IRanges missing S4Vectors_defines.h
1
0
Entering edit mode
@nathan-sheffield-7613
Last seen 3.4 years 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 • 1.2k views
ADD COMMENT
1
Entering edit mode
@herve-pages-1542
Last seen 3 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.

ADD COMMENT
0
Entering edit mode

@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 REPLY
0
Entering edit mode

@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 REPLY
0
Entering edit mode

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 REPLY

Login before adding your answer.

Traffic: 347 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6