Libreoffice给出“应用程序错误”。从R呼叫时 [英] Libreoffice gives "Application Error" when called from R

问题描述

在docker容器中，我尝试使用LibreOffice将XLSX文件转换为PDF。相关命令在命令行上有效，但从R调用时失败，并显示 Application Error。我使用此 Dockerfile ，这会添加一些（以我的经验为准）XLSX文件：

Inside a docker container I am trying to convert an XLSX file to PDF using LibreOffice. The relevant command works on the command line but fails with "Application Error" when called from R. I use this Dockerfile which adds some (in my experience arbitrary) XLSX file:

FROM rocker/r-ver:3.4.3

RUN apt-get update \
 && apt-get install --yes --no-install-recommends \
    default-jre-headless libreoffice-calc \
 && apt-get clean \
 && rm -rf /var/lib/apt/lists/* \
 && echo /usr/lib/libreoffice/program > /etc/ld.so.conf.d/libreoffice.conf \
 && ldconfig

COPY foo.xlsx /tmp

（ ldconfig 来自
R中系统功能存在共享库问题。

(The trick with ldconfig comes from shared library issue with the system function in R.)

然后在命令行上，我可以将XLSX文件转换为PDF：

On the command line I can then convert the XLSX file to PDF:

root@b395caeba33b:/# loffice --headless --convert-to pdf /tmp/foo.xlsx 
convert /tmp/foo.xlsx -> //foo.pdf using filter : calc_pdf_Export

但是，这从R失败：

> system("loffice --version")
LibreOffice 5.2.7.2 20m0(Build:2)

> system("loffice --headless --convert-to pdf /tmp/foo.xlsx")
convert /tmp/foo.xlsx -> //foo.pdf using filter : calc_pdf_Export
Application Error

如果我更改了基本图像从 rocker / r-ver：3.4.3 到 rocker / r-base 使用R 3.4.4和Debian测试/ sid结果仅略有变化：

If I change the base image from rocker/r-ver:3.4.3 to rocker/r-base which uses R 3.4.4 and Debian testing/sid the result changes only marginally:

> system("loffice --version")
LibreOffice 6.0.2.1.0 00m0(Build:1)

> system("loffice --headless --convert-to pdf /tmp/foo.xlsx")
Application Error

从R调用时，如何使LibreOffice将XLSX文件转换为PDF？

How can I get LibreOffice to convert XLSX files to PDF when called from R?

推荐答案

发生此问题是因为环境不同。通过系统

The issue happens because of the environment difference. When you run the env command through system

> system('env')
R_UNZIPCMD=/usr/bin/unzip
HOSTNAME=da4d504ddcb1
LD_LIBRARY_PATH=/usr/local/lib/R/lib:/usr/local/lib:/usr/lib/x86_64-linux-gnu:/usr/lib/jvm/java-8-openjdk-amd64/jre/lib/amd64/server
SHLVL=0
HOME=/root
R_LIBS_SITE=
R_BROWSER=xdg-open
PAGER=/usr/bin/pager
R_VERSION=3.4.3
BUILD_DATE=
R_SYSTEM_ABI=linux,gcc,gxx,gfortran,?
TAR=/bin/tar
R_LIBS_USER=/usr/local/lib/R/site-library
TERM=xterm
COLUMNS=200
R_ARCH=
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
R_BZIPCMD=/bin/bzip2
R_INCLUDE_DIR=/usr/local/lib/R/include
R_SESSION_TMPDIR=/tmp/RtmpJsaXba
LANG=en_US.UTF-8
R_GZIPCMD=/bin/gzip
SED=/bin/sed
LN_S=ln -s
R_PDFVIEWER=/usr/bin/xdg-open
R_TEXI2DVICMD=/usr/bin/texi2dvi
R_HOME=/usr/local/lib/R
R_PRINTCMD=/usr/bin/lpr
R_DOC_DIR=/usr/local/lib/R/doc
R_LIBS=/usr/local/lib/R/site-library:/usr/local/lib/R/library:/usr/lib/R/library
LC_ALL=en_US.UTF-8
R_SHARE_DIR=/usr/local/lib/R/share
PWD=/
R_ZIPCMD=/usr/bin/zip
R_PLATFORM=x86_64-pc-linux-gnu
R_PAPERSIZE=letter
LINES=50
MAKE=make
R_RD4PDF=times,inconsolata,hyper
EDITOR=vi

您可以看到默认的 R 有一组环境变量，其中一个是 LD _LIBRARY_PATH 。

You can see the default R has set of environment variables and one of them is LD_LIBRARY_PATH.

