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Posted to jira@arrow.apache.org by "Daniel Teske (Jira)" <ji...@apache.org> on 2021/11/02 14:04:00 UTC
[jira] [Updated] (ARROW-14555) install.packages("arrow") fails on
docker image rocker/r-ver:4.0.2
[ https://issues.apache.org/jira/browse/ARROW-14555?page=com.atlassian.jira.plugin.system.issuetabpanels:all-tabpanel ]
Daniel Teske updated ARROW-14555:
---------------------------------
Description:
Since last week we cannot build our R environment because the the arrow lib fails on
{code:java}
install.packages("arrow"){code}
We're using rocker/r-vers:4.0.2 as our base image. It seems that it's possible to install arrow on Windows an Mac, but not on Linux.
The effected part of the Dockerfile is the following:
{code:java}
FROM rocker/r-ver:4.0.2 AS builder
RUN apt-get update && apt-get install -y \
git-core \
libcurl4-openssl-dev \
libgit2-dev \
libglpk-dev \
libgmp-dev \
libicu-dev \
libssh2-1-dev \
libssl-dev \
libxml2-dev \
make pandoc pandoc-citeproc zlib1g-dev && rm -rf /var/lib/apt/lists/*
RUN echo "options(repos = c(CRAN = 'https://cran.rstudio.com/'), download.file.method = 'libcurl')" >> /usr/local/lib/R/etc/Rprofile.site
RUN R -e 'install.packages("remotes")'
RUN R -e 'remotes::install_github("r-lib/remotes", ref = "97bbf81")'
# copy the setup script, run it, then delete it
COPY dependencies/setup.R /
RUN Rscript setup.R && rm setup.R
{code}
the dependencies/setup.R script contains
{code:java}
install.packages(
c(
"arrow"
),
quiet = FALSE,
verbose = TRUE
)
arrow::install_arrow()
{code}
I attached the complete log output, but the interesting part ist the following:
{code:java}
#12 55.88 * installing *source* package ‘arrow’ ...
#12 55.96 ** package ‘arrow’ successfully unpacked and MD5 sums checked
#12 55.96 ** using staged installation
#12 56.46 *** Found local C++ source: 'tools/cpp'
#12 56.46 *** Building C++ libraries
#12 56.53 **** cmake
#12 62.22 **** arrow
#12 663.6 **** Error building Arrow C++. Re-run with ARROW_R_DEV=true for debug information.
#12 665.3 ------------------------- NOTE ---------------------------
#12 665.3 There was an issue preparing the Arrow C++ libraries.
#12 665.3 See https://arrow.apache.org/docs/r/articles/install.html
#12 665.3 ---------------------------------------------------------
#12 665.5 ERROR: configuration failed for package ‘arrow’
#12 665.5 * removing ‘/usr/local/lib/R/site-library/arrow’
#12 666.0
#12 666.0 The downloaded source packages are in
#12 666.0 ‘/tmp/RtmpDWxSqL/downloaded_packages’
#12 666.0 Warning message:
#12 666.0 In install.packages(c("arrow"), quiet = FALSE, verbose = TRUE) :
#12 666.0 installation of package ‘arrow’ had non-zero exit status
#12 666.1 Error in loadNamespace(name) : there is no package called ‘arrow’
#12 666.1 Calls: :: ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
#12 666.1 Execution halted
------
executor failed running [/bin/sh -c Rscript setup.R && rm setup.R]: exit code: 1
{code}
was:
Since last week we cannot build our R environment because the the arrow lib fails on
{code:java}
install.packages("arrow"){code}
We use the rocker/r-vers:4.0.2 as our base image. It seems that it's possible to install arrow on Windows an Mac, but not on Linux.
The effected part of the Dockerimage is the following:
{code:java}
FROM rocker/r-ver:4.0.2 AS builder
RUN apt-get update && apt-get install -y \
git-core \
libcurl4-openssl-dev \
libgit2-dev \
libglpk-dev \
libgmp-dev \
libicu-dev \
libssh2-1-dev \
libssl-dev \
libxml2-dev \
make pandoc pandoc-citeproc zlib1g-dev && rm -rf /var/lib/apt/lists/*
RUN echo "options(repos = c(CRAN = 'https://cran.rstudio.com/'), download.file.method = 'libcurl')" >> /usr/local/lib/R/etc/Rprofile.site
RUN R -e 'install.packages("remotes")'
RUN R -e 'remotes::install_github("r-lib/remotes", ref = "97bbf81")'
# copy the setup script, run it, then delete it
COPY dependencies/setup.R /
RUN Rscript setup.R && rm setup.R
{code}
the dependencies/setup.R script contains
{code:java}
install.packages(
c(
"arrow"
),
quiet = FALSE,
verbose = TRUE
)
arrow::install_arrow()
{code}
I attached the whole log output, but the interesting Part ist the following:
{code:java}
#12 55.88 * installing *source* package ‘arrow’ ...
