[Bioc-devel] moscato2 Windows build error reading IDAT file
Henrik Bengtsson
henrik.bengtsson at gmail.com
Tue Apr 12 01:01:05 CEST 2016
I *cannot* reproduce this:
% R --vanilla
## The IDAT file
> pathname <- system.file(package="minfiData", "extdata", "5723646053", "5723646053_R05C02_Grn.idat")
> file.info(pathname)$size
[1] 8091452
> unname(tools::md5sum(pathname))
[1] "dfc33fdaf3e91d872be896643a0c837f"
> packageVersion("minfiData")
[1] '0.13.0'
## Parsing it
> data <- illuminaio:::readIDAT_nonenc(pathname)
> str(data)
List of 12
$ fileSize : num 8091452
$ versionNumber: int 3
$ nFields : int 19
$ fields : num [1:19, 1:3] 1000 102 103 104 107 200 300 400 401 402 ...
..- attr(*, "dimnames")=List of 2
.. ..$ : chr [1:19] "nSNPsRead" "IlluminaID" "SD" "Mean" ...
.. ..$ : chr [1:3] "fieldCode" "byteOffset" "Bytes"
$ nSNPsRead : int 622399
$ Quants : int [1:622399, 1:3] 455 12883 2451 7650 4579 4955
1665 1953 5689 264 ...
..- attr(*, "dimnames")=List of 2
.. ..$ : chr [1:622399] "10600313" "10600322" "10600328" "10600336" ...
.. ..$ : chr [1:3] "Mean" "SD" "NBeads"
$ MidBlock : int [1:622399] 10600313 10600322 10600328 10600336
10600345 10600353 10600357 10600364 10600366 10600369 ...
$ RedGreen : int 0
$ Barcode : chr "5723646053"
$ ChipType : chr "BeadChip 12x8"
$ RunInfo : chr[0 , 1:5]
..- attr(*, "dimnames")=List of 2
.. ..$ : NULL
.. ..$ : chr [1:5] "RunTime" "BlockType" "BlockPars" "BlockCode" ...
$ Unknowns :List of 7
..$ MostlyNull: chr ""
..$ MostlyA : chr "R05C02"
..$ Unknown.1 : chr ""
..$ Unknown.2 : chr ""
..$ Unknown.3 : chr ""
..$ Unknown.4 : chr ""
..$ Unknown.5 : chr ""
> sessionInfo()
R version 3.3.0 beta (2016-04-08 r70447)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 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] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] base64_1.1 illuminaio_0.13.1
% R CMD config COMPILED_BY
gcc-4.9.3
/Henrik
On Mon, Apr 11, 2016 at 9:21 AM, Dan Tenenbaum <dtenenba at fredhutch.org> wrote:
> 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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>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
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