Question

RankProd crashing - stability issues?

0

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bhgyu ▴ 30

@bhgyu-13069

Last seen 6.4 years ago

Hi guys,

Anyone know why RankProd crashes R Studio when there are more than say 100 sample cases?

It consistently crashes R Studio for experiments with a larger number of subjects.

No error code or anything. R just encounters a fatal error.

Cheers

> sessionInfo()
R version 3.3.2 (2016-10-31)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X El Capitan 10.11.5

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

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

other attached packages:
[1] RankProd_3.0.0 Rmpfr_0.6-1    gmp_0.5-13.1  

loaded via a namespace (and not attached):
[1] tools_3.3.2
>

Crash report:

Process: RStudio [64386]
Path: /Applications/RStudio.app/Contents/MacOS/RStudio
Identifier: org.rstudio.RStudio
Version: 1.0.136 (1.0.136)
Code Type: X86-64 (Native)
Parent Process: ??? [1]
Responsible: RStudio [64386]
User ID: 501

Date/Time: 2017-06-16 16:13:17.807 +0100
OS Version: Mac OS X 10.11.5 (15F34)
Report Version: 11
Anonymous UUID: C80C5A19-D1DA-B4D5-393C-1C60B848093A

Sleep/Wake UUID: 56D8F5A1-BDD4-48C9-BD19-AF2EF89B7265

Time Awake Since Boot: 500000 seconds
Time Since Wake: 3500 seconds

System Integrity Protection: enabled

Crashed Thread: 0 Dispatch queue: com.apple.main-thread

Exception Type: EXC_BAD_ACCESS (SIGSEGV)
Exception Codes: KERN_INVALID_ADDRESS at 0x0000000011288c38
Exception Note: EXC_CORPSE_NOTIFY

VM Regions Near 0x11288c38:
-->
__TEXT 0000000100000000-00000001002d7000 [ 2908K] r-x/rwx SM=COW /Applications/RStudio.app/Contents/MacOS/RStudio

Application Specific Information:
objc_msgSend() selector name: _hasActiveAppearanceIgnoringKeyFocus

rankprod crash • 1.8k views

ADD COMMENT • link 7.5 years ago bhgyu ▴ 30

0

Entering edit mode

These types of question usually require a simple reproducible example, and information about the specific software you use. Please update your question to (a) include a reproducible example, e.g., using a data set from RankProd or simple simulated data and (b) include the output of the sessionInfo() command. For the later, I have

> sessionInfo()
R version 3.4.0 Patched (2017-05-24 r72729)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.2 LTS

Matrix products: default
BLAS: /home/mtmorgan/bin/R-3-4-branch/lib/libRblas.so
LAPACK: /home/mtmorgan/bin/R-3-4-branch/lib/libRlapack.so

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     

other attached packages:
[1] RankProd_3.2.0 Rmpfr_0.6-1    gmp_0.5-13.1  

loaded via a namespace (and not attached):
[1] compiler_3.4.0

Edit your question with this example and information, and ADD COMMENT to indicate that you have done so.

ADD REPLY • link 7.5 years ago Martin Morgan 25k

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Entering edit mode

Ok thank you.

ADD REPLY • link 7.5 years ago bhgyu ▴ 30

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Entering edit mode

You need to show us how you produce the problem -- a few lines of code that I can copy and paste into my own session and see what happens. You need to be using the current version of Bioconductor (R version 3.4.0, BiocInstaller version 1.26.0). It looks like you have an old version of R and RankProd. Install the current R (version 3.4.0) and be sure to follow standard Bioconductor installation instructions

source("https://bioconductor.org/biocLite.R")
biocLite("RankProd")

Since you already have a confused installation, be sure to try and validate your updated installation with

BiocInstaller::biocValid()

ADD REPLY • link 7.5 years ago Martin Morgan 25k

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Entering edit mode

Hi Martin,

Thank you. I did the above yesterday. I updated R to 3.4 and RankProd to 3.2

Bear in mind though, this all does work with a data set that has only 20 samples. Add 180 and it keeps crashing.

I also should add that I did gave this a go on a more powerful computer with the same problem (2.4Ghz, Core i7).

I run the following:

norm <- read.delim("norm.txt", header=T)

GSE.cl <- c(rep(1, each=90), rep(0, each=90))

origin <- rep(1,6)

symbol <- mapIds(huex10sttranscriptcluster.db,keys = as.vector(rownames(norm)),keytype="PROBEID",column = "ENTREZ")
gnames.27 <- symbol
RP <- RP.advance(norm, GSE.cl, origin, gene.names=gnames.27)

PS: Validation is True.

ADD REPLY • link 7.5 years ago bhgyu ▴ 30

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Entering edit mode

When I try and reproduce your code, I run into the following problem, for obvious reasons

> norm <- read.delim("norm.txt", header=T)
Error in file(file, "rt") : cannot open the connection
In addition: Warning message:
In file(file, "rt") :
  cannot open file 'norm.txt': No such file or directory

Maybe you can use rnorm() or similar to make your example reproducible by others, or use an existing data set (e.g., library(ALL)) that shows the problem.

ADD REPLY • link 7.5 years ago Martin Morgan 25k

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Entering edit mode

Sorry,

Let's try this: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE85426

The data set has to be large to test this so I cannot think of anything but an external one. Usually examples in R are rather small.

ADD REPLY • link 7.5 years ago bhgyu ▴ 30

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Entering edit mode

Hi,

I'm having the same issue. Did you find a solution?

Thanks

ADD REPLY • link 7.0 years ago tcalvo ▴ 100