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 <
kasperdanielhan...@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.bengts...@gmail.com> wrote:
>
>> No worries. Glad to hear it WS just a hiccup.
>>
>> Henrik
>> On Apr 11, 2016 4:53 PM, "Dan Tenenbaum" <dtene...@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.bengts...@gmail.com>
>> > > To: "Dan Tenenbaum" <dtene...@fredhutch.org>
>> > > Cc: "Maarten van Iterson" <mviter...@gmail.com>, "bioc-devel" <
>> > bioc-devel@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 <
>> dtene...@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" <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
>> > >>
>> > >> _______________________________________________
>> > >> Bioc-devel@r-project.org mailing list
>> > > > https://stat.ethz.ch/mailman/listinfo/bioc-devel
>> >
>>
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>>
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>
>
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