[Bioc-devel] moscato2 Windows build error reading IDAT file
Henrik Bengtsson
henrik.bengtsson at gmail.com
Tue Apr 12 02:18:36 CEST 2016
No worries. Glad to hear it WS just a hiccup.
Henrik
On Apr 11, 2016 4:53 PM, "Dan Tenenbaum" <dtenenba at fredhutch.org> wrote:
> 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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