date:20170330

[Bioc-devel] masking functions

2017-03-30 Thread Zimmermann, Michael T., Ph.D.

Dear BioConductor Devs,

I am working on submitting a package and have run into a warning from masking 
functions. The buildreport says:

Warning: replacing previous import gplots::plotCI by plotrix::plotCI when 
loading RITAN

I don't call plotCI. I assume that the other plotting methods I use call them 
internally. So, I'm not sure how to address this warning. Any advice you can 
provide would be appreciated.

Sincerely,

Michael T. Zimmermann
Ph. D. in Bioinformatics | Health Sciences Research | Division of Biomedical 
Statistics and Informatics
Mayo Clinic | 200 First Street SW | Rochester, MN 55905 | 
mayoclinic.org


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Re: [Bioc-devel] Question about R functions

2017-03-30 Thread Nathan Sheffield


HI Jing,

You should export FA FB and FC, but don't export FD. If using roxygen2 
for documentation you use "#' @export" on the ones to export, and just 
don't document FD and it won't be exported by default.


Hope that helps,

-Nathan


On 03/30/2017 04:02 PM, Jing Wang wrote:

Hi,

  


I have three functions (FA,FB,FC) in the package and all these functions need 
to call another function (FD). But I do not want other users to use the 
function FD and thus I do not want to create the document for FD in the R 
package.

  


Could you please give me some suggestion how to do that?

  


Thanks,

  

  

  



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Re: [Bioc-devel] Question about R functions

2017-03-30 Thread Juan David Henao Sanchez

Hi Wang

You can create internal functions calling them as ".function", the point is
necessary to declare an internal function. Additionally, you can put all
your internal functions in the same R file and is not necessary create the
documentation for this functions.

Best regards.

Juan D. Henao

2017-03-30 15:02 GMT-05:00 Jing Wang :

> Hi,
>
>
>
> I have three functions (FA,FB,FC) in the package and all these functions
> need to call another function (FD). But I do not want other users to use
> the function FD and thus I do not want to create the document for FD in the
> R package.
>
>
>
> Could you please give me some suggestion how to do that?
>
>
>
> Thanks,
>
>
>
>
>
>
>
>
> [[alternative HTML version deleted]]
>
> ___
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>



-- 
Juan David Henao
Maestría en Bioinformática
Universidad Nacional de Colombia

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[Bioc-devel] Question about R functions

2017-03-30 Thread Jing Wang

Hi,

 

I have three functions (FA,FB,FC) in the package and all these functions need 
to call another function (FD). But I do not want other users to use the 
function FD and thus I do not want to create the document for FD in the R 
package.

 

Could you please give me some suggestion how to do that?

 

Thanks,

 

 

 


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Re: [Bioc-devel] The story of tracing a derfinder bug on OSX that sometimes popped up, sometimes it didn't. Related to IRanges/S4Vectors '$<-'

2017-03-30 Thread Michael Lawrence

Yea I will have to port the recent fixes.

On Wed, Mar 29, 2017 at 11:32 PM, Hervé Pagès  wrote:
> On 03/27/2017 09:43 AM, Michael Lawrence wrote:
>>
>> I committed a fix into R trunk with a regression test.
>
>
> Thanks Michael. Any chance you can port the fix to the 3.4 branch?
>
> H.
>
>>
>> On Mon, Mar 27, 2017 at 8:41 AM, Michael Lawrence 
>> wrote:
>>>
>>> My bad guys, I'll fix when I get to work.
>>>
>>> On Mon, Mar 27, 2017 at 3:59 AM, Martin Morgan
>>>  wrote:

 On 03/22/2017 01:12 PM, Hervé Pagès wrote:
>
>
> Hi Martin,
>
> On 03/22/2017 03:17 AM, Martin Maechler wrote:
>>>
>>>
>>> Andrzej Oleś 
>>> on Wed, 22 Mar 2017 10:29:57 +0100 writes:
>>
>>
>>
>> > Just for the record, on R-3.3.2 Herve's code fails with the
>> following error:
>> > Error in x[TRUE] <- new("A") :
>> > incompatible types (from S4 to logical) in subassignment type
>> fix
>>
>> yes, (of course) and I would be interested in a small
>> reproducible example which uses _valid_ code.
>
>
>
> Looks like before performing the subassignment itself, [<- first tries
> to coerce the RHS to the "mode" of the LHS by calling as.vector() on
> the
> former. So if we define an as.vector S3 method for A objects:
>
>   setClass("A", representation(stuff="numeric"))
>   as.vector.A <- function (x, mode="any") x@stuff
>   a <- new("A", stuff=c(3.5, 0.1))
>   x <- numeric(10)
>   x[3:4] <- a



