Anaconda 环境下 R 包 ggraph_1.0.2 安装小记

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记录一下今天在 Anaconda3 环境下 R==3.4.3 中安装 ggraph 的一些问题。

install.packages("ggraph") 发现 libudunits2.so was not found 错误：

> install.packages("ggraph")
......
checking for gcc... x86_64-conda_cos6-linux-gnu-cc
checking whether we are using the GNU C compiler... yes
checking whether x86_64-conda_cos6-linux-gnu-cc accepts -g... yes
checking for x86_64-conda_cos6-linux-gnu-cc option to accept ISO C89... none needed
checking for XML_ParserCreate in -lexpat... yes
checking udunits2.h usability... no
checking udunits2.h presence... no
checking for udunits2.h... no
checking udunits2/udunits2.h usability... no
checking udunits2/udunits2.h presence... no
checking for udunits2/udunits2.h... no
checking for ut_read_xml in -ludunits2... no
configure: error: in `/tmp/RtmpDRI4FZ/R.INSTALL7d4f2d342516/units':
configure: error:
--------------------------------------------------------------------------------
  Configuration failed because libudunits2.so was not found. Try installing:
    * deb: libudunits2-dev (Debian, Ubuntu, ...)
    * rpm: udunits2-devel (Fedora, EPEL, ...)
    * brew: udunits (OSX)
  If udunits2 is already installed in a non-standard location, use:
    --configure-args='--with-udunits2-lib=/usr/local/lib'
  if the library was not found, and/or:
    --configure-args='--with-udunits2-include=/usr/include/udunits2'
  if the header was not found, replacing paths with appropriate values.
  You can alternatively set UDUNITS2_INCLUDE and UDUNITS2_LIBS manually.
--------------------------------------------------------------------------------

See `config.log' for more details
ERROR: configuration failed for package ‘units’
* removing ‘/usr/local/SoftWare/Anaconda3/lib/R/library/units’
ERROR: dependency ‘units’ is not available for package ‘ggforce’
* removing ‘/usr/local/SoftWare/Anaconda3/lib/R/library/ggforce’
ERROR: dependency ‘ggforce’ is not available for package ‘ggraph’
* removing ‘/usr/local/SoftWare/Anaconda3/lib/R/library/ggraph’

The downloaded source packages are in
        ‘/tmp/RtmpqBo0sm/downloaded_packages’
Updating HTML index of packages in '.Library'
Making 'packages.html' ... done
Warning messages:
1: In install.packages("ggraph") :
  installation of package ‘units’ had non-zero exit status
2: In install.packages("ggraph") :
  installation of package ‘ggforce’ had non-zero exit status
3: In install.packages("ggraph") :
  installation of package ‘ggraph’ had non-zero exit status

> install.packages("units")
......
checking for ut_read_xml in -ludunits2... no
configure: error: in `/tmp/Rtmp9xeJYe/R.INSTALL1e7523367a6/units':
configure: error:
--------------------------------------------------------------------------------
  Configuration failed because libudunits2.so was not found. Try installing:
    * deb: libudunits2-dev (Debian, Ubuntu, ...)
    * rpm: udunits2-devel (Fedora, EPEL, ...)
    * brew: udunits (OSX)
  If udunits2 is already installed in a non-standard location, use:
    --configure-args='--with-udunits2-lib=/usr/local/lib'
  if the library was not found, and/or:
    --configure-args='--with-udunits2-include=/usr/include/udunits2'
  if the header was not found, replacing paths with appropriate values.
  You can alternatively set UDUNITS2_INCLUDE and UDUNITS2_LIBS manually.
--------------------------------------------------------------------------------

See `config.log' for more details
ERROR: configuration failed for package ‘units’
* removing ‘/usr/local/SoftWare/Anaconda3/lib/R/library/units’

The downloaded source packages are in
        ‘/tmp/RtmpqBo0sm/downloaded_packages’
Updating HTML index of packages in '.Library'
Making 'packages.html' ... done
Warning message:
In install.packages("units") :
  installation of package ‘units’ had non-zero exit status

libudunits2.so not found，是 udunits2 相关的库存在问题，CentOS 下可以使用 sudo yum install udunits2-devel 解决，在这里也可以使用 conda 同时解决 units 安装及 udunits2 的库错误。

$ conda install r-units
#没有报错，正常安装成功

$ R
......
> library(units)
> install.packages("ggraph")
......
** R
** inst
** preparing package for lazy loading
Error : object ‘scale_type’ is not exported by 'namespace:ggplot2'
ERROR: lazy loading failed for package ‘ggforce’
* removing ‘/usr/local/SoftWare/Anaconda2/lib/R/library/ggforce’
ERROR: dependency ‘ggforce’ is not available for package ‘ggraph’
* removing ‘/usr/local/SoftWare/Anaconda2/lib/R/library/ggraph’

The downloaded source packages are in
        ‘/tmp/RtmpDK4vST/downloaded_packages’
Updating HTML index of packages in '.Library'
Making 'packages.html' ... done
Warning messages:
1: In install.packages("ggraph") :
  installation of package ‘ggforce’ had non-zero exit status
2: In install.packages("ggraph") :
  installation of package ‘ggraph’ had non-zero exit status

> library(ggforce)
Error in library(ggforce) : there is no package called ‘ggforce’
> install.packages("ggforce")
......
** inst
** preparing package for lazy loading
Error : object ‘scale_type’ is not exported by 'namespace:ggplot2'
ERROR: lazy loading failed for package ‘ggforce’
* removing ‘/usr/local/SoftWare/Anaconda2/lib/R/library/ggforce’
......

> install.packages("ggplot2")
......
Error : object ‘enexprs’ is not exported by 'namespace:rlang'
ERROR: lazy loading failed for package ‘ggplot2’
......

从 rlang 开始，依次更新 rlang、ggplot2、ggforce 包。

> install.packages("rlang")
trying URL 'http://mirror.lzu.edu.cn/CRAN/src/contrib/rlang_0.2.2.tar.gz'
Content type 'application/octet-stream' length 325128 bytes (317 KB)
==================================================
downloaded 317 KB
......

> install.packages("ggplot2")
trying URL 'http://mirror.lzu.edu.cn/CRAN/src/contrib/ggplot2_3.0.0.tar.gz'
Content type 'application/octet-stream' length 2847050 bytes (2.7 MB)
==================================================
downloaded 2.7 MB
......

> install.packages("ggforce")
trying URL 'http://mirror.lzu.edu.cn/CRAN/src/contrib/ggforce_0.1.3.tar.gz'
Content type 'application/octet-stream' length 1489319 bytes (1.4 MB)
==================================================
downloaded 1.4 MB
......

最后，安装 ggraph，问题解决。

> install.packages("ggraph")
trying URL 'http://mirror.lzu.edu.cn/CRAN/src/contrib/ggraph_1.0.2.tar.gz'
Content type 'application/octet-stream' length 2607278 bytes (2.5 MB)
==================================================
downloaded 2.5 MB
....

> library(ggraph)
Loading required package: ggplot2
>

最后，简单总结一下：

ggraph_1.0.2 安装需要满足两个依赖：R (≥ 2.10), ggplot2 (≥ 2.0.0)。各种包相互依赖调用，根据 log 可定位哪一个包存在问题，然后逐一去解决。

object ‘enexprs’ is not exported by ‘namespace:rlang’，某个包(rlnag)无法加载特定对象(enexprs)可能有两个原因：

• 该包没有安装。

• 该包版本问题，导致目标对象(函数)发生增删处理。

·end·

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