date:20160329

Re: [Rd] body(NULL) <- something; ditto formals() -- should not work

2016-03-29 Thread Hervé Pagès

Hi,

On 03/07/2016 09:26 AM, Martin Maechler wrote:

I'm proposing to signal an error (from R >= 3.3.0) in such
examples -- which do "work" in R 3.2.x and earlier :

f <- NULL; body(f) <- quote(sin(a+1)); f

function ()
sin(a + 1)

This works because formals() (the getter) works on things that are
not a function.

g <- NULL; formals(g) <- alist(x = pi, y=); g

function (x = pi, y)
NULL

And this works because body() (the getter) also works on things that
are not a function.

The proposal is that the underlying C code will signal an error
when such replacement functions would create a function out of
"something not a function".

Why modify the C code for this?

This is how formals() and body() are defined at the moment:

> formals
function (fun = sys.function(sys.parent()))
{
if (is.character(fun))
fun <- get(fun, mode = "function", envir = parent.frame())
.Internal(formals(fun))
}

> body
function (fun = sys.function(sys.parent()))
{
if (is.character(fun))
fun <- get(fun, mode = "function", envir = parent.frame())
.Internal(body(fun))
}

Not sure why they are not simply doing fun <- match.fun(fun) but if
they were, then they would signal an error when called on something
that is not a function.

H.

Martin Maechler, ETH Zurich

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--
Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024

E-mail: hpa...@fredhutch.org
Phone:  (206) 667-5791
Fax:(206) 667-1319

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Re: [Bioc-devel] Lack of Genomic RleList

2016-03-29 Thread Kasper Daniel Hansen

Thanks for the pointer, I'll experiment and update my materials.

Kasper

On Tue, Mar 29, 2016 at 2:43 PM, Hervé Pagès  wrote:

> Hi Dario,
>
> On 03/16/2016 04:00 AM, Dario Strbenac wrote:
>
>> Hello,
>>
>> I have a use case for which I notice other users have already asked about
>> https://stat.ethz.ch/pipermail/bioconductor/2013-December/056400.html
>> and
>> http://kasperdanielhansen.github.io/genbioconductor/html/GenomicRanges_Rle.html#rles-and-granges
>> I'm hoping that, by mentioning it again, it could be included in the future
>> plans for GenomicRanges. It would be nice to avoid making loops for
>> chromosomes and strands, which improves readability.
>>
>
> Janet was asking about subsetting a RleList using a GRanges object.
> I added this more than 2 years ago and it's documented (see last example
> in ?GRanges).
>
> Kasper's section "Rles and GRanges" could benefit from an update showing
> how to subset 'rl' by 'grView' instead of trying to create views on it.
>
> Creating views on a RleList object is not supported yet but could easily
> be done in the same way that I've done it for views on a BSgenome
> object (requested by Kasper 16 months ago):
>
>   https://support.bioconductor.org/p/62749/
>
> H.
>
>
>> --
>> Dario Strbenac
>> PhD Student
>> University of Sydney
>> Camperdown NSW 2050
>> Australia
>> ___
>> Bioc-devel@r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>
>>
> --
> Hervé Pagès
>
> Program in Computational Biology
> Division of Public Health Sciences
> Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N, M1-B514
> P.O. Box 19024
> Seattle, WA 98109-1024
>
> E-mail: hpa...@fredhutch.org
> Phone:  (206) 667-5791
> Fax:(206) 667-1319
>
>
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>

[[alternative HTML version deleted]]

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Re: [Bioc-devel] 49 software packages either have no vignettes or their vignettes are not built by R CMD build!

2016-03-29 Thread Dan Tenenbaum





- Original Message -
> From: "Karim Mezhoud" 
> To: "Dan Tenenbaum" 
> Cc: "bioc-devel" 
> Sent: Tuesday, March 29, 2016 12:05:03 PM
> Subject: Re: [Bioc-devel] 49 software packages either have no vignettes or 
> their vignettes are not built by R CMD build!

> Thank you,
> I am in devel branch (git checkout devel) .
> 
> when I "git svn rebase" I get all changed files with message: needs update.

This doesn't happen with me:

clone https://github.com/kmezhoud/canceR.git
cd canceR/
../mirror/update_remotes.sh
git checkout devel
git svn rebase


No error. You might try doing a fresh clone in another directory.

