date:20160402

Re: [Bioc-devel] Package Without a Vignette

2016-04-02 Thread Dan Tenenbaum

The nightly builds run every night (except Friday night) and if your commits 
are done before 5:20 PM (Seattle time) they will be reflected in the next day's 
build report.

But you don't need the build system or even travis to see if your vignette will 
be built by R CMD build.

All you have to do is run "R CMD build cogena" and if you see the line

* installing the package to build vignettes

then it means your vignettes will be created. If you don't see that line, the 
vignettes will not be built.

Dan




- Original Message -
> From: "Zhilong Jia" 
> To: "Dan Tenenbaum" 
> Cc: "Stefan Haunsberger" , "bioc-devel" 
> 
> Sent: Saturday, April 2, 2016 7:23:14 PM
> Subject: Re: [Bioc-devel] Package Without a Vignette

> Hi Dan,
> 
> Thank you. I updated it.
> 
> At the beginning,  knitr was used but would result in errors in travis-ci,
> like https://github.com/ropensci/rentrez/issues/71 and
> https://github.com/ropensci/rentrez/commit/8ee84ba29472f56f3f92bf65511e1a29121882d4
> so I changed knitr into rmarkdown and it works in travis-ci. I'm not sure
> what's the problem here exactly? Thank you.
> 
> For cogena's travis-ci
> 
> the knitr one is : https://travis-ci.org/zhilongjia/cogena/builds/119812514
> the rmarkdown one is:
> https://travis-ci.org/zhilongjia/cogena/builds/119819020
> 
> BTW, it seems there is a 2-3 days delay for  bioconductor to build the
> updated package. Is there a way for users to build it immediately by
> themselves?
> 
> Cheers,
> Zhilong
> 
> 
> On 3 April 2016 at 09:09, Dan Tenenbaum  wrote:
> 
>> In DESCRIPTION change
>>
>> VignetteBuilder: rmarkdown
>>
>> to
>>
>> VignetteBuilder: knitr
>>
>> Dan
>>
>>
>> - Original Message -
>> > From: "Zhilong Jia" 
>> > To: "Stefan Haunsberger" 
>> > Cc: "bioc-devel" 
>> > Sent: Saturday, April 2, 2016 5:48:59 PM
>> > Subject: Re: [Bioc-devel] Package Without a Vignette
>>
>> > Hi,
>> >
>> > I just found no vignette for my updated package cogena
>> >  (1.5.2),
>> > though there are vignettes  in the code. And the check CMD is
>> > /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings
>> > cogena_1.5.2.tar.gz in
>> >
>> http://bioconductor.org/checkResults/3.3/bioc-LATEST/cogena/zin2-checksrc.html
>> >
>> > And the similar section is here:
>> >
>> > vignette: >
>> >  %\VignetteIndexEntry{Vignette Title}
>> >  %\VignetteEngine{knitr::rmarkdown}
>> >  %\usepackage[utf8]{inputenc}
>> >
>> > No \\ here.
>> >
>> >
>> > Thank you.
>> >
>> > Regards,
>> > Zhilong
>> >
>> >
>> > On 22 March 2016 at 18:24, Stefan Haunsberger <
>> stefan.haunsber...@gmail.com>
>> > wrote:
>> >
>> >> Hi,
>> >>
>> >> Yes, my bad. I'm already on it.
>> >>
>> >> Thanks,
>> >> Stefan
>> >>
>> >> On Tue, Mar 22, 2016 at 10:14 AM Martin Morgan <
>> >> martin.mor...@roswellpark.org> wrote:
>> >>
>> >> >
>> >> >
>> >> > On 03/22/2016 03:00 AM, Dario Strbenac wrote:
>> >> > > Hello,
>> >> > >
>> >> > > The newly added Bioconductor package miRNAmeConverter has no
>> vignette,
>> >> > although a vignette is a requirement for Bioconductor packages which
>> are
>> >> > not simply annotation databases.
>> >> >
>> >> > Rather, the package has a vignette, but it is not built.
>> >> >
>> >> > This is because of the '\\' in the vignette header. Also, the 'html'
>> and
>> >> > 'pdf' versions of the vignette should not be in SVN.
>> >> >
>> >> > I've cc'd the maintainer.
>> >> >
>> >> > Martin
>> >> >
>> >> >
>> >> > Index: miRNAmeConverter-vignette.Rmd
>> >> > ===
>> >> > --- miRNAmeConverter-vignette.Rmd   (revision 115094)
>> >> > +++ miRNAmeConverter-vignette.Rmd   (working copy)
>> >> > @@ -9,9 +9,9 @@
>> >> >   csl: apa.csl
>> >> >   bibliography: references.bib
>> >> >   vignette: >
>> >> > -   %\\VignetteIndexEntry{miRNAmeConverter-vignette}
>> >> > -   %\\VignetteEncoding{UTF-8}
>> >> > -   %\\VignetteEngine{knitr::rmarkdown}
>> >> > +   %\VignetteIndexEntry{miRNAmeConverter-vignette}
>> >> > +   %\VignetteEncoding{UTF-8}
>> >> > +   %\VignetteEngine{knitr::rmarkdown}
>> >> >   ---
>> >> >
>> >> >   > >> > > 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
>> >> > >
>> >> >
>> >> >
>> >> > This email message may contain legally privileged and/or confidential
>> >> > information.  If you are not the intended recipient(s), or the
>> employee
>> >> or
>> >> > agent responsible for the delivery of this message to the intended
>> >> > recipient(s), you are hereby notified that any disclosure,

