Install Rsubread in win10, failed, how to proceed?
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0
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Yisong Zhen ▴ 200
@yisong-zhen-2952
Last seen 4.1 years ago

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 • 1.5k views
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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.

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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.

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@martin-morgan-1513
Last seen 11 days ago
United States

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.

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Wei Shi ★ 3.3k
@wei-shi-2183
Last seen 2 days ago
Australia/Melbourne/Olivia Newton-John …

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.

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@gordon-smyth
Last seen 9 hours ago
WEHI, Melbourne, Australia

Edit 29 August 2019

Rsubread finally become available for Windows starting version 1.99.0.

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Yang Liao ▴ 260
@yang-liao-6075
Last seen 19 days ago
Australia

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

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