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Posted to jira@arrow.apache.org by "Ofek Shilon (Jira)" <ji...@apache.org> on 2020/09/08 13:56:00 UTC
[jira] [Comment Edited] (ARROW-9932) R package fails to install on
Ubuntu 14
[ https://issues.apache.org/jira/browse/ARROW-9932?page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel&focusedCommentId=17192227#comment-17192227 ]
Ofek Shilon edited comment on ARROW-9932 at 9/8/20, 1:55 PM:
-------------------------------------------------------------
The previous suspicion is *not* the root cause of the installation failure.
The signature of dQuote changed in R3.6. It [accepted a single argument before|[https://www.rdocumentation.org/packages/base/versions/3.5.3/topics/sQuote]] but [accepts a second argument since 3.6.|https://www.rdocumentation.org/packages/base/versions/3.6.0/topics/sQuote] The arrow 1.0.1 R package is marked as dependent on R>=3.1, but the installation error message above seems to indicate that the installation script uses somewhere R3.6 syntax.
was (Author: ofek):
The previous suspicion is *not* the root cause of the installation failure.
The signature of dQuote changed in R3.6. It [accepted a single argument before|[https://www.rdocumentation.org/packages/base/versions/3.5.3/topics/sQuote|https://www.rdocumentation.org/packages/base/versions/3.5.3/topics/sQuote],]][,|https://www.rdocumentation.org/packages/base/versions/3.5.3/topics/sQuote],] but [accepts a second argument since 3.6.|https://www.rdocumentation.org/packages/base/versions/3.6.0/topics/sQuote] The arrow 1.0.1 R package is marked as dependent on R>=3.1, but the installation error message above seems to indicate that the installation script uses somewhere R3.6 syntax.
> R package fails to install on Ubuntu 14
> ---------------------------------------
>
> Key: ARROW-9932
> URL: https://issues.apache.org/jira/browse/ARROW-9932
> Project: Apache Arrow
> Issue Type: Bug
> Components: R
> Affects Versions: 1.0.1
> Environment: R version 3.4.0 (2015-04-16)
> Platform: x86_64-pc-linux-gnu (64-bit)
> Running under: Ubuntu 14.04.5 LTS
> Reporter: Ofek Shilon
> Priority: Major
>
> 1. From R (3.4) prompt, we run
> {{> install.packages("arrow")}}
> and it seems to succeed.
> 2. Next we run:
> {{> arrow::install_arrow()}}
> This is the full output:
> {{Installing package into '/opt/R-3.4.0.mkl/library'}}
> {{(as 'lib' is unspecified)}}
> {{trying URL 'https://cloud.r-project.org/src/contrib/arrow_1.0.1.tar.gz'}}
> {{Content type 'application/x-gzip' length 274865 bytes (268 KB)}}
> {{==================================================}}
> {{downloaded 268 KB}}
> {{installing *source* package 'arrow' ...}}
> {{** package 'arrow' successfully unpacked and MD5 sums checked}}
> {{*** No C++ binaries found for ubuntu-14.04}}
> {{*** Successfully retrieved C++ source}}
> {{*** Building C++ libraries}}
> {{**** cmake}}
> {color:#ff0000}*{{Error in dQuote(env_var_list, FALSE) : unused argument (FALSE)}}*{color}
> {color:#ff0000} *{{Calls: build_libarrow -> paste}}*{color}
> {color:#ff0000} *{{Execution halted}}*{color}
> {{------------------------- NOTE ---------------------------}}
> {{After installation, please run arrow::install_arrow()}}
> {{for help installing required runtime libraries}}
> {{---------------------------------------------------------}}
> {{** libs}}
> {{g++ -std=gnu++0x -I/opt/R-3.4.0.mkl/lib64/R/include -DNDEBUG -I"/opt/R-3.4.0.mkl/library/Rcpp/include" -I/usr/local/include -fpic -march=x86-64 -O3 -c array.cpp -o array.o}}
