date:20160412

Re: [Bioc-devel] package submission - problem with vignette

2016-04-12 Thread Karim Mezhoud

Hi,
I don't know why I have to use
%\VignetteEncoding{UTF-8}
instead
%\usepackage[UTF8]{inputenc}

it works.

On Tue, Apr 12, 2016 at 8:38 AM, Karim Mezhoud  wrote:

> Dear Lara and Dan,
> In my case I am having this error.  Thanks
>
> * creating vignettes ... ERROR
> Error: Vignette 'bioCancer.Rmd' is non-ASCII but has no declared encoding
> Execution halted
> Error: Command failed (1)
> Execution halted
>
> Exited with status 1.
>
> I am setting vignette using knitr package.
>
> In DESCRIPTION file I added:
>
> Suggests:
> BiocStyle,
> AnnotationHub,
> knitr,
> rmarkdown,
> testthat (>= 0.10.0),
> rappdirs
> VignetteBuilder: knitr
>
> In Rmd file, I started by:
>
> ---
> title: "bioCancer: Interactive Multi-OMICS Cancers Data Visualization and
> Analysis"
> author: "\\
> Karim Mezhoud ()\\
> Nuclear Science Center of Tunisia, Nuclear Safety & Security
> Department"
> date: "`r Sys.Date()`"
> output:
>   BiocStyle::html_document:
> toc: true
>   BiocStyle::pdf_document:
> toc: true
> vignette: >
>   %\VignetteIndexEntry{bioCancer: Interactive Multi-OMICS Cancers Data
> Visualization and Analysis}
>   %\VignetteEngine{knitr::rmarkdown}
>   %\VignetteDepends{AnnotationHub}
>   %\usepackage[utf8]{inputenc}
> ---
>
>
> On Mon, Apr 11, 2016 at 9:52 PM, Lara Urban 
> wrote:
>
>> Dear Dan,
>>
>> Many thanks, apparently I just had to update one of the knitr-associated
>> components.
>>
>> I hope it will go through now.
>>
>> Many thanks again and enjoy your evening,
>> Lara
>>
>> 2016-04-11 17:39 GMT+01:00 Dan Tenenbaum :
>>
>> >
>> >
>> > - Original Message -
>> > > From: "Dan Tenenbaum" 
>> > > To: "Lara Urban" 
>> > > Cc: "bioc-devel" 
>> > > Sent: Monday, April 11, 2016 9:29:30 AM
>> > > Subject: Re: [Bioc-devel] package submission - problem with vignette
>> >
>> > > It means that when you run R CMD build YourPackageName, the vignette
>> is
>> > not
>> > > built.
>> > >
>> > > It simply looks in the output of R CMD build for a line that starts:
>> > >
>> > >* creating vignettes ...
>> > >
>> > > If this line is present, it means `R` has not detected that a vignette
>> > > needs to be built.
>> >
>> > Oops, that should say: "If this line is NOT present..."
>> >
>> > Dan
>> >
>> > >
>> > > It's `REQUIRED` that the vignette be built.
>> > >
>> > > If you have vignette sources yet still get this message, there could
>> > > be several causes:
>> > >
>> > > * Missing or invalid `VignetteBuilder` line in the `DESCRIPTION` file.
>> > > * Missing or invalid `VignetteEngine` line in the vignette source.
>> > >
>> > > See `knitr`'s [package vignette](
>> http://yihui.name/knitr/demo/vignette/)
>> > > page, or the
>> > > [Non-Sweave
>> > > vignettes](
>> >
>> https://cran.r-project.org/doc/manuals/r-release/R-exts.html#Non_002dSweave-vignettes
>> > )
>> > > section of "Writing R Extensions" for more information.
>> > >
>> > > Dan
>> > >
>> > >
>> > > - Original Message -
>> > >> From: "Lara Urban" 
>> > >> To: "bioc-devel" 
>> > >> Sent: Monday, April 11, 2016 8:58:14 AM
>> > >> Subject: [Bioc-devel] package submission - problem with vignette
>> > >
>> > >> Dear BiocDevel,
>> > >>
>> > >> I have a question regarding the submission of my package; thank you
>> very
>> > >> much in advance.
>> > >>
>> > >> I have submitted my package to Bioconductor a few days ago and it
>> passed
>> > >> build, check and bioccheck. Now, that I had to change just one line
>> in
>> > my R
>> > >> code and submitted it again, I get an error on all three platforms,
>> > because
>> > >> it is required that my vignette is built by R CMD build; however, I
>> > still
>> > >> have my Rmd file in the order vignettes as before. Shouldn't it build
>> > >> automatically? Do you have any ideas what is going wrong here?
>> > >>
>> > >> Many thanks and kind regards,
>> > >> Lara
>> > >>
>> > >>
>> > >> --
>> > >> Lara Urban
>> > >>
>> > >> Predoctoral Fellow
>> > >> EMBL-European Bioinformatics Institute
>> > >> Wellcome Trust Genome Campus
>> > >> Hinxton, Cambridge
>> > >> CB10 1SD
>> > >> United Kingdom
>> > >>
>> > >> PhD Student
>> > >> Wolfson College
>> > >> University of Cambridge
>> > >>
>> > >> phone:  + 49 (0) 176 76 37 99 03
>> > <%2B%2044%20%280%29%201223%20494%20655>
>> > >> email: lara.h.ur...@ebi.ac.uk 
>> > >>
>> > >>  [[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
>> >
>>
>>
>>
>> --
>> Lara Urban
>>
>> Predoctoral Fellow
>>

Re: [Bioc-devel] package submission - problem with vignette

2016-04-12 Thread Karim Mezhoud

Dear Lara and Dan,
In my case I am having this error.  Thanks

* creating vignettes ... ERROR
Error: Vignette 'bioCancer.Rmd' is non-ASCII but has no declared encoding
Execution halted
Error: Command failed (1)
Execution halted

Exited with status 1.

