Closed PMassicotte closed 4 months ago
How did you install nanoparquet? If you compiled it, what compilation flags did you use? Eg. can you show the installation output?
let me try to install from source
Same error. Here is the installation ouput from building from source:
[nav] r$> install.packages('nanoparquet', repos = "https://cran.rstudio.com")
Installing package into ‘/home/filoche/R/x86_64-pc-linux-gnu-library/4.4’
(as ‘lib’ is unspecified)
trying URL 'https://cran.rstudio.com/src/contrib/nanoparquet_0.3.0.tar.gz'
Content type 'application/x-gzip' length 1025569 bytes (1001 KB)
==================================================
downloaded 1001 KB
* installing *source* package ‘nanoparquet’ ...
** package ‘nanoparquet’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 13.2.0-23ubuntu4) 13.2.0’
g++ -std=gnu++17 -I"/usr/bin/R/include" -DNDEBUG -Ithrift -I. -Izstd/include -I/usr/local/include -DR_NO_REMAP -fpic -g -O2 -c rwrapper.cpp -o rwrapper.o
g++ -std=gnu++17 -I"/usr/bin/R/include" -DNDEBUG -Ithrift -I. -Izstd/include -I/usr/local/include -DR_NO_REMAP -fpic -g -O2 -c protect.cpp -o protect.o
g++ -std=gnu++17 -I"/usr/bin/R/include" -DNDEBUG -Ithrift -I. -Izstd/include -I/usr/local/include -DR_NO_REMAP -fpic -g -O2 -c read.cpp -o read.o
g++ -std=gnu++17 -I"/usr/bin/R/include" -DNDEBUG -Ithrift -I. -Izstd/include -I/usr/local/include -DR_NO_REMAP -fpic -g -O2 -c write.cpp -o write.o
g++ -std=gnu++17 -I"/usr/bin/R/include" -DNDEBUG -Ithrift -I. -Izstd/include -I/usr/local/include -DR_NO_REMAP -fpic -g -O2 -c read-metadata.cpp -o read-metadata.o
g++ -std=gnu++17 -I"/usr/bin/R/include" -DNDEBUG -Ithrift -I. -Izstd/include -I/usr/local/include -DR_NO_REMAP -fpic -g -O2 -c read-pages.cpp -o read-pages.o
g++ -std=gnu++17 -I"/usr/bin/R/include" -DNDEBUG -Ithrift -I. -Izstd/include -I/usr/local/include -DR_NO_REMAP -fpic -g -O2 -c arrow-schema.cpp -o arrow-schema.o
g++ -std=gnu++17 -I"/usr/bin/R/include" -DNDEBUG -Ithrift -I. -Izstd/include -I/usr/local/include -DR_NO_REMAP -fpic -g -O2 -c base64.cpp -o base64.o
g++ -std=gnu++17 -I"/usr/bin/R/include" -DNDEBUG -Ithrift -I. -Izstd/include -I/usr/local/include -DR_NO_REMAP -fpic -g -O2 -c r-base64.cpp -o r-base64.o
g++ -std=gnu++17 -I"/usr/bin/R/include" -DNDEBUG -Ithrift -I. -Izstd/include -I/usr/local/include -DR_NO_REMAP -fpic -g -O2 -c snappy.cpp -o snappy.o
g++ -std=gnu++17 -I"/usr/bin/R/include" -DNDEBUG -Ithrift -I. -Izstd/include -I/usr/local/include -DR_NO_REMAP -fpic -g -O2 -c encodings.cpp -o encodings.o
g++ -std=gnu++17 -I"/usr/bin/R/include" -DNDEBUG -Ithrift -I. -Izstd/include -I/usr/local/include -DR_NO_REMAP -fpic -g -O2 -c dictionary-encoding.cpp -o dictionary-encoding.o
g++ -std=gnu++17 -I"/usr/bin/R/include" -DNDEBUG -Ithrift -I. -Izstd/include -I/usr/local/include -DR_NO_REMAP -fpic -g -O2 -c test.cpp -o test.o
g++ -std=gnu++17 -I"/usr/bin/R/include" -DNDEBUG -Ithrift -I. -Izstd/include -I/usr/local/include -DR_NO_REMAP -fpic -g -O2 -c lib/ParquetFile.cpp -o lib/ParquetFile.o
g++ -std=gnu++17 -I"/usr/bin/R/include" -DNDEBUG -Ithrift -I. -Izstd/include -I/usr/local/include -DR_NO_REMAP -fpic -g -O2 -c lib/ParquetOutFile.cpp -o lib/ParquetOutFile.o
g++ -std=gnu++17 -I"/usr/bin/R/include" -DNDEBUG -Ithrift -I. -Izstd/include -I/usr/local/include -DR_NO_REMAP -fpic -g -O2 -c lib/RleBpDecoder.cpp -o lib/RleBpDecoder.o
g++ -std=gnu++17 -I"/usr/bin/R/include" -DNDEBUG -Ithrift -I. -Izstd/include -I/usr/local/include -DR_NO_REMAP -fpic -g -O2 -c parquet/parquet_types.cpp -o parquet/parquet_types.o
