无法在 CentOS 上的 R 中安装 XML 包 [英] Unable to install XML package in R on CentOS

问题描述

当我尝试在 CENTOS 上的 R 中安装 xml 包时，我收到这样的警告:

<代码>>安装包(XML")将软件包安装到/opt/wpusers/r-mkosinski/R/x86_64-redhat-linux-gnu-library/3.1"(因为lib"未指定)尝试 URL 'http://cran.rstudio.com/src/contrib/XML_3.98-1.1.tar.gz'内容类型 'application/x-gzip' 长度 1582216 字节 (1.5 Mb)打开网址====================================================下载 1.5 Mb* 安装 *source* 包 ‘XML’ ...** 成功解包XML"包并检查 MD5 和检查 gcc ... gcc检查 C 编译器默认输出文件名...rm:无法删除'a.out.dSYM':是一个目录a.out检查 C 编译器是否工作......是的检查我们是否在交叉编译...否检查可执行文件的后缀...检查目标文件的后缀... o检查我们是否正在使用 GNU C 编译器...是的检查 gcc 是否接受 -g... 是检查 gcc 选项以接受 ISO C89... 不需要检查如何运行 C 预处理器... gcc -E检查 sed.../usr/bin/sed检查 pkg-config.../bin/pkg-config检查 xml2-config... 否找不到 xml2-config错误:包XML"的配置失败* 删除‘/opt/wpusers/r-mkosinski/R/x86_64-redhat-linux-gnu-library/3.1/XML’install.packages 中的警告:安装包XML"的退出状态非零下载的源码包在'/tmp/Rtmp3rqP3n/downloaded_pa​​ckages'>

我的会话信息是:

<代码>>会话信息()会话信息--------------------------------------------------------------------设定值版本 R 版本 3.1.2 (2014-10-31)系统 x86_64, linux-gnuui RStudio (0.98.1091)语言 (EN)整理 en_US.UTF-8tz 欧洲/华沙软件包-----------------------------------------------------------------------包 * 版本日期 来源档案管理员 1.2 2015-02-12 Github (pbiecek/archivist@d5305be)断言 * 0.1 2013-12-06 CRAN (R 3.1.2)bitops * 1.0-6 2013-08-17 CRAN (R 3.1.2)DBI 0.3.1 2014-09-24 CRAN (R 3.1.2)开发工具 1.7.0 2015-01-17 CRAN (R 3.1.2)摘要 * 0.6.8 2014-12-31 CRAN (R 3.1.2)dplyr 0.4.0 2015-01-08 CRAN (R 3.1.2)htmltools * 0.2.6 2014-09-08 CRAN (R 3.1.2)httpuv * 1.3.2 2014-10-23 CRAN (R 3.1.2)httr * 0.6.1 2015-01-01 CRAN (R 3.1.2)润滑 1.3.3 2013-12-31 CRAN (R 3.1.2)magrittr * 1.5 2014-11-22 CRAN (R 3.1.2)备忘录 * 0.2.1 2014-04-22 CRAN (R 3.1.2)哑剧 * 0.2 2014-09-26 CRAN (R 3.1.2)pbapply 1.1-1 2014-05-16 CRAN (R 3.1.2)plyr * 1.8.1 2014-02-26 CRAN (R 3.1.2)R6 * 2.0.1 2014-10-29 CRAN (R 3.1.2)Rcpp * 0.11.3 2014-09-29 CRAN (R 3.1.2)RCurl * 1.95-4.5 2014-12-28 CRAN (R 3.1.2)RJSONIO * 1.3-0 2014-07-28 CRAN (R 3.1.2)RSQLite 1.0.0 2014-10-25 CRAN (R 3.1.2)rstudio * 0.98.1091 2015-01-19 本地rstudioapi * 0.2 2014-12-31 CRAN (R 3.1.2)闪亮的 0.10.2.2 2014-12-08 CRAN (R 3.1.2)stringi 0.4-1 2014-12-14 CRAN (R 3.1.2)stringr * 0.6.2 2012-12-06 CRAN (R 3.1.2)xtable * 1.7-4 2014-09-12 CRAN (R 3.1.2)

可能是R版本的问题?

解决方案

你有两个问题在输出中明确说明:

1. 第一个是警告，你可能要删除 a.out/:

<块引用>

检查 C 编译器默认输出文件名...rm:无法删除'a.out.dSYM':是一个目录a.out检查 C 编译器是否工作......是的

1. 第二个错误是你的交易破坏者——你确实没有安装了 libxml2-dev(或任何 CentOS 调用的):

<块引用>

正在检查 xml2-config... 否找不到 xml2-config

如果没有 libxml2-dev 提供的 XML 开发工具，您根本无法从源代码构建包.

