUSED_PARAMETER
#0 4053.4 -- Performing Test CRC32C_HAVE_NO_UNUSED_PARAMETER - Success
#0 4053.4 -- Performing Test CRC32C_HAVE_NO_MISSING_FIELD_INITIALIZERS
#0 4053.5 -- Performing Test CRC32C_HAVE_NO_MISSING_FIELD_INITIALIZERS - Success
#0 4053.5 -- Performing Test HAVE_BUILTIN_PREFETCH
#0 4053.5 -- Performing Test HAVE_BUILTIN_PREFETCH - Success
#0 4053.5 -- Performing Test HAVE_MM_PREFETCH
#0 4053.6 -- Performing Test HAVE_MM_PREFETCH - Failed
#0 4053.6 -- Performing Test HAVE_SSE42
#0 4053.6 -- Performing Test HAVE_SSE42 - Failed
#0 4053.6 -- Performing Test HAVE_ARM64_CRC32C
#0 4053.8 -- Performing Test HAVE_ARM64_CRC32C - Success
#0 4053.8 -- Performing Test HAVE_STRONG_GETAUXVAL
#0 4053.9 -- Performing Test HAVE_STRONG_GETAUXVAL - Success
#0 4053.9 -- Performing Test HAVE_WEAK_GETAUXVAL
#0 4054.0 -- Performing Test HAVE_WEAK_GETAUXVAL - Success
#0 4054.0 -- Configuring done
#0 4054.0 -- Generating done
#0 4054.0 -- Build files have been written to: /root/gcssdk-install/v1.24.0/src/crc32-build-build
#0 4054.0 [ 61%] Performing build step for 'crc32-build'
#0 4054.0 [ 20%] Building CXX object CMakeFiles/crc32c_arm64.dir/src/crc32c_arm64.cc.o
#0 4054.2 [ 20%] Built target crc32c_arm64
#0 4054.2 [ 40%] Building CXX object CMakeFiles/crc32c_sse42.dir/src/crc32c_sse42.cc.o
#0 4054.2 [ 40%] Built target crc32c_sse42
#0 4054.2 [ 60%] Building CXX object CMakeFiles/crc32c.dir/src/crc32c_portable.cc.o
#0 4054.3 [ 80%] Building CXX object CMakeFiles/crc32c.dir/src/crc32c.cc.o
#0 4054.3 In file included from /root/gcssdk-install/v1.24.0/src/crc32-build/src/crc32c.cc:11:
#0 4054.3 /root/gcssdk-install/v1.24.0/src/crc32-build/src/./crc32c_arm64_linux_check.h: In function ‘bool crc32c::CanUseArm64Linux()’:
#0 4054.3 /root/gcssdk-install/v1.24.0/src/crc32-build/src/./crc32c_arm64_linux_check.h:36:37: error: the address of ‘long unsigned int getauxval(long unsigned int)’ will never be NULL [-Werror=address]
#0 4054.3 36 | unsigned long hwcap = (&getauxval != nullptr) ? getauxval(AT_HWCAP) : 0;
#0 4054.3 | ~~~~~~~~~~~^~~~~~~~~~
#0 4054.4 cc1plus: all warnings being treated as errors
#0 4054.4 make[5]: *** [CMakeFiles/crc32c.dir/build.make:90: CMakeFiles/crc32c.dir/src/crc32c.cc.o] Error 1
#0 4054.4 make[4]: *** [CMakeFiles/Makefile2:140: CMakeFiles/crc32c.dir/all] Error 2
#0 4054.4 make[3]: *** [Makefile:136: all] Error 2
#0 4054.4 make[2]: *** [dependencies/TileDB/CMakeFiles/crc32-build.dir/build.make:86: /root/gcssdk-install/v1.24.0/src/crc32-build-stamp/crc32-build-build] Error 2
#0 4054.4 make[1]: *** [CMakeFiles/Makefile2:822: dependencies/TileDB/CMakeFiles/crc32-build.dir/all] Error 2
#0 4054.4 make: *** [Makefile:146: all] Error 2
------
from genomicsdb.
nalinigans
commented on June 1, 2024
@lima1, just last week built GenomicsDB on a macOS m2 arm64 and it built fine using clang although I had a couple of tests failing. Can you please add the following information? Thanks.
- system macOS or Linux
- compiler and version, clang or gcc
- do you use the
gcscloud storage facilities available from GenomicsDB?
from genomicsdb.
lima1
commented on June 1, 2024
Just tried my amd64 Dockerimage on my new M2 MacBook Pro, although on a Linux image.
- Linux: bioconductor/bioconductor_docker:RELEASE_3_17 (Ubuntu 22.04)
- GCC GNU 11.3.0 (default of that image)
- No.
