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 _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel