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Posted to jira@arrow.apache.org by "Jonathan Keane (Jira)" <ji...@apache.org> on 2020/12/15 22:31:00 UTC
[jira] [Commented] (ARROW-10856) [R] CentOS 7 not correctly
identifying compiler version
[ https://issues.apache.org/jira/browse/ARROW-10856?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=17249988#comment-17249988 ]
Jonathan Keane commented on ARROW-10856:
----------------------------------------
Digging a little bit more, it looks like what was happening is that the environment variables `CC` and `CXX` weren't being picked up in the calls to cmake we used to identify what versions were available. On CentOS this resulted in the default versions of gcc being used even though newer versions were on the path and being used elsewhere. https://github.com/apache/arrow/pull/8932 adjusts the detection slightly to prevent this from happening.
> [R] CentOS 7 not correctly identifying compiler version
> -------------------------------------------------------
>
> Key: ARROW-10856
> URL: https://issues.apache.org/jira/browse/ARROW-10856
> Project: Apache Arrow
> Issue Type: Bug
> Components: R
> Reporter: Yi Hsiao
> Assignee: Jonathan Keane
> Priority: Major
> Labels: pull-request-available
> Fix For: 3.0.0
>
> Time Spent: 10m
> Remaining Estimate: 0h
>
> When I tried to use the example command like this in my R session:
> {code:java}
> df <- read_parquet(system.file("v0.7.1.parquet", package="arrow")){code}
>
> It shows error:
> {code:java}
> > df <- read_parquet(system.file("v0.7.1.parquet", package="arrow"))
> Error in io___MemoryMappedFile__Open(path, mode) :
> Cannot call io___MemoryMappedFile__Open(). Please use arrow::install_arrow() to install required runtime libraries.{code}
> I did try to install it with `arrow::install_arrow()` and it finishes successfully.
> However, I still get the same error message mentioned above after that.
> My session info is here:
>
> {code:java}
> > sessioninfo::session_info()
> ─ Session info ───────────────────────────────────────────────────────────────
> setting value
> version R version 4.0.2 (2020-06-22)
> os CentOS Linux 7 (Core)
> system x86_64, linux-gnu
> ui X11
> language (EN)
> collate en_US.UTF-8
> ctype en_US.UTF-8
> tz America/Detroit
> date 2020-12-08
> ─ Packages ───────────────────────────────────────────────────────────────────
> package * version date lib source
> arrow * 2.0.0 2020-10-20 [1] CRAN (R 4.0.2)
> assertthat 0.2.1 2019-03-21 [1] CRAN (R 4.0.2)
> bit 4.0.4 2020-08-04 [1] CRAN (R 4.0.2)
> bit64 4.0.5 2020-08-30 [1] CRAN (R 4.0.2)
> cli 2.2.0 2020-11-20 [1] CRAN (R 4.0.2)
> crayon 1.3.4 2017-09-16 [1] CRAN (R 4.0.2)
> fansi 0.4.1 2020-01-08 [1] CRAN (R 4.0.2)
> glue 1.4.2 2020-08-27 [1] CRAN (R 4.0.2)
> magrittr 2.0.1 2020-11-17 [1] CRAN (R 4.0.2)
> purrr 0.3.4 2020-04-17 [1] CRAN (R 4.0.2)
> R6 2.5.0 2020-10-28 [1] CRAN (R 4.0.2)
> rlang 0.4.9 2020-11-26 [1] CRAN (R 4.0.2)
> sessioninfo 1.1.1 2018-11-05 [1] CRAN (R 4.0.2)
> tidyselect 1.1.0 2020-05-11 [1] CRAN (R 4.0.2)
> vctrs 0.3.5 2020-11-17 [1] CRAN (R 4.0.2)
> withr 2.3.0 2020-09-22 [1] CRAN (R 4.0.2)
> [1] /home/yihsiao/R/x86_64-pc-linux-gnu-library/4.0
> [2] /sw/arcts/centos7/stacks/gcc/8.2.0/R/4.0.2/lib64/R/library
> {code}
>
> One thing I notice is that when installing the run time library, it doesn't get the correct compiler I have for C++ (8.2.0 rather than some version < 4.9)
>
> {code:java}
> > arrow::install_arrow()
> Installing package into '/home/yihsiao/R/x86_64-pc-linux-gnu-library/4.0'
> (as 'lib' is unspecified)
> trying URL 'https://cloud.r-project.org/src/contrib/arrow_2.0.0.tar.gz'
> Content type 'application/x-gzip' length 322592 bytes (315 KB)
> ==================================================
> downloaded 315 KB
> * installing *source* package 'arrow' ...
> ** package 'arrow' successfully unpacked and MD5 sums checked
> ** using staged installation
> *** No C++ binaries found for centos-7
> *** Successfully retrieved C++ source
> *** Building C++ libraries
> **** cmake
> **** S3 support not available for gcc < 4.9; building with ARROW_S3=OFF
> **** arrow
> {code}
>
>
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