Dan



> How can I update.
> km
> 
> 
> 
> 
> On Tue, Mar 29, 2016 at 4:16 PM, Dan Tenenbaum 
> wrote:
> 
>>
>>
>> - Original Message -
>> > From: "Karim Mezhoud" 
>> > To: "bioc-devel" 
>> > Cc: "Dan Tenenbaum" 
>> > Sent: Tuesday, March 29, 2016 6:11:15 AM
>> > Subject: Re: [Bioc-devel] 49 software packages either have no vignettes
>> or their vignettes are not built by R CMD build!
>>
>> > Dear Dr Dan,
>> > Thank you for this note.
>> > In my case (canceR), I am using sweave and having:
>> >
>> > checking PDF version of manual ... [8s/19s]   OK
>> >
>> > during R CMD Check.
>> >
>> > I need to sync devel version using git-mirrors (
>> > https://www.bioconductor.org/developers/how-to/git-mirrors/).
>> > I am following scenario 2.
>> > When I fork bioc-mirror/canceR I get two repo with the same name in my
>> > github.
>> >
>>
>> It sounds like you already had a github repository before the fork. In
>> this case, do not fork, just run the update_remotes.sh script.
>> Dan
>>
>>
>> > at step 4 of tutorial, I can not push some changes:
>> >
>> > error: unable to read askpass response from 'rpostback-askpass'
>> > fatal: could not read Username for 'https://github.com': Device not
>> > configured
>> >
>> > 1- How can I configure access to bioc-mirror/canceR.
>> >
>> > 2- What is the utility of the fork if we can commit directly to
>> > bioc-mirror/canceR?
>> >
>> > Thank you
>> > Karim
>> >
>> >
>> > On Wed, Mar 23, 2016 at 10:44 PM, Dan Tenenbaum 
>> > wrote:
>> >
>> >> Attention package maintainers,
>> >>
>> >> When building an R package, if R thinks there is a vignette, it will
>> emit
>> >> this line during R CMD build:
>> >>
>> >> * creating vignettes ... OK
>> >>
>> >> If there is either no vignette, or in the case of non-sweave vignettes,
>> >> something is not set up correctly (there are many things that can go
>> >> wrong), you won't see that line of output.
>> >>
>> >> This means your vignette will not be available on our web site, nor to
>> end
>> >> users who install your package.
>> >>
>> >> So going to the build system and looking through all R CMD build output
>> to
>> >> see which output files do NOT have that line, returns 49 matches:
>> >>
>> >> $ grep -L "creating vignettes ..." *.buildsrc-out.txt
>> >> a4Base.buildsrc-out.txt
>> >> a4Classif.buildsrc-out.txt
>> >> a4Core.buildsrc-out.txt
>> >> a4Preproc.buildsrc-out.txt
>> >> a4Reporting.buildsrc-out.txt
>> >> affxparser.buildsrc-out.txt
>> >> affyio.buildsrc-out.txt
>> >> AffyTiling.buildsrc-out.txt
>> >> aroma.light.buildsrc-out.txt
>> >> arrayQuality.buildsrc-out.txt
>> >> bigmemoryExtras.buildsrc-out.txt
>> >> BiocCaseStudies.buildsrc-out.txt
>> >> BiocGenerics.buildsrc-out.txt
>> >> BiocInstaller.buildsrc-out.txt
>> >> BufferedMatrixMethods.buildsrc-out.txt
>> >> canceR.buildsrc-out.txt
>> >> CGHbase.buildsrc-out.txt
>> >> CoCiteStats.buildsrc-out.txt
>> >> daMA.buildsrc-out.txt
>> >> dcGSA.buildsrc-out.txt
>> >> DynDoc.buildsrc-out.txt
>> >> ExperimentHub.buildsrc-out.txt
>> >> flipflop.buildsrc-out.txt
>> >> GraphAT.buildsrc-out.txt
>> >> HDF5Array.buildsrc-out.txt
>> >> hypergraph.buildsrc-out.txt
>> >> Icens.buildsrc-out.txt
>> >> impute.buildsrc-out.txt
>> >> mcaGUI.buildsrc-out.txt
>> >> microRNA.buildsrc-out.txt
>> >> minet.buildsrc-out.txt
>> >> MSstats.buildsrc-out.txt
>> >> multtest.buildsrc-out.txt
>> >> netresponse.buildsrc-out.txt
>> >> nondetects.buildsrc-out.txt
>> >> normalize450K.buildsrc-out.txt
>> >> oligoClasses.buildsrc-out.txt
>> >> parglms.buildsrc-out.txt
>> >> plier.buildsrc-out.txt
>> >> preprocessCore.buildsrc-out.txt
>> >> ProtGenerics.buildsrc-out.txt
>> >> QUALIFIER.buildsrc-out.txt
>> >> RPA.buildsrc-out.txt
>> >> scde.buildsrc-out.txt
>> >> seqplots.buildsrc-out.txt
>> >> SJava.buildsrc-out.txt
>> >> spotSegmentation.buildsrc-out.txt
>> >> stepNorm.buildsrc-out.txt
>> >> XVector.buildsrc-out.txt
>> >>
>> >> Some of these (a4Base, a4Classif and many more) just have no vignettes/
>> >> directory so no vignettes at all.
>> >>
>> >>
>> >> Others (ExperimentHub for example) have an empty vignettes directory.
>> >>
>> >> But others (QUALIFIER for example) have a vignettes directory with
>> >>

Re: [Bioc-devel] 49 software packages either have no vignettes or their vignettes are not built by R CMD build!

