Question

IRanges missing S4Vectors_defines.h

0

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Nathan Sheffield ▴ 10

@nathan-sheffield-7613

Last seen 7 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 • 1.7k views

ADD COMMENT • link updated 9.0 years ago by Hervé Pagès 16k • written 9.0 years ago by Nathan Sheffield ▴ 10

score 1 · Answer 1 · 2015-04-17

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Hervé Pagès 16k

@herve-pages-1542

Last seen 2 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 • link 9.0 years ago Hervé Pagès 16k

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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.

ADD REPLY • link 9.0 years ago Nathan Sheffield ▴ 10

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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?

ADD REPLY • link 9.0 years ago Nathan Sheffield ▴ 10

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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.

ADD REPLY • link 9.0 years ago Hervé Pagès 16k