Here's how I tried to compile:
ENV GENOMICSDB_PATH=/opt/GenomicsDB
ENV GENOMICSDB_BRANCH=develop
RUN mkdir $GENOMICSDB_PATH
ENV INSTALL_PREFIX=$GENOMICSDB_PATH
ENV PREREQS_ENV=$GENOMICSDB_PATH/genomicsdb_prereqs.sh
ENV JAVA_HOME=/usr/lib/jvm/java-17-openjdk-amd64
ENV JAVA_HOME=/usr/lib/jvm/java-17-openjdk-arm64
ENV MAVEN_VERSION=3.9.2
RUN ls $JAVA_HOME
WORKDIR /tmp
RUN git clone --recursive --branch $GENOMICSDB_BRANCH https://github.com/GenomicsDB/GenomicsDB.git && \
cd GenomicsDB/scripts/prereqs && \
./install_prereqs.sh && \
apt-get clean && \
rm -rf /var/lib/apt/lists/*
RUN chmod +x $PREREQS_ENV && \
$PREREQS_ENV && \
cmake -DCMAKE_INSTALL_PREFIX=$GENOMICSDB_PATH -DCMAKE_BUILD_TYPE=Release ./GenomicsDB && \
make && make install && \
rm -rf /tmp/GenomicsDB
from genomicsdb.
nalinigans
commented on June 1, 2024
@lima1, can you please try the develop branch and see if that fixes your issues building on amd64 Dockerimage on my new M2 MacBook Pro? Thanks.
from genomicsdb.
lima1
commented on June 1, 2024
Thanks @nalinigans. It compiled successfully last week, including the R bindings. Haven’t thoroughly tested yet. Any recent changes since then that I should try?
from genomicsdb.
nalinigans
commented on June 1, 2024
Thanks @lima1. Nothing recently added yet. But, you don't need to specify reference genome unless you are generating a vcf. I will be adding support for a protobuf export configuration later, this may be useful as you can use genomic coordinates directly, in addition to setting segment sizes, etc. almost like what GenotypeGVCFs offers.
from genomicsdb.
mr-c
commented on June 1, 2024
Hello from Debian. We are able to compile genomicsdb 1.5.0 for arm64/aarch64 but we get test failures:
Here are some excepts from the build log
test 5
Start 5: test_array_iterator
5: Test command: /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/genomicsdb-tiledb/test/test_array_iterator
5: Working Directory: /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/genomicsdb-tiledb/test
5: Test timeout computed to be: 10000000
5: [TileDB::utils] Error: (gzip_handle_error) Cannot compress with GZIP: deflateInit error: Z_STREAM_ERROR
5: [TileDB::Codec] Error: Could not compress with GZIP.
5: [TileDB::WriteState] Error: Cannot compress tile for /tmp/TileDBTestzmgk1D/array_iterator_test_ws/test_sparse_array_it_full/.__e38c070f-ad54-40f6-8b1c-b4bdc2e0ef58281473382141984_1688334784891/ATTR_INT32.tdb.
5:
5: ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
5: test_array_iterator is a Catch v2.13.10 host application.
5: Run with -? for options
5:
5: -------------------------------------------------------------------------------
5: Test sparse array iterator
5: -------------------------------------------------------------------------------
5: ./genomicsdb-tiledb/test/src/c_api/test_array_iterator.cc:193
5: ...............................................................................
5:
5: ./genomicsdb-tiledb/test/src/c_api/test_array_iterator.cc:106: FAILED:
5: CHECK( tiledb_array_write(tiledb_array, buffers, buffer_sizes) == 0 )
5: with expansion:
5: -1 == 0
5:
5: [TileDB::utils] Error: (gzip_handle_error) Cannot compress with GZIP: deflateInit error: Z_STREAM_ERROR
5: [TileDB::Codec] Error: Could not compress with GZIP.
5: [TileDB::WriteState] Error: Cannot compress tile for /tmp/TileDBTestzmgk1D/array_iterator_test_ws/test_sparse_array_it_full/.__e38c070f-ad54-40f6-8b1c-b4bdc2e0ef58281473382141984_1688334784891/ATTR_INT32.tdb.
5: ./genomicsdb-tiledb/test/src/c_api/test_array_iterator.cc:107: FAILED:
5: CHECK( tiledb_array_finalize(tiledb_array) == 0 )
5: with expansion:
5: -1 == 0
5:
5: ./genomicsdb-tiledb/test/src/c_api/test_array_iterator.cc:184: FAILED:
5: CHECK( i == nval )
5: with expansion:
5: 0 == 8
5:
5: [TileDB::utils] Error: (gzip_handle_error) Cannot compress with GZIP: deflateInit error: Z_STREAM_ERROR
5: [TileDB::Codec] Error: Could not compress with GZIP.
5: [TileDB::WriteState] Error: Cannot compress tile for /tmp/TileDBTestNm9PcM/array_iterator_test_ws/test_sparse_array_it_reset/.__f5d7dda5-66cc-45e0-a0b5-aaf415f7c2f6281473382141984_1688334784892/ATTR_INT32.tdb.
5: -------------------------------------------------------------------------------
5: Test sparse array iterator with reset
5: -------------------------------------------------------------------------------
5: ./genomicsdb-tiledb/test/src/c_api/test_array_iterator.cc:200
5: ...............................................................................
5:
5: ./genomicsdb-tiledb/test/src/c_api/test_array_iterator.cc:106: FAILED:
5: CHECK( tiledb_array_write(tiledb_array, buffers, buffer_sizes) == 0 )
5: with expansion:
5: -1 == 0
5:
5: [TileDB::utils] Error: (gzip_handle_error) Cannot compress with GZIP: deflateInit error: Z_STREAM_ERROR
5: [TileDB::Codec] Error: Could not compress with GZIP.
