R 安装包时找不到 GSL 库

Question

我正在安装学术期刊补充材料中的软件包 (https://www.degruyter.com/document/doi/10.1515/snde-2012-0064/html?lang=en）。

我已经设置了 Windows 系统环境变量 LIB_GSL （作为“C:/R/local323”）和 PATHS （作为“C:/rtools40/bin/”、“C:/rtools/mingw64/bin”、“C:/ R/R-4.1.2/bin")

当我运行 install.packages("/cobreak_0.1.tar.gz", repos=NULL, type="source") 时，会发生这种情况

* installing *source* package 'cobreak' ...
** using staged installation
** libs
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/R/R-4.1.2/include" -DNDEBUG  -I'C:/Users/Phat/Documents/R/win-library/4.1/Rcpp/include' -I'C:/Users/Phat/Documents/R/win-library/4.1/RcppArmadillo/include'        -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c cointmdl.cc -o cointmdl.o
In file included from genmdl.h:5,
                 from cointmdl.cc:1:
random_arma.h:4:10: fatal error: gsl/gsl_rng.h: No such file or directory
 #include <gsl/gsl_rng.h>
          ^~~~~~~~~~~~~~~
compilation terminated.
make: *** [C:/R/R-4.1.2/etc/x64/Makeconf:243: cointmdl.o] Error 1
ERROR: compilation failed for package 'cobreak'

我的猜测是问题出在 Makevars.win 文件中。这就是 Makevar 的样子

## This assume that we can call Rscript to ask Rcpp about its locations
## Use the R_HOME indirection to support installations of multiple R version
PKG_LIBS = $(shell $(R_HOME)/bin/Rscript.exe -e "Rcpp:::LdFlags()") $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS)

更新： 我刚刚在这里链接发现了类似的问题。但是，按照说明进行操作后，我遇到了新的错误。这次是 boost 的问题

** libs
C:/rtools40/mingw64/bin/g++  -std=gnu++11 -I"C:/R/R-4.1.2/include" -DNDEBUG -IC:/R/local323/include -I. -I../inst/include -I'C:/Users/Phat/Documents/R/win-library/4.1/Rcpp/include' -I'C:/Users/Phat/Documents/R/win-library/4.1/RcppArmadillo/include'        -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c cointmdl.cc -o cointmdl.o
C:/rtools40/mingw64/bin/g++  -std=gnu++11 -I"C:/R/R-4.1.2/include" -DNDEBUG -IC:/R/local323/include -I. -I../inst/include -I'C:/Users/Phat/Documents/R/win-library/4.1/Rcpp/include' -I'C:/Users/Phat/Documents/R/win-library/4.1/RcppArmadillo/include'        -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c cpp_r_interface.cc -o cpp_r_interface.o
cpp_r_interface.cc:2:10: fatal error: boost/ptr_container/ptr_vector.hpp: No such file or directory
 #include <boost/ptr_container/ptr_vector.hpp>
          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
compilation terminated.

，我尝试安装“BH”包，但问题仍然存在。

有人对如何解决这个问题有任何想法吗？

Answer 1

所以我下载了你引用的 zip 存档并将其解压。它包含一个 R cobreak_0.1.tar.gz 乍一看似乎很合理：

Package: cobreak
Title: Regime-switching cointegration
Description: MCMC estimation of regime-switching cointegration models
Version: 0.1
Date: 2013-12-11
Author: Markus Jochmann
Maintainer: Markus Jochmann <[email protected]>
License: GPL (>= 2)
Depends: Rcpp (>= 0.9.15), RcppArmadillo (>= 0.3.4.3)
LinkingTo: Rcpp, RcppArmadillo
Packaged: 2013-12-11 16:03:39 UTC; markus

但是，当我尝试将它安装到我的 Linux 系统上时，它遇到了函数 sympd() 的问题 已调用但未定义：

edd@rob:~/Downloads/regimeswitchcoint/cobreak$ install.r .
* installing *source* package ‘cobreak’ ...
** using staged installation
** libs
ccache g++-11 -I"/usr/share/R/include" -DNDEBUG  -I'/usr/local/lib/R/site-library/Rcpp/include' -I'/usr/local/lib/R/site-library/RcppArmadillo/include'    -fpic  -g -O3 -Wall -pipe -pedantic  -c cointmdl.cc -o cointmdl.o
ccache g++-11 -I"/usr/share/R/include" -DNDEBUG  -I'/usr/local/lib/R/site-library/Rcpp/include' -I'/usr/local/lib/R/site-library/RcppArmadillo/include'    -fpic  -g -O3 -Wall -pipe -pedantic  -c cpp_r_interface.cc -o cpp_r_interface.o
ccache g++-11 -I"/usr/share/R/include" -DNDEBUG  -I'/usr/local/lib/R/site-library/Rcpp/include' -I'/usr/local/lib/R/site-library/RcppArmadillo/include'    -fpic  -g -O3 -Wall -pipe -pedantic  -c dist_arma.cc -o dist_arma.o
dist_arma.cc: In function ‘double logpdfmn(const vec&, const mat&)’:
dist_arma.cc:52:37: error: ‘sympd’ was not declared in this scope
   52 |   result -= as_scalar( x.t() * inv( sympd( Sigma ) ) * x );
      |                                     ^~~~~
dist_arma.cc: In function ‘double logpdfmn(const vec&, const vec&, const mat&)’:
dist_arma.cc:62:39: error: ‘sympd’ was not declared in this scope
   62 |   result -= as_scalar( xmm.t() * inv( sympd( Sigma ) ) * xmm );
      |                                       ^~~~~
make: *** [/usr/lib/R/etc/Makeconf:175: dist_arma.o] Error 1
ERROR: compilation failed for package ‘cobreak’
* removing ‘/usr/local/lib/R/site-library/cobreak’
Warning message:
In install.packages(pkgs = f, lib = lib, repos = if (isMatchingFile(f)) NULL else repos) :
  installation of package ‘.’ had non-zero exit status
edd@rob:~/Downloads/regimeswitchcoint/cobreak$ 