Re: [Bioc-devel] Package Without a Vignette

2016-04-02 Thread Zhilong Jia

Hi Dan,

Thank you. I updated it.

At the beginning,  knitr was used but would result in errors in travis-ci,
like https://github.com/ropensci/rentrez/issues/71 and
https://github.com/ropensci/rentrez/commit/8ee84ba29472f56f3f92bf65511e1a29121882d4
so I changed knitr into rmarkdown and it works in travis-ci. I'm not sure
what's the problem here exactly? Thank you.

For cogena's travis-ci

the knitr one is : https://travis-ci.org/zhilongjia/cogena/builds/119812514
the rmarkdown one is:
https://travis-ci.org/zhilongjia/cogena/builds/119819020

BTW, it seems there is a 2-3 days delay for  bioconductor to build the
updated package. Is there a way for users to build it immediately by
themselves?

Cheers,
Zhilong


On 3 April 2016 at 09:09, Dan Tenenbaum  wrote:

> In DESCRIPTION change
>
> VignetteBuilder: rmarkdown
>
> to
>
> VignetteBuilder: knitr
>
> Dan
>
>
> - Original Message -
> > From: "Zhilong Jia" 
> > To: "Stefan Haunsberger" 
> > Cc: "bioc-devel" 
> > Sent: Saturday, April 2, 2016 5:48:59 PM
> > Subject: Re: [Bioc-devel] Package Without a Vignette
>
> > Hi,
> >
> > I just found no vignette for my updated package cogena
> >  (1.5.2),
> > though there are vignettes  in the code. And the check CMD is
> > /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings
> > cogena_1.5.2.tar.gz in
> >
> http://bioconductor.org/checkResults/3.3/bioc-LATEST/cogena/zin2-checksrc.html
> >
> > And the similar section is here:
> >
> > vignette: >
> >  %\VignetteIndexEntry{Vignette Title}
> >  %\VignetteEngine{knitr::rmarkdown}
> >  %\usepackage[utf8]{inputenc}
> >
> > No \\ here.
> >
> >
> > Thank you.
> >
> > Regards,
> > Zhilong
> >
> >
> > On 22 March 2016 at 18:24, Stefan Haunsberger <
> stefan.haunsber...@gmail.com>
> > wrote:
> >
> >> Hi,
> >>
> >> Yes, my bad. I'm already on it.
> >>
> >> Thanks,
> >> Stefan
> >>
> >> On Tue, Mar 22, 2016 at 10:14 AM Martin Morgan <
> >> martin.mor...@roswellpark.org> wrote:
> >>
> >> >
> >> >
> >> > On 03/22/2016 03:00 AM, Dario Strbenac wrote:
> >> > > Hello,
> >> > >
> >> > > The newly added Bioconductor package miRNAmeConverter has no
> vignette,
> >> > although a vignette is a requirement for Bioconductor packages which
> are
> >> > not simply annotation databases.
> >> >
> >> > Rather, the package has a vignette, but it is not built.
> >> >
> >> > This is because of the '\\' in the vignette header. Also, the 'html'
> and
> >> > 'pdf' versions of the vignette should not be in SVN.
> >> >
> >> > I've cc'd the maintainer.
> >> >
> >> > Martin
> >> >
> >> >
> >> > Index: miRNAmeConverter-vignette.Rmd
> >> > ===
> >> > --- miRNAmeConverter-vignette.Rmd   (revision 115094)
> >> > +++ miRNAmeConverter-vignette.Rmd   (working copy)
> >> > @@ -9,9 +9,9 @@
> >> >   csl: apa.csl
> >> >   bibliography: references.bib
> >> >   vignette: >
> >> > -   %\\VignetteIndexEntry{miRNAmeConverter-vignette}
> >> > -   %\\VignetteEncoding{UTF-8}
> >> > -   %\\VignetteEngine{knitr::rmarkdown}
> >> > +   %\VignetteIndexEntry{miRNAmeConverter-vignette}
> >> > +   %\VignetteEncoding{UTF-8}
> >> > +   %\VignetteEngine{knitr::rmarkdown}
> >> >   ---
> >> >
> >> >>> > > 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
> >> > >
> >> >
> >> >
> >> > This email message may contain legally privileged and/or confidential
> >> > information.  If you are not the intended recipient(s), or the
> employee
> >> or
> >> > agent responsible for the delivery of this message to the intended
> >> > recipient(s), you are hereby notified that any disclosure, copying,
> >> > distribution, or use of this email message is prohibited.  If you have
> >> > received this message in error, please notify the sender immediately
> by
> >> > e-mail and delete this email message from your computer. Thank you.
> >> >
> >>
> >> [[alternative HTML version deleted]]
> >>
> >> ___
> >> Bioc-devel@r-project.org mailing list
> >> https://stat.ethz.ch/mailman/listinfo/bioc-devel
> >>
> >
> >
> >
> > --
> > Zhilong JIA
> > zhilong...@gmail.com
> > https://github.com/zhilongjia
> >
> >   [[alternative HTML version deleted]]
> >
> > ___
> > Bioc-devel@r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
>



