[BioC] ParseMetaFromGtfFile is.na() error

Beth Wilmot [guest] guest at bioconductor.org
Thu Jun 5 19:38:47 CEST 2014

I am using SCAN.UPC and trying to create an annotation file from one concatenated GRCm38.73 fasta file.  I have the matched GRCm38.73.gtf file.  The .gtf file parsing halts near the end of the file and the following error message appears and no output file is generated.  Thanks, Beth

Done parsing 1140000 lines from /Mus_musculus.GRCm38.
Warning message:
In is.na(x) : is.na() applied to non-(list or vector) of type 'NULL'

 -- output of sessionInfo(): 

> sessionInfo()
R version 3.1.0 (2014-04-10)
Platform: x86_64-unknown-linux-gnu (64-bit)

 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=C

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

other attached packages:
 [1] SCAN.UPC_2.6.0       sva_3.10.0           mgcv_1.7-29
 [4] nlme_3.1-117         corpcor_1.6.6        foreach_1.4.2
 [7] affyio_1.32.0        affy_1.42.2          GEOquery_2.30.0
[10] oligo_1.28.2         Biostrings_2.32.0    XVector_0.4.0
[13] IRanges_1.22.2       oligoClasses_1.26.0  Biobase_2.24.0
[16] BiocGenerics_0.10.0  limma_3.20.1         Rsubread_1.14.0
[19] BiocInstaller_1.14.2

loaded via a namespace (and not attached):
 [1] affxparser_1.36.0     bit_1.1-12            codetools_0.2-8
 [4] DBI_0.2-7             ff_2.2-13             GenomeInfoDb_1.0.1
 [7] GenomicRanges_1.16.0  grid_3.1.0            iterators_1.0.7
[10] lattice_0.20-29       MASS_7.3-31           Matrix_1.1-3
[13] preprocessCore_1.26.1 RCurl_1.95-4.1        splines_3.1.0
[16] stats4_3.1.0          tools_3.1.0           XML_3.98-1.1
[19] zlibbioc_1.10.0

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