> {{g++ -std=gnu++0x -I/opt/R-3.4.0.mkl/lib64/R/include -DNDEBUG -I"/opt/R-3.4.0.mkl/library/Rcpp/include" -I/usr/local/include -fpic -march=x86-64 -O3 -c array_from_vector.cpp -o array_from_vector.o}}
> {{g++ -std=gnu++0x -I/opt/R-3.4.0.mkl/lib64/R/include -DNDEBUG -I"/opt/R-3.4.0.mkl/library/Rcpp/include" -I/usr/local/include -fpic -march=x86-64 -O3 -c array_to_vector.cpp -o array_to_vector.o}}
> {{g++ -std=gnu++0x -I/opt/R-3.4.0.mkl/lib64/R/include -DNDEBUG -I"/opt/R-3.4.0.mkl/library/Rcpp/include" -I/usr/local/include -fpic -march=x86-64 -O3 -c arraydata.cpp -o arraydata.o}}
> {{g++ -std=gnu++0x -I/opt/R-3.4.0.mkl/lib64/R/include -DNDEBUG -I"/opt/R-3.4.0.mkl/library/Rcpp/include" -I/usr/local/include -fpic -march=x86-64 -O3 -c arrowExports.cpp -o arrowExports.o}}
> {{g++ -std=gnu++0x -I/opt/R-3.4.0.mkl/lib64/R/include -DNDEBUG -I"/opt/R-3.4.0.mkl/library/Rcpp/include" -I/usr/local/include -fpic -march=x86-64 -O3 -c buffer.cpp -o buffer.o}}
> {{g++ -std=gnu++0x -I/opt/R-3.4.0.mkl/lib64/R/include -DNDEBUG -I"/opt/R-3.4.0.mkl/library/Rcpp/include" -I/usr/local/include -fpic -march=x86-64 -O3 -c chunkedarray.cpp -o chunkedarray.o}}
> {{g++ -std=gnu++0x -I/opt/R-3.4.0.mkl/lib64/R/include -DNDEBUG -I"/opt/R-3.4.0.mkl/library/Rcpp/include" -I/usr/local/include -fpic -march=x86-64 -O3 -c compression.cpp -o compression.o}}
> {{g++ -std=gnu++0x -I/opt/R-3.4.0.mkl/lib64/R/include -DNDEBUG -I"/opt/R-3.4.0.mkl/library/Rcpp/include" -I/usr/local/include -fpic -march=x86-64 -O3 -c compute.cpp -o compute.o}}
> {{g++ -std=gnu++0x -I/opt/R-3.4.0.mkl/lib64/R/include -DNDEBUG -I"/opt/R-3.4.0.mkl/library/Rcpp/include" -I/usr/local/include -fpic -march=x86-64 -O3 -c csv.cpp -o csv.o+}}{{g+ -std=gnu++0x -I/opt/R-3.4.0.mkl/lib64/R/include -DNDEBUG -I"/opt/R-3.4.0.mkl/library/Rcpp/include" -I/usr/local/include -fpic -march=x86-64 -O3 -c dataset.cpp -o dataset.o}}
> {{g++ -std=gnu++0x -I/opt/R-3.4.0.mkl/lib64/R/include -DNDEBUG -I"/opt/R-3.4.0.mkl/library/Rcpp/include" -I/usr/local/include -fpic -march=x86-64 -O3 -c datatype.cpp -o datatype.o}}
> {{g++ -std=gnu++0x -I/opt/R-3.4.0.mkl/lib64/R/include -DNDEBUG -I"/opt/R-3.4.0.mkl/library/Rcpp/include" -I/usr/local/include -fpic -march=x86-64 -O3 -c expression.cpp -o expression.o}}
> {{g++ -std=gnu++0x -I/opt/R-3.4.0.mkl/lib64/R/include -DNDEBUG -I"/opt/R-3.4.0.mkl/library/Rcpp/include" -I/usr/local/include -fpic -march=x86-64 -O3 -c feather.cpp -o feather.o}}
> {{g++ -std=gnu++0x -I/opt/R-3.4.0.mkl/lib64/R/include -DNDEBUG -I"/opt/R-3.4.0.mkl/library/Rcpp/include" -I/usr/local/include -fpic -march=x86-64 -O3 -c field.cpp -o field.o}}
> {{g++ -std=gnu++0x -I/opt/R-3.4.0.mkl/lib64/R/include -DNDEBUG -I"/opt/R-3.4.0.mkl/library/Rcpp/include" -I/usr/local/include -fpic -march=x86-64 -O3 -c filesystem.cpp -o filesystem.o}}
> {{g++ -std=gnu++0x -I/opt/R-3.4.0.mkl/lib64/R/include -DNDEBUG -I"/opt/R-3.4.0.mkl/library/Rcpp/include" -I/usr/local/include -fpic -march=x86-64 -O3 -c imports.cpp -o imports.o}}
> {{g++ -std=gnu++0x -I/opt/R-3.4.0.mkl/lib64/R/include -DNDEBUG -I"/opt/R-3.4.0.mkl/library/Rcpp/include" -I/usr/local/include -fpic -march=x86-64 -O3 -c io.cpp -o io.o}}
> {{g++ -std=gnu++0x -I/opt/R-3.4.0.mkl/lib64/R/include -DNDEBUG -I"/opt/R-3.4.0.mkl/library/Rcpp/include" -I/usr/local/include -fpic -march=x86-64 -O3 -c json.cpp -o json.o+}}{{g+ -std=gnu++0x -I/opt/R-3.4.0.mkl/lib64/R/include -DNDEBUG -I"/opt/R-3.4.0.mkl/library/Rcpp/include" -I/usr/local/include -fpic -march=x86-64 -O3 -c memorypool.cpp -o memorypool.o}}
