Re: [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 <
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
Re: [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 <
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_1.1illuminaio_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(illum
Re: [Bioc-devel] moscato2 Windows build error reading IDAT file
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_1.1illuminaio_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
Re: [Bioc-devel] moscato2 Windows build error reading IDAT file
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_1.1illuminaio_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.
Re: [Bioc-devel] moscato2 Windows build error reading IDAT file
se_0.4-7
> [7] mime_0.4 R6_2.1.2 plyr_1.8.3
> [10] chron_2.3-47 RSQLite_1.0.0ggplot2_2.1.0
> [13] zlibbioc_1.17.1 GenomicFeatures_1.23.29 data.table_1.9.6
> [16] annotate_1.49.1 hexbin_1.27.1preprocessCore_1.33.0
> [19] splines_3.3.0BiocParallel_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_0.22htmltools_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_1.53.3doRNG_1.6limma_3.27.15
> [52] nor1mix_1.2-1RColorBrewer_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
Re: [Bioc-devel] moscato2 Windows build error reading IDAT file
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] stats4parallel 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_1.0.0ggplot2_2.1.0
[13] zlibbioc_1.17.1 GenomicFeatures_1.23.29 data.table_1.9.6
[16] annotate_1.49.1 hexbin_1.27.1preprocessCore_1.33.0
[19] splines_3.3.0BiocParallel_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_0.22htmltools_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_1.53.3doRNG_1.6limma_3.27.15
[52] nor1mix_1.2-1RColorBrewer_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] 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