I am setting vignette using knitr package.

In DESCRIPTION file I added:

Suggests:
BiocStyle,
AnnotationHub,
knitr,
rmarkdown,
testthat (>= 0.10.0),
rappdirs
VignetteBuilder: knitr

In Rmd file, I started by:

---
title: "bioCancer: Interactive Multi-OMICS Cancers Data Visualization and
Analysis"
author: "\\
Karim Mezhoud ()\\
Nuclear Science Center of Tunisia, Nuclear Safety & Security
Department"
date: "`r Sys.Date()`"
output:
  BiocStyle::html_document:
toc: true
  BiocStyle::pdf_document:
toc: true
vignette: >
  %\VignetteIndexEntry{bioCancer: Interactive Multi-OMICS Cancers Data
Visualization and Analysis}
  %\VignetteEngine{knitr::rmarkdown}
  %\VignetteDepends{AnnotationHub}
  %\usepackage[utf8]{inputenc}
---


On Mon, Apr 11, 2016 at 9:52 PM, Lara Urban  wrote:

> Dear Dan,
>
> Many thanks, apparently I just had to update one of the knitr-associated
> components.
>
> I hope it will go through now.
>
> Many thanks again and enjoy your evening,
> Lara
>
> 2016-04-11 17:39 GMT+01:00 Dan Tenenbaum :
>
> >
> >
> > - Original Message -
> > > From: "Dan Tenenbaum" 
> > > To: "Lara Urban" 
> > > Cc: "bioc-devel" 
> > > Sent: Monday, April 11, 2016 9:29:30 AM
> > > Subject: Re: [Bioc-devel] package submission - problem with vignette
> >
> > > It means that when you run R CMD build YourPackageName, the vignette is
> > not
> > > built.
> > >
> > > It simply looks in the output of R CMD build for a line that starts:
> > >
> > >* creating vignettes ...
> > >
> > > If this line is present, it means `R` has not detected that a vignette
> > > needs to be built.
> >
> > Oops, that should say: "If this line is NOT present..."
> >
> > Dan
> >
> > >
> > > It's `REQUIRED` that the vignette be built.
> > >
> > > If you have vignette sources yet still get this message, there could
> > > be several causes:
> > >
> > > * Missing or invalid `VignetteBuilder` line in the `DESCRIPTION` file.
> > > * Missing or invalid `VignetteEngine` line in the vignette source.
> > >
> > > See `knitr`'s [package vignette](
> http://yihui.name/knitr/demo/vignette/)
> > > page, or the
> > > [Non-Sweave
> > > vignettes](
> >
> https://cran.r-project.org/doc/manuals/r-release/R-exts.html#Non_002dSweave-vignettes
> > )
> > > section of "Writing R Extensions" for more information.
> > >
> > > Dan
> > >
> > >
> > > - Original Message -
> > >> From: "Lara Urban" 
> > >> To: "bioc-devel" 
> > >> Sent: Monday, April 11, 2016 8:58:14 AM
> > >> Subject: [Bioc-devel] package submission - problem with vignette
> > >
> > >> Dear BiocDevel,
> > >>
> > >> I have a question regarding the submission of my package; thank you
> very
> > >> much in advance.
> > >>
> > >> I have submitted my package to Bioconductor a few days ago and it
> passed
> > >> build, check and bioccheck. Now, that I had to change just one line in
> > my R
> > >> code and submitted it again, I get an error on all three platforms,
> > because
> > >> it is required that my vignette is built by R CMD build; however, I
> > still
> > >> have my Rmd file in the order vignettes as before. Shouldn't it build
> > >> automatically? Do you have any ideas what is going wrong here?
> > >>
> > >> Many thanks and kind regards,
> > >> Lara
> > >>
> > >>
> > >> --
> > >> Lara Urban
> > >>
> > >> Predoctoral Fellow
> > >> EMBL-European Bioinformatics Institute
> > >> Wellcome Trust Genome Campus
> > >> Hinxton, Cambridge
> > >> CB10 1SD
> > >> United Kingdom
> > >>
> > >> PhD Student
> > >> Wolfson College
> > >> University of Cambridge
> > >>
> > >> phone:  + 49 (0) 176 76 37 99 03
> > <%2B%2044%20%280%29%201223%20494%20655>
> > >> email: lara.h.ur...@ebi.ac.uk 
> > >>
> > >>  [[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
> >
>
>
>
> --
> Lara Urban
>
> Predoctoral Fellow
> EMBL-European Bioinformatics Institute
> Wellcome Trust Genome Campus
> Hinxton, Cambridge
> CB10 1SD
> United Kingdom
>
> PhD Student
> Wolfson College
> University of Cambridge
>
> phone:  + 49 (0) 176 76 37 99 03 <%2B%2044%20%280%29%201223%20494%20655>
> email: lara.h.ur...@ebi.ac.uk 
>
> [[alternative HTML version deleted]]
>
> ___
>

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

2016-04-12 Thread Maarten van Iterson

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"  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" 
>> > > To: "Dan Tenenbaum" 
>> > > Cc: "Maarten van Iterson" , "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

Re: [Bioc-devel] package submission - problem with vignette

Re: [Bioc-devel] package submission - problem with vignette

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

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