5: [TileDB::WriteState] Error: Cannot compress tile for /tmp/TileDBTestNm9PcM/array_iterator_test_ws/test_sparse_array_it_reset/.__f5d7dda5-66cc-45e0-a0b5-aaf415f7c2f6281473382141984_1688334784892/ATTR_INT32.tdb.
5: ./genomicsdb-tiledb/test/src/c_api/test_array_iterator.cc:107: FAILED:
5: CHECK( tiledb_array_finalize(tiledb_array) == 0 )
5: with expansion:
5: -1 == 0
5:
5: ./genomicsdb-tiledb/test/src/c_api/test_array_iterator.cc:184: FAILED:
5: CHECK( i == nval )
5: with expansion:
5: 0 == 8
5:
5: ./genomicsdb-tiledb/test/src/c_api/test_array_iterator.cc:184: FAILED:
5: CHECK( i == nval )
5: with expansion:
5: 0 == 8
5:
5: [TileDB::utils] Error: (gzip_handle_error) Cannot compress with GZIP: deflateInit error: Z_STREAM_ERROR
5: [TileDB::Codec] Error: Could not compress with GZIP.
5: [TileDB::WriteState] Error: Cannot compress tile for /tmp/TileDBTestHjv52m/array_iterator_test_ws/test_sparse_array_it_reset_subarray/.__110d6e71-2706-4e63-b93b-a5147687fde3281473382141984_1688334784893/ATTR_INT32.tdb.
5: -------------------------------------------------------------------------------
5: Test sparse array iterator with reset subarray
5: -------------------------------------------------------------------------------
5: ./genomicsdb-tiledb/test/src/c_api/test_array_iterator.cc:210
5: ...............................................................................
5:
5: ./genomicsdb-tiledb/test/src/c_api/test_array_iterator.cc:106: FAILED:
5: CHECK( tiledb_array_write(tiledb_array, buffers, buffer_sizes) == 0 )
5: with expansion:
5: -1 == 0
5:
5: [TileDB::utils] Error: (gzip_handle_error) Cannot compress with GZIP: deflateInit error: Z_STREAM_ERROR
5: [TileDB::Codec] Error: Could not compress with GZIP.
5: [TileDB::WriteState] Error: Cannot compress tile for /tmp/TileDBTestHjv52m/array_iterator_test_ws/test_sparse_array_it_reset_subarray/.__110d6e71-2706-4e63-b93b-a5147687fde3281473382141984_1688334784893/ATTR_INT32.tdb.
5: ./genomicsdb-tiledb/test/src/c_api/test_array_iterator.cc:107: FAILED:
5: CHECK( tiledb_array_finalize(tiledb_array) == 0 )
5: with expansion:
5: -1 == 0
5:
5: ./genomicsdb-tiledb/test/src/c_api/test_array_iterator.cc:184: FAILED:
5: CHECK( i == nval )
5: with expansion:
5: 0 == 8
5:
5: ./genomicsdb-tiledb/test/src/c_api/test_array_iterator.cc:184: FAILED:
5: CHECK( i == nval )
5: with expansion:
5: 0 == 5
5:
5: [TileDB::utils] Error: (gzip_handle_error) Cannot compress with GZIP: deflateInit error: Z_STREAM_ERROR
5: [TileDB::Codec] Error: Could not compress with GZIP.
5: [TileDB::WriteState] Error: Cannot compress tile for /tmp/TileDBTestGR6Kaq/array_iterator_test_ws/test_sparse_array_it_filter/.__804d85e2-ab0b-4ae4-8f2d-ab1b6add4505281473382141984_1688334784894/ATTR_INT32.tdb.
5: -------------------------------------------------------------------------------
5: Test sparse array iterator with filter
5: -------------------------------------------------------------------------------
5: ./genomicsdb-tiledb/test/src/c_api/test_array_iterator.cc:220
5: ...............................................................................
5:
5: ./genomicsdb-tiledb/test/src/c_api/test_array_iterator.cc:106: FAILED:
5: CHECK( tiledb_array_write(tiledb_array, buffers, buffer_sizes) == 0 )
5: with expansion:
5: -1 == 0
5:
5: [TileDB::utils] Error: (gzip_handle_error) Cannot compress with GZIP: deflateInit error: Z_STREAM_ERROR
5: [TileDB::Codec] Error: Could not compress with GZIP.
5: [TileDB::WriteState] Error: Cannot compress tile for /tmp/TileDBTestGR6Kaq/array_iterator_test_ws/test_sparse_array_it_filter/.__804d85e2-ab0b-4ae4-8f2d-ab1b6add4505281473382141984_1688334784894/ATTR_INT32.tdb.
5: ./genomicsdb-tiledb/test/src/c_api/test_array_iterator.cc:107: FAILED:
5: CHECK( tiledb_array_finalize(tiledb_array) == 0 )
5: with expansion:
5: -1 == 0
5:
5: ./genomicsdb-tiledb/test/src/c_api/test_array_iterator.cc:184: FAILED:
5: CHECK( i == nval )
5: with expansion:
5: 0 == 4
5:
5: [TileDB::utils] Error: (gzip_handle_error) Cannot compress with GZIP: deflateInit error: Z_STREAM_ERROR
5: [TileDB::Codec] Error: Could not compress with GZIP.
