impute2mach error

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lckarssen
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Re: impute2mach error

Postby lckarssen » Wed Aug 27, 2014 8:23 pm

We have just finished a new release of DatABEL that seems to solve the problem. We will upload it to CRAN in the coming days.
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Lennart Karssen
PolyOmica
The Netherlands
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matthew.law
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Joined: Wed Aug 27, 2014 1:13 am

Re: impute2mach error

Postby matthew.law » Thu Aug 28, 2014 12:35 am

That is excellent news, thanks for the speedy response

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

Re: impute2mach error

Postby matthew.law » Tue Sep 30, 2014 5:45 am

Hello again

I have installed the new version of DatABEL and the problem still occurs. Please let me know if I can supply or test anything else.

Error:

Code: Select all

Error in .Call("iterator", tmp_fv@data, as.integer(0), as.integer(0),  :
  "iterator" not resolved from current namespace (GenABEL)
Calls: impute2mach -> impute2databel -> .Call


System info:

Code: Select all

sessionInfo() #updated 30/09/2014
R version 3.1.1 (2014-07-10)
Platform: x86_64-unknown-linux-gnu (64-bit)

locale:
 [1] LC_CTYPE=en_AU.UTF-8       LC_NUMERIC=C             
 [3] LC_TIME=en_AU.UTF-8        LC_COLLATE=en_AU.UTF-8   
 [5] LC_MONETARY=en_AU.UTF-8    LC_MESSAGES=en_AU.UTF-8   
 [7] LC_PAPER=en_AU.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C           
[11] LC_MEASUREMENT=en_AU.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
[1] GenABEL_1.8-0      GenABEL.data_1.0.0 MASS_7.3-34        DatABEL_0.9-5     
[5] ggplot2_1.0.0     

loaded via a namespace (and not attached):
 [1] colorspace_1.2-4 digest_0.6.4     grid_3.1.1       gtable_0.1.2   
 [5] munsell_0.4.2    plyr_1.8.1       proto_0.3-10     Rcpp_0.11.2     
 [9] reshape2_1.4     scales_0.2.4     stringr_0.6.2    tools_3.1.1   


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

Re: impute2mach error

Postby matthew.law » Wed May 13, 2015 2:27 am

Just downloaded the latest version of DatABEL (0.9.6) and I am still having this problem.

Error in .Call("iterator", tmp_fv@data, as.integer(0), as.integer(0), :
"iterator" not resolved from current namespace (GenABEL)
Calls: impute2mach -> impute2databel -> .Call

Are there any further suggestions on how to resolve this problem?

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

Re: impute2mach error

Postby lckarssen » Fri Jun 05, 2015 11:04 am

I recently looked into this and it turns out that the fix inadvertently wasn't incorporated in the latest GenABEL release. Please wait for the next release of the GenABEL package. Until then, please use the updated code from here.
-------
Lennart Karssen
PolyOmica
The Netherlands
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danny.park
Posts: 2
Joined: Fri Sep 11, 2015 7:15 pm

Re: impute2mach error

Postby danny.park » Fri Sep 11, 2015 7:21 pm

Hello,

I'm seeing the same error. I've tried on unix and os x machines, both times using the updated impute2databel.R script. Any help would be appreciated. Thanks!

Code: Select all

> sessionInfo()
R version 3.2.1 (2015-06-18)
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] DatABEL_0.9-6      GenABEL_1.8-0      GenABEL.data_1.0.0 MASS_7.3-40
 


Code: Select all

> sessionInfo()
R version 3.0.2 (2013-09-25)
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_0.9-6      GenABEL_1.8-0      GenABEL.data_1.0.0 MASS_7.3-26 

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

Re: impute2mach error

Postby lckarssen » Fri Sep 11, 2015 8:48 pm

Hmm, sorry to hear that it doesn't work with the updated script either... :?
I'll have to look at it again in more detail, but won't have to time to do so this month.
-------
Lennart Karssen
PolyOmica
The Netherlands
-------

danny.park
Posts: 2
Joined: Fri Sep 11, 2015 7:15 pm

Re: impute2mach error

Postby danny.park » Fri Sep 11, 2015 9:11 pm

Thanks, please keep me updated.

tboutin
Posts: 1
Joined: Mon Oct 26, 2015 8:43 am

Re: impute2mach error

Postby tboutin » Mon Oct 26, 2015 8:48 am

Hi,

I was wondering if there is any update on this issue.

Thanks

tpalviai
Posts: 1
Joined: Thu Jan 14, 2016 9:34 am

Re: impute2mach error

Postby tpalviai » Thu Jan 14, 2016 9:45 am

I got this issue solved using that external impute2databel.R mentioned before. At least the conversion works now using windows R 3.2.3 x64 and newest GenABEL and DatABEL libraries downloaded from cran.


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