Implement skip_rows + column_names in R #4
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A separate ticket sounds fine. |
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@@ Coverage Diff @@
## ARROW-5747-csv-column-names #4 +/- ##
==============================================================
Coverage ? 75.27%
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Files ? 57
Lines ? 3713
Branches ? 0
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Hits ? 2795
Misses ? 918
Partials ? 0
Continue to review full report at Codecov.
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Codecov Report
@@ Coverage Diff @@
## ARROW-5747-csv-column-names #4 +/- ##
==============================================================
Coverage ? 75.27%
==============================================================
Files ? 57
Lines ? 3713
Branches ? 0
==============================================================
Hits ? 2795
Misses ? 918
Partials ? 0
Continue to review full report at Codecov.
|
pitrou
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Jul 23, 2019
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Feb 24, 2020
…comments. The reset method allow the data structures to be re-used so they don't have to be allocated over and over again. Closes apache#6430 from richardartoul/ra/merge-upstream and squashes the following commits: 5a08281 <Richard Artoul> Add license to test file d76be05 <Richard Artoul> Add test for data reset d102b1f <Richard Artoul> Add tests d3e6e67 <Richard Artoul> cleanup comments c8525ae <Richard Artoul> Add Reset method to int array (#5) 489ca25 <Richard Artoul> Fix array.setData() to retain before release (#4) 88cd05f <Richard Artoul> Add reset method to Data (#3) 6d1b277 <Richard Artoul> Add Reset() method to String array (#2) dca2303 <Richard Artoul> Add Reset method to buffer and cleanup comments (#1) Lead-authored-by: Richard Artoul <richard.artoul@datadoghq.com> Co-authored-by: Richard Artoul <richardartoul@gmail.com> Signed-off-by: Sebastien Binet <binet@cern.ch>
pitrou
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This PR enables tests for `ARROW_COMPUTE`, `ARROW_DATASET`, `ARROW_FILESYSTEM`, `ARROW_HDFS`, `ARROW_ORC`, and `ARROW_IPC` (default on). apache#7131 enabled a minimal set of tests as a starting point. I confirmed that these tests pass locally with the current master. In the current TravisCI environment, we cannot see this result due to a lot of error messages in `arrow-utility-test`. ``` $ git log | head -1 commit ed5f534 % ctest ... Start 1: arrow-array-test 1/51 Test #1: arrow-array-test ..................... Passed 4.62 sec Start 2: arrow-buffer-test 2/51 Test #2: arrow-buffer-test .................... Passed 0.14 sec Start 3: arrow-extension-type-test 3/51 Test #3: arrow-extension-type-test ............ Passed 0.12 sec Start 4: arrow-misc-test 4/51 Test #4: arrow-misc-test ...................... Passed 0.14 sec Start 5: arrow-public-api-test 5/51 Test #5: arrow-public-api-test ................ Passed 0.12 sec Start 6: arrow-scalar-test 6/51 Test #6: arrow-scalar-test .................... Passed 0.13 sec Start 7: arrow-type-test 7/51 Test #7: arrow-type-test ...................... Passed 0.14 sec Start 8: arrow-table-test 8/51 Test #8: arrow-table-test ..................... Passed 0.13 sec Start 9: arrow-tensor-test 9/51 Test #9: arrow-tensor-test .................... Passed 0.13 sec Start 10: arrow-sparse-tensor-test 10/51 Test #10: arrow-sparse-tensor-test ............. Passed 0.16 sec Start 11: arrow-stl-test 11/51 Test #11: arrow-stl-test ....................... Passed 0.12 sec Start 12: arrow-concatenate-test 12/51 Test #12: arrow-concatenate-test ............... Passed 0.53 sec Start 13: arrow-diff-test 13/51 Test #13: arrow-diff-test ...................... Passed 1.45 sec Start 14: arrow-c-bridge-test 14/51 Test apache#14: arrow-c-bridge-test .................. Passed 0.18 sec Start 15: arrow-io-buffered-test 15/51 Test apache#15: arrow-io-buffered-test ............... Passed 0.20 sec Start 16: arrow-io-compressed-test 16/51 Test apache#16: arrow-io-compressed-test ............. Passed 3.48 sec Start 17: arrow-io-file-test 17/51 Test apache#17: arrow-io-file-test ................... Passed 0.74 sec Start 18: arrow-io-hdfs-test 18/51 Test apache#18: arrow-io-hdfs-test ................... Passed 0.12 sec Start 19: arrow-io-memory-test 19/51 Test apache#19: arrow-io-memory-test ................. Passed 2.77 sec Start 20: arrow-utility-test 20/51 Test apache#20: arrow-utility-test ...................