Question: Install Rsubread in win10, failed, how to proceed?
0
gravatar for Yisong Zhen
2.3 years 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

```

rsubread windows10 rtools • 1.2k views
ADD COMMENTlink modified 4 weeks ago by Yang Liao130 • written 2.3 years 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 2.3 years 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 2.3 years ago by Martin Morgan ♦♦ 23k
Answer: Install Rsubread in win10, failed, how to proceed?
1
gravatar for Martin Morgan
2.3 years ago by
Martin Morgan ♦♦ 23k
United States
Martin Morgan ♦♦ 23k 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 2.3 years ago by Martin Morgan ♦♦ 23k
Answer: Install Rsubread in win10, failed, how to proceed?
1
gravatar for Wei Shi
2.3 years ago by
Wei Shi3.2k
Australia
Wei Shi3.2k 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 2.3 years ago by Wei Shi3.2k
Answer: Install Rsubread in win10, failed, how to proceed?
0
gravatar for Gordon Smyth
2.3 years ago by
Gordon Smyth38k
Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia
Gordon Smyth38k wrote:

Edit 29 August 2019

Rsubread finally become available for Windows starting version 1.99.0.

ADD COMMENTlink modified 7 weeks ago • written 2.3 years ago by Gordon Smyth38k
Answer: Install Rsubread in win10, failed, how to proceed?
0
gravatar for Yang Liao
4 weeks ago by
Yang Liao130
Australia
Yang Liao130 wrote:

Hi Yisong,

The Rsubread package now supports Windows (64-bit) platforms. This includes the 64-bit Windows 10. Please follow the instructions on

https://bioconductor.org/packages/release/bioc/html/Rsubread.html

to install Rsubread on a Windows (64-bit) computer. It is recommended to run Rsubread on a computer with at least 16GB of memory.

Cheers, Yang

ADD COMMENTlink written 4 weeks ago by Yang Liao130
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