2016-03-29 Thread Karim Mezhoud

Thank you,
I am in devel branch (git checkout devel) .

when I "git svn rebase" I get all changed files with message: needs update.
How can I update.
km




On Tue, Mar 29, 2016 at 4:16 PM, Dan Tenenbaum 
wrote:

>
>
> - Original Message -
> > From: "Karim Mezhoud" 
> > To: "bioc-devel" 
> > Cc: "Dan Tenenbaum" 
> > Sent: Tuesday, March 29, 2016 6:11:15 AM
> > Subject: Re: [Bioc-devel] 49 software packages either have no vignettes
> or their vignettes are not built by R CMD build!
>
> > Dear Dr Dan,
> > Thank you for this note.
> > In my case (canceR), I am using sweave and having:
> >
> > checking PDF version of manual ... [8s/19s]   OK
> >
> > during R CMD Check.
> >
> > I need to sync devel version using git-mirrors (
> > https://www.bioconductor.org/developers/how-to/git-mirrors/).
> > I am following scenario 2.
> > When I fork bioc-mirror/canceR I get two repo with the same name in my
> > github.
> >
>
> It sounds like you already had a github repository before the fork. In
> this case, do not fork, just run the update_remotes.sh script.
> Dan
>
>
> > at step 4 of tutorial, I can not push some changes:
> >
> > error: unable to read askpass response from 'rpostback-askpass'
> > fatal: could not read Username for 'https://github.com': Device not
> > configured
> >
> > 1- How can I configure access to bioc-mirror/canceR.
> >
> > 2- What is the utility of the fork if we can commit directly to
> > bioc-mirror/canceR?
> >
> > Thank you
> > Karim
> >
> >
> > On Wed, Mar 23, 2016 at 10:44 PM, Dan Tenenbaum 
> > wrote:
> >
> >> Attention package maintainers,
> >>
> >> When building an R package, if R thinks there is a vignette, it will
> emit
> >> this line during R CMD build:
> >>
> >> * creating vignettes ... OK
> >>
> >> If there is either no vignette, or in the case of non-sweave vignettes,
> >> something is not set up correctly (there are many things that can go
> >> wrong), you won't see that line of output.
> >>
> >> This means your vignette will not be available on our web site, nor to
> end
> >> users who install your package.
> >>
> >> So going to the build system and looking through all R CMD build output
> to
> >> see which output files do NOT have that line, returns 49 matches:
> >>
> >> $ grep -L "creating vignettes ..." *.buildsrc-out.txt
> >> a4Base.buildsrc-out.txt
> >> a4Classif.buildsrc-out.txt
> >> a4Core.buildsrc-out.txt
> >> a4Preproc.buildsrc-out.txt
> >> a4Reporting.buildsrc-out.txt
> >> affxparser.buildsrc-out.txt
> >> affyio.buildsrc-out.txt
> >> AffyTiling.buildsrc-out.txt
> >> aroma.light.buildsrc-out.txt
> >> arrayQuality.buildsrc-out.txt
> >> bigmemoryExtras.buildsrc-out.txt
> >> BiocCaseStudies.buildsrc-out.txt
> >> BiocGenerics.buildsrc-out.txt
> >> BiocInstaller.buildsrc-out.txt
> >> BufferedMatrixMethods.buildsrc-out.txt
> >> canceR.buildsrc-out.txt
> >> CGHbase.buildsrc-out.txt
> >> CoCiteStats.buildsrc-out.txt
> >> daMA.buildsrc-out.txt
> >> dcGSA.buildsrc-out.txt
> >> DynDoc.buildsrc-out.txt
> >> ExperimentHub.buildsrc-out.txt
> >> flipflop.buildsrc-out.txt
> >> GraphAT.buildsrc-out.txt
> >> HDF5Array.buildsrc-out.txt
> >> hypergraph.buildsrc-out.txt
> >> Icens.buildsrc-out.txt
> >> impute.buildsrc-out.txt
> >> mcaGUI.buildsrc-out.txt
> >> microRNA.buildsrc-out.txt
> >> minet.buildsrc-out.txt
> >> MSstats.buildsrc-out.txt
> >> multtest.buildsrc-out.txt
> >> netresponse.buildsrc-out.txt
> >> nondetects.buildsrc-out.txt
> >> normalize450K.buildsrc-out.txt
> >> oligoClasses.buildsrc-out.txt
> >> parglms.buildsrc-out.txt
> >> plier.buildsrc-out.txt
> >> preprocessCore.buildsrc-out.txt
> >> ProtGenerics.buildsrc-out.txt
> >> QUALIFIER.buildsrc-out.txt
> >> RPA.buildsrc-out.txt
> >> scde.buildsrc-out.txt
> >> seqplots.buildsrc-out.txt
> >> SJava.buildsrc-out.txt
> >> spotSegmentation.buildsrc-out.txt
> >> stepNorm.buildsrc-out.txt
> >> XVector.buildsrc-out.txt
> >>
> >> Some of these (a4Base, a4Classif and many more) just have no vignettes/
> >> directory so no vignettes at all.
> >>
> >>
> >> Others (ExperimentHub for example) have an empty vignettes directory.
> >>
> >> But others (QUALIFIER for example) have a vignettes directory with
> >> vignette files.
> >>
> >> If any packages you maintain do not have a vignette, please add one.
> >>
> >> If your package has a vignette in the vignettes/ directory but is in the
> >> above list, then you need to fix it.
> >>
> >> This page is a good place to start tracking down the problem:
> >>
> >> http://yihui.name/knitr/demo/vignette/
> >>
> >> For non-sweave (usually knitr) vignettes, the important things to check
> >> are:
> >>
> >> - knitr should be in the Suggests field in DESCRIPTION
> >>   (if using BiocStyle with rmarkdown, be sure BiocStyle and rmarkdown
> are
> >>   also in Suggests).
> >> - VignetteBuilder: knitr should be in DESCRIPTION
> >> - The actual vignette file should have a %\VignetteEngine