#12 55.96 ** package ‘arrow’ successfully unpacked and MD5 sums checked
#12 55.96 ** using staged installation
#12 56.46 *** Found local C++ source: 'tools/cpp'
#12 56.46 *** Building C++ libraries
#12 56.53 **** cmake
#12 62.22 **** arrow
#12 663.6 **** Error building Arrow C++. Re-run with ARROW_R_DEV=true for debug information.
#12 665.3 ------------------------- NOTE ---------------------------
#12 665.3 There was an issue preparing the Arrow C++ libraries.
#12 665.3 See https://arrow.apache.org/docs/r/articles/install.html
#12 665.3 ---------------------------------------------------------
#12 665.5 ERROR: configuration failed for package ‘arrow’
#12 665.5 * removing ‘/usr/local/lib/R/site-library/arrow’
#12 666.0
#12 666.0 The downloaded source packages are in
#12 666.0 ‘/tmp/RtmpDWxSqL/downloaded_packages’
#12 666.0 Warning message:
#12 666.0 In install.packages(c("arrow"), quiet = FALSE, verbose = TRUE) :
#12 666.0 installation of package ‘arrow’ had non-zero exit status
#12 666.1 Error in loadNamespace(name) : there is no package called ‘arrow’
#12 666.1 Calls: :: ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
#12 666.1 Execution halted
------
executor failed running [/bin/sh -c Rscript setup.R && rm setup.R]: exit code: 1
{code}
> install.packages("arrow") fails on docker image rocker/r-ver:4.0.2
> ------------------------------------------------------------------
>
> Key: ARROW-14555
> URL: https://issues.apache.org/jira/browse/ARROW-14555
> Project: Apache Arrow
> Issue Type: Bug
> Components: R
> Affects Versions: 6.0.0
> Reporter: Daniel Teske
> Priority: Major
> Attachments: complete-output.log
>
>
> Since last week we cannot build our R environment because the the arrow lib fails on
> {code:java}
> install.packages("arrow"){code}
> We're using rocker/r-vers:4.0.2 as our base image. It seems that it's possible to install arrow on Windows an Mac, but not on Linux.
> The effected part of the Dockerfile is the following:
> {code:java}
> FROM rocker/r-ver:4.0.2 AS builder
> RUN apt-get update && apt-get install -y \
> git-core \
> libcurl4-openssl-dev \
> libgit2-dev \
> libglpk-dev \
> libgmp-dev \
> libicu-dev \
> libssh2-1-dev \
> libssl-dev \
> libxml2-dev \
> make pandoc pandoc-citeproc zlib1g-dev && rm -rf /var/lib/apt/lists/*
> RUN echo "options(repos = c(CRAN = 'https://cran.rstudio.com/'), download.file.method = 'libcurl')" >> /usr/local/lib/R/etc/Rprofile.site
> RUN R -e 'install.packages("remotes")'
> RUN R -e 'remotes::install_github("r-lib/remotes", ref = "97bbf81")'
> # copy the setup script, run it, then delete it
> COPY dependencies/setup.R /
> RUN Rscript setup.R && rm setup.R
> {code}
> the dependencies/setup.R script contains
> {code:java}
> install.packages(
> c(
> "arrow"
> ),
> quiet = FALSE,
> verbose = TRUE
> )
> arrow::install_arrow()
> {code}
> I attached the complete log output, but the interesting part ist the following:
> {code:java}
> #12 55.88 * installing *source* package ‘arrow’ ...
> #12 55.96 ** package ‘arrow’ successfully unpacked and MD5 sums checked
> #12 55.96 ** using staged installation
> #12 56.46 *** Found local C++ source: 'tools/cpp'
> #12 56.46 *** Building C++ libraries
> #12 56.53 **** cmake
> #12 62.22 **** arrow
> #12 663.6 **** Error building Arrow C++. Re-run with ARROW_R_DEV=true for debug information.
> #12 665.3 ------------------------- NOTE ---------------------------
> #12 665.3 There was an issue preparing the Arrow C++ libraries.
> #12 665.3 See https://arrow.apache.org/docs/r/articles/install.html
> #12 665.3 ---------------------------------------------------------
> #12 665.5 ERROR: configuration failed for package ‘arrow’
> #12 665.5 * removing ‘/usr/local/lib/R/site-library/arrow’
> #12 666.0
> #12 666.0 The downloaded source packages are in
> #12 666.0 ‘/tmp/RtmpDWxSqL/downloaded_packages’
> #12 666.0 Warning message:
> #12 666.0 In install.packages(c("arrow"), quiet = FALSE, verbose = TRUE) :
> #12 666.0 installation of package ‘arrow’ had non-zero exit status
> #12 666.1 Error in loadNamespace(name) : there is no package called ‘arrow’
> #12 666.1 Calls: :: ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
> #12 666.1 Execution halted
> ------
> executor failed running [/bin/sh -c Rscript setup.R && rm setup.R]: exit code: 1
> {code}
>
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