安装 R 3.5 软件包时 rcpp 编译错误（ubuntu 16.04）答案

【问题标题】：rcpp compiling error when installing R 3.5 packages (ubuntu 16.04)安装 R 3.5 软件包时 rcpp 编译错误（ubuntu 16.04）
【发布时间】：2020-02-13 19:44:30
【问题描述】：

我无法安装 tidyverse 或 devtools，并且收到此错误：

/usr/lib/R/etc/Makeconf:172: recipe for target 'RcppExports.o' failed
make: *** [RcppExports.o] Error 1

例如，这些是 install.packages("tidyverse", dependencies = TRUE) 的结果：

 ^
/usr/lib/R/etc/Makeconf:172: recipe for target 'RcppExports.o' failed
make: *** [RcppExports.o] Error 1
ERROR: compilation failed for package ‘xml2’
* removing ‘/usr/local/lib/R/site-library/xml2’
ERROR: dependency ‘xml2’ is not available for package ‘rvest’
* removing ‘/usr/local/lib/R/site-library/rvest’
ERROR: dependencies ‘rvest’, ‘xml2’ are not available for package ‘tidyverse’
* removing ‘/usr/local/lib/R/site-library/tidyverse’

我的 R 版本：

platform       x86_64-pc-linux-gnu         
arch           x86_64                      
os             linux-gnu                   
system         x86_64, linux-gnu           
status                                     
major          3                           
minor          5.3                         
year           2019                        
month          03                          
day            11                          
svn rev        76217                       
language       R                           
version.string R version 3.5.3 (2019-03-11)
nickname       Great Truth

我尝试安装每个单独的依赖项，但每次都得到相同的错误（有时使用不同的依赖项：rvest、roxygen2、rversions、lintr 等）。我也试过卸载 Rcpp 并重新安装它。我已经尝试更新我的软件包（update.packages（checkBuilt=TRUE，ask=FALSE）。我没有弄乱任何其他设置。这是在具有 2GB RAM 的 Ubuntu 16.04 上运行的。这可能是内存问题吗？做我需要从头开始重新安装吗？

Distributor ID: Ubuntu
Description:    Ubuntu 16.04.6 LTS
Release:    16.04
Codename:   xenial

              total        used        free      shared  buff/cache   available
Mem:           1971         932         653          16         385         830
Swap:           999         518         481

添加信息：我在别处看到有人建议尝试从 github 安装最新版本的 xml2：remotes::install_github("hadley/xml2")

这是我在执行此操作时遇到的错误（类似于之前的错误）：

  ^
   /usr/lib/R/etc/Makeconf:172: recipe for target 'RcppExports.o' failed
   make: *** [RcppExports.o] Error 1
   ERROR: compilation failed for package ‘xml2’
─  removing ‘/tmp/RtmpNcUpLL/Rinst1bbc679e28bc/xml2’
         -----------------------------------
   ERROR: package installation failed
Error: Failed to install 'xml2' from GitHub:
  System command 'R' failed, exit status: 1, stdout + stderr (last 10 lines):
>                  from RcppExports.cpp:4:
> /usr/include/unicode/ucnv.h:585:1: error: ‘unique_ptr’ in namespace ‘std’ does not name a template type
>  U_DEFINE_LOCAL_OPEN_POINTER(LocalUConverterPointer, UConverter, ucnv_close);
>  ^
> /usr/lib/R/etc/Makeconf:172: recipe for target 'RcppExports.o' failed
> make: *** [RcppExports.o] Error 1
> ERROR: compilation failed for package ‘xml2’
> * removing ‘/tmp/RtmpNcUpLL/Rinst1bbc679e28bc/xml2’
>       -----------------------------------
> ERROR: package installation failed
>

