Error message in Rsubread detectionCall command
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raf4 ▴ 20
@raf4-8249
Last seen 14 months ago
United States

Dear Bioconductor users and (I hope) Rsubread developers,

I have the following error message using the detectionCall command on

Rsubread run on a Mac:

 

################################################################
R version 3.2.3 (2015-12-10) -- "Wooden Christmas-Tree"
Copyright (C) 2015 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin13.4.0 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

  Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

[R.app GUI 1.66 (7060) x86_64-apple-darwin13.4.0]

[History restored from /Users/friedman/.Rapp.history]

2016-02-16 17:21:57.285 R[914:19328] *** WARNING: Method convertPointFromBase: in class NSView is deprecated on 10.7 and later. It should not be used in new applications.
> library(Rsubread)
> sessionInfo()
R version 3.2.3 (2015-12-10)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.10.4 (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] Rsubread_1.20.3
> detectionCall("Dclk1p_zt001-GRCh38.sbrd.sam",species="mm", plot=FALSE)

 *** caught segfault ***
address 0x68, cause 'memory not mapped'

Traceback:
 1: .C("detectionCall", as.character(dataset), as.character(exon_file),     as.character(ir_file), as.character(temp_header), PACKAGE = "Rsubread")
 2: detectionCall("Dclk1p_zt001-GRCh38.sbrd.sam", species = "mm",     plot = FALSE)

Possible actions:
1: abort (with core dump, if enabled)
2: normal R exit
3: exit R without saving workspace
4: exit R saving workspace
Selection:

################################################################

I would appreciate help in getting this to work properly.

Thanks and best wishes,

Rich

Richard A. Friedman, PhD
Associate Research Scientist,
Biomedical Informatics Shared Resource
Herbert Irving Comprehensive Cancer Center (HICCC)
Lecturer,
Department of Biomedical Informatics (DBMI)
Room 824
Irving Cancer Research Center
Columbia University
1130 St. Nicholas Ave
New York, NY 10032
(212)851-4765 (voice)
raf4@cumc.columbia.edu

http://www.columbia.edu/~raf4/index.html

"Light enables the physical perception of space by leading the eye to distinguish dark from light". -Rose Friedman, age 19

 

 

 

 

Rsubread • 1.1k views
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