IRanges missing S4Vectors_defines.h
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@nathan-sheffield-7613
Last seen 15 months ago
University of Virginia

Hi,

I'm trying to install my R package IRangeKernels, which extends IRanges, which you can see/install the code from here:

https://github.com/sheffien/IRangeKernels

I get this error:
 

In file included from IRangeKernels.h:1:0,
                 from R_init_IRangeKernels.c:1:
/home/nsheffield/R/x86_64-pc-linux-gnu-library/3.1/IRanges/include/IRanges_defines.h:18:31: fatal error: S4Vectors_defines.h: No such file or directory
 #include "S4Vectors_defines.h"
                               ^

I guess something changed with IRanges and S4Vectors in the last few months. If I drop the file from

S4Vectors/includes/S4Vectors_defines.h

into:

IRanges/includes/S4Vectors_defines.h

Now my package will compile and install as expected.  Can anyone shed some light on this for me? It looks like I'm not the only one to run into this: https://bitbucket.org/leslielab/chipkernels/issue/2/support-for-iranges-201

-Nathan

sessionInfo()
R version 3.1.3 (2015-03-09)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 14.04.2 LTS

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

 

iranges s4vectors • 1.9k views
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@herve-pages-1542
Last seen 5 days ago
Seattle, WA, United States

Hi sheffien,

It looks like a version mismatch issue to me. Please make sure you keep your packages up-to-date by running biocLite() (with no arguments) on a regular basis. This advice is true for BioC users and developers but for developers it's even more important (they should do it at least twice a week). Also developers should always develop against BioC devel, not BioC release. One last thing: the bioc-devel mailing list is a much better place than this forum to ask questions about package development.

Cheers,

H.

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@Hervé Pagès Thanks for the advice. After updating R, and all bioC stuff with `biocLite()`, I still have the same error on the release version, and also on the devel version. -- I discovered that the issue only happens when I use install_github, but goes away when I clone and install locally, so perhaps it's a  devtools issue.

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@Hervé Pagès  Incidentally, since you're an author of IRanges, would you be interested in accepting a code contribution to add this functionality from IRangeKernels directly into IRanges? It's a small update... Then I wouldn't have to worry about these packing and linking issues... and maybe others will find this useful?

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Hi sheffien,

Not sure what viewMuls does exactly. Could you provide a little bit more details? The README file on github is kind of vague and viewMuls.Rd doesn't describe the returned value and has no example. Thanks,

H.

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