Re: [Bioc-devel] Lack of Genomic RleList

2016-03-29 Thread Hervé Pagès

Hi Dario,

On 03/16/2016 04:00 AM, Dario Strbenac wrote:

Hello,

I have a use case for which I notice other users have already asked about
https://stat.ethz.ch/pipermail/bioconductor/2013-December/056400.html and
http://kasperdanielhansen.github.io/genbioconductor/html/GenomicRanges_Rle.html#rles-and-granges
I'm hoping that, by mentioning it again, it could be included in the future
plans for GenomicRanges. It would be nice to avoid making loops for chromosomes
and strands, which improves readability.

Janet was asking about subsetting a RleList using a GRanges object.
I added this more than 2 years ago and it's documented (see last example
in ?GRanges).

Kasper's section "Rles and GRanges" could benefit from an update showing
how to subset 'rl' by 'grView' instead of trying to create views on it.

Creating views on a RleList object is not supported yet but could easily
be done in the same way that I've done it for views on a BSgenome
object (requested by Kasper 16 months ago):

https://support.bioconductor.org/p/62749/

--
Dario Strbenac
PhD Student
University of Sydney
Camperdown NSW 2050
Australia
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--
Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024

E-mail: hpa...@fredhutch.org
Phone: (206) 667-5791
Fax:(206) 667-1319

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Re: [Bioc-devel] package build failing in Windows with "Failed to locate the 'texi2pdf' output file"

2016-03-29 Thread Ramon Diaz-Uriarte

Thanks Dan.

Best,

R.


On Tue, 29-03-2016, at 17:03, Dan Tenenbaum  wrote:
> This error happens once in a while. It's very hard to reproduce because of 
> that (which is probably why I never received a reply when reporting the issue 
> on R-devel), but the 'solution' is to wait until the next build report and it 
> will be gone.
>
> I just manually built your package on moscato2 and it was fine.
>
> Dan
>
>
> - Original Message -
>> From: "Ramon Diaz-Uriarte" 
>> To: "bioc-devel" 
>> Cc: "ramon diaz" 
>> Sent: Tuesday, March 29, 2016 1:34:04 AM
>> Subject: [Bioc-devel] package build failing in Windows with "Failed to   
>> locate the 'texi2pdf' output file"
>
>> Dear All,
>> 
>> I have a package, ADaCGH2, that I just noticed has failed to build in
>> Windows in the latest report
>> (https://www.bioconductor.org/checkResults/devel/bioc-LATEST/ADaCGH2/moscato2-buildsrc.html).
>> The
>> error is the dreaded
>> 
>> Error in find_vignette_product(name, by = "texi2pdf", engine = engine) :
>>  Failed to locate the 'texi2pdf' output file (by engine 'utils::Sweave')
>>  for vignette
>> 
>> 
>> But I just run the build and check three times on a local windows machine
>> (with 3.3.0 alpha, r70387) and build and check are fine. Moreover, this
>> package has not changed at all in a long time, so I do not understand why
>> it should be failing now when it was not failing in previous reports
>> (though I am not sure when it first started failing) and there is, in fact,
>> a Windows binary for this version from the BioC page
>> (https://www.bioconductor.org/packages/3.3/bioc/html/ADaCGH2.html).
>> 
>> I am not sure how to proceed.
>> 
>> Best,
>> 
>> R.
>> 
>> --
>> Ramon Diaz-Uriarte
>> Department of Biochemistry, Lab B-25
>> Facultad de Medicina
>> Universidad Autónoma de Madrid
>> Arzobispo Morcillo, 4
>> 28029 Madrid
>> Spain
>> 
>> Phone: +34-91-497-2412
>> 
>> Email: rdia...@gmail.com
>>   ramon.d...@iib.uam.es
>> 
>> http://ligarto.org/rdiaz
>> 
>> ___
>> Bioc-devel@r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel


-- 
Ramon Diaz-Uriarte
Department of Biochemistry, Lab B-25
Facultad de Medicina
Universidad Autónoma de Madrid 
Arzobispo Morcillo, 4
28029 Madrid
Spain

Phone: +34-91-497-2412

Email: rdia...@gmail.com
   ramon.d...@iib.uam.es

http://ligarto.org/rdiaz

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Re: [Bioc-devel] 49 software packages either have no vignettes or their vignettes are not built by R CMD build!