5: [TileDB::WriteState] Error: Cannot compress tile for /tmp/TileDBTest9tc7IW/array_iterator_test_ws/test_sparse_array_it_filter_reset/.__7e66b381-84bf-436b-932a-cad138365032281473382141984_1688334784896/ATTR_INT32.tdb.
5: -------------------------------------------------------------------------------
5: Test sparse array iterator with filter with subarray
5: -------------------------------------------------------------------------------
5: ./genomicsdb-tiledb/test/src/c_api/test_array_iterator.cc:227
5: ...............................................................................
5:
5: ./genomicsdb-tiledb/test/src/c_api/test_array_iterator.cc:106: FAILED:
5: CHECK( tiledb_array_write(tiledb_array, buffers, buffer_sizes) == 0 )
5: with expansion:
5: -1 == 0
5:
5: [TileDB::utils] Error: (gzip_handle_error) Cannot compress with GZIP: deflateInit error: Z_STREAM_ERROR
5: [TileDB::Codec] Error: Could not compress with GZIP.
5: [TileDB::WriteState] Error: Cannot compress tile for /tmp/TileDBTest9tc7IW/array_iterator_test_ws/test_sparse_array_it_filter_reset/.__7e66b381-84bf-436b-932a-cad138365032281473382141984_1688334784896/ATTR_INT32.tdb.
5: ./genomicsdb-tiledb/test/src/c_api/test_array_iterator.cc:107: FAILED:
5: CHECK( tiledb_array_finalize(tiledb_array) == 0 )
5: with expansion:
5: -1 == 0
5:
5: ./genomicsdb-tiledb/test/src/c_api/test_array_iterator.cc:184: FAILED:
5: CHECK( i == nval )
5: with expansion:
5: 0 == 4
5:
5: ./genomicsdb-tiledb/test/src/c_api/test_array_iterator.cc:184: FAILED:
5: CHECK( i == nval )
5: with expansion:
5: 0 == 1
5:
5: [TileDB::utils] Error: (gzip_handle_error) Cannot compress with GZIP: deflateInit error: Z_STREAM_ERROR
5: [TileDB::Codec] Error: Could not compress with GZIP.
5: [TileDB::WriteState] Error: Cannot compress tile for /tmp/TileDBTestcWIZ2d/array_iterator_test_ws/test_sparse_array_it_filter_with_empty_value/.__8beaeba5-e1cd-402f-9fb3-a00f104d7489281473382141984_1688334784897/ATTR_INT32.tdb.
5: -------------------------------------------------------------------------------
5: Test sparse array iterator with filteri with empty value
5: -------------------------------------------------------------------------------
5: ./genomicsdb-tiledb/test/src/c_api/test_array_iterator.cc:237
5: ...............................................................................
5:
5: ./genomicsdb-tiledb/test/src/c_api/test_array_iterator.cc:106: FAILED:
5: CHECK( tiledb_array_write(tiledb_array, buffers, buffer_sizes) == 0 )
5: with expansion:
5: -1 == 0
5:
5: [TileDB::utils] Error: (gzip_handle_error) Cannot compress with GZIP: deflateInit error: Z_STREAM_ERROR
5: [TileDB::Codec] Error: Could not compress with GZIP.
5: [TileDB::WriteState] Error: Cannot compress tile for /tmp/TileDBTestcWIZ2d/array_iterator_test_ws/test_sparse_array_it_filter_with_empty_value/.__8beaeba5-e1cd-402f-9fb3-a00f104d7489281473382141984_1688334784897/ATTR_INT32.tdb.
5: ./genomicsdb-tiledb/test/src/c_api/test_array_iterator.cc:107: FAILED:
5: CHECK( tiledb_array_finalize(tiledb_array) == 0 )
5: with expansion:
5: -1 == 0
5:
5: [TileDB::utils] Error: (gzip_handle_error) Cannot compress with GZIP: deflateInit error: Z_STREAM_ERROR
5: [TileDB::Codec] Error: Could not compress with GZIP.
5: [TileDB::WriteState] Error: Cannot compress tile for /tmp/TileDBTestcWIZ2d/array_iterator_test_ws/test_sparse_array_it_filter_with_empty_value/.__78263663-df68-463f-ac7b-fd5321190655281473382141984_1688334784897/ATTR_INT32.tdb.
5: ./genomicsdb-tiledb/test/src/c_api/test_array_iterator.cc:125: FAILED:
5: CHECK( tiledb_array_write(tiledb_array, buffers, buffer_sizes) == 0 )
5: with expansion:
5: -1 == 0
5:
5: [TileDB::utils] Error: (gzip_handle_error) Cannot compress with GZIP: deflateInit error: Z_STREAM_ERROR
5: [TileDB::Codec] Error: Could not compress with GZIP.
5: [TileDB::WriteState] Error: Cannot compress tile for /tmp/TileDBTestcWIZ2d/array_iterator_test_ws/test_sparse_array_it_filter_with_empty_value/.__78263663-df68-463f-ac7b-fd5321190655281473382141984_1688334784897/ATTR_INT32.tdb.
