Question: Error trying to run "seqlm" example
0
gravatar for calen.p.ryan
3.3 years ago by
calen.p.ryan0 wrote:

I'm trying to get the seqlm package running for a DMR analysis I'd like to conduct, first by simply running the example provided with the package, but am already getting an error I have no idea how to deal with.

After installing the required packages (and all dependencies), followed by update.packages():

library(seqlm)
data(tissue_small)

segments = seqlm(values = tissue_small$values, genome_information = tissue_small$genome_information, annotation =  tissue_small$annotation)

 

I get this error:

 

Error: 'as.vector' is not an exported object from 'namespace:IRanges'

 

Could this be a problem with some updated packages but not others? I don't even know what a namespace is!

sessionInfo below. Any help would be appreciated!


---

R version 3.3.1 (2016-06-21)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.10.5 (Yosemite)

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

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

other attached packages:
[1] seqlm_0.1            devtools_1.12.0      BiocInstaller_1.22.3

loaded via a namespace (and not attached):
[1] Rcpp_0.12.5          magrittr_1.5         XVector_0.12.0       GenomicRanges_1.24.2 BiocGenerics_0.18.0
[6] zlibbioc_1.18.0      IRanges_2.6.1        munsell_0.4.3        lattice_0.20-33      colorspace_1.2-6   
[11] foreach_1.4.3        stringr_1.0.0        GenomeInfoDb_1.8.1   plyr_1.8.4           tools_3.3.1        
[16] parallel_3.3.1       grid_3.3.1           gtable_0.2.0         withr_1.0.2          iterators_1.0.8    
[21] digest_0.6.9         Matrix_1.2-6         reshape2_1.4.1       ggplot2_2.1.0        S4Vectors_0.10.2   
[26] codetools_0.2-14     memoise_1.0.0        stringi_1.1.1        scales_0.4.0         stats4_3.3.1

 

ADD COMMENTlink modified 3.3 years ago • written 3.3 years ago by calen.p.ryan0
Answer: Error trying to run "seqlm" example
1
gravatar for Martin Morgan
3.3 years ago by
Martin Morgan ♦♦ 23k
United States
Martin Morgan ♦♦ 23k wrote:

seqlm isn't a Bioconductor package so you should contact maintainer("seqlm"). It looks like the version you are using has not been updated to work with the current version of Bioconductor.

ADD COMMENTlink written 3.3 years ago by Martin Morgan ♦♦ 23k

Ok thanks @Martin Morgan . I thought this might be bioconductor solvable but I'll contact the maintainer. If there's a workaround should I post it here for others, or restrict to bioconductor packages? Thanks again.

ADD REPLYlink written 3.3 years ago by calen.p.ryan0
Answer: Error trying to run "seqlm" example
0
gravatar for calen.p.ryan
3.3 years ago by
calen.p.ryan0 wrote:

Problem has been solved by the package maintainer and is now working.

ADD COMMENTlink written 3.3 years ago by calen.p.ryan0
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