R CMD config --all 的结果


CC = gcc -std=gnu99
CFLAGS = -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g
CPICFLAGS = -fpic
CPP = gcc -std=gnu99 -E
CPPFLAGS =
CXX = g++
CXXCPP = g++ -E
CXXFLAGS = -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g
CXXPICFLAGS = -fpic
CXX11 = g++
CXX11STD = -std=gnu++11
CXX11FLAGS = -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g
CXX11PICFLAGS = -fpic
CXX14 = g++
CXX14STD = -std=gnu++14
CXX14FLAGS = -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g
CXX14PICFLAGS = -fpic
CXX98 = g++
CXX98STD = -std=gnu++98
CXX98FLAGS = -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g
CXX98PICFLAGS = -fpic
CXX17 =
CXX17STD =
CXX17FLAGS =
CXX17PICFLAGS =
CXX1X = g++
CXX1XSTD = -std=gnu++11
CXX1XFLAGS = -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g
CXX1XPICFLAGS = -fpic
DYLIB_EXT = .so
DYLIB_LD = gcc -std=gnu99
DYLIB_LDFLAGS = -shared -fopenmp
F77 = gfortran
FFLAGS = -g -O2 -fstack-protector-strong
FPICFLAGS = -fpic
FLIBS = -lgfortran -lm -lquadmath
SAFE_FFLAGS = -g -O2 -fstack-protector-strong -msse2 -mfpmath=sse
FC = gfortran
FCFLAGS = -g -O2 -fstack-protector-strong
FCPICFLAGS = -fpic
OBJC =
OBJCFLAGS =
JAVA = /usr/lib/jvm/default-java/jre/bin/java
JAVAC = /usr/lib/jvm/default-java/bin/javac
JAVAH = /usr/lib/jvm/default-java/bin/javah
JAR = /usr/lib/jvm/default-java/bin/jar
JAVA_HOME = /usr/lib/jvm/default-java
JAVA_LIBS = -L/usr/lib/jvm/default-java/jre/lib/amd64/server -ljvm
JAVA_CPPFLAGS = -I/usr/lib/jvm/default-java/include -I/usr/lib/jvm/default-java/include/linux
LDFLAGS = -Wl,-Bsymbolic-functions -Wl,-z,relro
SHLIB_CFLAGS =
SHLIB_CXXLD = g++
SHLIB_CXXLDFLAGS = -shared
SHLIB_CXX98LD = g++ -std=gnu++98
SHLIB_CXX98LDFLAGS = -shared
SHLIB_CXX11LD = g++ -std=gnu++11
SHLIB_CXX11LDFLAGS = -shared
SHLIB_CXX14LD = g++ -std=gnu++14
SHLIB_CXX14LDFLAGS = -shared
SHLIB_CXX17LD =
SHLIB_CXX17LDFLAGS = -shared
SHLIB_EXT = .so
SHLIB_FFLAGS =
SHLIB_LD = gcc -std=gnu99
SHLIB_LDFLAGS = -shared
SHLIB_FCLD = gfortran
SHLIB_FCLDFLAGS = -shared
SHLIB_CXX1XLD = g++ -std=gnu++11
SHLIB_CXX1XLDFLAGS = -shared
TCLTK_CPPFLAGS = -I/usr/include/tcl8.6 -I/usr/include/tcl8.6
TCLTK_LIBS = -L/usr/lib/x86_64-linux-gnu -ltcl8.6 -L/usr/lib/x86_64-linux-gnu -ltk8.6 -lX11 -lXss -lXext
BLAS_LIBS = -lblas
LAPACK_LIBS = -llapack
MAKE = make
LIBnn = lib
LOCAL_SOFT =
COMPILED_BY =

【问题讨论】：

您的 ubuntu 构建中需要开发库 sudo apt-get install libxml2-dev libssl-dev
谢谢，我应该提到开发库已经安装：libssl-dev 已经是最新版本（1.1.1d-1+ubuntu16.04.1+deb.sury.org+2）。 libxml2-dev 已经是最新版本了（2.9.9+dfsg-1+ubuntu16.04.1+deb.sury.org+2）。
我在上面添加了更多信息以及 R CMD config --all 的结果

标签： r

【解决方案1】：

通过在命令行中执行此操作，我最终能够将 xml2 安装到不同的库目录中：

sudo apt-get install r-cran-xml2

这会将 xml2 安装到 /usr/lib/R/site-library 目录中，而使用 R 和 install.packages 默认安装到 /usr/local/lib/R/site-library 目录中，这就是不工作。

一旦安装了 xml2，它就允许我安装 devtools 并且有点排序解决了我的问题，但是如果我尝试使用 sudo R-->install 安装 tidyverse 或其他几个软件包，我仍然会收到 rcpp 错误。包（“xml2”）。如果有人对此有任何见解并且有任何见解，我很想知道发生了什么！

【讨论】：