r - “lib64/R/include：没有这样的文件或目录”错误

Question

我最近更新到 R 版本 4.0.0。但是更新后安装新包失败，以“Rcpp”为例。错误消息说“lib64/R/include：没有这样的文件或目录”。实际上，该目录确实存在。

通过在步骤中使用--prefix参数将更新版本安装到与旧版本完全相同的目录中。configure

当我遇到这个问题时，我尝试过并发现：

1. 删除旧版本后将 R-4.0.0 重新安装到同一目录中。但是错误信息仍然存在。
2. 一些包有同样的问题，包括testthat.
3. 有些包没有这个问题，可以成功安装，包括tibble.
4. 回到 R 版本 3.6.1。Rcpp可以成功安装。

谢谢！

> BiocManager::install("Rcpp")
Bioconductor version 3.11 (BiocManager 1.30.10), R 4.0.0 (2020-04-24)
Installing package(s) 'Rcpp'
trying URL 'https://cran.rstudio.com/src/contrib/Rcpp_1.0.4.6.tar.gz'
Content type 'application/x-gzip' length 2751467 bytes (2.6 MB)
==================================================
downloaded 2.6 MB

* installing *source* package 'Rcpp' ...
** package 'Rcpp' successfully unpacked and MD5 sums checked
** using staged installation
** libs
I"/path/to/soft/R/R_soft/lib64/R/include" -DNDEBUG -I../inst/include/  -I/path/to/soft/lib/packages/bzip2-1.0.6/include/ -I/path/to/soft/lib/packages/readline-6.3/include/ -I/path/to/soft/lib/packages/zlib-1.2.8/include/ -I/path/to/soft/lib/packages/curl-7.52.1/include/ -I/path/to/soft/lib/packages/xz-5.2.2/include/ -I/path/to/soft/lib/packages/pcre-8.39/include/ -I/path/to/soft/lib/packages/ncurses-5.8/include/ -I/path/to/soft/lib/packages/pcre2-10.34/include/ -I/path/to/soft/lib/packages/curl-7.52.1/include/     -O3 -mtune=native -march=native -Wno-unused-variable -Wno-unused-function -Wno-macro-redefined -c api.cpp -o api.o
/bin/sh: I/path/to/soft/R/R_soft/lib64/R/include: No such file or directory
make: [api.o] Error 127 (ignored)
I"/path/to/soft/R/R_soft/lib64/R/include" -DNDEBUG -I../inst/include/  -I/path/to/soft/lib/packages/bzip2-1.0.6/include/ -I/path/to/soft/lib/packages/readline-6.3/include/ -I/path/to/soft/lib/packages/zlib-1.2.8/include/ -I/path/to/soft/lib/packages/curl-7.52.1/include/ -I/path/to/soft/lib/packages/xz-5.2.2/include/ -I/path/to/soft/lib/packages/pcre-8.39/include/ -I/path/to/soft/lib/packages/ncurses-5.8/include/ -I/path/to/soft/lib/packages/pcre2-10.34/include/ -I/path/to/soft/lib/packages/curl-7.52.1/include/     -O3 -mtune=native -march=native -Wno-unused-variable -Wno-unused-function -Wno-macro-redefined -c attributes.cpp -o attributes.o
/bin/sh: I/path/to/soft/R/R_soft/lib64/R/include: No such file or directory
make: [attributes.o] Error 127 (ignored)
I"/path/to/soft/R/R_soft/lib64/R/include" -DNDEBUG -I../inst/include/  -I/path/to/soft/lib/packages/bzip2-1.0.6/include/ -I/path/to/soft/lib/packages/readline-6.3/include/ -I/path/to/soft/lib/packages/zlib-1.2.8/include/ -I/path/to/soft/lib/packages/curl-7.52.1/include/ -I/path/to/soft/lib/packages/xz-5.2.2/include/ -I/path/to/soft/lib/packages/pcre-8.39/include/ -I/path/to/soft/lib/packages/ncurses-5.8/include/ -I/path/to/soft/lib/packages/pcre2-10.34/include/ -I/path/to/soft/lib/packages/curl-7.52.1/include/     -O3 -mtune=native -march=native -Wno-unused-variable -Wno-unused-function -Wno-macro-redefined -c barrier.cpp -o barrier.o
/bin/sh: I/path/to/soft/R/R_soft/lib64/R/include: No such file or directory
make: [barrier.o] Error 127 (ignored)
I"/path/to/soft/R/R_soft/lib64/R/include" -DNDEBUG -I../inst/include/  -I/path/to/soft/lib/packages/bzip2-1.0.6/include/ -I/path/to/soft/lib/packages/readline-6.3/include/ -I/path/to/soft/lib/packages/zlib-1.2.8/include/ -I/path/to/soft/lib/packages/curl-7.52.1/include/ -I/path/to/soft/lib/packages/xz-5.2.2/include/ -I/path/to/soft/lib/packages/pcre-8.39/include/ -I/path/to/soft/lib/packages/ncurses-5.8/include/ -I/path/to/soft/lib/packages/pcre2-10.34/include/ -I/path/to/soft/lib/packages/curl-7.52.1/include/     -O3 -mtune=native -march=native -Wno-unused-variable -Wno-unused-function -Wno-macro-redefined -c date.cpp -o date.o