2016-03-29 Thread Dan Tenenbaum



- Original Message -
> From: "Karim Mezhoud" 
> To: "bioc-devel" 
> Cc: "Dan Tenenbaum" 
> Sent: Tuesday, March 29, 2016 6:11:15 AM
> Subject: Re: [Bioc-devel] 49 software packages either have no vignettes or 
> their vignettes are not built by R CMD build!

> Dear Dr Dan,
> Thank you for this note.
> In my case (canceR), I am using sweave and having:
> 
> checking PDF version of manual ... [8s/19s]   OK
> 
> during R CMD Check.
> 
> I need to sync devel version using git-mirrors (
> https://www.bioconductor.org/developers/how-to/git-mirrors/).
> I am following scenario 2.
> When I fork bioc-mirror/canceR I get two repo with the same name in my
> github.
> 

It sounds like you already had a github repository before the fork. In this 
case, do not fork, just run the update_remotes.sh script.
Dan


> at step 4 of tutorial, I can not push some changes:
> 
> error: unable to read askpass response from 'rpostback-askpass'
> fatal: could not read Username for 'https://github.com': Device not
> configured
> 
> 1- How can I configure access to bioc-mirror/canceR.
> 
> 2- What is the utility of the fork if we can commit directly to
> bioc-mirror/canceR?
> 
> Thank you
> Karim
> 
> 
> On Wed, Mar 23, 2016 at 10:44 PM, Dan Tenenbaum 
> wrote:
> 
>> Attention package maintainers,
>>
>> When building an R package, if R thinks there is a vignette, it will emit
>> this line during R CMD build:
>>
>> * creating vignettes ... OK
>>
>> If there is either no vignette, or in the case of non-sweave vignettes,
>> something is not set up correctly (there are many things that can go
>> wrong), you won't see that line of output.
>>
>> This means your vignette will not be available on our web site, nor to end
>> users who install your package.
>>
>> So going to the build system and looking through all R CMD build output to
>> see which output files do NOT have that line, returns 49 matches:
>>
>> $ grep -L "creating vignettes ..." *.buildsrc-out.txt
>> a4Base.buildsrc-out.txt
>> a4Classif.buildsrc-out.txt
>> a4Core.buildsrc-out.txt
>> a4Preproc.buildsrc-out.txt
>> a4Reporting.buildsrc-out.txt
>> affxparser.buildsrc-out.txt
>> affyio.buildsrc-out.txt
>> AffyTiling.buildsrc-out.txt
>> aroma.light.buildsrc-out.txt
>> arrayQuality.buildsrc-out.txt
>> bigmemoryExtras.buildsrc-out.txt
>> BiocCaseStudies.buildsrc-out.txt
>> BiocGenerics.buildsrc-out.txt
>> BiocInstaller.buildsrc-out.txt
>> BufferedMatrixMethods.buildsrc-out.txt
>> canceR.buildsrc-out.txt
>> CGHbase.buildsrc-out.txt
>> CoCiteStats.buildsrc-out.txt
>> daMA.buildsrc-out.txt
>> dcGSA.buildsrc-out.txt
>> DynDoc.buildsrc-out.txt
>> ExperimentHub.buildsrc-out.txt
>> flipflop.buildsrc-out.txt
>> GraphAT.buildsrc-out.txt
>> HDF5Array.buildsrc-out.txt
>> hypergraph.buildsrc-out.txt
>> Icens.buildsrc-out.txt
>> impute.buildsrc-out.txt
>> mcaGUI.buildsrc-out.txt
>> microRNA.buildsrc-out.txt
>> minet.buildsrc-out.txt
>> MSstats.buildsrc-out.txt
>> multtest.buildsrc-out.txt
>> netresponse.buildsrc-out.txt
>> nondetects.buildsrc-out.txt
>> normalize450K.buildsrc-out.txt
>> oligoClasses.buildsrc-out.txt
>> parglms.buildsrc-out.txt
>> plier.buildsrc-out.txt
>> preprocessCore.buildsrc-out.txt
>> ProtGenerics.buildsrc-out.txt
>> QUALIFIER.buildsrc-out.txt
>> RPA.buildsrc-out.txt
>> scde.buildsrc-out.txt
>> seqplots.buildsrc-out.txt
>> SJava.buildsrc-out.txt
>> spotSegmentation.buildsrc-out.txt
>> stepNorm.buildsrc-out.txt
>> XVector.buildsrc-out.txt
>>
>> Some of these (a4Base, a4Classif and many more) just have no vignettes/
>> directory so no vignettes at all.
>>
>>
>> Others (ExperimentHub for example) have an empty vignettes directory.
>>
>> But others (QUALIFIER for example) have a vignettes directory with
>> vignette files.
>>
>> If any packages you maintain do not have a vignette, please add one.
>>
>> If your package has a vignette in the vignettes/ directory but is in the
>> above list, then you need to fix it.
>>
>> This page is a good place to start tracking down the problem:
>>
>> http://yihui.name/knitr/demo/vignette/
>>
>> For non-sweave (usually knitr) vignettes, the important things to check
>> are:
>>
>> - knitr should be in the Suggests field in DESCRIPTION
>>   (if using BiocStyle with rmarkdown, be sure BiocStyle and rmarkdown are
>>   also in Suggests).
>> - VignetteBuilder: knitr should be in DESCRIPTION
>> - The actual vignette file should have a %\VignetteEngine line; see link
>> above
>>   for more information.
>>
>> How can you tell if you've fixed the problem?
>> run R CMD build on your package and look for the line
>>
>> * creating vignettes ... OK
>>
>> In the output. If you don't see that line, your vignette has not been
>> built.
>>
>> If you've tried all these things and are still running into problems,
>> contact bioc-devel.
>>
>> Dan
>>
>> ___
>> Bioc-devel@r-project.org mailing list
>>

