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
?myreadPairedAlignments?\n <anonymous>: no visible global function
definition for ?ScanBamParam?\n <anonymous>: no visible global function
definition for ?scanBamFlag?\n <anonymous>: no visible global function
definition for ?matchBamToNames?\n <anonymous>: no visible binding for
global variable ?GRangesList?\n <anonymous>: no visible binding for
global variable ?align2GRanges?\n <anonymous>: no visible binding for
global variable ?GRangesList?\n <anonymous>: no visible binding for
global variable ?align2GRanges?\n <anonymous>: no visible binding for
global variable ?align2GRanges?\n <anonymous>: no visible binding for
global variable ?align2GRanges?\n <anonymous>: no visible global
function definition for ?values?\n <anonymous>: no visible global
function definition for ?getTxIdsByGene?\n <anonymous>: no visible
global function definition for ?exonsBy?\n <anonymous>: no visible
global function definition for ?endoapply?\n <anonymous>: no visible
binding for global variable ?reduce?\n <anonymous> : <anonymous>: no
visible global function definition for ?alignPairs2Tx?\n <anonymous>: no
visible global function definition for ?seqnames?\n <anonymous> :
<anonymous> : <anonymous>: no visible global function definition for
?alignPairs2Tx?\n <anonymous> : <anonymous>: no visible global
function
definition for ?alignPairs2Ex?\n <anonymous>: no visible global function
definition for ?seqnames?\n <anonymous> : <anonymous> :
<anonymous>: no
visible global function definition for ?alignPairs2Ex?\n <anonymous>: no
visible global function definition for ?mclapply?\n <anonymous>: no
visible binding for global variable ?.tabulateReads?\n <anonymous>: no
visible binding for global variable ?.tabulateReads?\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