 The relevant stack trace is

   * frame #0: 0x00010dded77a
 libR.dylib`R_has_methods(op=)
 + 74 at objects.c:1415
 frame #1: 0x00010ddaabf4
 libR.dylib`Rf_DispatchOrEval(call=0x7fcea36f68a8,
 op=0x7fcea201a178,
 generic=0x00010df0a185, args=, rho=0x7fcea2053318,
 ans=0x7fff51f60c48, dropmissing=, argsevald=1) + 404 at
 eval.c:3150
 frame #2: 0x00010de4e658 libR.dylib`SubassignTypeFix [inlined]
 dispatch_asvector(x=, call=0x7fcea36f68a8,
 rho=0x7fcea2053318) + 295 at subassign.c:283


 The segfault is at objects.c:1415

 offset = PRIMOFFSET(op);
 if(offset > curMaxOffset || prim_methods[offset] == NO_METHODS
|| prim_methods[offset] == SUPPRESSED)

 where offset is negative and prim_methods[offset] fails.

 (lldb) p *op
 (SEXPREC) $8 = {
   sxpinfo = (type = 0, obj = 0, named = 2, gp = 0, mark = 1, debug = 0,
 trace = 0, spare = 0, gcgen = 1, gccls = 0)
   attrib = 0x7fcea201a178
   gengc_next_node = 0x7fcea21874e8
   gengc_prev_node = 0x7fcea2019ff0
   u = {
 primsxp = (offset = -1576951432)
 symsxp = {


 'op' is assigned from subassign.c:287, op = R_Primitive("as.vector")

 static Rboolean dispatch_asvector(SEXP *x, SEXP call, SEXP rho) {
 static SEXP op = NULL;
 SEXP args;
 Rboolean ans;
 if (op == NULL)
 op = R_Primitive("as.vector");
 PROTECT(args = list2(*x, mkString("any")));
 ans = DispatchOrEval(call, op, "as.vector", args, rho, x, 0, 1);
 UNPROTECT(1);
 return ans;
 }

 But as.vector is not a primitive, so gets R_NilValue. This is passed to
 DispatchOrEval, and then to R_has_methods.

 It seems like dispatch_asvector() was introduced by

 $ svn log -c69747
 
 r69747 | lawrence | 2015-12-09 09:04:56 -0500 (Wed, 09 Dec 2015) | 3
 lines

 subassignment of an S4 value into an atomic vector coerces the value
 with as.vector

 

 So maybe Michael can tell us about his thinking here.

 Also, should R_has_methods be robust to R_NilValue? And R_NilValue
 explicitly zero it's data?

 Martin



>
> then the code is now valid and we still get the segfault on Mac.
>
> I didn't define as.vector.A in my original minimalist reproducible
> code in order to keep it as simple as possible.
>
> H.
>
>
>> We have seen such examples with something (more complicated
>> than, but basically like)
>>
>>   df <- data.frame(x=1:5, y=5:1, m=matrix(-pi*1:30, 5,6))
>>   M <- Matrix::Matrix(exp(0:3),2)
>>   df[1:2,1:2] <- M
>>
>> which actually calls `[<-`, and then `[<-.data.frame`  and
>> always works for me but does seg.fault (in the CRAN checks of
>> package FastImputation (on 3 of the dozen platforms,
>>
>>
>> https://urldefense.proofpoint.com/v2/url?u=https-3A__cran.r-2Dproject.org_web_checks_check-5Fresults-5FFastImputation.html&d=DwIGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=ILfV0tHrE_BxAkWYlvUUwWcBdBdtVD7BlEljGiO3W

Re: [Bioc-devel] Cannot find SummarizedExperiment's function assays()

2017-03-30 Thread Martin Morgan

On 03/30/2017 05:21 AM, Sokratis Kariotis wrote:

