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Posted to jira@arrow.apache.org by "Nicola Crane (Jira)" <ji...@apache.org> on 2022/09/13 10:51:00 UTC
[jira] [Commented] (ARROW-17692) [R] Arrow Package Installation: undefined symbol error
[ https://issues.apache.org/jira/browse/ARROW-17692?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=17603509#comment-17603509 ]
Nicola Crane commented on ARROW-17692:
--------------------------------------
Thanks for reporting this [~wtacct77]. A couple of questions; is there are longer installation log that you can provide? It'll give us a little more context to see exactly what has gone wrong as the last message isn't always the most relevant one for diagnosing the issue.
That said, the last message there refers to something to do with AWS. Looking at the [dependencies list in the installation guide|https://arrow.apache.org/docs/r/articles/install.html#dependencies-for-s3-and-gcs-support], it looks like you have a sufficient version of gcc, but would you mind you confirming the versions of CURL and OpenSSL that you have installed, so I can rule out a dependency mismatch?
> [R] Arrow Package Installation: undefined symbol error
> -------------------------------------------------------
>
> Key: ARROW-17692
> URL: https://issues.apache.org/jira/browse/ARROW-17692
> Project: Apache Arrow
> Issue Type: Bug
> Components: R
> Reporter: Wayne Tu
> Priority: Major
>
> Hi,
> I encountered "undefined symbol: _ZTIN3Aws4Auth22AWSCredentialsProviderE
> Error: loading failed
> Execution halted
> ERROR: loading failed" errors when trying to install arrow under R 4.1.3 with devtoolset-8 (gcc version 8.3.1).
> > Sys.getenv("LD_LIBRARY_PATH")
> [1] "/usr/local/lib64:/usr/local/lib64/cmake:/lib64:/opt/rh/devtoolset-8/root/usr/lib64:/opt/rh/devtoolset-8/root/usr/lib/gcc/x86_64-redhat-linux/8:/opt/rh/devtoolset-8/root/usr/libexec/gcc/x86_64-redhat-linux/8:/opt/R/4.1.3/lib/R/lib:/usr/local/lib:/usr/lib/jvm/java-1.8.0-openjdk-1.8.0.322.b06-1.el7_9.x86_64/jre/lib/amd64/server"
> > Sys.getenv("PATH")
> [1] "/apps/Python/3.9.12/bin:/usr/local/cmake-3.21.4-linux-x86_64/bin:/opt/rh/devtoolset-8/root/usr/bin:/apps/bin:/usr/local/bin:/bin:/usr/bin"
> > Sys.setenv("NOT_CRAN"=TRUE)
> > Sys.setenv("LIBARROW_BINARY" = FALSE)
> > Sys.setenv("ARROW_R_DEV" = TRUE)
> > Sys.setenv("ARROW_USE_PKG_CONFIG" = FALSE)
> > Sys.setenv(ARROW_S3 = "ON")
> > Sys.setenv(CMAKE = "/apps/cmake-3.21.4-linux-x86_64/bin/cmake")
> > sessionInfo()
> R version 4.1.3 (2022-03-10)
> Platform: x86_64-pc-linux-gnu (64-bit)
> Running under: Red Hat Enterprise Linux Server 7.9 (Maipo)
> Matrix products: default
> BLAS/LAPACK: /usr/lib64/libopenblasp-r0.3.3.so
> locale:
> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
> [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
> [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
> [7] LC_PAPER=en_US.UTF-8 LC_NAME=C
> [9] LC_ADDRESS=C LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
> attached base packages:
> [1] stats graphics grDevices utils datasets methods base
> loaded via a namespace (and not attached):
> [1] compiler_4.1.3
> > arrow::arrow_available()
> Error in loadNamespace(x) : there is no package called ‘arrow’
> > system("gcc -v")
> Using built-in specs.
> COLLECT_GCC=gcc
> COLLECT_LTO_WRAPPER=/opt/rh/devtoolset-8/root/usr/libexec/gcc/x86_64-redhat-linux/8/lto-wrapper
> Target: x86_64-redhat-linux
> Configured with: ../configure --enable-bootstrap --enable-languages=c,c++,fortran,lto --prefix=/opt/rh/devtoolset-8/root/usr --mandir=/opt/rh/devtoolset-8/root/usr/share/man --infodir=/opt/rh/devtoolset-8/root/usr/share/info --with-bugurl=http://bugzilla.redhat.com/bugzilla --enable-shared --enable-threads=posix --enable-checking=release --enable-multilib --with-system-zlib --enable-__cxa_atexit --disable-libunwind-exceptions --enable-gnu-unique-object --enable-linker-build-id --with-gcc-major-version-only --with-linker-hash-style=gnu --with-default-libstdcxx-abi=gcc4-compatible --enable-plugin --enable-initfini-array --with-isl=/builddir/build/BUILD/gcc-8.3.1-20190311/obj-x86_64-redhat-linux/isl-install --disable-libmpx --enable-gnu-indirect-function --with-tune=generic --with-arch_32=x86-64 --build=x86_64-redhat-linux
> Thread model: posix
> gcc version 8.3.1 20190311 (Red Hat 8.3.1-3) (GCC)
>
> > install.packages(mpkg, repos=NULL, type="source")
> ......
> ......
> ** building package indices
> ** installing vignettes
> ** testing if installed package can be loaded from temporary location
> Error: package or namespace load failed for ‘arrow’ in dyn.load(file, DLLpath = DLLpath, ...):
> unable to load shared object '/home/user1/R/x86_64-pc-linux-gnu/4.1.3/00LOCK-arrow/00new/arrow/libs/arrow.so':
> /home/user1/R/x86_64-pc-linux-gnu/4.1.3/00LOCK-arrow/00new/arrow/libs/arrow.so: undefined symbol: _ZTIN3Aws4Auth22AWSCredentialsProviderE
> Error: loading failed
> Execution halted
> ERROR: loading failed
> * removing ‘/home/user1/R/x86_64-pc-linux-gnu/4.1.3/arrow’
> Warning message:
> In install.packages(mpkg, repos = NULL, type = "source") :
> installation of package ‘/apps/tmp/RtmpEqJN3J/downloaded_packages/arrow_8.0.0.tar.gz’ had non-zero exit status
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