impute2mach error

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Heather
Posts: 1
Joined: Wed Jul 31, 2013 11:41 pm

impute2mach error

Postby Heather » Thu Aug 01, 2013 1:41 am

I'm trying to convert impute2 output files (gen format) into dosage files, like those output by MACH. I've installed and loaded the libraries for GenABEL as well as DatABEL and am running impute2mach. The tmp .fvi and .fvd files are generated, but get an error and no mach files are created. The full command and error are below.

Any suggestions would be greatly appreciated.

Code: Select all

impute2mach("/blah/chr.12.impute", "/blah/chr.12.impute_info", "/blah/chr.cov.sample", "/blah/mach12",maketextdosefile=TRUE, order_geno_snp_a0_a1=c(2, 4:5), skip_geno=0,  order_info_snp_pos_freq1_info_qual_type=c(2:7), skip_info=1)
Options in effect:
    --infile    = /blah/chr.12.impute
    --outfile   = ./tmp948566
    --skiprows  = OFF
    --skipcols  = 5
    --cnrow     = OFF
    --rncol     = ON, using column 2 of '/blah/chr.12.impute'
    --transpose = ON
    --Rmatrix   = OFF
    --nanString = NA
Number of lines in source file is 1819438
Number of words in source file is 4853
skiprows = 0
cnrow = 0
skipcols = 5
rncol = 2
Rmatrix = 0
numWords = 4853
Creating file with numRows = 1819438
Creating file with numColumns = 4848
text2fvf finished.
Error in .Call("iterator", tmp_fv@data, as.integer(0), as.integer(0),  :
  "iterator" not resolved from current namespace (GenABEL)

lckarssen
Site Admin
Site Admin
Posts: 322
Joined: Tue Jan 04, 2011 3:04 pm
Location: Utrecht, The Netherlands

Re: impute2mach error

Postby lckarssen » Wed Aug 07, 2013 8:39 am

That doesn't look good. I haven't used impute2mach in a while, so I'll have to look into it.
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Lennart Karssen
PolyOmica
The Netherlands
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jhuffman
Posts: 3
Joined: Thu Jun 02, 2011 3:48 pm
Location: Edinburgh, UK

Re: impute2mach error

Postby jhuffman » Mon Aug 19, 2013 10:21 am

Hi! I have found the same thing. It only seems to happen when using the versions of the package for R v3.0, not R v2.15. I hope this helps with the debugging.

lckarssen
Site Admin
Site Admin
Posts: 322
Joined: Tue Jan 04, 2011 3:04 pm
Location: Utrecht, The Netherlands

Re: impute2mach error

Postby lckarssen » Mon Aug 26, 2013 2:03 pm

Thanks, that helped nailing the issue down.
I turns out that we already ran into this bug, but I didn't realise it had to do with R v2 -> v3 at the time. The bug reports can be found here.

I've fixed the issue, so it will be available in the next release of GenABEL. If you want to start using it now, then save the content of the file impute2databel.R from our version control system to a file on your computer and run the following:

Code: Select all

library(GenABEL)
library(DatABEL)
source("/path/to/your/impute2databel.R")

and then run impute2mach() as you did before.

Let us know if this works.
-------
Lennart Karssen
PolyOmica
The Netherlands
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Edith
Posts: 1
Joined: Tue Aug 27, 2013 1:36 pm

Re: impute2mach error

Postby Edith » Tue Aug 27, 2013 1:44 pm

I also have this problem I tried to solve it using the new impute2databel.R file you provided but unfortunately I still get the same error message.

li9636
Posts: 1
Joined: Wed Mar 12, 2014 3:25 pm

Re: impute2mach error

Postby li9636 » Wed Mar 12, 2014 3:55 pm

I also got the same error message even after using the new impute2datable.R script that you posted here.

Joni
Posts: 1
Joined: Tue May 20, 2014 6:16 pm

Re: impute2mach error

Postby Joni » Tue May 20, 2014 6:17 pm

I also get this error, and it is not fixed by the impute2databel file. The version of GenABEL is the latest release

Jodie
Posts: 1
Joined: Thu May 29, 2014 5:38 am

Re: impute2mach error

Postby Jodie » Thu May 29, 2014 5:42 am

Hello! I'm getting this error too (using R v3, with GenABEL for this version of R). I don't suppose anyone has managed to find a solution or a work-around? Thanks!

zx8754
Posts: 1
Joined: Mon Nov 05, 2012 5:05 pm

Re: impute2mach error

Postby zx8754 » Thu Jun 05, 2014 2:39 pm

I am having the same error here, any solutions?

Error:

Code: Select all

Error in .Call("iterator", tmp_fv@data, as.integer(0), as.integer(0),  :
  "iterator" not resolved from current namespace (GenABEL)


System info:

Code: Select all

sessionInfo()
R version 3.0.2 (2013-09-25)
Platform: x86_64-pc-linux-gnu (64-bit)

locale:
[1] C

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

other attached packages:
[1] DatABEL_0.9-4      GenABEL_1.8-0      GenABEL.data_1.0.0 MASS_7.3-29

matthew.law
Posts: 4
Joined: Wed Aug 27, 2014 1:13 am

Re: impute2mach error

Postby matthew.law » Wed Aug 27, 2014 1:56 am

I am also having the described problem. I have tried the latest R and packages as detailed below, as well as combinations of older builds of R and GenABEL packages. (e.g R 2.15, DatABEL 0.9.2, GenABEL 1.7.6) without success. I have also tried the 'source("impute2databel.R") solution in another thread without resolving the problem.


The following session information is the set up for the majority of our cluster, as well as my desktop:

Error:

Code: Select all

Error in .Call("iterator", tmp_fv@data, as.integer(0), as.integer(0),  :
  "iterator" not resolved from current namespace (GenABEL)


System info:

Code: Select all

sessionInfo()
R version 3.1.1 (2014-07-10)
Platform: x86_64-pc-linux-gnu (64-bit)

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] DatABEL_0.9-4.1    GenABEL_1.8-0      GenABEL.data_1.0.0 MASS_7.3-34 


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