Hey all,

Thanks for the input! I followed Marcel's advice and included the library
in my vignette. Also, I replaced lazyData with a datalist. The datalist
file includes "compressed_result : result" which is in turn loaded in the
vignette using "data(compressed_result)". However, I got:

Warning in data(compressed_result) :
  data set ‘compressed_result’ not found

Error: processing vignette 'usingPathprintGEOData.Rnw' failed with diagnostics:
 chunk 1
Error in assays(result) : object 'result' not found

I Stangle'd the vignette

  cd pathprintGEOData/vignettes
  R CMD Stangle usingPathprintGEOData.Rnw

and then walked through the lines of R code. I got to

> data(compressed_result)
Warning message:
In data(compressed_result) : data set 'compressed_result' not found

The data 'compressed_result' is not found, because it is in the 
pathprintGEOData package, and the pathprintGEOData package is not on the 
search path.

> search()
 [1] ".GlobalEnv"   "package:SummarizedExperiment"
 [3] "package:DelayedArray" "package:matrixStats"
 [5] "package:Biobase"  "package:GenomicRanges"
 [7] "package:GenomeInfoDb" "package:IRanges"
 [9] "package:S4Vectors""package:BiocGenerics"
[11] "package:parallel" "package:stats4"
[13] "package:pathprint""ESSR"
[15] "package:BiocInstaller""package:stats"
[17] "package:graphics" "package:grDevices"
[19] "package:utils""package:datasets"
[21] "package:methods"  "Autoloads"
[23] "package:base"

It is not on the search path because, originally, pathprint had Depends: 
pathprintGEOData, but that was modified, as you know, to Suggests: 
pathprintGEOData, to avoid circular dependencies that thwart our build 
system. So previously library(pathprint) was enough to make the data 
available, but now you must either load the package

  library(pathprintGEOData)
  data(compressed_result)

or tell data() where the data set is

  data(compressed_result, package="pathprintGEOData")

One would still like to use an informative name for the data (first 
argument of data) and presumably an identical name for the object that 
is loaded.

Martin

So the dataset is still not loaded (again, these errors did not exist
prior to package acceptance). I have been using devtools to
build/check the package (since the github issue was closed) and these
warnings/errors dont show up, which imakes it difficult for me to fix
them. Thanks again for any input!

Regards,

Sokratis

On 27 March 2017 at 19:58, Michael Lawrence 
wrote:

Actually, I don't see where the package itself is loaded in the
vignette. If it were, this error would not occur.

Unsurprisingly, I get this when trying to run the vignette code:

Warning message:
In data(list = ds) : data set ‘pathprintSummarizedGEOData’ not found

I noticed that pathprintGEOData just provides compressed_result, not
the "pathprintSummarizedGEOData" so I'm not sure where that lives now.
You might also consider turning off lazy data and using a datalist
file for that package since the file is somewhat large.

I also think that the datalist file for pathprint is out of date.

Michael

On Mon, Mar 27, 2017 at 11:26 AM, Marcel Ramos
 wrote:

Hi Sokratis,

You can resolve this issue by moving `SummarizedExperiment` to the
Suggests field and

including a `library(SummarizedExperiment)` call in your vignette.

Best regards,

Marcel

On Mon, Mar 27, 2017 at 11:09 AM Sokratis Kariotis
mailto:s.kario...@sheffield.ac.uk>> wrote:

Hey,

I have submitted the package pathprintGEOData, which got accepted,
but the
build/check report is now producing the following error:

*Error: processing vignette 'usingPathprintGEOData.Rnw' failed with
diagnostics:  chunk 1 Error in assays(result) : could not find

function

"assays"*

*assays *is a function from the SummarizedExperiment package which I
have
added on my Depends in DESCRIPTION. This error was not present during
building/checking before this package was accepted. Besides adding
SummarizedExperiment
to my Imports what else might be responsible for that error?

Thank you for any help on the matter!

-Sokratis

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Roswell Park Cancer Institute

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[Bioc-devel] Using LaTeX packages in vignettes

2017-03-30 Thread Janssen-10, R.R.E.

Hello all,

We wrote our vignette in Sweave/LaTeX, and I am running into a problem with 
citing to other papers.
I would like to use the APA style of citing which looks like: "Determine the 
optimal factorization rank using the NMF package (Gaujoux and Seoighe, 2010). 
..."

