Error and solutions - xiaolei-lab/rMVP GitHub Wiki

The names of all SNPs must be unique, please check 'BIM' file!

You can use the following code to make sure the SNPs name in the 'BIM' file is unique.

mv snp.filter.bim snp.filter.bim.old
cat snp.filter.bim.old | awk -vOFS='\t' '{print $1,$1"-"$4,$3,$4,$5,$6}' > snp.filter.bim

X11 is not available

R> capabilities()
       jpeg         png        tiff       tcltk         X11        aqua
       TRUE        TRUE        TRUE        TRUE       FALSE       FALSE
   http/ftp     sockets      libxml        fifo      cledit       iconv
       TRUE        TRUE        TRUE        TRUE        TRUE        TRUE
        NLS     profmem       cairo         ICU long.double     libcurl
       TRUE        TRUE        TRUE        TRUE        TRUE        TRUE
  1. install X11 or
  2. set 'bitmapType' to 'cairo' by option(bitmapType = 'cairo')

OpenBLAS Warning : Detect OpenMP Loop and this application may hang. Please rebuild the library with USE_OPENMP=1 option.

OpenBLAS Warning : Detect OpenMP Loop and this application may hang. Please rebuild the library with USE_OPENMP=1 option.
OpenBLAS Warning : Detect OpenMP Loop and this application may hang. Please rebuild the library with USE_OPENMP=1 option.
OpenBLAS Warning : Detect OpenMP Loop and this application may hang. Please rebuild the library with USE_OPENMP=1 option.
OpenBLAS Warning : Detect OpenMP Loop and this application may hang. Please rebuild the library with USE_OPENMP=1 option.
OpenBLAS Warning : Detect OpenMP Loop and this application may hang. Please rebuild the library with USE_OPENMP=1 option.
OpenBLAS Warning : Detect OpenMP Loop and this application may hang. Please rebuild the library with USE_OPENMP=1 option.
address 0x6f0, cause 'memory not mapped'
An irrecoverable exception occurred. R is aborting now ...
OpenBLAS Warning : Detect OpenMP Loop and this application may hang. Please rebuild the library with USE_OPENMP=1 option.

If you encounter a problem similar to the above, it means that the linear algebra backend used by your R conflicts with the parallel strategy of rMVP. You can solve this problem by the following methods

  1. Using Microsoft R Open (https://mran.microsoft.com/open) or
  2. Recompile OpenBLAS and set the compile option USE_OPENMP=1