-- 
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zhilong...@gmail.com
https://github.com/zhilongjia

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Re: [Bioc-devel] Package Without a Vignette

2016-04-02 Thread Dan Tenenbaum

In DESCRIPTION change 

VignetteBuilder: rmarkdown

to 

VignetteBuilder: knitr

Dan


- Original Message -
> From: "Zhilong Jia" 
> To: "Stefan Haunsberger" 
> Cc: "bioc-devel" 
> Sent: Saturday, April 2, 2016 5:48:59 PM
> Subject: Re: [Bioc-devel] Package Without a Vignette

> Hi,
> 
> I just found no vignette for my updated package cogena
>  (1.5.2),
> though there are vignettes  in the code. And the check CMD is
> /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings
> cogena_1.5.2.tar.gz in
> http://bioconductor.org/checkResults/3.3/bioc-LATEST/cogena/zin2-checksrc.html
> 
> And the similar section is here:
> 
> vignette: >
>  %\VignetteIndexEntry{Vignette Title}
>  %\VignetteEngine{knitr::rmarkdown}
>  %\usepackage[utf8]{inputenc}
> 
> No \\ here.
> 
> 
> Thank you.
> 
> Regards,
> Zhilong
> 
> 
> On 22 March 2016 at 18:24, Stefan Haunsberger 
> wrote:
> 
>> Hi,
>>
>> Yes, my bad. I'm already on it.
>>
>> Thanks,
>> Stefan
>>
>> On Tue, Mar 22, 2016 at 10:14 AM Martin Morgan <
>> martin.mor...@roswellpark.org> wrote:
>>
>> >
>> >
>> > On 03/22/2016 03:00 AM, Dario Strbenac wrote:
>> > > Hello,
>> > >
>> > > The newly added Bioconductor package miRNAmeConverter has no vignette,
>> > although a vignette is a requirement for Bioconductor packages which are
>> > not simply annotation databases.
>> >
>> > Rather, the package has a vignette, but it is not built.
>> >
>> > This is because of the '\\' in the vignette header. Also, the 'html' and
>> > 'pdf' versions of the vignette should not be in SVN.
>> >
>> > I've cc'd the maintainer.
>> >
>> > Martin
>> >
>> >
>> > Index: miRNAmeConverter-vignette.Rmd
>> > ===
>> > --- miRNAmeConverter-vignette.Rmd   (revision 115094)
>> > +++ miRNAmeConverter-vignette.Rmd   (working copy)
>> > @@ -9,9 +9,9 @@
>> >   csl: apa.csl
>> >   bibliography: references.bib
>> >   vignette: >
>> > -   %\\VignetteIndexEntry{miRNAmeConverter-vignette}
>> > -   %\\VignetteEncoding{UTF-8}
>> > -   %\\VignetteEngine{knitr::rmarkdown}
>> > +   %\VignetteIndexEntry{miRNAmeConverter-vignette}
>> > +   %\VignetteEncoding{UTF-8}
>> > +   %\VignetteEngine{knitr::rmarkdown}
>> >   ---
>> >
>> >   > > > 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
>> > >
>> >
>> >
>> > This email message may contain legally privileged and/or confidential
>> > information.  If you are not the intended recipient(s), or the employee
>> or
>> > agent responsible for the delivery of this message to the intended
>> > recipient(s), you are hereby notified that any disclosure, copying,
>> > distribution, or use of this email message is prohibited.  If you have
>> > received this message in error, please notify the sender immediately by
>> > e-mail and delete this email message from your computer. Thank you.
>> >
>>
>> [[alternative HTML version deleted]]
>>
>> ___
>> Bioc-devel@r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>
> 
> 
> 
> --
> Zhilong JIA
> zhilong...@gmail.com
> https://github.com/zhilongjia
> 
>   [[alternative HTML version deleted]]
> 
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel

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Re: [Bioc-devel] Package Without a Vignette

2016-04-02 Thread Zhilong Jia

Hi,

I just found no vignette for my updated package cogena
 (1.5.2),
though there are vignettes  in the code. And the check CMD is
/home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings
cogena_1.5.2.tar.gz in
http://bioconductor.org/checkResults/3.3/bioc-LATEST/cogena/zin2-checksrc.html

And the similar section is here:

vignette: >
  %\VignetteIndexEntry{Vignette Title}
  %\VignetteEngine{knitr::rmarkdown}
  %\usepackage[utf8]{inputenc}

No \\ here.


Thank you.

Regards,
Zhilong


On 22 March 2016 at 18:24, Stefan Haunsberger 
wrote:

> Hi,
>
> Yes, my bad. I'm already on it.
>
> Thanks,
> Stefan
>
> On Tue, Mar 22, 2016 at 10:14 AM Martin Morgan <
> martin.mor...@roswellpark.org> wrote:
>
> >
> >
> > On 03/22/2016 03:00 AM, Dario Strbenac wrote:
> > > Hello,
> > >
> > > The newly added Bioconductor package miRNAmeConverter has no vignette,
> > although a vignette is a requirement for Bioconductor packages which are
> > not simply annotation databases.
> >
> > Rather, the package has a vignette, but it is not built.
> >
> > This is because of the '\\' in the vignette header. Also, the 'html' and
> > 'pdf' versions of the vignette should not be in SVN.
> >
> > I've cc'd the maintainer.
> >
> > Martin
> >
> >
> > Index: miRNAmeConverter-vignette.Rmd
> > ===
> > --- miRNAmeConverter-vignette.Rmd   (revision 115094)
> > +++ miRNAmeConverter-vignette.Rmd   (working copy)
> > @@ -9,9 +9,9 @@
> >   csl: apa.csl
> >   bibliography: references.bib
> >   vignette: >
> > -   %\\VignetteIndexEntry{miRNAmeConverter-vignette}
> > -   %\\VignetteEncoding{UTF-8}
> > -   %\\VignetteEngine{knitr::rmarkdown}
> > +   %\VignetteIndexEntry{miRNAmeConverter-vignette}
> > +   %\VignetteEncoding{UTF-8}
> > +   %\VignetteEngine{knitr::rmarkdown}
> >   ---
> >
> >> > 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
> > >
> >
> >
> > This email message may contain legally privileged and/or confidential
> > information.  If you are not the intended recipient(s), or the employee
> or
> > agent responsible for the delivery of this message to the intended
> > recipient(s), you are hereby notified that any disclosure, copying,
> > distribution, or use of this email message is prohibited.  If you have
> > received this message in error, please notify the sender immediately by
> > e-mail and delete this email message from your computer. Thank you.
> >
>
> [[alternative HTML version deleted]]
>
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>



-- 
Zhilong JIA
zhilong...@gmail.com
https://github.com/zhilongjia

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Re: [Bioc-devel] namespace question

2016-04-02 Thread Dan Tenenbaum

BTW, looks like the change has been made to R-devel:

 CHANGES IN R-devel NEW FEATURES 

  * The ‘import()’ namespace directive now accepts an argument ‘except’ which 
names symbols to exclude from the imports. The ‘except’ expression should 
evaluate to a character vector (after substituting symbols for strings). See 
Writing R Extensions.

URL: 
http://developer.r-project.org/blosxom.cgi/R-devel/NEWS/2016/04/02#n2016-04-02



- Original Message -
> From: "Michael Lawrence" 
> To: "Hervé Pagès" 
> Cc: "Michael Lawrence" , "bioc-devel" 
> 
> Sent: Saturday, April 2, 2016 4:10:10 AM
> Subject: Re: [Bioc-devel] namespace question