/bin/sh: I/path/to/soft/R/R_soft/lib64/R/include: No such file or directory
make: [date.o] Error 127 (ignored)
I"/path/to/soft/R/R_soft/lib64/R/include" -DNDEBUG -I../inst/include/  -I/path/to/soft/lib/packages/bzip2-1.0.6/include/ -I/path/to/soft/lib/packages/readline-6.3/include/ -I/path/to/soft/lib/packages/zlib-1.2.8/include/ -I/path/to/soft/lib/packages/curl-7.52.1/include/ -I/path/to/soft/lib/packages/xz-5.2.2/include/ -I/path/to/soft/lib/packages/pcre-8.39/include/ -I/path/to/soft/lib/packages/ncurses-5.8/include/ -I/path/to/soft/lib/packages/pcre2-10.34/include/ -I/path/to/soft/lib/packages/curl-7.52.1/include/     -O3 -mtune=native -march=native -Wno-unused-variable -Wno-unused-function -Wno-macro-redefined -c module.cpp -o module.o
/bin/sh: I/path/to/soft/R/R_soft/lib64/R/include: No such file or directory
make: [module.o] Error 127 (ignored)
I"/path/to/soft/R/R_soft/lib64/R/include" -DNDEBUG -I../inst/include/  -I/path/to/soft/lib/packages/bzip2-1.0.6/include/ -I/path/to/soft/lib/packages/readline-6.3/include/ -I/path/to/soft/lib/packages/zlib-1.2.8/include/ -I/path/to/soft/lib/packages/curl-7.52.1/include/ -I/path/to/soft/lib/packages/xz-5.2.2/include/ -I/path/to/soft/lib/packages/pcre-8.39/include/ -I/path/to/soft/lib/packages/ncurses-5.8/include/ -I/path/to/soft/lib/packages/pcre2-10.34/include/ -I/path/to/soft/lib/packages/curl-7.52.1/include/     -O3 -mtune=native -march=native -Wno-unused-variable -Wno-unused-function -Wno-macro-redefined -c rcpp_init.cpp -o rcpp_init.o
/bin/sh: I/path/to/soft/R/R_soft/lib64/R/include: No such file or directory
make: [rcpp_init.o] Error 127 (ignored)
-L/path/to/soft/R/R_soft/lib64/R/lib -L/path/to/soft/lib/packages/xz-5.2.2/lib/ -L/path/to/soft/lib/packages/ncurses-5.8/lib/ -L/path/to/soft/lib/packages/readline-6.3/lib/ -L/path/to/soft/lib/packages/zlib-1.2.8/lib/ -L/path/to/soft/lib/packages/bzip2-1.0.6/lib/ -L/path/to/soft/lib/packages/pcre-8.39/lib/ -L/path/to/soft/lib/packages/pcre2-10.34/lib/ -L/path/to/soft/lib/packages/curl-7.52.1/lib/ -o Rcpp.so api.o attributes.o barrier.o date.o module.o rcpp_init.o -L/path/to/soft/R/R_soft/lib64/R/lib -lR
/bin/sh: line 2: -L/path/to/soft/R/R_soft/lib64/R/lib: No such file or directory
make: *** [Rcpp.so] Error 127
ERROR: compilation failed for package 'Rcpp'
* removing '/path/to/soft/R/R_soft/lib64/R/library/Rcpp'

The downloaded source packages are in
        '/tmp/RtmpM3149V/downloaded_packages'
Updating HTML index of packages in '.Library'
Making 'packages.html' ... done
Old packages: 'KernSmooth', 'MASS', 'boot', 'class', 'foreign', 'nnet',
  'spatial'
Update all/some/none? [a/s/n]: n
Warning message:
In install.packages(...) :
  installation of package 'Rcpp' had non-zero exit status

系统信息如下：

> sessionInfo()
R version 4.0.0 (2020-04-24)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Red Hat Enterprise Linux Server release 6.3 (Santiago)

Matrix products: default
BLAS:   /path/to/soft/R/R_soft/lib64/R/lib/libRblas.so
LAPACK: /path/to/soft/R/R_soft/lib64/R/lib/libRlapack.so

locale:
[1] C

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

loaded via a namespace (and not attached):
[1] compiler_4.0.0

标签： rinstallationupdatesrcpp