Re: [Bioc-devel] package build failing in Windows with "Failed to locate the 'texi2pdf' output file"

2016-03-29 Thread Dan Tenenbaum

Actually your problem is different and does not affect windows.

Which branch have you committed your changes to? 

Can you do the following?

git checkout release-3.2
git checkout -b issue/vignette-problem 
# fix the problem
git commit -a
git push # then copy and paste the command that git suggests

Then let me know and I will investigate merging that branch with release-3.2.

Dan


- Original Message -
> From: "Tiphaine Martin" 
> To: "bioc-devel" 
> Sent: Tuesday, March 29, 2016 1:55:25 AM
> Subject: Re: [Bioc-devel] package build failing in Windows with "Failed   
> to  locate the 'texi2pdf' output file"

> Hi,
> I have the same issue build failing in Windows and Mac for the release 
> version,
> but not for devel version that are similar as I didn't do some update from the
> last release.
> 
> I did some update on my GitHub recently and I tried to follow different advice
> to push my update to SVN of Bioconductor. I have the same error that I want to
> update any branch when I run "git svn dcommit --add-author-from".
> 
> Unable to determine upstream SVN information from HEAD history.
> Perhaps the repository is empty. at /usr/lib/git-core/git-svn line 866.
> 
> Beforehand, I used git-svn bridge that could be the origin of issue, but I 
> don't
> know how to handle because I tried to cherry-pick, it told me that I have 
> empty
> pick.
> 
>  When I did Sunday, it creates a request for a pull on
>  https://github.com/Bioconductor-mirror/coMET. This request is not more here
>  and no of my branch are updated.
> 
> I don't know what to do. If one of you have any advice, I am happy to try it.
> 
> Regards,
> Tiphaine
> 
> 
> Tiphaine Martin
> PhD Research Student | King's College
> The Department of Twin Research & Genetic Epidemiology | Genetics & Molecular
> Medicine Division
> St Thomas' Hospital
> 4th Floor, Block D, South Wing
> SE1 7EH, London
> United Kingdom
> 
> email : tiphaine.mar...@kcl.ac.uk
> Fax: +44 (0) 207 188 6761
> 
> 
> From: Bioc-devel  on behalf of Ramon
> Diaz-Uriarte 
> Sent: 29 March 2016 09:34
> To: bioc-devel@r-project.org
> Cc: ramon.d...@iib.uam.es
> Subject: [Bioc-devel] package build failing in Windows with "Failed to  locate
> the 'texi2pdf' output file"
> 
> Dear All,
> 
> I have a package, ADaCGH2, that I just noticed has failed to build in
> Windows in the latest report
> (https://www.bioconductor.org/checkResults/devel/bioc-LATEST/ADaCGH2/moscato2-buildsrc.html).
> The
> error is the dreaded
> 
> Error in find_vignette_product(name, by = "texi2pdf", engine = engine) :
>  Failed to locate the 'texi2pdf' output file (by engine 'utils::Sweave')
>  for vignette
> 
> 
> But I just run the build and check three times on a local windows machine
> (with 3.3.0 alpha, r70387) and build and check are fine. Moreover, this
> package has not changed at all in a long time, so I do not understand why
> it should be failing now when it was not failing in previous reports
> (though I am not sure when it first started failing) and there is, in fact,
> a Windows binary for this version from the BioC page
> (https://www.bioconductor.org/packages/3.3/bioc/html/ADaCGH2.html).
> 
> I am not sure how to proceed.
> 
> Best,
> 
> R.
> 
> --
> Ramon Diaz-Uriarte
> Department of Biochemistry, Lab B-25
> Facultad de Medicina
> Universidad Autónoma de Madrid
> Arzobispo Morcillo, 4
> 28029 Madrid
> Spain
> 
> Phone: +34-91-497-2412
> 
> Email: rdia...@gmail.com
>   ramon.d...@iib.uam.es
> 
> http://ligarto.org/rdiaz
> 
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
> 
> ___
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> https://stat.ethz.ch/mailman/listinfo/bioc-devel