> Also, just btw, there are two other places where arbitrary R code can
> be evaluated in the NAMESPACE, but no one has abused them yet. as far
> as I know. The first argument to if() and the .fixes argument to
> useDynLib(). The latter sets the precedent for the except= behavior.
> Although someone forgot to document it, you can do .fixes=c("prefix",
> "suffix") to both prefix and suffix incoming native symbols.
> Currently, the documentation only mentions prefixing. Not sure when
> suffixing would be desirable.
> 
> 
> On Fri, Apr 1, 2016 at 4:14 PM, Hervé Pagès  wrote:
>> On 04/01/2016 01:39 PM, Michael Lawrence wrote:
>>>
>>> Yes, it's arbitrary R code that is evaluated, so paste0() would work.
>>> You're right that it's a big door and could let people do weird
>>> things. Do you foresee a problem with that?
>>
>>
>> Opening such a big door raises many questions. In addition to allowing
>> people do weird/crazy things (like putting calls to library()
>> or requireNamespace() etc... in them), NAMESPACE files with arbitrary
>> R code in them become more complicated to maintain and the tools for
>> parsing/processing them also become more complicated to write and
>> maintain.
>>
>> Now we have a new category of errors that can happen at package
>> installation time: errors triggered by the evaluation of the R
>> expressions embedded in the NAMESPACE file. Hopefully 'R CMD INSTALL'
>> will report something that can be understood by mere mortals when this
>> happens.
>>
>> Once you create the feeling that a NAMESPACE file is just a file
>> that contains arbitrary R code then people expect import(), export()
>> etc.. to be ordinary R functions with a man page (being able to do
>> ?import would not hurt actually) and they'll naturally try to do
>> things like
>>
>>   unwanted_foo_symbols <- ... long and complicated expression
>>   eventually calling user-defined helper
>>   functions located in the NAMESPACE file ...
>>   import(foo, except=unwanted_foo_symbols)
>>
>> Can't blame them for that. But is this the kind of things that we're
>> ready to see in NAMESPACE files?
>>
>> Also once you've open that door, people will naturally wonder why they
>> can use an R expression in the 'except' part of import( , except=) but
>> not elsewhere e.g. in
>>
>>   import(foo, only=paste0("bar", 1:10))
>>
>> as a more elegant way of doing importFrom(foo, bar1, bar2, ..., bar10).
>> This dissymmetry between the syntax of "import only this" and "import
>> all except this" feels very arbitrary. If you don't support the
>> import( , only=) syntax, people might legitimately ask things like
>>
>>   do.call(importFrom, c(list("foo"), as.list(paste0("bar", 1:10
>>
>> to work. Again, can't blame them for that. But do we want this kind of
>> things to work? I'm worried debugging NAMESPACE files would become a
>> full-time job...
>>
>>> I guess one could have implemented NAMESPACE parsing by evaluating the
>>> code in an environment (inheriting from the base namespace) where
>>> import(), export(), etc, were defined. Maybe there's a good reason why
>>> it was not implemented that way.
>>
>>
>> I'm sure there is ;-)
>>
>> H.
>>
>>
>>>
>>> On Fri, Apr 1, 2016 at 12:55 PM, Hervé Pagès  wrote:

 On 03/31/2016 04:07 PM, Michael Lawrence wrote:
>
>
> I agree. The importExcept idea also works that way: importExcept(foo,
> bar,
> baz)
>
> But import(foo, except=c(bar, baz)) reads better.



 mmh... so R expressions with calls to base functions like base::c() are
 making their way in the NAMESPACE file. That's opening a big door. Does
 that mean that we'll be able to do things like:

 import(foo, except=paste0("bar", 1:10))

 Or maybe c(bar, baz) in your above example is just an arbitrary syntax
 that just happens to look like an R expression but won't be evaluated
 as such?


 H.

>
>
> On Thu, Mar 31, 2016 at 4:00 PM,   wrote:
>>
>>
>> I don't think you want to separate it from the import. Better to allow
>> something like
>>
>> import(foo,

Re: [Bioc-devel] SVN credentials

2016-04-02 Thread Dan Tenenbaum

The error with pd.genomewidesnp.6 is related to a move to a new windows 
toolchain (which has been discussed on this list) and the fallout affecting a 
package (affxparser) which pd.genomewidesnp.6 depends on.

THe biovizBase issue will be resolved in the next build report (on Sunday 
afternoon Seattle time).
Dan



- Original Message -
> From: "Krithika Bhuvaneshwar" 
> To: "bioc-devel" 
> Sent: Saturday, April 2, 2016 5:01:42 AM
> Subject: [Bioc-devel] SVN credentials

> Hello
> We are authors of the newly accepted CINdex package.
> 
> We have not received our SVN credentials yet. I believe today is the last
> day to make changes to the package before the new  release .
> 
> Also our package build was error free two days ago. Yesterday there was a
> build error only in windows saying " "pd.genomewidesnp.6" was missing.
> 
> Today I see a build error in all three platforms saying 'biovizbase' is
> missing.
> 
> These packages are listed in our namespace.
> Need advice on what to do ?
> 
> Thanks,
> -Krithika
> 
>   [[alternative HTML version deleted]]
> 
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Re: [Bioc-devel] ggbio error

2016-04-02 Thread Dan Tenenbaum

Yes, the ggbio issue is fixed and this will be reflected in tomorrow's build 
report.
Dan


- Original Message -
> From: "Michael Lawrence" 
> To: "Ludwig Geistlinger" 
> Cc: "bioc-devel" 
> Sent: Saturday, April 2, 2016 4:00:20 AM
> Subject: Re: [Bioc-devel] ggbio error

> I think I fixed those things since the build report was generated.
> 
> Michael
> 
> On Sat, Apr 2, 2016 at 1:48 AM, Ludwig Geistlinger
>  wrote:
>> Hi,
>>
>> I am wondering whether this is only something temporary, but given that
>> the new Bioc release is upcoming and packages should pass R CMD
>> build/check by now, I am reporting that a ggbio R CMD check error
>>
>> http://bioconductor.org/checkResults/devel/bioc-LATEST/ggbio/zin2-checksrc.html
>>
>> causes ReportingTools to fail:
>>
>>> ERROR: dependency ‘ggbio’ is not available for package ‘ReportingTools’
>>
>> and, eventually, EnrichmentBrowser to fail:
>>
>>> ERROR: dependency ‘ReportingTools’ is not available for package
>> ‘EnrichmentBrowser’
>>
>> Which steps need to be undertaken here?
>>
>> Thx,
>> Ludwig
>>
>>
>> --
>> Dipl.-Bioinf. Ludwig Geistlinger
>>
>> Lehr- und Forschungseinheit für Bioinformatik
>> Institut für Informatik
>> Ludwig-Maximilians-Universität München
>> Amalienstrasse 17, 2. Stock, Büro A201
>> 80333 München
>>
>> Tel.: 089-2180-4067
>> eMail: ludwig.geistlin...@bio.ifi.lmu.de
>>
>> ___
>> Bioc-devel@r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
> 
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Re: [Bioc-devel] SVN credentials

2016-04-02 Thread Krithika Bhuvaneshwar

Yes, that would be great. I will be the one  making the updates. Thank you.

-Krithika
On Apr 2, 2016 10:45 AM, "Martin Morgan" 
wrote:
>
>
>
> On 04/02/2016 08:01 AM, Krithika Bhuvaneshwar wrote:
>>
>> Hello
>> We are authors of the newly accepted CINdex package.
>>
>> We have not received our SVN credentials yet. I believe today is the last
>> day to make changes to the package before the new  release .
>
>
> Credentials were sent to the maintainer ('cre') on March 30. Let me know
if you would also like svn access.
>
> Martin
>
>>
>> Also our package build was error free two days ago. Yesterday there was a
>> build error only in windows saying " "pd.genomewidesnp.6" was missing.
>>
>> Today I see a build error in all three platforms saying 'biovizbase' is
>> missing.
>>
>> These packages are listed in our namespace.
>> Need advice on what to do ?
>>
>> Thanks,
>> -Krithika
>>
>> [[alternative HTML version deleted]]
>>
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>>
>
>
> This email message may contain legally privileged and/or confidential
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Re: [Bioc-devel] SVN credentials

2016-04-02 Thread Martin Morgan




On 04/02/2016 08:01 AM, Krithika Bhuvaneshwar wrote:

Hello
We are authors of the newly accepted CINdex package.

We have not received our SVN credentials yet. I believe today is the last
day to make changes to the package before the new  release .


Credentials were sent to the maintainer ('cre') on March 30. Let me know 
if you would also like svn access.


Martin



Also our package build was error free two days ago. Yesterday there was a
build error only in windows saying " "pd.genomewidesnp.6" was missing.

Today I see a build error in all three platforms saying 'biovizbase' is
missing.

These packages are listed in our namespace.
Need advice on what to do ?

Thanks,
-Krithika

[[alternative HTML version deleted]]

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This email message may contain legally privileged and/or confidential 
information.  If you are not the intended recipient(s), or the employee or 
agent responsible for the delivery of this message to the intended 
recipient(s), you are hereby notified that any disclosure, copying, 
distribution, or use of this email message is prohibited.  If you have received 
this message in error, please notify the sender immediately by e-mail and 
delete this email message from your computer. Thank you.

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[Bioc-devel] SVN credentials

2016-04-02 Thread Krithika Bhuvaneshwar

Hello
We are authors of the newly accepted CINdex package.

We have not received our SVN credentials yet. I believe today is the last
day to make changes to the package before the new  release .

Also our package build was error free two days ago. Yesterday there was a
build error only in windows saying " "pd.genomewidesnp.6" was missing.

Today I see a build error in all three platforms saying 'biovizbase' is
missing.

These packages are listed in our namespace.
Need advice on what to do ?

