Failing to compile R package from source

[gavinsimpson]

I am running into errors when building the filzback R package from source, specifically an error is thrown during R CMD check filzbach_1.2-1.tar.gz when trying to install the package for checking. The error I am seeing is for example using build.sh, but I see the same when I build outside the R source tree:

* checking for file ‘filzbach/DESCRIPTION’ ... OK
* preparing ‘filzbach’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* checking for LF line-endings in source and make files
* checking for empty or unneeded directories
* building ‘filzbach_1.2-1.tar.gz’

* using log directory ‘/home/gavin/work/git/filzbach/src/R/filzbach.Rcheck’
* using R version 3.2.3 Patched (2015-12-10 r69760)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* checking for file ‘filzbach/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘filzbach’ version ‘1.2-1’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘filzbach’ can be installed ... ERROR
Installation failed.
See ‘/home/gavin/work/git/filzbach/src/R/filzbach.Rcheck/00install.out’ for details.
* DONE

Status: 1 ERROR
See
  ‘/home/gavin/work/git/filzbach/src/R/filzbach.Rcheck/00check.log’
for details.

The log in 00install.out contains:

$ cat filzbach.Rcheck/00install.out 
* installing *source* package ‘filzbach’ ...
** libs
ccache g++ -std=c++11 -I/home/gavin/R/build/3.2-patched/include -DNDEBUG -DFILZBACH_LIB -I/usr/local/include    -fpic  -ggdb -O2 -m64 -pipe -Wall -pedantic -mtune=native -c catherine_loader.cpp -o catherine_loader.o
ccache g++ -std=c++11 -I/home/gavin/R/build/3.2-patched/include -DNDEBUG -DFILZBACH_LIB -I/usr/local/include    -fpic  -ggdb -O2 -m64 -pipe -Wall -pedantic -mtune=native -c filzbachR.cpp -o filzbachR.o
ccache g++ -std=c++11 -I/home/gavin/R/build/3.2-patched/include -DNDEBUG -DFILZBACH_LIB -I/usr/local/include    -fpic  -ggdb -O2 -m64 -pipe -Wall -pedantic -mtune=native -c metropolis.cpp -o metropolis.o
metropolis.cpp:98:0: warning: ignoring #pragma omp threadprivate [-Wunknown-pragmas]
 #pragma omp threadprivate(currentchain)
 ^
metropolis.cpp:102:0: warning: ignoring #pragma omp threadprivate [-Wunknown-pragmas]
 #pragma omp threadprivate(metr_k)
 ^
metropolis.cpp:182:0: warning: ignoring #pragma warning  [-Wunknown-pragmas]
 #pragma warning(push)
 ^
metropolis.cpp:183:0: warning: ignoring #pragma warning  [-Wunknown-pragmas]
 #pragma warning(disable:4996)
 ^
metropolis.cpp:185:0: warning: ignoring #pragma warning  [-Wunknown-pragmas]
 #pragma warning(pop)
 ^
metropolis.cpp:856:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
   #pragma omp parallel for /* reduction(+:ltotnew_currentchain)*/
 ^
metropolis.cpp:1705:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
  #pragma omp parallel for
 ^
metropolis.cpp:1869:0: warning: ignoring #pragma omp critical [-Wunknown-pragmas]
     #pragma omp critical
 ^
metropolis.cpp:2041:0: warning: ignoring #pragma omp critical [-Wunknown-pragmas]
 #pragma omp critical
 ^
metropolis.cpp:2113:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
  #pragma omp parallel for
 ^
metropolis.cpp:2146:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
  #pragma omp parallel for
 ^
In file included from metropolis.cpp:3:0:
dwp_stats.h:8:22: error: declaration of ‘double gamma(double)’ has a different exception specifier
 double gamma(double x);
                      ^
In file included from /usr/include/math.h:69:0,
                 from /usr/include/c++/5.3.1/cmath:44,
                 from stdafx.h:17,
                 from metropolis.cpp:1:
/usr/include/bits/mathcalls.h:264:15: error: from previous declaration ‘double gamma(double) throw ()’
 __MATHCALL (gamma,, (_Mdouble_));
               ^
metropolis.cpp: In function ‘int _mkdir(const char*)’:
metropolis.cpp:14:62: warning: no return statement in function returning non-void [-Wreturn-type]
 inline int _mkdir(const char* dirname){ mkdir(dirname, 0777);}
                                                              ^
metropolis.cpp: In function ‘void executeLikelihood()’:
metropolis.cpp:824:10: warning: unused variable ‘ltotnew_currentchain’ [-Wunused-variable]
   double ltotnew_currentchain=0.0;
          ^
metropolis.cpp: In function ‘void calc_IC()’:
metropolis.cpp:1438:9: warning: unused variable ‘pD’ [-Wunused-variable]
  double pD = dmean_sum1 - datmean;
         ^
/home/gavin/R/build/3.2-patched/etc/Makeconf:141: recipe for target 'metropolis.o' failed
