Dear Bioconductor users,
Following is the error message, and I think the rsubread uses the sys/ioctl.h. But the current Rtools failed to find the corresponding library in its compling tool. Do I need extra step to provide any location information to C library?
Any suggestions are apprecaited.
My Rtools is its most update version (Rtools3.4)
R is the most updated version 'single candle'
sessionInfo()
R version 3.4.1 (2017-06-30)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows >= 8 x64 (build 9200)
Matrix products: default
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
other attached packages:
[1] BiocInstaller_1.26.0
loaded via a namespace (and not attached):
[1] compiler_3.4.1 tools_3.4.1
Thrown-out error:
```
** libs
c:/Rtools/mingw_64/bin/gcc -I"D:/Program/R-3.4.1/include" -DNDEBUG -I"d:/Compiler/gcc-4.9.3/local330/include" -DMAKE_FOR_EXON -D SUBREAD_VERSION="\"Rsubread 1.26.0\"" -O2 -Wall -std=gnu99 -mtune=core2 -c HelperFunctions.c -o HelperFunctions.o
HelperFunctions.c:39:23: fatal error: sys/ioctl.h: No such file or directory
#include <sys/ioctl.h>
^
compilation terminated.
make: *** [HelperFunctions.o] Error 1
```
Thanks, @Gordon & @Martin. I tried to downsample my rawdata and use the same code to process them at the server side. This seems to be a dead-end.
Why downsample? That doesn't sound like the right approach, just do the summary on the full data.
For what it's worth,
GenomicAlignments::summarizeOverlaps() will work across platforms (although not as performant / robust) as Rsubread.