Thanks,
-Krithika

[[alternative HTML version deleted]]

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Re: [Bioc-devel] namespace question

2016-04-02 Thread Michael Lawrence

Also, just btw, there are two other places where arbitrary R code can
be evaluated in the NAMESPACE, but no one has abused them yet. as far
as I know. The first argument to if() and the .fixes argument to
useDynLib(). The latter sets the precedent for the except= behavior.
Although someone forgot to document it, you can do .fixes=c("prefix",
"suffix") to both prefix and suffix incoming native symbols.
Currently, the documentation only mentions prefixing. Not sure when
suffixing would be desirable.


On Fri, Apr 1, 2016 at 4:14 PM, Hervé Pagès  wrote:
> On 04/01/2016 01:39 PM, Michael Lawrence wrote:
>>
>> Yes, it's arbitrary R code that is evaluated, so paste0() would work.
>> You're right that it's a big door and could let people do weird
>> things. Do you foresee a problem with that?
>
>
> Opening such a big door raises many questions. In addition to allowing
> people do weird/crazy things (like putting calls to library()
> or requireNamespace() etc... in them), NAMESPACE files with arbitrary
> R code in them become more complicated to maintain and the tools for
> parsing/processing them also become more complicated to write and
> maintain.
>
> Now we have a new category of errors that can happen at package
> installation time: errors triggered by the evaluation of the R
> expressions embedded in the NAMESPACE file. Hopefully 'R CMD INSTALL'
> will report something that can be understood by mere mortals when this
> happens.
>
> Once you create the feeling that a NAMESPACE file is just a file
> that contains arbitrary R code then people expect import(), export()
> etc.. to be ordinary R functions with a man page (being able to do
> ?import would not hurt actually) and they'll naturally try to do
> things like
>
>   unwanted_foo_symbols <- ... long and complicated expression
>   eventually calling user-defined helper
>   functions located in the NAMESPACE file ...
>   import(foo, except=unwanted_foo_symbols)
>
> Can't blame them for that. But is this the kind of things that we're
> ready to see in NAMESPACE files?
>
> Also once you've open that door, people will naturally wonder why they
> can use an R expression in the 'except' part of import( , except=) but
> not elsewhere e.g. in
>
>   import(foo, only=paste0("bar", 1:10))
>
> as a more elegant way of doing importFrom(foo, bar1, bar2, ..., bar10).
> This dissymmetry between the syntax of "import only this" and "import
> all except this" feels very arbitrary. If you don't support the
> import( , only=) syntax, people might legitimately ask things like
>
>   do.call(importFrom, c(list("foo"), as.list(paste0("bar", 1:10
>
> to work. Again, can't blame them for that. But do we want this kind of
> things to work? I'm worried debugging NAMESPACE files would become a
> full-time job...
>
>> I guess one could have implemented NAMESPACE parsing by evaluating the
>> code in an environment (inheriting from the base namespace) where
>> import(), export(), etc, were defined. Maybe there's a good reason why
>> it was not implemented that way.
>
>
> I'm sure there is ;-)
>
> H.
>
>
>>
>> On Fri, Apr 1, 2016 at 12:55 PM, Hervé Pagès  wrote:
>>>
>>> On 03/31/2016 04:07 PM, Michael Lawrence wrote:


 I agree. The importExcept idea also works that way: importExcept(foo,
 bar,
 baz)

 But import(foo, except=c(bar, baz)) reads better.
>>>
>>>
>>>
>>> mmh... so R expressions with calls to base functions like base::c() are
>>> making their way in the NAMESPACE file. That's opening a big door. Does
>>> that mean that we'll be able to do things like:
>>>
>>> import(foo, except=paste0("bar", 1:10))
>>>
>>> Or maybe c(bar, baz) in your above example is just an arbitrary syntax
>>> that just happens to look like an R expression but won't be evaluated
>>> as such?
>>>
>>>
>>> H.
>>>


 On Thu, Mar 31, 2016 at 4:00 PM,   wrote:
>
>
> I don't think you want to separate it from the import. Better to allow
> something like
>
> import(foo, exclude=bar)
>
> or
>
> import(foo, exclude=c("bar", "baz"))
>
> This seems reasonably natural and shouldn't be too hard to
> implement. (But is has been a while since I've worked on this code).
>
> Best,
>
> luke
>
>
> On Thu, 31 Mar 2016, Karim Mezhoud wrote:
>
>> I think "From" is needed to specify which package we want to exlude
>> functions.
>>
>> I think  excludeFrom (package, function)  seems to be intuitive.
>>
>> thanks,
>> Karim
>>
>>
>>
>> On Thu, Mar 31, 2016 at 9:54 PM, Hervé Pagès 
>> wrote:
>>
>>> On 03/31/2016 12:55 PM, Michael Lawrence wrote:
>>>
 Probably should just stick to exact symbols for now. If there is a
 case where a pattern is actually useful, rather than just an

Re: [Bioc-devel] ggbio error

2016-04-02 Thread Michael Lawrence

I think I fixed those things since the build report was generated.