g++ -std=gnu++17 -I"/usr/bin/R/include" -DNDEBUG -Ithrift -I. -Izstd/include -I/usr/local/include -DR_NO_REMAP -fpic -g -O2 -c thrift/protocol/TProtocol.cpp -o thrift/protocol/TProtocol.o
g++ -std=gnu++17 -I"/usr/bin/R/include" -DNDEBUG -Ithrift -I. -Izstd/include -I/usr/local/include -DR_NO_REMAP -fpic -g -O2 -c thrift/transport/TTransportException.cpp -o thrift/transport/TTransportException.o
g++ -std=gnu++17 -I"/usr/bin/R/include" -DNDEBUG -Ithrift -I. -Izstd/include -I/usr/local/include -DR_NO_REMAP -fpic -g -O2 -c thrift/transport/TBufferTransports.cpp -o thrift/transport/TBufferTransports.o
g++ -std=gnu++17 -I"/usr/bin/R/include" -DNDEBUG -Ithrift -I. -Izstd/include -I/usr/local/include -DR_NO_REMAP -fpic -g -O2 -c fastpforlib/bitpacking.cpp -o fastpforlib/bitpacking.o
g++ -std=gnu++17 -I"/usr/bin/R/include" -DNDEBUG -Ithrift -I. -Izstd/include -I/usr/local/include -DR_NO_REMAP -fpic -g -O2 -c snappy/snappy.cc -o snappy/snappy.o
g++ -std=gnu++17 -I"/usr/bin/R/include" -DNDEBUG -Ithrift -I. -Izstd/include -I/usr/local/include -DR_NO_REMAP -fpic -g -O2 -c snappy/snappy-sinksource.cc -o snappy/snappy-sinksource.o
g++ -std=gnu++17 -I"/usr/bin/R/include" -DNDEBUG -Ithrift -I. -Izstd/include -I/usr/local/include -DR_NO_REMAP -fpic -g -O2 -c miniz/miniz.cpp -o miniz/miniz.o
g++ -std=gnu++17 -I"/usr/bin/R/include" -DNDEBUG -Ithrift -I. -Izstd/include -I/usr/local/include -DR_NO_REMAP -fpic -g -O2 -c zstd/common/entropy_common.cpp -o zstd/common/entropy_common.o
g++ -std=gnu++17 -I"/usr/bin/R/include" -DNDEBUG -Ithrift -I. -Izstd/include -I/usr/local/include -DR_NO_REMAP -fpic -g -O2 -c zstd/common/error_private.cpp -o zstd/common/error_private.o
g++ -std=gnu++17 -I"/usr/bin/R/include" -DNDEBUG -Ithrift -I. -Izstd/include -I/usr/local/include -DR_NO_REMAP -fpic -g -O2 -c zstd/common/fse_decompress.cpp -o zstd/common/fse_decompress.o
g++ -std=gnu++17 -I"/usr/bin/R/include" -DNDEBUG -Ithrift -I. -Izstd/include -I/usr/local/include -DR_NO_REMAP -fpic -g -O2 -c zstd/common/xxhash.cpp -o zstd/common/xxhash.o
g++ -std=gnu++17 -I"/usr/bin/R/include" -DNDEBUG -Ithrift -I. -Izstd/include -I/usr/local/include -DR_NO_REMAP -fpic -g -O2 -c zstd/common/zstd_common.cpp -o zstd/common/zstd_common.o
g++ -std=gnu++17 -I"/usr/bin/R/include" -DNDEBUG -Ithrift -I. -Izstd/include -I/usr/local/include -DR_NO_REMAP -fpic -g -O2 -c zstd/decompress/huf_decompress.cpp -o zstd/decompress/huf_decompress.o
g++ -std=gnu++17 -I"/usr/bin/R/include" -DNDEBUG -Ithrift -I. -Izstd/include -I/usr/local/include -DR_NO_REMAP -fpic -g -O2 -c zstd/decompress/zstd_ddict.cpp -o zstd/decompress/zstd_ddict.o
g++ -std=gnu++17 -I"/usr/bin/R/include" -DNDEBUG -Ithrift -I. -Izstd/include -I/usr/local/include -DR_NO_REMAP -fpic -g -O2 -c zstd/decompress/zstd_decompress.cpp -o zstd/decompress/zstd_decompress.o
g++ -std=gnu++17 -I"/usr/bin/R/include" -DNDEBUG -Ithrift -I. -Izstd/include -I/usr/local/include -DR_NO_REMAP -fpic -g -O2 -c zstd/decompress/zstd_decompress_block.cpp -o zstd/decompress/zstd_decompress_block.o
g++ -std=gnu++17 -I"/usr/bin/R/include" -DNDEBUG -Ithrift -I. -Izstd/include -I/usr/local/include -DR_NO_REMAP -fpic -g -O2 -c zstd/compress/fse_compress.cpp -o zstd/compress/fse_compress.o
g++ -std=gnu++17 -I"/usr/bin/R/include" -DNDEBUG -Ithrift -I. -Izstd/include -I/usr/local/include -DR_NO_REMAP -fpic -g -O2 -c zstd/compress/hist.cpp -o zstd/compress/hist.o