Now, to achieve that, I could use the package "apacite", but I wonder whether 
it's available on the build nodes of Bioconductor, and whether it's desired to 
choose our own citation style.  Can we choose our own citation style in 
vignettes? And if so, is "apacite" available on the build infrastructure of 
Bioconductor?

Thanks!

Kind regards,
Roel Janssen

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Re: [Bioc-devel] Cannot find SummarizedExperiment's function assays()

2017-03-30 Thread Sokratis Kariotis

Hey all,

Thanks for the input! I followed Marcel's advice and included the library
in my vignette. Also, I replaced lazyData with a datalist. The datalist
file includes "compressed_result : result" which is in turn loaded in the
vignette using "data(compressed_result)". However, I got:

Warning in data(compressed_result) :
  data set ‘compressed_result’ not found

Error: processing vignette 'usingPathprintGEOData.Rnw' failed with diagnostics:
 chunk 1
Error in assays(result) : object 'result' not found

So the dataset is still not loaded (again, these errors did not exist
prior to package acceptance). I have been using devtools to
build/check the package (since the github issue was closed) and these
warnings/errors dont show up, which imakes it difficult for me to fix
them. Thanks again for any input!

Regards,

Sokratis


On 27 March 2017 at 19:58, Michael Lawrence 
wrote:

> Actually, I don't see where the package itself is loaded in the
> vignette. If it were, this error would not occur.
>
> Unsurprisingly, I get this when trying to run the vignette code:
>
> Warning message:
> In data(list = ds) : data set ‘pathprintSummarizedGEOData’ not found
>
> I noticed that pathprintGEOData just provides compressed_result, not
> the "pathprintSummarizedGEOData" so I'm not sure where that lives now.
> You might also consider turning off lazy data and using a datalist
> file for that package since the file is somewhat large.
>
> I also think that the datalist file for pathprint is out of date.
>
> Michael
>
> On Mon, Mar 27, 2017 at 11:26 AM, Marcel Ramos
>  wrote:
> > Hi Sokratis,
> >
> > You can resolve this issue by moving `SummarizedExperiment` to the
> > Suggests field and
> >
> > including a `library(SummarizedExperiment)` call in your vignette.
> >
> > Best regards,
> >
> > Marcel
> >
> >
> > On Mon, Mar 27, 2017 at 11:09 AM Sokratis Kariotis
> > mailto:s.kario...@sheffield.ac.uk>> wrote:
> >
> > Hey,
> >
> > I have submitted the package pathprintGEOData, which got accepted,
> > but the
> > build/check report is now producing the following error:
> >
> >
> >
> > *Error: processing vignette 'usingPathprintGEOData.Rnw' failed with
> > diagnostics:  chunk 1 Error in assays(result) : could not find
> function
> > "assays"*
> >
> > *assays *is a function from the SummarizedExperiment package which I
> > have
> > added on my Depends in DESCRIPTION. This error was not present during
> > building/checking before this package was accepted. Besides adding
> > SummarizedExperiment
> > to my Imports what else might be responsible for that error?
> >
> > Thank you for any help on the matter!
> >
> > -Sokratis
> >
> >  [[alternative HTML version deleted]]
> >
> > ___
> > Bioc-devel@r-project.org mailing
> list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> > 
> >
> > --
> > Marcel Ramos
> > Bioconductor Core Team Member
> > Roswell Park Cancer Institute
> >
> >
> >
> > This email message may contain legally privileged and/or...{{dropped:4}}
> >
> > ___
> > Bioc-devel@r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
>

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Re: [Bioc-devel] Trouble checking out svn with username and password

2017-03-30 Thread Riebenbauer, Thomas

The problem is already solved:
My username was entered incorrectly.

