R 4.4版本安装退役plyr包失败的解决方法咨询

问题背景 #

将R版本更新至4.4后，大部分包丢失需要重新安装。尽管plyr包已退役，但由于安装phyloseq包依赖它，尝试安装plyr时出现编译错误，错误信息如下：

> install.packages("plyr")
Installing package into ‘/home/sskoldas/R/x86_64-pc-linux-gnu-library/4.4’
(as ‘lib’ is unspecified)
trying URL 'https://cloud.r-project.org/src/contrib/plyr_1.8.9.tar.gz'
Content type 'application/x-gzip' length 401488 bytes (392 KB)
==================================================
downloaded 392 KB

* installing *source* package ‘plyr’ ...
** package ‘plyr’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
g++ -std=gnu++17 -I"/usr/share/R/include" -DNDEBUG  -I'/usr/local/lib/R/site-library/Rcpp/include'     -fpic  -g -O2 -ffile-prefix-map=/build/r-base-H8urij/r-base-4.4.0=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2   -c RcppExports.cpp -o RcppExports.o
In file included from /usr/local/lib/R/site-library/Rcpp/include/Rcpp/routines.h:26,
                 from /usr/local/lib/R/site-library/Rcpp/include/RcppCommon.h:128,
                 from /usr/local/lib/R/site-library/Rcpp/include/Rcpp.h:27,
                 from RcppExports.cpp:4:
/usr/local/lib/R/site-library/Rcpp/include/Rcpp/iostream/Rstreambuf.h: In member function ‘std::streamsize Rcpp::Rstreambuf<OUTPUT>::xsputn(const char*, std::streamsize) [with bool OUTPUT = true; std::streamsize = long int]’:
/usr/local/lib/R/site-library/Rcpp/include/Rcpp/iostream/Rstreambuf.h:53:20: warning: field precision specifier ‘.*’ expects argument of type ‘int’, but argument 2 has type ‘std::streamsize’ {aka ‘long int’} [-Wformat=]
   53 |         Rprintf("%.*s", num, s);
      |                  ~~^~   ~~~
      |                    |    |
      |                    int  std::streamsize {aka ‘long int’}
/usr/local/lib/R/site-library/Rcpp/include/Rcpp/iostream/Rstreambuf.h: In member function ‘std::streamsize Rcpp::Rstreambuf<OUTPUT>::xsputn(const char*, std::streamsize) [with bool OUTPUT = false; std::streamsize = long int]’:
/usr/local/lib/R/site-library/Rcpp/include/Rcpp/iostream/Rstreambuf.h:57:21: warning: field precision specifier ‘.*’ expects argument of type ‘int’, but argument 2 has type ‘std::streamsize’ {aka ‘long int’} [-Wformat=]
   57 |         REprintf("%.*s", num, s);
      |                   ~~^~   ~~~
      |                     |    |
      |                     int  std::streamsize {aka ‘long int’}
In file included from /usr/local/lib/R/site-library/Rcpp/include/RcppCommon.h:181,
                 from /usr/local/lib/R/site-library/Rcpp/include/Rcpp.h:27,
                 from RcppExports.cpp:4:
/usr/local/lib/R/site-library/Rcpp/include/Rcpp/print.h: In function ‘void Rcpp::warningcall(SEXP, const string&)’:
/usr/local/lib/R/site-library/Rcpp/include/Rcpp/print.h:30:19: error: format not a string literal and no format arguments [-Werror=format-security]
   30 |     Rf_warningcall(call, s.c_str());
      |     ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~
cc1plus: some warnings being treated as errors
make: *** [/usr/lib/R/etc/Makeconf:204: RcppExports.o] Error 1
ERROR: compilation failed for package ‘plyr’
* removing ‘/home/sskoldas/R/x86_64-pc-linux-gnu-library/4.4/plyr’
Warning in install.packages :
  installation of package ‘plyr’ had non-zero exit status

The downloaded source packages are in
    ‘/tmp/RtmpWy0Zao/downloaded_packages’

解决办法 #

方法一：临时禁用格式安全编译警告 #

错误核心是编译器将-Wformat-security相关警告当作错误处理，导致编译失败。可以临时修改环境变量关闭该错误检查：

# 设置编译选项，禁用format-security错误
Sys.setenv(CFLAGS="-Wno-error=format-security", CXXFLAGS="-Wno-error=format-security")
# 重新安装plyr
install.packages("plyr")

安装完成后，若不需要保留该设置，可执行Sys.unsetenv(c("CFLAGS", "CXXFLAGS"))恢复默认。

方法二：安装系统二进制包（Linux用户） #

如果是Debian/Ubuntu系列系统，可以直接通过系统包管理器安装预编译好的plyr包，避免编译问题：

sudo apt-get install r-cran-plyr

安装完成后，在R中即可直接加载使用。

方法三：指定安装旧版本（若上述方法失效） #

若新版本plyr在R4.4下兼容性问题无法解决，可以尝试安装适配性更好的旧版本：

# 先安装devtools（若未安装）
install.packages("devtools")
# 安装指定版本的plyr
devtools::install_version("plyr", version = "1.8.8")

内容的提问来源于stack exchange，提问作者Seda Koldas