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[Rd] DESCRIPTION file: Space after colon mandatory?

2016-03-29 Thread Kirill Müller

According to R-exts, DESCRIPTION is a DCF variant, and " Fields start 
with an ASCII name immediately followed by a colon: the value starts 
after the colon and a space." However, according to the linked 
https://www.debian.org/doc/debian-policy/ch-controlfields.html, 
horizontal space before and after a value are trimmed, this is also the 
behavior of read.dcf().


Is this an omission in the documentation, or is the space after the 
colon actually required? Thanks.



Best regards

Kirill

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Re: [Bioc-devel] 49 software packages either have no vignettes or their vignettes are not built by R CMD build!

2016-03-29 Thread Karim Mezhoud

Dear Dr Dan,
Thank you for this note.
In my case (canceR), I am using sweave and having:

 checking PDF version of manual ... [8s/19s]   OK

during R CMD Check.

I need to sync devel version using git-mirrors (
https://www.bioconductor.org/developers/how-to/git-mirrors/).
I am following scenario 2.
When I fork bioc-mirror/canceR I get two repo with the same name in my
github.

at step 4 of tutorial, I can not push some changes:

error: unable to read askpass response from 'rpostback-askpass'
fatal: could not read Username for 'https://github.com': Device not
configured

1- How can I configure access to bioc-mirror/canceR.

2- What is the utility of the fork if we can commit directly to
bioc-mirror/canceR?

Thank you
Karim


On Wed, Mar 23, 2016 at 10:44 PM, Dan Tenenbaum 
wrote:

> Attention package maintainers,
>
> When building an R package, if R thinks there is a vignette, it will emit
> this line during R CMD build:
>
> * creating vignettes ... OK
>
> If there is either no vignette, or in the case of non-sweave vignettes,
> something is not set up correctly (there are many things that can go
> wrong), you won't see that line of output.
>
> This means your vignette will not be available on our web site, nor to end
> users who install your package.
>
> So going to the build system and looking through all R CMD build output to
> see which output files do NOT have that line, returns 49 matches:
>
> $ grep -L "creating vignettes ..." *.buildsrc-out.txt
> a4Base.buildsrc-out.txt
> a4Classif.buildsrc-out.txt
> a4Core.buildsrc-out.txt
> a4Preproc.buildsrc-out.txt
> a4Reporting.buildsrc-out.txt
> affxparser.buildsrc-out.txt
> affyio.buildsrc-out.txt
> AffyTiling.buildsrc-out.txt
> aroma.light.buildsrc-out.txt
> arrayQuality.buildsrc-out.txt
> bigmemoryExtras.buildsrc-out.txt
> BiocCaseStudies.buildsrc-out.txt
> BiocGenerics.buildsrc-out.txt
> BiocInstaller.buildsrc-out.txt
> BufferedMatrixMethods.buildsrc-out.txt
> canceR.buildsrc-out.txt
> CGHbase.buildsrc-out.txt
> CoCiteStats.buildsrc-out.txt
> daMA.buildsrc-out.txt
> dcGSA.buildsrc-out.txt
> DynDoc.buildsrc-out.txt
> ExperimentHub.buildsrc-out.txt
> flipflop.buildsrc-out.txt
> GraphAT.buildsrc-out.txt
> HDF5Array.buildsrc-out.txt
> hypergraph.buildsrc-out.txt
> Icens.buildsrc-out.txt
> impute.buildsrc-out.txt
> mcaGUI.buildsrc-out.txt
> microRNA.buildsrc-out.txt
> minet.buildsrc-out.txt
> MSstats.buildsrc-out.txt
> multtest.buildsrc-out.txt
> netresponse.buildsrc-out.txt
> nondetects.buildsrc-out.txt
> normalize450K.buildsrc-out.txt
> oligoClasses.buildsrc-out.txt
> parglms.buildsrc-out.txt
> plier.buildsrc-out.txt
> preprocessCore.buildsrc-out.txt
> ProtGenerics.buildsrc-out.txt
> QUALIFIER.buildsrc-out.txt
> RPA.buildsrc-out.txt
> scde.buildsrc-out.txt
> seqplots.buildsrc-out.txt
> SJava.buildsrc-out.txt
> spotSegmentation.buildsrc-out.txt
> stepNorm.buildsrc-out.txt
> XVector.buildsrc-out.txt
>
> Some of these (a4Base, a4Classif and many more) just have no vignettes/
> directory so no vignettes at all.
>
>
> Others (ExperimentHub for example) have an empty vignettes directory.
>
> But others (QUALIFIER for example) have a vignettes directory with
> vignette files.
>
> If any packages you maintain do not have a vignette, please add one.
>
> If your package has a vignette in the vignettes/ directory but is in the
> above list, then you need to fix it.
>
> This page is a good place to start tracking down the problem:
>
> http://yihui.name/knitr/demo/vignette/
>
> For non-sweave (usually knitr) vignettes, the important things to check
> are:
>
> - knitr should be in the Suggests field in DESCRIPTION
>   (if using BiocStyle with rmarkdown, be sure BiocStyle and rmarkdown are
>   also in Suggests).
> - VignetteBuilder: knitr should be in DESCRIPTION
> - The actual vignette file should have a %\VignetteEngine line; see link
> above
>   for more information.
>
> How can you tell if you've fixed the problem?
> run R CMD build on your package and look for the line
>
> * creating vignettes ... OK
>
> In the output. If you don't see that line, your vignette has not been
> built.
>
> If you've tried all these things and are still running into problems,
> contact bioc-devel.
>
> Dan
>
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>