make: *** [metropolis.o] Error 1
ccache g++ -std=c++11 -I/home/gavin/R/build/3.2-patched/include -DNDEBUG -DFILZBACH_LIB -I/usr/local/include    -fpic  -ggdb -O2 -m64 -pipe -Wall -pedantic -mtune=native -c metropolis.cpp -o metropolis.o
metropolis.cpp:98:0: warning: ignoring #pragma omp threadprivate [-Wunknown-pragmas]
 #pragma omp threadprivate(currentchain)
 ^
metropolis.cpp:102:0: warning: ignoring #pragma omp threadprivate [-Wunknown-pragmas]
 #pragma omp threadprivate(metr_k)
 ^
metropolis.cpp:182:0: warning: ignoring #pragma warning  [-Wunknown-pragmas]
 #pragma warning(push)
 ^
metropolis.cpp:183:0: warning: ignoring #pragma warning  [-Wunknown-pragmas]
 #pragma warning(disable:4996)
 ^
metropolis.cpp:185:0: warning: ignoring #pragma warning  [-Wunknown-pragmas]
 #pragma warning(pop)
 ^
metropolis.cpp:856:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
   #pragma omp parallel for /* reduction(+:ltotnew_currentchain)*/
 ^
metropolis.cpp:1705:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
  #pragma omp parallel for
 ^
metropolis.cpp:1869:0: warning: ignoring #pragma omp critical [-Wunknown-pragmas]
     #pragma omp critical
 ^
metropolis.cpp:2041:0: warning: ignoring #pragma omp critical [-Wunknown-pragmas]
 #pragma omp critical
 ^
metropolis.cpp:2113:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
  #pragma omp parallel for
 ^
metropolis.cpp:2146:0: warning: ignoring #pragma omp parallel [-Wunknown-pragmas]
  #pragma omp parallel for
 ^
In file included from metropolis.cpp:3:0:
dwp_stats.h:8:22: error: declaration of ‘double gamma(double)’ has a different exception specifier
 double gamma(double x);
                      ^
In file included from /usr/include/math.h:69:0,
                 from /usr/include/c++/5.3.1/cmath:44,
                 from stdafx.h:17,
                 from metropolis.cpp:1:
/usr/include/bits/mathcalls.h:264:15: error: from previous declaration ‘double gamma(double) throw ()’
 __MATHCALL (gamma,, (_Mdouble_));
               ^
metropolis.cpp: In function ‘int _mkdir(const char*)’:
metropolis.cpp:14:62: warning: no return statement in function returning non-void [-Wreturn-type]
 inline int _mkdir(const char* dirname){ mkdir(dirname, 0777);}
                                                              ^
metropolis.cpp: In function ‘void executeLikelihood()’:
metropolis.cpp:824:10: warning: unused variable ‘ltotnew_currentchain’ [-Wunused-variable]
   double ltotnew_currentchain=0.0;
          ^
metropolis.cpp: In function ‘void calc_IC()’:
metropolis.cpp:1438:9: warning: unused variable ‘pD’ [-Wunused-variable]
  double pD = dmean_sum1 - datmean;
         ^
/home/gavin/R/build/3.2-patched/etc/Makeconf:141: recipe for target 'metropolis.o' failed
make: *** [metropolis.o] Error 1
ERROR: compilation failed for package ‘filzbach’
* removing ‘/home/gavin/work/git/filzbach/filzbach.Rcheck/filzbach’

This is on (Fedora) Linux with

> version
               _                                          
platform       x86_64-pc-linux-gnu                        
arch           x86_64                                     
os             linux-gnu                                  
system         x86_64, linux-gnu                          
status         Patched                                    
major          3                                          
minor          2.3                                        
year           2015                                       
month          12                                         
day            10                                         
svn rev        69760                                      
language       R                                          
version.string R version 3.2.3 Patched (2015-12-10 r69760)
nickname       Wooden Christmas-Tree

[vassilyl]

@gavinsimpson which g++ version do you have (g++ --version)?

[gavinsimpson]

@vassilyl my GCC tool chain is v 5.3.1

$ g++ --version
g++ (GCC) 5.3.1 20151207 (Red Hat 5.3.1-2)

The definition that seems to be clashing and causing the error is supplied in the glibc library, which is v 2.21-8.fc22.

Let me know if you need anything further.

[vassilyl]

@gavinsimpson I failed to reproduce the error you mentioned. On my fresh Fedora 23 system with R 3.2.3 and gcc 5.3.1 the package sets up without errors. Can you please try install on your system the source package 1.2-2 from the latest release v1.2-beta2?