GNU Guix系统R安装Rcpp/ggplot2时std::__throw_bad_array_new_length错误求助

我在GNU Guix Linux-libre系统中安装了R 4.2.2版本，尝试安装Rcpp包时出现编译错误，提示std::__throw_bad_array_new_length()不是std的成员；安装ggplot2时也触发相同错误（实际是依赖的farver包编译失败）。怀疑系统缺少R依赖的必要包，但不清楚具体是哪个，相关报错及系统环境信息如下：

安装Rcpp时的报错 #

> install.packages("Rcpp")
Installing package into ‘/home/guix/R/x86_64-unknown-linux-gnu-library/4.2’
(as ‘lib’ is unspecified)
--- Please select a CRAN mirror for use in this session ---
trying URL 'https://cloud.r-project.org/src/contrib/Rcpp_1.0.10.tar.gz'
Content type 'application/x-gzip' length 2936173 bytes (2.8 MB)
==================================================
downloaded 2.8 MB

* installing *source* package ‘Rcpp’ ...
** package ‘Rcpp’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
g++ -std=gnu++14 -I"/gnu/store/kjd4gfz8frchb8n4ada2l6nssa9pnin6-r-minimal-4.2.2/lib/R/include" -DNDEBUG -I../inst/include/  -I/usr/local/include   -fpic  -g -O2  -c api.cpp -o api.o
In file included from /gnu/store/fyc3x8nd2ln090y4ng020rvspwl5pc78-gcc-12.2.0/include/c++/x86_64-unknown-linux-gnu/bits/c++allocator.h:33,
                 from /home/guix/.guix-profile/include/c++/bits/allocator.h:46,
                 from /home/guix/.guix-profile/include/c++/unordered_map:40,
                 from ../inst/include/Rcpp/platform/compiler.h:153,
                 from ../inst/include/Rcpp/r/headers.h:62,
                 from ../inst/include/RcppCommon.h:30,
                 from ../inst/include/Rcpp.h:27,
                 from api.cpp:26:
/home/guix/.guix-profile/include/c++/bits/new_allocator.h: In member function ‘_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*)’:
/home/guix/.guix-profile/include/c++/bits/new_allocator.h:125:20: error: ‘__throw_bad_array_new_length’ is not a member of ‘std’; did you mean ‘bad_array_new_length’?
  125 |               std::__throw_bad_array_new_length();
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                    bad_array_new_length
make: *** [/gnu/store/kjd4gfz8frchb8n4ada2l6nssa9pnin6-r-minimal-4.2.2/lib/R/etc/Makeconf:178: api.o] Error 1
ERROR: compilation failed for package ‘Rcpp’
* removing ‘/home/guix/R/x86_64-unknown-linux-gnu-library/4.2/Rcpp’

The downloaded source packages are in
    ‘/tmp/RtmptAJQ9x/downloaded_packages’
Warning message:
In install.packages("Rcpp") :
  installation of package ‘Rcpp’ had non-zero exit status

安装ggplot2时的报错（触发farver包错误） #

* installing *source* package ‘farver’ ...
** package ‘farver’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
g++ -std=gnu++11 -I"/gnu/store/kjd4gfz8frchb8n4ada2l6nssa9pnin6-r-minimal-4.2.2/lib/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -c ColorSpace.cpp -o ColorSpace.o
g++ -std=gnu++11 -I"/gnu/store/kjd4gfz8frchb8n4ada2l6nssa9pnin6-r-minimal-4.2.2/lib/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -c Comparison.cpp -o Comparison.o
g++ -std=gnu++11 -I"/gnu/store/kjd4gfz8frchb8n4ada2l6nssa9pnin6-r-minimal-4.2.2/lib/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -c Conversion.cpp -o Conversion.o
g++ -std=gnu++11 -I"/gnu/store/kjd4gfz8frchb8n4ada2l6nssa9pnin6-r-minimal-4.2.2/lib/R/include" -DNDEBUG   -I/usr/local/include   -fpic  -g -O2  -c encode.cpp -o encode.o
In file included from /gnu/store/fyc3x8nd2ln090y4ng020rvspwl5pc78-gcc-12.2.0/include/c++/x86_64-unknown-linux-gnu/bits/c++allocator.h:33,
                 from /home/guix/.guix-profile/include/c++/bits/allocator.h:46,
                 from /home/guix/.guix-profile/include/c++/unordered_map:40,
                 from encode.h:4,
                 from encode.cpp:1:
/home/guix/.guix-profile/include/c++/bits/new_allocator.h: In member function ‘_Tp* std::__new_allocator<_Tp>::allocate(size_type, const void*)’:
/home/guix/.guix-profile/include/c++/bits/new_allocator.h:125:20: error: ‘__throw_bad_array_new_length’ is not a member of ‘std’; did you mean ‘bad_array_new_length’?
  125 |               std::__throw_bad_array_new_length();
      |                    ^~~~~~~~~~~~~~~~~~~~~~~~~~~~
      |                    bad_array_new_length
make: *** [/gnu/store/kjd4gfz8frchb8n4ada2l6nssa9pnin6-r-minimal-4.2.2/lib/R/etc/Makeconf:178: encode.o] Error 1
ERROR: compilation failed for package ‘farver’
* removing ‘/home/guix/R/x86_64-unknown-linux-gnu-library/4.2/farver’

系统环境信息 #

> sessionInfo()
R version 4.2.2 (2022-10-31)
Platform: x86_64-unknown-linux-gnu (64-bit)
Running under: Guix System

Matrix products: default
BLAS/LAPACK: /gnu/store/xghpgl3fnr603z16vg7hldmpxygriqm2-openblas-0.3.20/lib/libopenblasp-r0.3.20.so

locale:
 [1] LC_CTYPE=en_US.utf8       LC_NUMERIC=C             
 [3] LC_TIME=en_US.utf8        LC_COLLATE=en_US.utf8    
 [5] LC_MONETARY=en_US.utf8    LC_MESSAGES=en_US.utf8   
 [7] LC_PAPER=en_US.utf8       LC_NAME=C                
 [9] LC_ADDRESS=C              LC_TELEPHONE=C           
[11] LC_MEASUREMENT=en_US.utf8 LC_IDENTIFICATION=C      

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

loaded via a namespace (and not attached):
[1] compiler_4.2.2 tools_4.2.2    tcltk_4.2.2   

解决方法 #

1. 使用Guix官方包安装（推荐）
   Guix的包管理系统会自动处理所有依赖，避免环境冲突。直接在终端执行以下命令安装所需R包：

guix install r-rcpp r-ggplot2

安装完成后，启动R即可直接调用这些包。

2. 修复编译环境冲突
   如果坚持要通过R的install.packages安装，需要确保编译环境的一致性：

• 先进入包含R和对应GCC版本的隔离环境：

guix environment r-minimal --ad-hoc gcc-toolchain

• 在该环境中启动R，再执行install.packages("Rcpp")或install.packages("ggplot2")

错误根源是系统中混合了不同路径的C++标准库头文件（系统GCC的头文件和用户profile中的头文件版本不匹配），导致编译器无法找到内部函数std::__throw_bad_array_new_length()。Guix的隔离环境可以彻底解决这类依赖冲突问题。

内容的提问来源于stack exchange，提问作者Давид Пирић