[Bioc-devel] moscato2 Windows build error reading IDAT file
Dan Tenenbaum
dtenenba at fredhutch.org
Tue Apr 12 01:53:43 CEST 2016
I upgraded to r70462 and I cannot reproduce it now either. I guess it was an issue in R-alpha, since fixed.
Sorry for the trouble.
Dan
----- Original Message -----
> From: "Henrik Bengtsson" <henrik.bengtsson at gmail.com>
> To: "Dan Tenenbaum" <dtenenba at fredhutch.org>
> Cc: "Maarten van Iterson" <mviterson at gmail.com>, "bioc-devel" <bioc-devel at r-project.org>
> Sent: Monday, April 11, 2016 4:01:05 PM
> Subject: Re: [Bioc-devel] moscato2 Windows build error reading IDAT file
> 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]]
>>>
>>> _______________________________________________
>>> Bioc-devel at r-project.org mailing list
>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>
>> _______________________________________________
>> Bioc-devel at r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
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