[Bioc-devel] moscato2 Windows build error reading IDAT file
Maarten van Iterson
mviterson at gmail.com
Fri Apr 15 08:45:47 CEST 2016
Indeed, build/check reports were generated now on the moscato2 windows
server as well and the error has disappeared!
Thanks again,
Maarten
On Tue, Apr 12, 2016 at 3:23 PM, Kasper Daniel Hansen <
kasperdanielhansen at gmail.com> wrote:
> 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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>>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>>>
>>>
>>>
>>
>
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