> system('loffice --headless --convert-to pdf /tmp/foo.xlsx')
Application Error
> system('LD_LIBRARY_PATH= loffice --headless --convert-to pdf /tmp/foo.xlsx')
convert /tmp/foo.xlsx -> //foo.pdf using filter : calc_pdf_Export

将其清除，即可使用。它在bash中起作用的原因是因为默认环境变量集很小

Blank it out and it works. The reason it works in bash is because the default environment variable set is small

root@5c5bbcfcebf2:/# env
LC_ALL=en_US.UTF-8
LANG=en_US.UTF-8
HOSTNAME=5c5bbcfcebf2
PWD=/
HOME=/root
R_VERSION=3.4.3
BUILD_DATE=
TERM=xterm
SHLVL=1
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
_=/usr/bin/env

启动时 r 而不是bash中的 R

Also when you launch r instead of R from bash

root@5c5bbcfcebf2:/# r -i
system('env')
R_UNZIPCMD=/usr/bin/unzip
HOSTNAME=5c5bbcfcebf2
SHLVL=1
R_INSTALL_PKG=littler
HOME=/root
R_ENVIRON=
R_LIBS_SITE=
R_BROWSER=xdg-open
PAGER=/usr/bin/pager
R_VERSION=3.4.3
BUILD_DATE=
R_SYSTEM_ABI=linux,gcc,gxx,gfortran,?
R_PROFILE_USER=
TAR=/bin/tar
_=/usr/local/bin/r
R_LIBS_USER=/usr/local/lib/R/site-library
TERM=xterm
R_ARCH=
R_PAPERSIZE_USER=letter
PATH=/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin
R_BZIPCMD=/bin/bzip2
R_INCLUDE_DIR=/usr/local/lib/R/include
R_SESSION_TMPDIR=/tmp
R_OSTYPE=unix
LANG=en_US.UTF-8
R_CMD=/usr/local/lib/R/bin/Rcmd
R_DEFAULT_PACKAGES=NULL
R_PACKAGE_NAME=littler
R_GZIPCMD=/bin/gzip
LN_S=ln -s
SED=/bin/sed
R_PDFVIEWER=/usr/bin/xdg-open
R_PROFILE=
R_ENVIRON_USER=
R_TEXI2DVICMD=/usr/bin/texi2dvi
R_HOME=/usr/local/lib/R
R_PRINTCMD=/usr/bin/lpr
R_DOC_DIR=/usr/local/lib/R/doc
R_LIBS=/usr/local/lib/R/site-library:/usr/local/lib/R/library:/usr/lib/R/library
LC_ALL=en_US.UTF-8
PWD=/
R_SHARE_DIR=/usr/local/lib/R/share
R_ZIPCMD=/usr/bin/zip
R_PAPERSIZE=letter
R_PLATFORM=x86_64-pc-linux-gnu
MAKE=make
R_RD4PDF=times,inconsolata,hyper
EDITOR=vi

在从bash启动的交互式shell中使用 r -i

In the interactive shell launch from bash using r -i

system('LD_LIBRARY_PATH= loffice --headless --convert-to pdf /tmp/foo.xlsx')
convert /tmp/foo.xlsx -> //foo.pdf using filter : calc_pdf_Export

system('loffice --headless --convert-to pdf /tmp/foo.xlsx')
convert /tmp/foo.xlsx -> //foo.pdf using filter : calc_pdf_Export
Overwriting: //foo.pdf

它是从父级继承的子进程环境，在您的情况下会导致问题

It is the child process environment inherited from the parent that causes the issue in your case

这篇关于Libreoffice给出“应用程序错误”。从R呼叫时的文章就介绍到这了，希望我们推荐的答案对大家有所帮助，也希望大家多多支持IT屋！