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Question: Install Rsubread in win10, failed, how to proceed?
0
gravatar for Yisong Zhen
4 months ago by
Yisong Zhen200
Yisong Zhen200 wrote:

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

```

ADD COMMENTlink modified 4 months ago by Wei Shi2.7k • written 4 months ago by Yisong Zhen200

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.

ADD REPLYlink written 4 months ago by Yisong Zhen200

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.

ADD REPLYlink written 4 months ago by Martin Morgan ♦♦ 20k
1
gravatar for Martin Morgan
4 months ago by
Martin Morgan ♦♦ 20k
United States
Martin Morgan ♦♦ 20k wrote:

Unfortunately, Rsubread is not supported on Windows. You can see this from it's landing page where the 'platforms' badge indicates only 'some' and the 'Package Archives' section at the bottom of the page indicates no Windows availability.

ADD COMMENTlink written 4 months ago by Martin Morgan ♦♦ 20k
1
gravatar for Wei Shi
4 months ago by
Wei Shi2.7k
Australia
Wei Shi2.7k wrote:

You may run Rsubread on Linux Bash Shell on Windows 10. The Linux Bash Shell is a new feature Microsoft adds to Windows 10. We found Rsubread runs smoothly on this shell.

ADD COMMENTlink written 4 months ago by Wei Shi2.7k
0
gravatar for Gordon Smyth
4 months ago by
Gordon Smyth32k
Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
Gordon Smyth32k wrote:

There's no work-around. To achieve full performance, Rsubread relies on some C tools that not available under Windows.

You really will need something bigger than a personal computer to do read alignments on any scale anyway.

ADD COMMENTlink modified 4 months ago • written 4 months ago by Gordon Smyth32k
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