5: ./genomicsdb-tiledb/test/src/c_api/test_array_iterator.cc:126: FAILED:
5: CHECK( tiledb_array_finalize(tiledb_array) == 0 )
5: with expansion:
5: -1 == 0
5:
5: ./genomicsdb-tiledb/test/src/c_api/test_array_iterator.cc:184: FAILED:
5: CHECK( i == nval )
5: with expansion:
5: 0 == 4
5:
5: ===============================================================================
5: test cases: 6 | 0 passed | 6 failed
5: assertions: 81 | 58 passed | 23 failed
5:
6: Test command: /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/genomicsdb-tiledb/test/test_array_schema_api
6: Working Directory: /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/genomicsdb-tiledb/test
6: Test timeout computed to be: 10000000
6:
6: ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
6: test_array_schema_api is a Catch v2.13.10 host application.
6: Run with -? for options
6:
6: -------------------------------------------------------------------------------
6: Test array schema backward compatibility 2
6: -------------------------------------------------------------------------------
6: ./genomicsdb-tiledb/test/src/c_api/test_array_schema_api.cc:349
6: ...............................................................................
6:
6: ./genomicsdb-tiledb/test/src/c_api/test_array_schema_api.cc:368: FAILED:
6: CHECK( array_schema.compression_level_[1] == -1 )
6: with expansion:
6: 255 == -1
6:
6: ===============================================================================
6: test cases: 13 | 12 passed | 1 failed
6: assertions: 335 | 334 passed | 1 failed
6:
19: Test command: /<<PKGBUILDDIR>>/genomicsdb-tiledb/examples/run_examples.sh
19: Working Directory: /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples
19: Test timeout computed to be: 10000000
19: Example 1: Running ./tiledb_workspace_group_create...
19: Example 1: Done running ./tiledb_workspace_group_create
19: Example 2: Running ./tiledb_ls_workspaces...
19: my_workspace
19: Example 2: Done running ./tiledb_ls_workspaces
19: Example 3: Running ./tiledb_array_create_dense...
19: Example 3: Done running ./tiledb_array_create_dense
19: Example 4: Running ./tiledb_array_create_sparse...
19: Example 4: Done running ./tiledb_array_create_sparse
19: Example 5: Running ./tiledb_array_primitive...
19: Array name: my_workspace/dense_arrays/my_array_A
19: Attributes: a1 a2 a3
19: The array is dense
19: Array name: my_workspace/sparse_arrays/my_array_B
19: Attributes: a1 a2 a3
19: The array is sparse
19: Example 5: Done running ./tiledb_array_primitive
19: Example 6: Running ./tiledb_array_write_dense_1...
19: [TileDB::utils] Error: (gzip_handle_error) Cannot compress with GZIP: deflateInit error: Z_STREAM_ERROR
19: [TileDB::Codec] Error: Could not compress with GZIP.
19: [TileDB::WriteState] Error: Cannot compress tile for /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples/my_workspace/dense_arrays/my_array_A/.__e3770d96-3113-4f9e-8089-24c0178c6400281473779200032_1688334785380/a1.tdb.
19: [TileDB::WriteState] Error: Cannot compress tile for /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/genomicsdb-tiledb/examples/my_workspace/dense_arrays/my_array_A/.__e3770d96-3113-4f9e-8089-24c0178c6400281473779200032_1688334785380/a1.tdb[Examples::./genomicsdb-tiledb/examples/src/tiledb_array_write_dense_1.cc] Runtime Error.
19:
19: Exit Status=255. Quitting execution of run_examples.sh
20: Test command: /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/src/test/cpp/ctests "-d" "yes"
20: Working Directory: /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/src/test/cpp
20: Test timeout computed to be: 10000000
20: 21:53:05.118 DEBUG NativeGenomicsDB - pid=3527814 tid=3527814 json file /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn
20: 21:53:05.119 WARN NativeGenomicsDB - pid=3527814 tid=3527814 Could not deserialize loader file /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead
20: 21:53:05.123 DEBUG NativeGenomicsDB - pid=3527814 tid=3527814 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name
20: 0.015 s: Check loader configuration with json file
20: 21:53:05.129 DEBUG NativeGenomicsDB - pid=3527814 tid=3527814 json file /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn
20: 21:53:05.130 WARN NativeGenomicsDB - pid=3527814 tid=3527814 Could not deserialize loader file /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead
20: 21:53:05.131 DEBUG NativeGenomicsDB - pid=3527814 tid=3527814 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name
20: 0.003 s: Check configuration with json file
20: 21:53:05.135 DEBUG NativeGenomicsDB - pid=3527814 tid=3527814 json file /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn
20: 21:53:05.137 WARN NativeGenomicsDB - pid=3527814 tid=3527814 Could not deserialize loader file /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead
20: 21:53:05.139 DEBUG NativeGenomicsDB - pid=3527814 tid=3527814 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name
20: 0.009 s: Check configuration with json file and shared posifs optim
20: 21:53:05.144 DEBUG NativeGenomicsDB - pid=3527814 tid=3527814 json file /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn
20: 21:53:05.145 WARN NativeGenomicsDB - pid=3527814 tid=3527814 Could not deserialize loader file /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead
20: 21:53:05.147 DEBUG NativeGenomicsDB - pid=3527814 tid=3527814 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name
20: 0.007 s: Compare configuration with json file and string
20: 0.000 s: genotype_ordering haploid_5_alleles
20: 0.000 s: genotype_ordering diploid_2_alleles
20: 0.000 s: genotype_ordering diploid_3_alleles
20: 0.000 s: genotype_ordering diploid_4_alleles
20: 0.000 s: genotype_ordering triploid_2_alleles
20: 0.000 s: genotype_ordering triploid_3_alleles
20: 0.000 s: genotype_ordering triploid_4_alleles
20: 0.000 s: genotype_ordering triploid_4_alleles_reordered_alleles
20: 0.000 s: genotype_ordering triploid_4_alleles_reordered_alleles_without_NON_REF
20: 0.001 s: multid_vector 2D_test
20: 0.000 s: multid_vector 3D_test
20: 0.000 s: multid_vector 2D_test_with_missing_values
20: 0.000 s: multid_vector 2D_float_test
20: 0.000 s: multid_vector 2D_tuple_test
20: 0.000 s: pb_query_config_test
20: 0.004 s: pb_vid_mapping_test
20: 21:53:05.178 INFO NativeGenomicsDB - pid=3527814 tid=3527814 Contig/chromosome 2 begins at TileDB column 249250601 and intersects with contig/chromosome 1 that spans columns [0, 249250620]
20: 0.004 s: pb_overlapping_vid_mapping_test
20: 21:53:05.180 INFO NativeGenomicsDB - pid=3527814 tid=3527814 This is a test
20: 21:53:05.180 WARN NativeGenomicsDB - pid=3527814 tid=3527814 This is a test
20: 21:53:05.180 ERROR NativeGenomicsDB - pid=3527814 tid=3527814 This is a test
20: 21:53:05.181 DEBUG NativeGenomicsDB - pid=3527814 tid=3527814 This is a test
20: This is a test
20: This is a test
20: This is a test
20: This is a test
20: This is a once_only test
20: Trying format Hello1 Hello2
20: 0.005 s: test logger
20: 21:53:05.186 INFO NativeGenomicsDB - pid=3527814 tid=3527814 i=1 str=This is a test
20: 21:53:05.186 WARN NativeGenomicsDB - pid=3527814 tid=3527814 i=2 str=This is a test
20: 21:53:05.186 ERROR NativeGenomicsDB - pid=3527814 tid=3527814 i=3 str=This is a test
20: 21:53:05.187 DEBUG NativeGenomicsDB - pid=3527814 tid=3527814 i=4 str=This is a test
20: 21:53:05.187 INFO NativeGenomicsDB - pid=3527814 tid=3527814 i=6 str=This is a once_only test
20: 21:53:05.187 WARN NativeGenomicsDB - pid=3527814 tid=3527814 i=7 str=This is a once_only test
20: 0.001 s: test logger format
20: 21:53:05.187 ERROR NativeGenomicsDB - pid=3527814 tid=3527814 i=1 str=This is a test
20: 21:53:05.187 ERROR NativeGenomicsDB - pid=3527814 tid=3527814 Test Exception
20: 21:53:05.187 ERROR NativeGenomicsDB - pid=3527814 tid=3527814 Test Exception
20: 21:53:05.187 ERROR NativeGenomicsDB - pid=3527814 tid=3527814 Test Exception
20: 21:53:05.188 ERROR NativeGenomicsDB - pid=3527814 tid=3527814 Native Stack Trace:
20: /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/src/test/cpp/ctests(+0xd2f74) [0xaaaae30a2f74]
20: /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/src/test/cpp/ctests(+0xc70c4) [0xaaaae30970c4]
20: /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/src/test/cpp/ctests(+0x4e0e8) [0xaaaae301e0e8]
20: /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/src/test/cpp/ctests(+0x6688c) [0xaaaae303688c]
20: /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/src/test/cpp/ctests(+0x6cde4) [0xaaaae303cde4]
20: /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/src/test/cpp/ctests(+0x6ea70) [0xaaaae303ea70]
20: /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/src/test/cpp/ctests(+0x6f0c0) [0xaaaae303f0c0]
20: /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/src/test/cpp/ctests(+0x3fee0) [0xaaaae300fee0]
20: /lib/aarch64-linux-gnu/libc.so.6(+0x27780) [0xffffab0e7780]
20: 21:53:05.188 ERROR NativeGenomicsDB - pid=3527814 tid=3527814 Test Exception
20: 21:53:05.188 ERROR NativeGenomicsDB - pid=3527814 tid=3527814 Native Stack Trace:
20: /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/src/test/cpp/ctests(+0xd2f74) [0xaaaae30a2f74]
20: /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/src/test/cpp/ctests(+0xc70d4) [0xaaaae30970d4]
20: /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/src/test/cpp/ctests(+0x4e0e8) [0xaaaae301e0e8]
20: /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/src/test/cpp/ctests(+0x6688c) [0xaaaae303688c]
20: /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/src/test/cpp/ctests(+0x6cde4) [0xaaaae303cde4]
