R fail to find GSL library while installing package - r

Question

I am installing a package from the Supplementary materials of an academic journal (https://www.degruyter.com/document/doi/10.1515/snde-2012-0064/html?lang=en).
I've set the Windows system environment variables LIB_GSL (as "C:/R/local323") and PATHS (as "C:/rtools40/bin/", "C:/rtools/mingw64/bin", "C:/R/R-4.1.2/bin")
When I run install.packages("/cobreak_0.1.tar.gz", repos=NULL, type="source"), this happens
* 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'
My guess is the issue was in the Makevars.win file. This is what the Makevars looks like
## 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)
Update:
I just found a similar problem here link. However, after following the instruction, I encounter a new error. This time it's a problem with boost
** 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.
I tried to install the "BH" package but the problem still persists.
Does anyone have any ideas on how to fix this?

Answer 1

So I downloaded the zip archive you referenced unpacked it. It contains an R cobreak_0.1.tar.gz which at first glance looks reasonable:
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 <markus.jochmann#ncl.ac.uk>
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
However, when I try to install it on my Linux system it hits a wall over a function sympd() called but not defined:
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$
Fundamentally, I do not understand why you asked this question at StackOverflow. This is published and peer-reviewed work, and you are given a name and address of an author (or if you must a journal editor). I would contact them.
Edit Turns out this is due to 'stale' package sources, a CRAN archive would have that changed. As the documentation for Armadillo shows, the inv(sympd(...)) is no longer available but inv_sympd(). Making that change on two lines allows the package to build and install. No issues for me:
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$
Edit 2: I should add that the package does in fact have undeclared dependencies, for example if wants to link with GNU GSL (i.e. the system library provided for example by the package libgsl-dev on the Ubuntu system I use (and for which I am the Debian maintainer, but that is a side detail)) as well as the one inclusion of the Boost header file you noticed. So in sum this reflects poor on the SNDE journal where editors should have enforced stricter reproducibility rules. These are more common now, thanks in part due to leadership by journals such as JStatSoft (where I help as an Associate Editor) but that was not always the case with older papers. Anyway: you can build this package, you "just" need to learn how to use the GSL on Windows which is documented in the support material for R on Windows.