Michael

On Sat, Apr 2, 2016 at 1:48 AM, Ludwig Geistlinger
 wrote:
> Hi,
>
> I am wondering whether this is only something temporary, but given that
> the new Bioc release is upcoming and packages should pass R CMD
> build/check by now, I am reporting that a ggbio R CMD check error
>
> http://bioconductor.org/checkResults/devel/bioc-LATEST/ggbio/zin2-checksrc.html
>
> causes ReportingTools to fail:
>
>> ERROR: dependency ‘ggbio’ is not available for package ‘ReportingTools’
>
> and, eventually, EnrichmentBrowser to fail:
>
>> ERROR: dependency ‘ReportingTools’ is not available for package
> ‘EnrichmentBrowser’
>
> Which steps need to be undertaken here?
>
> Thx,
> Ludwig
>
>
> --
> Dipl.-Bioinf. Ludwig Geistlinger
>
> Lehr- und Forschungseinheit für Bioinformatik
> Institut für Informatik
> Ludwig-Maximilians-Universität München
> Amalienstrasse 17, 2. Stock, Büro A201
> 80333 München
>
> Tel.: 089-2180-4067
> eMail: ludwig.geistlin...@bio.ifi.lmu.de
>
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel

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Re: [Bioc-devel] ggbio error

2016-04-02 Thread Leonardo Collado Torres

Hi,

ggbio's error also cause some of my packages to fail the latest build.
But I'm confident it'll get fixed before the release.

Best,
Leo

On Sat, Apr 2, 2016 at 4:48 AM, Ludwig Geistlinger
 wrote:
> Hi,
>
> I am wondering whether this is only something temporary, but given that
> the new Bioc release is upcoming and packages should pass R CMD
> build/check by now, I am reporting that a ggbio R CMD check error
>
> http://bioconductor.org/checkResults/devel/bioc-LATEST/ggbio/zin2-checksrc.html
>
> causes ReportingTools to fail:
>
>> ERROR: dependency 'ggbio' is not available for package 'ReportingTools'
>
> and, eventually, EnrichmentBrowser to fail:
>
>> ERROR: dependency 'ReportingTools' is not available for package
> 'EnrichmentBrowser'
>
> Which steps need to be undertaken here?
>
> Thx,
> Ludwig
>
>
> --
> Dipl.-Bioinf. Ludwig Geistlinger
>
> Lehr- und Forschungseinheit für Bioinformatik
> Institut für Informatik
> Ludwig-Maximilians-Universität München
> Amalienstrasse 17, 2. Stock, Büro A201
> 80333 München
>
> Tel.: 089-2180-4067
> eMail: ludwig.geistlin...@bio.ifi.lmu.de
>
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> https://stat.ethz.ch/mailman/listinfo/bioc-devel

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[Bioc-devel] ggbio error

2016-04-02 Thread Ludwig Geistlinger

Hi,

I am wondering whether this is only something temporary, but given that
the new Bioc release is upcoming and packages should pass R CMD
build/check by now, I am reporting that a ggbio R CMD check error

http://bioconductor.org/checkResults/devel/bioc-LATEST/ggbio/zin2-checksrc.html

causes ReportingTools to fail:

> ERROR: dependency ggbio is not available for package ReportingTools

and, eventually, EnrichmentBrowser to fail:

> ERROR: dependency ReportingTools is not available for package
EnrichmentBrowser

Which steps need to be undertaken here?

Thx,
Ludwig


-- 
Dipl.-Bioinf. Ludwig Geistlinger

Lehr- und Forschungseinheit für Bioinformatik
Institut für Informatik
Ludwig-Maximilians-Universität München
Amalienstrasse 17, 2. Stock, Büro A201
80333 München

Tel.: 089-2180-4067
eMail: ludwig.geistlin...@bio.ifi.lmu.de

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Re: [Bioc-devel] Package Without a Vignette

Re: [Bioc-devel] Package Without a Vignette

Re: [Bioc-devel] Package Without a Vignette

Re: [Bioc-devel] Package Without a Vignette

Re: [Bioc-devel] namespace question

Re: [Bioc-devel] SVN credentials

Re: [Bioc-devel] ggbio error

Re: [Bioc-devel] SVN credentials

Re: [Bioc-devel] SVN credentials

[Bioc-devel] SVN credentials

Re: [Bioc-devel] namespace question

Re: [Bioc-devel] ggbio error

Re: [Bioc-devel] ggbio error

[Bioc-devel] ggbio error

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