[Bioc-devel] moscato2 Windows build error reading IDAT file

[Dan Tenenbaum]

The problem seems to have to do with illuminaio and possibly minfiData; it can be reduced to / reproduced by the following:

library(illuminaio)
file <- "e:/biocbld/bbs-3.3-bioc/R/library/minfiData/extdata/5723646053/5723646053_R05C02_Grn.idat" 
illuminaio:::readIDAT_nonenc(file)

Specifically the error occurs on line 59 of illuminaio/R/readIDAT_nonenc.R, in the readString() function inside readIDAT_nonenc().

I'll leave it to the maintainer(s) of those packages to trobuleshoot further what the problem is.

> traceback()
5: readString(con = con)
4: readField(con = con, field = xx)
3: FUN(X[[i]], ...)
2: lapply(res, function(xx) {
       where <- fields[xx, "byteOffset"]
       seek(con, where = where, origin = "start")
       readField(con = con, field = xx)
   })
1: illuminaio:::readIDAT_nonenc(file) 


> sessionInfo()
R version 3.3.0 alpha (2016-03-28 r70390)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows Server 2008 R2 x64 (build 7601) Service Pack 1

locale:
[1] LC_COLLATE=English_United States.1252
[2] LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C
[5] LC_TIME=English_United States.1252

attached base packages:
[1] stats4    parallel  stats     graphics  grDevices utils     datasets
[8] methods   base

other attached packages:
 [1] illuminaio_0.13.1
 [2] minfiData_0.13.0
 [3] IlluminaHumanMethylation450kanno.ilmn12.hg19_0.2.1
 [4] IlluminaHumanMethylation450kmanifest_0.4.0
 [5] minfi_1.17.10
 [6] bumphunter_1.11.5
 [7] locfit_1.5-9.1
 [8] iterators_1.0.8
 [9] foreach_1.4.3
[10] Biostrings_2.39.12
[11] XVector_0.11.8
[12] SummarizedExperiment_1.1.24
[13] GenomicRanges_1.23.26
[14] GenomeInfoDb_1.7.6
[15] IRanges_2.5.43
[16] S4Vectors_0.9.46
[17] lattice_0.20-33
[18] Biobase_2.31.3
[19] BiocGenerics_0.17.5
[20] MethylAid_1.5.4

loaded via a namespace (and not attached):
 [1] mclust_5.2               base64_1.1               Rcpp_0.12.4
 [4] Rsamtools_1.23.8         digest_0.6.9             gridBase_0.4-7
 [7] mime_0.4                 R6_2.1.2                 plyr_1.8.3
[10] chron_2.3-47             RSQLite_1.0.0            ggplot2_2.1.0
[13] zlibbioc_1.17.1          GenomicFeatures_1.23.29  data.table_1.9.6
[16] annotate_1.49.1          hexbin_1.27.1            preprocessCore_1.33.0
[19] splines_3.3.0            BiocParallel_1.5.21      stringr_1.0.0
[22] RCurl_1.95-4.8           biomaRt_2.27.2           munsell_0.4.3
[25] shiny_0.13.2             httpuv_1.3.3             rtracklayer_1.31.10
[28] multtest_2.27.0          pkgmaker_0.22            htmltools_0.3.5
[31] GEOquery_2.37.0          quadprog_1.5-5           codetools_0.2-14
[34] matrixStats_0.50.1       XML_3.98-1.4             reshape_0.8.5
[37] GenomicAlignments_1.7.20 MASS_7.3-45              bitops_1.0-6
[40] grid_3.3.0               nlme_3.1-126             xtable_1.8-2
[43] gtable_0.2.0             registry_0.3             DBI_0.3.1
[46] magrittr_1.5             scales_0.4.0             stringi_1.0-1
[49] genefilter_1.53.3        doRNG_1.6                limma_3.27.15
[52] nor1mix_1.2-1            RColorBrewer_1.1-2       siggenes_1.45.0
[55] tools_3.3.0              rngtools_1.2.4           survival_2.38-3
[58] AnnotationDbi_1.33.8     colorspace_1.2-6         beanplot_1.2

Dan


----- Original Message -----
> From: "Maarten van Iterson" <mviterson at gmail.com>
> To: "bioc-devel" <bioc-devel at r-project.org>
> Sent: Monday, April 11, 2016 4:01:05 AM
> Subject: [Bioc-devel] moscato2 Windows build error reading IDAT file

> Dear all,
> 
> My package MethylAid does not pass check on moscato2.
> 
> I got
> 
> "Error in while (m%/%128 == 1) { : argument is of length zero
> Calls: summarize ... readIDAT_nonenc -> lapply -> FUN -> readField ->
> readString"
> 
> the summarize function calls read.metharray.exp from minfi which calls
> readIDAT/readIDAT_nonenc
> from illuminaio. However, both packages do pass check on moscato2.
> 
> I don't know how to fix this or if the error is related to the new
> windows toolchain?
> 
> Any idea's or suggestions are welcome!
> 
> Cheers,
> Maarten
> 
>	[[alternative HTML version deleted]]
> 
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