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[Bioc-devel] package build failing in Windows with "Failed to locate the 'texi2pdf' output file"

2016-03-29 Thread Ramon Diaz-Uriarte

Dear All,

I have a package, ADaCGH2, that I just noticed has failed to build in
Windows in the latest report
(https://www.bioconductor.org/checkResults/devel/bioc-LATEST/ADaCGH2/moscato2-buildsrc.html).
 The
error is the dreaded

Error in find_vignette_product(name, by = "texi2pdf", engine = engine) : 
  Failed to locate the 'texi2pdf' output file (by engine 'utils::Sweave')
  for vignette


But I just run the build and check three times on a local windows machine
(with 3.3.0 alpha, r70387) and build and check are fine. Moreover, this
package has not changed at all in a long time, so I do not understand why
it should be failing now when it was not failing in previous reports
(though I am not sure when it first started failing) and there is, in fact,
a Windows binary for this version from the BioC page
(https://www.bioconductor.org/packages/3.3/bioc/html/ADaCGH2.html).

I am not sure how to proceed.

Best,

R.

-- 
Ramon Diaz-Uriarte
Department of Biochemistry, Lab B-25
Facultad de Medicina
Universidad Autónoma de Madrid 
Arzobispo Morcillo, 4
28029 Madrid
Spain

Phone: +34-91-497-2412

Email: rdia...@gmail.com
   ramon.d...@iib.uam.es

http://ligarto.org/rdiaz

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[Rd] documentation / warning when passing a vector as lower/upper bound in stats::integrate()

2016-03-29 Thread Baptiste Auguie

Dear R-dev list,

I wonder if stats::integrate shouldn't warn the user when a numeric vector
of length > 1 is passed as lower or upper bounds. If a vector is passed,
only the first value is used and the others are silently ignored:

integrate(sin, lower=0, upper=pi)
integrate(sin, lower=0:10, upper=pi)

?integrate doesn't appear to mention explicitly that the function is not
vectorised over those arguments.

It's probably not a common mistake, but it can have unfortunate
consequences in the iterative calculation of multiple integrals. Someone
was puzzled by this today (http://stackoverflow.com/q/36275909/471093) and
it wasn't immediately obvious what had led to incorrect results (and worse,
it could have gone unnoticed).

Best regards,

baptiste

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Re: [Rd] body(NULL) <- something; ditto formals() -- should not work

Re: [Bioc-devel] Lack of Genomic RleList

Re: [Bioc-devel] 49 software packages either have no vignettes or their vignettes are not built by R CMD build!

Re: [Bioc-devel] 49 software packages either have no vignettes or their vignettes are not built by R CMD build!

Re: [Bioc-devel] Lack of Genomic RleList

Re: [Bioc-devel] package build failing in Windows with "Failed to locate the 'texi2pdf' output file"

Re: [Bioc-devel] 49 software packages either have no vignettes or their vignettes are not built by R CMD build!

Re: [Bioc-devel] package build failing in Windows with "Failed to locate the 'texi2pdf' output file"

[Rd] DESCRIPTION file: Space after colon mandatory?

Re: [Bioc-devel] 49 software packages either have no vignettes or their vignettes are not built by R CMD build!

[Bioc-devel] package build failing in Windows with "Failed to locate the 'texi2pdf' output file"

[Rd] documentation / warning when passing a vector as lower/upper bound in stats::integrate()

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