20: /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/src/test/cpp/ctests(+0x6ea70) [0xaaaae303ea70]
20: /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/src/test/cpp/ctests(+0x6f0c0) [0xaaaae303f0c0]
20: /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/src/test/cpp/ctests(+0x3fee0) [0xaaaae300fee0]
20: /lib/aarch64-linux-gnu/libc.so.6(+0x27780) [0xffffab0e7780]
20: 0.003 s: test logger exceptions
20: /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/src/test/cpp/ctests(+0xd2f74) [0xaaaae30a2f74]
20: /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/src/test/cpp/ctests(+0xc9c98) [0xaaaae3099c98]
20: /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/src/test/cpp/ctests(+0x4e0e8) [0xaaaae301e0e8]
20: /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/src/test/cpp/ctests(+0x6688c) [0xaaaae303688c]
20: /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/src/test/cpp/ctests(+0x6cde4) [0xaaaae303cde4]
20: /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/src/test/cpp/ctests(+0x6ea70) [0xaaaae303ea70]
20: /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/src/test/cpp/ctests(+0x6f0c0) [0xaaaae303f0c0]
20: /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/src/test/cpp/ctests(+0x3fee0) [0xaaaae300fee0]
20: /lib/aarch64-linux-gnu/libc.so.6(+0x27780) [0xffffab0e7780]
20: /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/src/test/cpp/ctests(+0xd2f74) [0xaaaae30a2f74]
20: /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/src/test/cpp/ctests(+0xc9d28) [0xaaaae3099d28]
20: /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/src/test/cpp/ctests(+0x4e0e8) [0xaaaae301e0e8]
20: /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/src/test/cpp/ctests(+0x6688c) [0xaaaae303688c]
20: /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/src/test/cpp/ctests(+0x6cde4) [0xaaaae303cde4]
20: /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/src/test/cpp/ctests(+0x6ea70) [0xaaaae303ea70]
20: /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/src/test/cpp/ctests(+0x6f0c0) [0xaaaae303f0c0]
20: /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/src/test/cpp/ctests(+0x3fee0) [0xaaaae300fee0]
20: /lib/aarch64-linux-gnu/libc.so.6(+0x27780) [0xffffab0e7780]
20: This is a test
20: 0.004 s: test explicit logger
20: 21:53:05.196 DEBUG NativeGenomicsDB - pid=3527814 tid=3527814 json file /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn
20: 21:53:05.197 WARN NativeGenomicsDB - pid=3527814 tid=3527814 Could not deserialize loader file /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead
20: 21:53:05.202 DEBUG NativeGenomicsDB - pid=3527814 tid=3527814 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name
20: 0.055 s: gvcf iterator
20: 21:53:05.253 DEBUG NativeGenomicsDB - pid=3527814 tid=3527814 json file /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn
20: 21:53:05.254 WARN NativeGenomicsDB - pid=3527814 tid=3527814 Could not deserialize loader file /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead
20: 21:53:05.255 DEBUG NativeGenomicsDB - pid=3527814 tid=3527814 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name
20: 0.043 s: columnar_gvcf_iterator_test
20: [TileDB] Error: No TileDB support for URL=dfdfd://ddd.
20: 21:53:05.297 ERROR NativeGenomicsDB - pid=3527814 tid=3527814 htslib_plugin could not open file dfdfd://ddd No TileDB support for URL=dfdfd://ddd
20: [TileDB::FileSystem] Error: (write_to_file) Cannot write to file; File opening error path=/dfdfd/dfdfd/non-existent-file errno=2(No such file or directory)
20: 21:53:05.299 ERROR NativeGenomicsDB - pid=3527814 tid=3527814 hts_plugin read /dfdfd/dfdfd/non-existent-file error [TileDB::FileSystem] Error: (write_to_file) Cannot write to file; File opening error path=/dfdfd/dfdfd/non-existent-file errno=2(No such file or directory)
20: [TileDB::FileSystem] Error: (read_from_file) Cannot read from file; File opening error path=non-existent-file errno=2(No such file or directory)
20: 21:53:05.301 ERROR NativeGenomicsDB - pid=3527814 tid=3527814 hts_plugin read non-existent-file error [TileDB::FileSystem] Error: (read_from_file) Cannot read from file; File opening error path=non-existent-file errno=2(No such file or directory)
20: 0.008 s: test htslib plugin
20: 0.000 s: alleles_combiner
20: 0.000 s: gt_remapper
20:
20: ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
20: ctests is a Catch v2.13.10 host application.
20: Run with -? for options
20:
20: -------------------------------------------------------------------------------
20: test bgen
20: -------------------------------------------------------------------------------
20: ./src/test/cpp/src/test_bgen.cc:11
20: ...............................................................................
20:
20: ./src/test/cpp/src/test_bgen.cc:11: FAILED:
20: due to unexpected exception with message:
20: Direct - first BGEN test output did not match reference output
20:
20: 0.000 s: test bgen
20: 21:53:05.961 ERROR NativeGenomicsDB - pid=3527814 tid=3527814 VariantStorageManagerException exception : Could not open workspace
20: 21:53:05.961 ERROR NativeGenomicsDB - pid=3527814 tid=3527814 Could not open array non_existent_array in workspace /tmp/GenomicsDB7P2Z05/ws
20: 21:53:05.961 ERROR NativeGenomicsDB - pid=3527814 tid=3527814 VariantQueryProcessorException : Could not open array non_existent_array at workspace /tmp/GenomicsDB7P2Z05/ws
20: 0.001 s: constructor
20: 21:53:05.964 DEBUG NativeGenomicsDB - pid=3527814 tid=3527814 json file /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(column_partitions[0].begin): invalid value 0 for type type.googleapis.com/GenomicsDBColumn
20: 21:53:05.966 WARN NativeGenomicsDB - pid=3527814 tid=3527814 Could not deserialize loader file /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/src/test/cpp/inputs/loader.json as protobuf. Trying to parse as a regular JSON file instead
20: 21:53:05.967 DEBUG NativeGenomicsDB - pid=3527814 tid=3527814 json file inputs/vid.json does not seem to be serialized protobuf - error:INVALID_ARGUMENT:(contigs): missing field name
20: 21:53:05.979 ERROR NativeGenomicsDB - pid=3527814 tid=3527814 Invalid query attribute : non_existent_attribute
20: 0.019 s: test basic queries
20: ===============================================================================
20: test cases: 33 | 32 passed | 1 failed
20: assertions: 1434 | 1433 passed | 1 failed
20:
20: 21:53:05.982 DEBUG NativeGenomicsDB - pid=3527814 tid=3527814 Deleting htslib_fs_adapter tiledb_ctx_map
22: Test command: /<<PKGBUILDDIR>>/tests/test_tools.sh "/<<PKGBUILDDIR>>/tests/inputs/vcfs" "/<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/tools" "1"
22: Working Directory: /<<PKGBUILDDIR>>/obj-aarch64-linux-gnu/tools
22: Test timeout computed to be: 10000000
22: 21:53:06.657 INFO NativeGenomicsDB - pid=3527929 tid=3527929 Reading 1 vcfs
22: 21:53:06.660 INFO NativeGenomicsDB - pid=3527929 tid=3527929 [STAGE 1 / 3] Reading 1 / 1 = 100.00%
22: 21:53:06.780 INFO NativeGenomicsDB - pid=3527929 tid=3527929 [STAGE 2 / 3] read_next_batch 0 / 1 = 0.00%
22: 21:53:06.782 INFO NativeGenomicsDB - pid=3527929 tid=3527929 [STAGE 3 / 3] progress: 12140 / 249250620 = 0.00%
22: [TileDB::utils] Error: (gzip_handle_error) Cannot compress with GZIP: deflateInit error: Z_STREAM_ERROR
22: [TileDB::Codec] Error: Could not compress with GZIP.
22: [TileDB::WriteState] Error: Cannot compress tile for /tmp/test_tools-3MWKYDtPtg/ws_27716/1$1$249250621/.__a6fea7aa-d4a5-4028-9541-375ffb29be3a281473138085952_1688334786747/END.tdb.
22: 21:53:06.784 ERROR NativeGenomicsDB - pid=3527929 tid=3527929 VariantStorageManagerException exception : Error while finalizing GenomicsDB array 1$1$249250621 : [TileDB::WriteState] Error: Cannot compress tile for /tmp/test_tools-3MWKYDtPtg/ws_27716/1$1$249250621/.__a6fea7aa-d4a5-4028-9541-375ffb29be3a281473138085952_1688334786747/END.tdb
22: command 'vcf2genomicsdb --progress /tmp/test_tools-3MWKYDtPtg/ws_27716/loader.json' returned 139 unexpectedly
77% tests passed, 5 tests failed out of 22
Total Test time (real) = 5.37 sec
The following tests FAILED:
5 - test_array_iterator (Failed)
6 - test_array_schema_api (Failed)
19 - ci_tests (Failed)
20 - ctests (Failed)
22 - tools_tests (Failed)
from genomicsdb.
Related Issues (20)
- GenomicsDB api returns a null list when querying for variant calls with no rows specified
- Maven wget url invalid HOT 2
- Add ID field and handle duplicate names in INFO/FMT/FILTER fields correctly in vcf2genomicsdb_init
- Annotation Service needs to be extended to support multiple alternate alleles HOT 1
- Excessive logging with --max-alternate-alleles HOT 6
- plink support has introduced mpi dependency in test_gen.cc
- Import should automatically increase buffer size as needed HOT 3
- Allow for multiple inputs(bed, etc.) to be ingested into GenomicsDB
- string_view needs c++-17
- Changes to JsonFormat methods when building with protobuf-java-format 1.3 instead of 1.2
- Missing links to fmt
- Dependencies missing in the pom HOT 2
- Use unflattened genomic coordinates in GenomicsDB error messages
- Compilation on Ubuntu jammy fails in aws-cpp-sdk HOT 4
- Porting to gcc-13 HOT 2
- ERROR: failed to solve: failed to compute cache key HOT 3
- The compatibility of array_schema.cc HOT 1
- Ambiguous call to Assert in the tests HOT 1
- Moving to 24.04 for the docker builds is broken.
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from genomicsdb.