> {{g++ -std=gnu++0x -I/opt/R-3.4.0.mkl/lib64/R/include -DNDEBUG -I"/opt/R-3.4.0.mkl/library/Rcpp/include" -I/usr/local/include -fpic -march=x86-64 -O3 -c message.cpp -o message.o}}
> {{g++ -std=gnu++0x -I/opt/R-3.4.0.mkl/lib64/R/include -DNDEBUG -I"/opt/R-3.4.0.mkl/library/Rcpp/include" -I/usr/local/include -fpic -march=x86-64 -O3 -c parquet.cpp -o parquet.o}}
> {{g++ -std=gnu++0x -I/opt/R-3.4.0.mkl/lib64/R/include -DNDEBUG -I"/opt/R-3.4.0.mkl/library/Rcpp/include" -I/usr/local/include -fpic -march=x86-64 -O3 -c py-to-r.cpp -o py-to-r.o}}
> {{g++ -std=gnu++0x -I/opt/R-3.4.0.mkl/lib64/R/include -DNDEBUG -I"/opt/R-3.4.0.mkl/library/Rcpp/include" -I/usr/local/include -fpic -march=x86-64 -O3 -c recordbatch.cpp -o recordbatch.o}}
> {{g++ -std=gnu++0x -I/opt/R-3.4.0.mkl/lib64/R/include -DNDEBUG -I"/opt/R-3.4.0.mkl/library/Rcpp/include" -I/usr/local/include -fpic -march=x86-64 -O3 -c recordbatchreader.cpp -o recordbatchreader.o}}
> {{g++ -std=gnu++0x -I/opt/R-3.4.0.mkl/lib64/R/include -DNDEBUG -I"/opt/R-3.4.0.mkl/library/Rcpp/include" -I/usr/local/include -fpic -march=x86-64 -O3 -c recordbatchwriter.cpp -o recordbatchwriter.o}}
> {{g++ -std=gnu++0x -I/opt/R-3.4.0.mkl/lib64/R/include -DNDEBUG -I"/opt/R-3.4.0.mkl/library/Rcpp/include" -I/usr/local/include -fpic -march=x86-64 -O3 -c scalar.cpp -o scalar.o}}
> {{g++ -std=gnu++0x -I/opt/R-3.4.0.mkl/lib64/R/include -DNDEBUG -I"/opt/R-3.4.0.mkl/library/Rcpp/include" -I/usr/local/include -fpic -march=x86-64 -O3 -c schema.cpp -o schema.o}}
> {{g++ -std=gnu++0x -I/opt/R-3.4.0.mkl/lib64/R/include -DNDEBUG -I"/opt/R-3.4.0.mkl/library/Rcpp/include" -I/usr/local/include -fpic -march=x86-64 -O3 -c symbols.cpp -o symbols.o}}
> {{g++ -std=gnu++0x -I/opt/R-3.4.0.mkl/lib64/R/include -DNDEBUG -I"/opt/R-3.4.0.mkl/library/Rcpp/include" -I/usr/local/include -fpic -march=x86-64 -O3 -c table.cpp -o table.o+}}{{g+ -std=gnu++0x -I/opt/R-3.4.0.mkl/lib64/R/include -DNDEBUG -I"/opt/R-3.4.0.mkl/library/Rcpp/include" -I/usr/local/include -fpic -march=x86-64 -O3 -c threadpool.cpp -o threadpool.o+}}{{g+ -std=gnu++0x -shared -L/opt/R-3.4.0.mkl/lib64/R/lib -L/usr/local/lib64 -o arrow.so array.o array_from_vector.o array_to_vector.o arraydata.o arrowExports.o buffer.o chunkedarray.o compression.o compute.o csv.o dataset.o datatype.o expression.o feather.o field.o filesystem.o imports.o io.o json.o memorypool.o message.o parquet.o py-to-r.o recordbatch.o recordbatchreader.o recordbatchwriter.o scalar.o schema.o symbols.o table.o threadpool.o -L/opt/R-3.4.0.mkl/lib64/R/lib -lR}}
> {{installing to /opt/R-3.4.0.mkl/library/arrow/libs}}{{** R}}
> {{** inst}}
> {{** preparing package for lazy loading}}
> {{** help}}
> {{*** installing help indices}}
> {{** building package indices}}
> {{** installing vignettes}}{{** testing if installed package can be loaded}}
> {{* DONE (arrow)}}{{The downloaded source packages are inThe downloaded source packages are in '/tmp/RtmppBCBzR/downloaded_packages'}}{{Please restart R to use the 'arrow' package.}}
> 3. We restart R, and run -
> {{> arrow::arrow_available()}}
> {color:#ff0000}{{*[1] FALSE*}}{color}
>
> And indeed all arrow functionality fails:
> {{> x <- arrow::Table$create(data.frame(a=1:2)) }}
> {{{color:#FF0000}Error in Table__from_dots(dots, schema) :{color}}}
> {{{color:#ff0000}Cannot call Table__from_dots(). Please use arrow::install_arrow() to install required runtime libraries.{color}}}}}
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