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Question: IRanges missing S4Vectors_defines.h
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gravatar for Nathan Sheffield
2.7 years ago by
University of Virginia
Nathan Sheffield10 wrote:

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

 

ADD COMMENTlink modified 2.7 years ago by Hervé Pagès ♦♦ 13k • written 2.7 years ago by Nathan Sheffield10
1
gravatar for Hervé Pagès
2.7 years ago by
Hervé Pagès ♦♦ 13k
United States
Hervé Pagès ♦♦ 13k wrote:

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.

ADD COMMENTlink written 2.7 years ago by Hervé Pagès ♦♦ 13k

@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.

ADD REPLYlink written 2.7 years ago by Nathan Sheffield10

@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?

ADD REPLYlink written 2.7 years ago by Nathan Sheffield10

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.

ADD REPLYlink written 2.7 years ago by Hervé Pagès ♦♦ 13k
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