github install issue

[edward130603]

@senbaikang

I'm having some issues installing your latest version.

** libs
using C++ compiler: 'G__~1.EXE (GCC) 13.2.0'
using C++17
g++  -std=gnu++17 -I"C:/Users/zhaoej/AppData/Local/Programs/R/R-44~1.1/include" -DNDEBUG  -I'C:/Users/zhaoej/AppData/Local/Programs/R/R-4.4.1/library/Rcpp/include' -I'C:/Users/zhaoej/AppData/Local/Programs/R/R-4.4.1/library/RcppArmadillo/include' -I'C:/Users/zhaoej/AppData/Local/Programs/R/R-4.4.1/library/RcppDist/include' -I'C:/Users/zhaoej/AppData/Local/Programs/R/R-4.4.1/library/RcppProgress/include'   -I"c:/rtools44/x86_64-w64-mingw32.static.posix/include"  -Iindicators/include -fopenmp   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c RcppExports.cpp -o RcppExports.o
g++  -std=gnu++17 -I"C:/Users/zhaoej/AppData/Local/Programs/R/R-44~1.1/include" -DNDEBUG  -I'C:/Users/zhaoej/AppData/Local/Programs/R/R-4.4.1/library/Rcpp/include' -I'C:/Users/zhaoej/AppData/Local/Programs/R/R-4.4.1/library/RcppArmadillo/include' -I'C:/Users/zhaoej/AppData/Local/Programs/R/R-4.4.1/library/RcppDist/include' -I'C:/Users/zhaoej/AppData/Local/Programs/R/R-4.4.1/library/RcppProgress/include'   -I"c:/rtools44/x86_64-w64-mingw32.static.posix/include"  -Iindicators/include -fopenmp   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c cluster.cpp -o cluster.o
cluster.cpp:12:10: fatal error: indicators/cursor_control.hpp: No such file or directory
   12 | #include <indicators/cursor_control.hpp>
      |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
compilation terminated.
make: *** [C:/Users/zhaoej/AppData/Local/Programs/R/R-44~1.1/etc/x64/Makeconf:296: cluster.o] Error 1
ERROR: compilation failed for package 'BayesSpace'
* removing 'C:/Users/zhaoej/AppData/Local/Programs/R/R-4.4.1/library/BayesSpace'

I have a fresh R and Rtools install so I don't think there's any issues there. Have you tested the package on Windows? I'll look into this more this week if I have time.

[senbaikang]

Hi Edward,

It seems that the indicators package is not downloaded, which should be taken care of in configure file in the root directory. Although I haven't tested the package on Windows, may I ask how you installed it? Can you try remotes::install_github("bdsc-tds/BayesSpace") if you haven't tried it?

Senbai

[edward130603]

I did use that command to install. It works on my linux HPC. On windows I get various warnings and errors.

   Warning: file 'BayesSpace/configure' did not have execute permissions: corrected

   **********************************************
   WARNING: this package has a configure script
         It probably needs manual configuration
   **********************************************
** libs
using C++ compiler: 'G__~1.EXE (GCC) 13.2.0'
using C++17
g++  -std=gnu++17 -I"C:/Users/zhaoej/AppData/Local/Programs/R/R-44~1.1/include" -DNDEBUG  -I'C:/Users/zhaoej/AppData/Local/Programs/R/R-4.4.1/library/Rcpp/include' -I'C:/Users/zhaoej/AppData/Local/Programs/R/R-4.4.1/library/RcppArmadillo/include' -I'C:/Users/zhaoej/AppData/Local/Programs/R/R-4.4.1/library/RcppDist/include' -I'C:/Users/zhaoej/AppData/Local/Programs/R/R-4.4.1/library/RcppProgress/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -Iindicators/include -fopenmp   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c RcppExports.cpp -o RcppExports.o
g++  -std=gnu++17 -I"C:/Users/zhaoej/AppData/Local/Programs/R/R-44~1.1/include" -DNDEBUG  -I'C:/Users/zhaoej/AppData/Local/Programs/R/R-4.4.1/library/Rcpp/include' -I'C:/Users/zhaoej/AppData/Local/Programs/R/R-4.4.1/library/RcppArmadillo/include' -I'C:/Users/zhaoej/AppData/Local/Programs/R/R-4.4.1/library/RcppDist/include' -I'C:/Users/zhaoej/AppData/Local/Programs/R/R-4.4.1/library/RcppProgress/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"  -Iindicators/include -fopenmp   -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c cluster.cpp -o cluster.o
cluster.cpp:12:10: fatal error: indicators/cursor_control.hpp: No such file or directory
   12 | #include <indicators/cursor_control.hpp>
      |          ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
compilation terminated.

Whereas on linux, it correctly cloned indicators as written in configure. From my googling, it seems like we might need a configure.win script as well.

[edward130603]

@senbaikang Can you try the SBK_windows branch? It worked for me on a fresh R/4.4 windows install.

[senbaikang]

Hi Edward, I finally managed to test the installation on my old windows PC. Your fix indeed works. Thanks for fixing it!