failed installation

[Faber81]

Hi my DECoN installation fails in Ubuntu. Below the output of setup.log:

Please help

`* installing source package ‘packrat’ ...
** package ‘packrat’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path

• DONE (packrat)
  Installing BiocGenerics (0.12.1) ... OK (built source)
  Installing DBI (0.3.1) ... OK (built source)
  Installing R.methodsS3 (1.7.0) ... OK (built source)
  Installing R6 (2.0.1) ... OK (built source)
  Installing RColorBrewer (1.1-2) ... OK (built source)
  Installing RJSONIO (1.3-0) ... OK (built source)
  Installing Rcpp (0.11.6) ... [1] "Command failed (1)\n\nFailed to run system command:\n\n\t'/usr/lib/R/bin/R' --vanilla CMD INSTALL '/tmp/Rtmp2tJxun/Rcpp' --library='/home/faber/BioIT/tools/DECoN-1.0.1/Linux/packrat/lib/x86_64-pc-linux-gnu/3.6.3' --install-tests --no-docs --no-multiarch --no-demo \n\nThe command failed with output:\n* installing source package 'Rcpp' ...\n** package 'Rcpp' successfully unpacked and MD5 sums checked\n** using staged installation\n** libs\ng++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I../inst/include/ -fpic -g -O2 -fdebug-prefix-map=/build/r-base-V28x5H/r-base-3.6.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c Date.cpp -o Date.o\nIn file included from ../inst/include/Rcpp/Module.h:335:0,\n from ../inst/include/Rcpp.h:64,\n from Date.cpp:31:\n../inst/include/Rcpp/module/Module_Property.h:103:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]\n void set(Class* object, SEXP value) throw(std::range_error,Rcpp::not_compatible){\n ^~~~~\n../inst/include/Rcpp/module/Module_Property.h:161:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]\n void set(Class* object, SEXP value) throw(std::range_error,Rcpp::not_compatible){\n ^~~~~\nIn file included from ../inst/include/Rcpp.h:73:0,\n from Date.cpp:31:\n../inst/include/Rcpp/Rmath.h: In function 'double R::pythag(double, double)':\n../inst/include/Rcpp/Rmath.h:222:57: error: '::Rf_pythag' has not been declared\n inline double pythag(double a, double b) { return ::Rf_pythag(a, b); }\n ^~~~~~~~~\n../inst/include/Rcpp/Rmath.h:222:57: note: suggested alternative: 'pythag'\n inline double pythag(double a, double b) { return ::Rf_pythag(a, b); }\n ^~~~~~~~~\n pythag\n/usr/lib/R/etc/Makeconf:177: recipe for target 'Date.o' failed\nmake: *** [Date.o] Error 1\nERROR: compilation failed for package 'Rcpp'\n* removing '/home/faber/BioIT/tools/DECoN-1.0.1/Linux/packrat/lib/x86_64-pc-linux-gnu/3.6.3/Rcpp'"
  Error: Command failed (1)

Failed to run system command:

'/usr/lib/R/bin/R' --vanilla CMD INSTALL '/tmp/Rtmp2tJxun/Rcpp' --library='/home/faber/BioIT/tools/DECoN-1.0.1/Linux/packrat/lib/x86_64-pc-linux-gnu/3.6.3' --install-tests --no-docs --no-multiarch --no-demo 

The command failed with output:

• installing source package 'Rcpp' ...
  ** package 'Rcpp' successfully unpacked and MD5 sums checked
  ** using staged installation
  ** libs
  g++ -std=gnu++11 -I"/usr/share/R/include" -DNDEBUG -I../inst/include/ -fpic -g -O2 -fdebug-prefix-map=/build/r-base-V28x5H/r-base-3.6.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c Date.cpp -o Date.o
  In file included from ../inst/include/Rcpp/Module.h:335:0,
  from ../inst/include/Rcpp.h:64,
  from Date.cpp:31:
  ../inst/include/Rcpp/module/Module_Property.h:103:41: warning: dynamic exception specifications are deprecated in C++11 [-Wdeprecated]
  void set(Class* obj
  In addition: There were 15 warnings (use warnings() to see them)
  Execution halted
  `

[tgurbich]

Hi,

I had the same error when using R 3.6.1. It looks like DECoN requires an earlier version of R (according to their documentation, 3.1.2).

I installed 3.1.2, modified the setup.sh file by adding the path to Rscript version 3.1.2, ran it again and this error was gone.