从根本上讲，我不明白您为什么在 StackOverflow 上问这个问题。这是已发表并经过同行评审的作品，并且您会获得作者的姓名和地址（或者如果您必须是期刊编辑）。我会联系他们。

编辑 事实证明，这是由于“过时”的软件包源造成的，CRAN 存档会对此进行更改。正如犰狳文档所示，inv(sympd(...)) 不再可用，但 inv_sympd() 可用。在两行中进行更改允许构建和安装包。对我来说没有问题：

edd@rob:~/Downloads/regimeswitchcoint/cobreak$ install.r .
* installing *source* package ‘cobreak’ ...
** using staged installation
** libs
ccache g++-11 -I"/usr/share/R/include" -DNDEBUG  -I'/usr/local/lib/R/site-library/Rcpp/include' -I'/usr/local/lib/R/site-library/RcppArmadillo/include'    -fpic  -g -O3 -Wall -pipe -pedantic  -c dist_arma.cc -o dist_arma.o
ccache g++-11 -I"/usr/share/R/include" -DNDEBUG  -I'/usr/local/lib/R/site-library/Rcpp/include' -I'/usr/local/lib/R/site-library/RcppArmadillo/include'    -fpic  -g -O3 -Wall -pipe -pedantic  -c ext_arma.cc -o ext_arma.o
ccache g++-11 -I"/usr/share/R/include" -DNDEBUG  -I'/usr/local/lib/R/site-library/Rcpp/include' -I'/usr/local/lib/R/site-library/RcppArmadillo/include'    -fpic  -g -O3 -Wall -pipe -pedantic  -c genmdl.cc -o genmdl.o
ccache g++-11 -I"/usr/share/R/include" -DNDEBUG  -I'/usr/local/lib/R/site-library/Rcpp/include' -I'/usr/local/lib/R/site-library/RcppArmadillo/include'    -fpic  -g -O3 -Wall -pipe -pedantic  -c markovmdl.cc -o markovmdl.o
markovmdl.cc: In member function ‘void MarkovMdl::logisdXi(const mat&, arma::vec&)’:
markovmdl.cc:218:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const uword’ {aka ‘const unsigned int’} [-Wsign-compare]
  218 |   for( int l=0; l<logp.n_elem; l++ )
      |                 ~^~~~~~~~~~~~
markovmdl.cc: In member function ‘void MarkovMdl::save_parmem(arma::mat&, arma::mat&, arma::mat&, arma::mat&, arma::mat&, arma::mat&, arma::mat&, arma::mat&, arma::mat&, arma::imat&)’:
markovmdl.cc:521:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<arma::Mat<double> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  521 |   for( int i=0; i<ximem.size(); i++ )
      |                 ~^~~~~~~~~~~~~
markovmdl.cc: In member function ‘void MarkovMdl::save_parmem(arma::mat&, arma::mat&, arma::mat&, arma::mat&, arma::mat&, arma::mat&, arma::mat&, arma::mat&, arma::mat&, arma::mat&, arma::mat&, arma::mat&, arma::mat&, arma::imat&)’:
markovmdl.cc:547:18: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<arma::Mat<double> >::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
  547 |   for( int i=0; i<ximem.size(); i++ )
      |                 ~^~~~~~~~~~~~~
ccache g++-11 -I"/usr/share/R/include" -DNDEBUG  -I'/usr/local/lib/R/site-library/Rcpp/include' -I'/usr/local/lib/R/site-library/RcppArmadillo/include'    -fpic  -g -O3 -Wall -pipe -pedantic  -c mvlinmdl.cc -o mvlinmdl.o
ccache g++-11 -I"/usr/share/R/include" -DNDEBUG  -I'/usr/local/lib/R/site-library/Rcpp/include' -I'/usr/local/lib/R/site-library/RcppArmadillo/include'    -fpic  -g -O3 -Wall -pipe -pedantic  -c random_arma.cc -o random_arma.o
ccache g++-11 -Wl,-S -shared -L/usr/lib/R/lib -Wl,-Bsymbolic-functions -flto=auto -Wl,-z,relro -o cobreak.so cointmdl.o cpp_r_interface.o dist_arma.o ext_arma.o genmdl.o markovmdl.o mvlinmdl.o random_arma.o -llapack -lblas -lgfortran -lm -lquadmath -lgsl -L/usr/lib/R/lib -lR
installing to /usr/local/lib/R/site-library/00LOCK-cobreak/00new/cobreak/libs
** R
** data
** byte-compile and prepare package for lazy loading
** help
No man pages found in package  ‘cobreak’ 
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (cobreak)
edd@rob:~/Downloads/regimeswitchcoint/cobreak$ 

编辑2：我应该补充一点，该包实际上确实具有未声明的依赖项，例如，如果想要与 GNU GSL 链接（即由包提供的系统库libgsl-dev （我是 Debian 维护者，但这是一个侧面细节））以及您注意到的 Boost 头文件的一个包含内容。总而言之，这反映了 SNDE 期刊的糟糕状况，编辑们应该执行更严格的再现性规则。这些现在更加常见，部分归功于 JStatSoft（我在其中担任副编辑）等期刊的领导，但旧论文的情况并非总是如此。无论如何：您可以构建这个包，您“只”需要学习如何在 Windows 上使用 GSL，这在 Windows 上的 R 支持材料中进行了记录。