Error: Cannot export ++gnu_lto_v1: symbol not defined collect2.exe: error ld returned 1 exit status

[Jesse Wolfhagen]

Hello,

I am trying to install rstan and am continually getting this error that prevents any C++ code (from rstan or the test code snippets) from running correctly. I can't find any straightforward venues to solve this issue outside of the rstan community, so even if you could just point me to the right place that'd be extremely helpful!

I have been following the "RStan Getting Started" guide and have consistently run into the same issue - I have reinstalled everything multiple times and keep hitting a wall here.

This is the output when I try to run the code found at https://github.com/stan-dev/rstan/wiki/RStan-Getting-Started to "Verify that your toolchain works by executing in R":

> fx <- inline::cxxfunction( signature(x = "integer", y = "numeric" ) , '

+ return ScalarReal( INTEGER(x)[0] * REAL(y)[0] ) ;

+                    ' )

Cannot export __gnu_lto_v1: symbol not defined

collect2.exe: error: ld returned 1 exit status

ERROR(s) during compilation: source code errors or compiler configuration errors!

Program source:

  1: 

  2: // includes from the plugin

  3: #include <R.h>

  4: #include <Rdefines.h>

  5: #include <R_ext/Error.h>

  6: 

  7: 

  8: // user includes

  9: 

 10: 

 11: // declarations

 12: extern "C" {

 13: SEXP file24f838966efd( SEXP x, SEXP y) ;

 14: }

 15: 

 16: // definition

 17: 

 18: SEXP file24f838966efd( SEXP x, SEXP y ){

 19: 

 20: return ScalarReal( INTEGER(x)[0] * REAL(y)[0] ) ;

 21:                     

 22: Rf_warning("your C++ program does not return anything"); 

 23:  return R_NilValue ; 

 24: }

 25: 

 26: 

Error in compileCode(f, code, language = language, verbose = verbose) : 

  Compilation ERROR, function(s)/method(s) not created! Cannot export __gnu_lto_v1: symbol not defined

collect2.exe: error: ld returned 1 exit status

The error continues if I blindly ignore reality and then try to use the Stan 8 schools data example.

rstan and all of the related packages install without issues. Their versions:

> packageVersion("rstan")

[1] ‘2.10.1’

> packageVersion("inline")

[1] ‘0.3.14’

> packageVersion("Rcpp")

[1] ‘0.12.5’

> sessionInfo()

R version 3.3.1 (2016-06-21)

Platform: x86_64-w64-mingw32/x64 (64-bit)

Running under: Windows >= 8 x64 (build 9200)

locale:

[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252   

[3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C                          

[5] LC_TIME=English_United States.1252    

attached base packages:

[1] stats     graphics  grDevices utils     datasets  methods   base     

loaded via a namespace (and not attached):

[1] rsconnect_0.4.3 tools_3.3.1     inline_0.3.14

I am using Rtools33 (located in c:/Rtools) - the beginning of my PATH is thus:

> Sys.getenv("PATH")

[1] "C:\\R\\R-3.3.1\\bin\\x64;c:\\Rtools\\bin;c:\\Rtools\\mingw_64\\bin;C:\\ProgramData\\Oracle\\Java\\javapath;C:\\WINDOWS\\system32;C:\\WINDOWS;C:\\WINDOWS\\system32\\wbem;C:\\Program Files (x86)...

My version of g++ is:

> system("g++ --version")

G__~1.EXE (x86_64-posix-seh, Built by MinGW-W64 project) 4.9.3

Copyright (C) 2015 Free Software Foundation, Inc.

This is free software; see the source for copying conditions.  There is NO

warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

Thank you! I am at an archaeological dig and so have limited windows of internet access each day - I would really appreciate any help with this!

[Bob Carpenter]

Does that cxxfunction thing still work? I thought Daniel had
found that the diagnostics no longer worked.

- Bob

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[Ben Goodrich]

On Friday, July 8, 2016 at 1:03:22 PM UTC-4, Bob Carpenter wrote:

Does that cxxfunction thing still work?  I thought Daniel had
found that the diagnostics no longer worked.

It works generally, but the fortran part doesn't unless you have gfortran installed.

I don't know why it is not working in this case but I would suggest to start by taking -flto and -ffat-lto-objects out of the file that is returned by

normalizePath("~/.R/Makevars")

Ben

[Jesse Wolfhagen]

Thank you so much, that worked perfectly! Had to eventually move R to a path without a space after getting a new error (as mentioned in another thread here), but your advice fixed my problem immediately and now rstan appears to be working.

Thanks again!

[Soutik Ghosal]

Hi Jesse , I am having the same problem as you had, but I didn't understand the suggestion by Ben Goodrich. Can someone illustrate a bit ?

[Avraham Adler]

The error "gnu_lto_v1" relates to link-time optimization. By removing "-flto" from Makevars you are no longer asking GCC to perform LTO, so the problem should go away. On Windows, the current gcc is 4.9.3 whose LTO is existent but not a flawless as later versions of GCC and it tends to cause R-related packages to fail.

Avi

[Avraham Adler]

On Saturday, September 10, 2016 at 4:59:26 PM UTC-4, Soutik Ghosal wrote:Hi Jesse , I am having the same problem as you had, but I didn't understand the suggestion by Ben Goodrich. Can someone illustrate a bit ?

On Sunday, September 11, 2016 at 1:29:45 AM UTC-4, Avraham Adler wrote:

The error "gnu_lto_v1" relates to link-time optimization. By removing "-flto" from Makevars you are no longer asking GCC to perform LTO, so the problem should go away. On Windows, the current gcc is 4.9.3 whose LTO is existent but not a flawless as later versions of GCC and it tends to cause R-related packages to fail.

The other option that may work, but will void your warranty, is to go to R_HOME/etc/x64 and edit Makeconf to add "gcc-" in front of AR, NM, and RANLIB. E.g. Change AR = $(BINPREF)ar to AR = $(BINPREF)gcc-ar, and same for NM and RANLIB. In GCC 4.x, only the "gcc-" headed files have scripts that allow them to process LTO properly.

Avi