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" <mviter...@gmail.com>
> To: "bioc-devel" <bioc-devel@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]]
>
> _______________________________________________
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
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