compilation failed

[eduardszoecs]

During installation I get the error message:

g++ -I/usr/share/R/include -DNDEBUG -I/home/user/RDKit/Code  -I/usr/lib64  -I"/home/user/R/library/Rcpp/include"   -fpic  -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -c rcpp_rdkit_ws.cpp -o rcpp_rdkit_ws.o

rcpp_rdkit_ws.cpp: In function ‘void p_writeSdf(std::string, SEXP, bool)’:
rcpp_rdkit_ws.cpp:243:5: error: ‘RDKit::SDWriter::SDWriter’ names the constructor, not the type
     SDWriter::SDWriter  sdw  = SDWriter::SDWriter(file); 
     ^
rcpp_rdkit_ws.cpp:243:25: error: expected ‘;’ before ‘sdw’
     SDWriter::SDWriter  sdw  = SDWriter::SDWriter(file); 
                         ^
rcpp_rdkit_ws.cpp:243:56: error: statement cannot resolve address of overloaded function
     SDWriter::SDWriter  sdw  = SDWriter::SDWriter(file); 
                                                        ^
rcpp_rdkit_ws.cpp:244:5: error: ‘sdw’ was not declared in this scope
     sdw.setForceV3000(setForceV3000);
     ^
make: *** [rcpp_rdkit_ws.o] Error 1
ERROR: compilation failed for package ‘rrdkit’
* removing ‘/home/user/R/library/rrdkit’
Error: Command failed (1)

Any Ideas how to fix?

> sessionInfo()
R version 3.3.1 (2016-06-21)
Platform: i686-pc-linux-gnu (32-bit)
Running under: Ubuntu 14.04.5 LTS

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=de_DE.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=de_DE.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=de_DE.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

loaded via a namespace (and not attached):
[1] httr_1.2.1      R6_2.1.3        tools_3.3.1     withr_1.0.2    
[5] curl_2.1        memoise_1.0.0   git2r_0.15.0    digest_0.6.10  
[9] devtools_1.12.0

> Sys.info()
                                             sysname 
                                             "Linux" 
                                             release 
                                 "3.16.0-38-generic" 
                                             version 
"#52~14.04.1-Ubuntu SMP Fri May 8 09:44:48 UTC 2015" 
                                            nodename 
                               "user-OptiPlex-GX280" 
                                             machine 
                                              "i686" 
                                               login 
                                              "user" 
                                                user 
                                              "user" 
                                      effective_user 
                                              "user" 

[pauca]

which RDKit version are you using?

2016-09-28 10:36 GMT+02:00 Eduard Szöcs notifications@github.com:

During installation I get the error message:

g++ -I/usr/share/R/include -DNDEBUG -I/home/user/RDKit/Code -I/usr/lib64 -I"/home/user/R/library/Rcpp/include" -fpic -g -O2 -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g -c rcpp_rdkit_ws.cpp -o rcpp_rdkit_ws.o rcpp_rdkit_ws.cpp: In function ‘void p_writeSdf(std::string, SEXP, bool)’:rcpp_rdkit_ws.cpp:243:5: error: ‘RDKit::SDWriter::SDWriter’ names the constructor, not the type SDWriter::SDWriter sdw = SDWriter::SDWriter(file); ^rcpp_rdkit_ws.cpp:243:25: error: expected ‘;’ before ‘sdw’ SDWriter::SDWriter sdw = SDWriter::SDWriter(file); ^rcpp_rdkit_ws.cpp:243:56: error: statement cannot resolve address of overloaded function SDWriter::SDWriter sdw = SDWriter::SDWriter(file); ^rcpp_rdkit_ws.cpp:244:5: error: ‘sdw’ was not declared in this scope sdw.setForceV3000(setForceV3000); ^make: ** [rcpp_rdkit_ws.o] Error 1ERROR: compilation failed for package ‘rrdkit’\ removing ‘/home/user/R/library/rrdkit’Error: Command failed (1)

Any Ideas how to fix?

sessionInfo() R version 3.3.1 (2016-06-21) Platform: i686-pc-linux-gnu (32-bit) Running under: Ubuntu 14.04.5 LTS

locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=de_DE.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=de_DE.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=de_DE.UTF-8 LC_IDENTIFICATION=C

attached base packages: [1] stats graphics grDevices utils datasets methods base

loaded via a namespace (and not attached): [1] httr_1.2.1 R6_2.1.3 tools_3.3.1 withr_1.0.2 [5] curl_2.1 memoise_1.0.0 git2r_0.15.0 digest_0.6.10 [9] devtools_1.12.0

Sys.info() sysname "Linux" release "3.16.0-38-generic" version "#52~14.04.1-Ubuntu SMP Fri May 8 09:44:48 UTC 2015" nodename "user-OptiPlex-GX280" machine "i686" login "user" user "user" effective_user "user"

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[eduardszoecs]

The newest from here (Release_2016.03.4). I got this error independently on two machines (both Linux, with same RDKit, but different architecture and distribution)

With the suggested fix I can run rrdkit from the command line. [Can't run it from RStudio because of a problem with LD_LIBRARY_PATH]

[pauca]

Solution merged