duckdb fails to compile on RHEL7.9 on R 4.1 session.

[Nishantha2006]

Hi,
Im using install.packages("duckdb") to install duckdb (version 1.3.2) on my R 4.1 session, running on a RHEL 7.9 OS/system. And it fails to compile (I use devtoolset-12) returning below error attached.

The compilation log was quite length, but I've captured the initial section for reference:

install.packages('duckdb')
Installing package into ‘/home//R/x86_64-pc-linux-gnu-library/4.1’
(as ‘lib’ is unspecified)
trying URL 'https:///prod-cran/linux/centos7/latest/src/contrib/duckdb_1.3.2.tar.gz'
Content type 'application/x-gzip' length 4176759 bytes (4.0 MB)
==================================================
downloaded 4.0 MB

• installing source package ‘duckdb’ ...
  ** package ‘duckdb’ successfully unpacked and MD5 sums checked
  ** using staged installation
  ++ dirname ./configure

• cd ./src
• echo DUCKDB_RSTRTMGR=1
• echo DUCKDB_RSTRTMGR_LIB=
• '[' -f '' ']'
• cp include/to-tar.mk Makevars.duckdb
• '[' -f duckdb.tar.xz ']'
• tar xJf duckdb.tar.xz
  ** libs
  Makevars:22: include/deps.mk: No such file or directory
  touch -r $(ls -t *.cpp | head -n 1) "include/deps.mk"
  /opt/rh/devtoolset-12/root/usr/bin/g++ -std=gnu++17 -I"/opt/R/4.1.0/lib/R/include" -DNDEBUG -Iinclude -I../inst/include -DDUCKDB_DISABLE_PRINT -DDUCKDB_R_BUILD -DBROTLI_ENCODER_CLEANUP_ON_OOM -DDUCKDB_EXTENSION_AUTOLOAD_DEFAULT -DDUCKDB_RSTRTMGR=1 -Iduckdb/src/include -Iduckdb/third_party/concurrentqueue -Iduckdb/third_party/fast_float -Iduckdb/third_party/fastpforlib -Iduckdb/third_party/fmt/include -Iduckdb/third_party/fsst -Iduckdb/third_party/httplib -Iduckdb/third_party/hyperloglog -Iduckdb/third_party/jaro_winkler -Iduckdb/third_party/jaro_winkler/details -Iduckdb/third_party/libpg_query -Iduckdb/third_party/libpg_query/include -Iduckdb/third_party/lz4 -Iduckdb/third_party/brotli/include -Iduckdb/third_party/brotli/common -Iduckdb/third_party/brotli/dec -Iduckdb/third_party/brotli/enc -Iduckdb/third_party/mbedtls/include -Iduckdb/third_party/mbedtls/library -Iduckdb/third_party/miniz -Iduckdb/third_party/pcg -Iduckdb/third_party/re2 -Iduckdb/third_party/skiplist -Iduckdb/third_party/tdigest -Iduckdb/third_party/utf8proc -Iduckdb/third_party/utf8proc/include -Iduckdb/third_party/yyjson/include -Iduckdb/third_party/zstd/include -Iduckdb/extension/parquet/include -Iduckdb/third_party/parquet -Iduckdb/third_party/thrift -Iduckdb/third_party/lz4 -Iduckdb/third_party/brotli/include -Iduckdb/third_party/brotli/common -Iduckdb/third_party/brotli/dec -Iduckdb/third_party/brotli/enc -Iduckdb/third_party/snappy -Iduckdb/third_party/mbedtls -Iduckdb/third_party/mbedtls/include -Iduckdb/third_party/zstd/include -Iduckdb/extension/core_functions/include -I../inst/include -Iduckdb -DDUCKDB_EXTENSION_PARQUET_LINKED -DDUCKDB_BUILD_LIBRARY -DDUCKDB_EXTENSION_CORE_FUNCTIONS_LINKED -DDUCKDB_BUILD_LIBRARY -I/usr/local/include -fpic -g -O2 -c rfuns.cpp -o rfuns.o
  /opt/rh/devtoolset-12/root/usr/bin/g++ -std=gnu++17 -I"/opt/R/4.1.0/lib/R/include" -DNDEBUG -Iinclude -I../inst/include -DDUCKDB_DISABLE_PRINT -DDUCKDB_R_BUILD -DBROTLI_ENCODER_CLEANUP_ON_OOM -DDUCKDB_EXTENSION_AUTOLOAD_DEFAULT -DDUCKDB_RSTRTMGR=1 -Iduckdb/src/include -Iduckdb/third_party/concurrentqueue -Iduckdb/third_party/fast_float -Iduckdb/third_party/fastpforlib -Iduckdb/third_party/fmt/include -Iduckdb/third_party/fsst -Iduckdb/third_party/httplib -Iduckdb/third_party/hyperloglog -Iduckdb/third_party/jaro_winkler -Iduckdb/third_party/jaro_winkler/details -Iduckdb/third_party/libpg_query -Iduckdb/third_party/libpg_query/include -Iduckdb/third_party/lz4 -Iduckdb/third_party/brotli/include -Iduckdb/third_party/brotli/common -Iduckdb/third_party/brotli/dec -Iduckdb/third_party/brotli/enc -Iduckdb/third_party/mbedtls/include -Iduckdb/third_party/mbedtls/library -Iduckdb/third_party/miniz -Iduckdb/third_party/pcg -Iduckdb/third_party/re2 -Iduckdb/third_party/skiplist -Iduckdb/third_party/tdigest -Iduckdb/third_party/utf8proc -Iduckdb/third_party/utf8proc/include -Iduckdb/third_party/yyjson/include -Iduckdb/third_party/zstd/include -Iduckdb/extension/parquet/include -Iduckdb/third_party/parquet -Iduckdb/third_party/thrift -Iduckdb/third_party/lz4 -Iduckdb/third_party/brotli/include -Iduckdb/third_party/brotli/common -Iduckdb/third_party/brotli/dec -Iduckdb/third_party/brotli/enc -Iduckdb/third_party/snappy -Iduckdb/third_party/mbedtls -Iduckdb/third_party/mbedtls/include -Iduckdb/third_party/zstd/include -Iduckdb/extension/core_functions/include -I../inst/include -Iduckdb -DDUCKDB_EXTENSION_PARQUET_LINKED -DDUCKDB_BUILD_LIBRARY -DDUCKDB_EXTENSION_CORE_FUNCTIONS_LINKED -DDUCKDB_BUILD_LIBRARY -I/usr/local/include -fpic -g -O2 -c database.cpp -o database.o

Can you please advise how I could resolve this?

Thanks,

[krlmlr]

Thanks. This is a fairly old OS. Can you please try duckdb 1.2.2 or older?

https://cran.r-project.org/src/contrib/Archive/duckdb/

[Nishantha2006]

Thanks. Yes duckdb 1.2.2 installs fine on my R 4.1 session. Although I was trying to install the latest version if can, to leverage new features. Does that mean duckdb 1.2.2 is the highest version we could get on RHEL7.9 perhaps? Is there any other method to get the latest duckdb working on RHEL7.9?
Cheers.

[krlmlr]

Thanks. Can you compile the upstream C++ library on your OS: https://github.com/duckdb/duckdb ?