g++ -std=gnu++17 -I"/usr/bin/R/include" -DNDEBUG -Ithrift -I. -Izstd/include -I/usr/local/include -DR_NO_REMAP -f
pic -g -O2 -c zstd/compress/huf_compress.cpp -o zstd/compress/huf_compress.o
g++ -std=gnu++17 -I"/usr/bin/R/include" -DNDEBUG -Ithrift -I. -Izstd/include -I/usr/local/include -DR_NO_REMAP -fpic -g -O2 -c zstd/compress/zstd_compress.cpp -o zstd/compress/zstd_compress.o
g++ -std=gnu++17 -I"/usr/bin/R/include" -DNDEBUG -Ithrift -I. -Izstd/include -I/usr/local/include -DR_NO_REMAP -fpic -g -O2 -c zstd/compress/zstd_compress_literals.cpp -o zstd/compress/zstd_compress_literals.o
g++ -std=gnu++17 -I"/usr/bin/R/include" -DNDEBUG -Ithrift -I. -Izstd/include -I/usr/local/include -DR_NO_REMAP -fpic -g -O2 -c zstd/compress/zstd_compress_sequences.cpp -o zstd/compress/zstd_compress_sequences.o
g++ -std=gnu++17 -I"/usr/bin/R/include" -DNDEBUG -Ithrift -I. -Izstd/include -I/usr/local/include -DR_NO_REMAP -fpic -g -O2 -c zstd/compress/zstd_compress_superblock.cpp -o zstd/compress/zstd_compress_superblock.o
g++ -std=gnu++17 -I"/usr/bin/R/include" -DNDEBUG -Ithrift -I. -Izstd/include -I/usr/local/include -DR_NO_REMAP -fpic -g -O2 -c zstd/compress/zstd_double_fast.cpp -o zstd/compress/zstd_double_fast.o
g++ -std=gnu++17 -I"/usr/bin/R/include" -DNDEBUG -Ithrift -I. -Izstd/include -I/usr/local/include -DR_NO_REMAP -fpic -g -O2 -c zstd/compress/zstd_fast.cpp -o zstd/compress/zstd_fast.o
g++ -std=gnu++17 -I"/usr/bin/R/include" -DNDEBUG -Ithrift -I. -Izstd/include -I/usr/local/include -DR_NO_REMAP -fpic -g -O2 -c zstd/compress/zstd_lazy.cpp -o zstd/compress/zstd_lazy.o
g++ -std=gnu++17 -I"/usr/bin/R/include" -DNDEBUG -Ithrift -I. -Izstd/include -I/usr/local/include -DR_NO_REMAP -fpic -g -O2 -c zstd/compress/zstd_ldm.cpp -o zstd/compress/zstd_ldm.o
g++ -std=gnu++17 -I"/usr/bin/R/include" -DNDEBUG -Ithrift -I. -Izstd/include -I/usr/local/include -DR_NO_REMAP -fpic -g -O2 -c zstd/compress/zstd_opt.cpp -o zstd/compress/zstd_opt.o
g++ -std=gnu++17 -shared -L/usr/bin/R/lib -L/usr/local/lib -o nanoparquet.so rwrapper.o protect.o read.o write.o read-metadata.o read-pages.o arrow-schema.o base64.o r-base64.o snappy.o encodings.o dictionary-encoding.o test.o lib/ParquetFile.o lib/ParquetOutFile.o lib/RleBpDecoder.o parquet/parquet_types.o thrift/protocol/TProtocol.o thrift/transport/TTransportException.o thrift/transport/TBufferTransports.o fastpforlib/bitpacking.o snappy/snappy.o snappy/snappy-sinksource.o miniz/miniz.o zstd/common/entropy_common.o zstd/common/error_private.o zstd/common/fse_decompress.o zstd/common/xxhash.o zstd/common/zstd_common.o zstd/decompress/huf_decompress.o zstd/decompress/zstd_ddict.o zstd/decompress/zstd_decompress.o zstd/decompress/zstd_decompress_block.o zstd/compress/fse_compress.o zstd/compress/hist.o zstd/compress/huf_compress.o zstd/compress/zstd_compress.o zstd/compress/zstd_compress_literals.o zstd/compress/zstd_compress_sequences.o zstd/compress/zstd_compress_superblock.o zstd/compress/zstd_double_fast.o zstd/compress/zstd_fast.o zstd/compress/zstd_lazy.o zstd/compress/zstd_ldm.o zstd/compress/zstd_opt.o -L/usr/bin/R/lib -lR
installing to /home/filoche/R/x86_64-pc-linux-gnu-library/4.4/00LOCK-nanoparquet/00new/nanoparquet/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (nanoparquet)
Please install from GH for now, we'll have another release soon. I have no clue why this only happens on Ubuntu Noble...
Launching R with
R -d lldb
gives me:It crashes whatever compression method I am using.
Session info: