[Bioc-devel] moscato2 Windows build error reading IDAT file
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
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