[Bioc-devel] moscato2 Windows build error reading IDAT file
Kasper Daniel Hansen
kasperdanielhansen at gmail.com
Tue Apr 12 15:23:42 CEST 2016
Yes. But I agree it is _really_ weird since minfi and illuminaio builds
without problems on Windows.
Kasper
On Tue, Apr 12, 2016 at 2:53 AM, Maarten van Iterson <mviterson at gmail.com>
wrote:
> Dear Dan and Henrik,
>
> Thank you for looking into this!
>
> So if I understand correctly the check error will disappear once the new
> build/check reports has been generated.
>
> Cheers,
> Maarten
>
> On Tue, Apr 12, 2016 at 3:00 AM, Kasper Daniel Hansen <
> kasperdanielhansen at gmail.com> wrote:
>
>> Thanks for checking; minfi reads some (but not this exact one) of these
>> IDATs as part of the build process.
>>
>> On Mon, Apr 11, 2016 at 8:18 PM, Henrik Bengtsson <
>> henrik.bengtsson at gmail.com> wrote:
>>
>>> 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
>>> >
>>>
>>> [[alternative HTML version deleted]]
>>>
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>>
>>
>
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