***Failed 5.65 sec Start 21: arrow-threading-utility-test 21/51 Test apache#21: arrow-threading-utility-test ......... Passed 1.34 sec Start 22: arrow-compute-compute-test 22/51 Test apache#22: arrow-compute-compute-test ........... Passed 0.13 sec Start 23: arrow-compute-boolean-test 23/51 Test apache#23: arrow-compute-boolean-test ........... Passed 0.15 sec Start 24: arrow-compute-cast-test 24/51 Test apache#24: arrow-compute-cast-test .............. Passed 0.22 sec Start 25: arrow-compute-hash-test 25/51 Test apache#25: arrow-compute-hash-test .............. Passed 2.61 sec Start 26: arrow-compute-isin-test 26/51 Test apache#26: arrow-compute-isin-test .............. Passed 0.81 sec Start 27: arrow-compute-match-test 27/51 Test apache#27: arrow-compute-match-test ............. Passed 0.40 sec Start 28: arrow-compute-sort-to-indices-test 28/51 Test apache#28: arrow-compute-sort-to-indices-test ... Passed 3.33 sec Start 29: arrow-compute-nth-to-indices-test 29/51 Test apache#29: arrow-compute-nth-to-indices-test .... Passed 1.51 sec Start 30: arrow-compute-util-internal-test 30/51 Test apache#30: arrow-compute-util-internal-test ..... Passed 0.13 sec Start 31: arrow-compute-add-test 31/51 Test apache#31: arrow-compute-add-test ............... Passed 0.12 sec Start 32: arrow-compute-aggregate-test 32/51 Test apache#32: arrow-compute-aggregate-test ......... Passed 14.70 sec Start 33: arrow-compute-compare-test 33/51 Test apache#33: arrow-compute-compare-test ........... Passed 7.96 sec Start 34: arrow-compute-take-test 34/51 Test apache#34: arrow-compute-take-test .............. Passed 4.80 sec Start 35: arrow-compute-filter-test 35/51 Test apache#35: arrow-compute-filter-test ............ Passed 8.23 sec Start 36: arrow-dataset-dataset-test 36/51 Test apache#36: arrow-dataset-dataset-test ........... Passed 0.25 sec Start 37: arrow-dataset-discovery-test 37/51 Test apache#37: arrow-dataset-discovery-test ......... Passed 0.13 sec Start 38: arrow-dataset-file-ipc-test 38/51 Test apache#38: arrow-dataset-file-ipc-test .......... Passed 0.21 sec Start 39: arrow-dataset-file-test 39/51 Test apache#39: arrow-dataset-file-test .............. Passed 0.12 sec Start 40: arrow-dataset-filter-test 40/51 Test apache#40: arrow-dataset-filter-test ............ Passed 0.16 sec Start 41: arrow-dataset-partition-test 41/51 Test apache#41: arrow-dataset-partition-test ......... Passed 0.13 sec Start 42: arrow-dataset-scanner-test 42/51 Test apache#42: arrow-dataset-scanner-test ........... Passed 0.20 sec Start 43: arrow-filesystem-test 43/51 Test apache#43: arrow-filesystem-test ................ Passed 1.62 sec Start 44: arrow-hdfs-test 44/51 Test apache#44: arrow-hdfs-test ...................... Passed 0.13 sec Start 45: arrow-feather-test 45/51 Test apache#45: arrow-feather-test ................... Passed 0.91 sec Start 46: arrow-ipc-read-write-test 46/51 Test apache#46: arrow-ipc-read-write-test ............ Passed 5.77 sec Start 47: arrow-ipc-json-simple-test 47/51 Test apache#47: arrow-ipc-json-simple-test ........... Passed 0.16 sec Start 48: arrow-ipc-json-test 48/51 Test apache#48: arrow-ipc-json-test .................. Passed 0.27 sec Start 49: arrow-json-integration-test 49/51 Test apache#49: arrow-json-integration-test .......... Passed 0.13 sec Start 50: arrow-json-test 50/51 Test apache#50: arrow-json-test ...................... Passed 0.26 sec Start 51: arrow-orc-adapter-test 51/51 Test apache#51: arrow-orc-adapter-test ............... Passed 1.92 sec 98% tests passed, 1 tests failed out of 51 Label Time Summary: arrow-tests = 27.38 sec (27 tests) arrow_compute = 45.11 sec (14 tests) arrow_dataset = 1.21 sec (7 tests) arrow_ipc = 6.20 sec (3 tests) unittest = 79.91 sec (51 tests) Total Test time (real) = 79.99 sec The following tests FAILED: 20 - arrow-utility-test (Failed) Errors while running CTest ``` Closes apache#7142 from kiszk/ARROW-8754 Authored-by: Kazuaki Ishizaki <ishizaki@jp.ibm.com> Signed-off-by: Sutou Kouhei <kou@clear-code.com>
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From a deadlocked run... ``` #0 0x00007f8a5d48dccd in __lll_lock_wait () from /lib64/libpthread.so.0 #1 0x00007f8a5d486f05 in pthread_mutex_lock () from /lib64/libpthread.so.0 #2 0x00007f8a566e7e89 in arrow::internal::FnOnce<void ()>::FnImpl<arrow::Future<Aws::Utils::Outcome<Aws::S3::Model::ListObjectsV2Result, Aws::S3::S3Error> >::Callback<arrow::fs::(anonymous namespace)::TreeWalker::ListObjectsV2Handler> >::invoke() () from /arrow/r/check/arrow.Rcheck/arrow/libs/arrow.so #3 0x00007f8a5650efa0 in arrow::FutureImpl::AddCallback(arrow::internal::FnOnce<void ()>) () from /arrow/r/check/arrow.Rcheck/arrow/libs/arrow.so #4 0x00007f8a566e67a9 in arrow::fs::(anonymous namespace)::TreeWalker::ListObjectsV2Handler::SpawnListObjectsV2() () from /arrow/r/check/arrow.Rcheck/arrow/libs/arrow.so #5 0x00007f8a566e723f in arrow::fs::(anonymous namespace)::TreeWalker::WalkChild(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, int) () from /arrow/r/check/arrow.Rcheck/arrow/libs/arrow.so #6 0x00007f8a566e827d in arrow::internal::FnOnce<void ()>::FnImpl<arrow::Future<Aws::Utils::Outcome<Aws::S3::Model::ListObjectsV2Result, Aws::S3::S3Error> >::Callback<arrow::fs::(anonymous namespace)::TreeWalker::ListObjectsV2Handler> >::invoke() () from /arrow/r/check/arrow.Rcheck/arrow/libs/arrow.so #7 0x00007f8a5650efa0 in arrow::FutureImpl::AddCallback(arrow::internal::FnOnce<void ()>) () from /arrow/r/check/arrow.Rcheck/arrow/libs/arrow.so #8 0x00007f8a566e67a9 in arrow::fs::(anonymous namespace)::TreeWalker::ListObjectsV2Handler::SpawnListObjectsV2() () from /arrow/r/check/arrow.Rcheck/arrow/libs/arrow.so #9 0x00007f8a566e723f in arrow::fs::(anonymous namespace)::TreeWalker::WalkChild(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> >, int) () from /arrow/r/check/arrow.Rcheck/arrow/libs/arrow.so #10 0x00007f8a566e74b1 in arrow::fs::(anonymous namespace)::TreeWalker::DoWalk() () from /arrow/r/check/arrow.Rcheck/arrow/libs/arrow.so ``` The callback `ListObjectsV2Handler` is being called recursively and the mutex is non-reentrant thus deadlock. To fix it I got rid of the mutex on `TreeWalker` by using `arrow::util::internal::TaskGroup` instead of manually tracking the #/status of in-flight requests. Closes apache#9842 from westonpace/bugfix/arrow-12040 Lead-authored-by: Weston Pace <weston.pace@gmail.com> Co-authored-by: Antoine Pitrou <antoine@python.org> Signed-off-by: Antoine Pitrou <antoine@python.org>
pitrou
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Jun 16, 2021
Before change:
```
Direct leak of 65536 byte(s) in 1 object(s) allocated from:
#0 0x522f09 in
#1 0x7f28ae5826f4 in
#2 0x7f28ae57fa5d in
#3 0x7f28ae58cb0f in
#4 0x7f28ae58bda0 in
...
```
After change:
```
Direct leak of 65536 byte(s) in 1 object(s) allocated from:
#0 0x522f09 in posix_memalign (/build/cpp/debug/arrow-dataset-file-csv-test+0x522f09)
#1 0x7f28ae5826f4 in arrow::(anonymous namespace)::SystemAllocator::AllocateAligned(long, unsigned char**) /arrow/cpp/src/arrow/memory_pool.cc:213:24
#2 0x7f28ae57fa5d in arrow::BaseMemoryPoolImpl<arrow::(anonymous namespace)::SystemAllocator>::Allocate(long, unsigned char**) /arrow/cpp/src/arrow/memory_pool.cc:405:5
#3 0x7f28ae58cb0f in arrow::PoolBuffer::Reserve(long) /arrow/cpp/src/arrow/memory_pool.cc:717:9
#4 0x7f28ae58bda0 in arrow::PoolBuffer::Resize(long, bool) /arrow/cpp/src/arrow/memory_pool.cc:741:7
...
```
Closes apache#10498 from westonpace/feature/ARROW-13027--c-fix-asan-stack-traces-in-ci
Authored-by: Weston Pace <weston.pace@gmail.com>
Signed-off-by: Antoine Pitrou <antoine@python.org>
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The new behavior is working as expected now. Two other observations:
Invalid: Empty CSV file, same as what I was getting before your latest change to the skip_rows behavior. It would be nice if the error message were accurate, and even better if it were more specific so that I as a user might know how to fix my bad input.ignore_empty_linesis false and there are empty lines, it fails to parse (again, withInvalid: Empty CSV file).Happy to take those up in a separate ticket if you prefer, just observed them while working on this.