[R] GridR error

[Elizabeth Purdom]

Hi,
I am trying to use 'GridR' package for the first time, and I'm running 
into a strange error from grid.check:

 > grid.check(gridFun)
Error in exists(add) : invalid first argument

After playing around in recover mode, I see that this because the 
variable 'add' created by grid.check is blank:

Browse[1]> split[[1]][k]
[1] " : "
Browse[1]> add
[1] ""

The problem appears to be that my grid.input.Parameters (shown in full 
below) has components that look like this:
'<anonymous> : <anonymous>'
so when it is split by '<anonymous>' I get add that is "", and this 
gives me an error in 'exists(add)'. I have no real idea what this 
function is doing, but is there a work around for what ever is going on?

My function is quite complicated and calls a lot of local variables 
which are themselves quite intricate, so I don't really know what other 
information I can give. Any help is appreciated!

 > sessionInfo()
R version 2.11.1 (2010-05-31)
x86_64-unknown-linux-gnu

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=C              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] GridR_0.9.1           codetools_0.2-2       multicore_0.1-3
 [4] Rsamtools_1.0.7       Biostrings_2.16.9     GenomicFeatures_1.0.6
 [7] GenomicRanges_1.0.7   IRanges_1.6.11        projectManager_1.0
[10] XML_3.1-0

loaded via a namespace (and not attached):
[1] Biobase_2.8.0     biomaRt_2.4.0     BSgenome_1.16.5   DBI_0.2-5
[5] RCurl_1.4-3       RSQLite_0.9-2     rtracklayer_1.8.1 tools_2.11.1


Thanks,
Elizabeth

The full grid.input.Parameters:

Browse[1]> grid.input.Parameters
[1] " <anonymous>: no visible global function definition for 
âmyreadPairedAlignmentsâ\n <anonymous>: no visible global function 
definition for âScanBamParamâ\n <anonymous>: no visible global function 
definition for âscanBamFlagâ\n <anonymous>: no visible global function 
definition for âmatchBamToNamesâ\n <anonymous>: no visible binding for 
global variable âGRangesListâ\n <anonymous>: no visible binding for 
global variable âalign2GRangesâ\n <anonymous>: no visible binding for 
global variable âGRangesListâ\n <anonymous>: no visible binding for 
global variable âalign2GRangesâ\n <anonymous>: no visible binding for 
global variable âalign2GRangesâ\n <anonymous>: no visible binding for 
global variable âalign2GRangesâ\n <anonymous>: no visible global 
function definition for âvaluesâ\n <anonymous>: no visible global 
function definition for âgetTxIdsByGeneâ\n <anonymous>: no visible 
global function definition for âexonsByâ\n <anonymous>: no visible 
global function definition for âendoapplyâ\n <anonymous>: no visible 
binding for global variable âreduceâ\n <anonymous> : <anonymous>: no 
visible global function definition for âalignPairs2Txâ\n <anonymous>: no 
visible global function definition for âseqnamesâ\n <anonymous> : 
<anonymous> : <anonymous>: no visible global function definition for 
âalignPairs2Txâ\n <anonymous> : <anonymous>: no visible global function 
definition for âalignPairs2Exâ\n <anonymous>: no visible global function 
definition for âseqnamesâ\n <anonymous> : <anonymous> : <anonymous>: no 
visible global function definition for âalignPairs2Exâ\n <anonymous>: no 
visible global function definition for âmclapplyâ\n <anonymous>: no 
visible binding for global variable â.tabulateReadsâ\n <anonymous>: no 
visible binding for global variable â.tabulateReadsâ\n"

-- 
-------------
Elizabeth Purdom
Assistant Professor
Department of Statistics
UC, Berkeley

Office: 433 Evans Hall
(510) 642-6154 (office)
(510) 642-7892 (fax)
Mailing: 367 Evans Hall Berkeley, CA 94720-3860
epurdom at stat.berkeley.edu