When I try to install xml package in R on CENTOS i recieve such warning:

> install.packages("XML")
Installing package into ‘/opt/wpusers/r-mkosinski/R/x86_64-redhat-linux-gnu-library/3.1’
(as ‘lib’ is unspecified)
trying URL 'http://cran.rstudio.com/src/contrib/XML_3.98-1.1.tar.gz'
Content type 'application/x-gzip' length 1582216 bytes (1.5 Mb)
opened URL
==================================================
downloaded 1.5 Mb

* installing *source* package ‘XML’ ...
** package ‘XML’ successfully unpacked and MD5 sums checked
checking for gcc... gcc
checking for C compiler default output file name... 
rm: cannot remove 'a.out.dSYM': Is a directory
a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables... 
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking how to run the C preprocessor... gcc -E
checking for sed... /usr/bin/sed
checking for pkg-config... /bin/pkg-config
checking for xml2-config... no
Cannot find xml2-config
ERROR: configuration failed for package ‘XML’
* removing ‘/opt/wpusers/r-mkosinski/R/x86_64-redhat-linux-gnu-library/3.1/XML’
Warning in install.packages :
  installation of package ‘XML’ had non-zero exit status

The downloaded source packages are in
    ‘/tmp/Rtmp3rqP3n/downloaded_packages’

>

My session info is:

> session_info()
Session info --------------------------------------------------------------------
 setting  value                       
 version  R version 3.1.2 (2014-10-31)
 system   x86_64, linux-gnu           
 ui       RStudio (0.98.1091)         
 language (EN)                        
 collate  en_US.UTF-8                 
 tz       Europe/Warsaw               

Packages ------------------------------------------------------------------------
 package    * version   date       source                            
 archivist    1.2       2015-02-12 Github (pbiecek/archivist@d5305be)
 assertthat * 0.1       2013-12-06 CRAN (R 3.1.2)                    
 bitops     * 1.0-6     2013-08-17 CRAN (R 3.1.2)                    
 DBI          0.3.1     2014-09-24 CRAN (R 3.1.2)                    
 devtools     1.7.0     2015-01-17 CRAN (R 3.1.2)                    
 digest     * 0.6.8     2014-12-31 CRAN (R 3.1.2)                    
 dplyr        0.4.0     2015-01-08 CRAN (R 3.1.2)                    
 htmltools  * 0.2.6     2014-09-08 CRAN (R 3.1.2)                    
 httpuv     * 1.3.2     2014-10-23 CRAN (R 3.1.2)                    
 httr       * 0.6.1     2015-01-01 CRAN (R 3.1.2)                    
 lubridate    1.3.3     2013-12-31 CRAN (R 3.1.2)                    
 magrittr   * 1.5       2014-11-22 CRAN (R 3.1.2)                    
 memoise    * 0.2.1     2014-04-22 CRAN (R 3.1.2)                    
 mime       * 0.2       2014-09-26 CRAN (R 3.1.2)                    
 pbapply      1.1-1     2014-05-16 CRAN (R 3.1.2)                    
 plyr       * 1.8.1     2014-02-26 CRAN (R 3.1.2)                    
 R6         * 2.0.1     2014-10-29 CRAN (R 3.1.2)                    
 Rcpp       * 0.11.3    2014-09-29 CRAN (R 3.1.2)                    
 RCurl      * 1.95-4.5  2014-12-28 CRAN (R 3.1.2)                    
 RJSONIO    * 1.3-0     2014-07-28 CRAN (R 3.1.2)                    
 RSQLite      1.0.0     2014-10-25 CRAN (R 3.1.2)                    
 rstudio    * 0.98.1091 2015-01-19 local                             
 rstudioapi * 0.2       2014-12-31 CRAN (R 3.1.2)                    
 shiny        0.10.2.2  2014-12-08 CRAN (R 3.1.2)                    
 stringi      0.4-1     2014-12-14 CRAN (R 3.1.2)                    
 stringr    * 0.6.2     2012-12-06 CRAN (R 3.1.2)                    
 xtable     * 1.7-4     2014-09-12 CRAN (R 3.1.2) 

Maybe it is a matter of R version?

解决方案

You have two problems clearly stated in the output:

1. The first is a warning, you may want to remove a.out/:

checking for C compiler default output file name... 
rm: cannot remove 'a.out.dSYM': Is a directory
a.out
checking whether the C compiler works... yes

2. The second is an error and your dealbreaker -- you do not have libxml2-dev (or whatever CentOS calls this) installed:

checking for xml2-config... no
Cannot find xml2-config

Without the XML development tools provided by libxml2-dev you simply cannot build the package from source.

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