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

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 <

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

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