Best regards,
Thomas


> -Original Message-
> From: Bioc-devel [mailto:bioc-devel-boun...@r-project.org] On Behalf Of
> Riebenbauer, Thomas
> Sent: Wednesday, March 29, 2017 6:56 PM
> To: bioc-devel
> Subject: Re: [Bioc-devel] Trouble checking out svn with username and
> password
> 
> Hello all,
> 
> I think that I'm running into a similar problam as Brad:
> 
> If I try the link
> https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_4/madman/
> Rpacks/IPO/ for my package IPO, I'm prompted to insert my login-data.
> Readonly works as expected. But with my username t.riebenbauer (and the
> password provided, when my package was added) I get "500 Internal Server
> Error". Similar things happened on checking out the package with git-svn.
> 
> Thanks in advance for your help!
> Thomas
> 
> 
> > -Original Message-
> > From: Bioc-devel [mailto:bioc-devel-boun...@r-project.org] On Behalf
> > Of Martin Morgan
> > Sent: Sunday, September 04, 2016 12:01 AM
> > To: Dan Tenenbaum; Brad Nelms
> > Cc: bioc-devel
> > Subject: Re: [Bioc-devel] Trouble checking out svn with username and
> > password
> >
> > On 09/03/2016 04:29 PM, Dan Tenenbaum wrote:
> > > Your username is b.nelms
> >
> > actually, it appears that the user was assigned bnelms (breaking the
> > usual convention), but the permissions file mentioned b.nelms; the
> > permissions file has been updated, please let me know about the
> > success of bnelms and your assigned password.
> >
> > Martin
> >
> > >
> > > (note the dot).
> > >
> > > Dan
> > >
> > >
> > > - Original Message -
> > >> From: "Brad Nelms" 
> > >> To: "bioc-devel" 
> > >> Sent: Saturday, September 3, 2016 1:23:18 PM
> > >> Subject: [Bioc-devel] Trouble checking out svn with username and
> > >> password
> > >
> > >> Hi all,
> > >>
> > >> I'm trying to checkout a package that was recently accepted to
> > >> Bioconductor ('CellMapperData'), but am unable to check this out
> > >> using my provided svn credentials. If I type:
> > >>
> > >> svn co
> > >> https://hedgehog.fhcrc.org/bioc-
> > data/trunk/experiment/pkgs/CellMapper
> > >> Data
> > >> --username "bnelms" --password xxx
> > >>
> > >> where 'xxx' is my svn password. I get the following error:
> > >>
> > >> svn: E170013: Unable to connect to a repository at URL '
> > >> https://hedgehog.fhcrc.org/bioc-
> > data/trunk/experiment/pkgs/CellMapperData'
> > >> svn: E175013: Access to
> > >> '/bioc-data/trunk/experiment/pkgs/CellMapperData' forbidden
> > >>
> > >> I have also tried using my full email as my username (
> > >> bnelms.resea...@gmail.com), but then I get this error:
> > >>
> > >> svn co
> > >> https://hedgehog.fhcrc.org/bioc-
> > data/trunk/experiment/pkgs/CellMapper
> > >> Data --username "bnelms.resea...@gmail.com" --password xxx
> > >> svn: E170013: Unable to connect to a repository at URL '
> > >> https://hedgehog.fhcrc.org/bioc-
> > data/trunk/experiment/pkgs/CellMapperData'
> > >> svn: E175002: Unexpected server error 500 'Internal Server Error'
> > >> on '/bioc-data/trunk/experiment/pkgs/CellMapperData'
> > >>
> > >> I can checkout the package using readonly as the password and
> > username:
> > >>
> > >> svn co
> > >> https://hedgehog.fhcrc.org/bioc-
> > data/trunk/experiment/pkgs/CellMapper
> > >> Data --username "readonly" --password readonly
> > >> ACellMapperData/vignettes
> > >> ACellMapperData/man
> > >> .
> > >> Checked out revision 3880.
> > >>
> > >> I see there was a similar bioc-devel question last May (
> > >> https://stat.ethz.ch/pipermail/bioc-devel/2016-May/009226.html),
> > >> but it is not clear to me what solved the problem for that user. My
> > >> svn version can access https. What can I do to resolve this issue?
> > >>
> > >> Thanks in advance for your help!
> > >> Brad
> > >>
> > >>  [[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
> > >
> >
> >
> > This email message may contain legally privileged
> > and/or...{{dropped:2}}
> >
> > ___
> > Bioc-devel@r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel
> 
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[Bioc-devel] masking functions

Re: [Bioc-devel] Question about R functions

Re: [Bioc-devel] Question about R functions

[Bioc-devel] Question about R functions

Re: [Bioc-devel] The story of tracing a derfinder bug on OSX that sometimes popped up, sometimes it didn't. Related to IRanges/S4Vectors '$<-'

Re: [Bioc-devel] Cannot find SummarizedExperiment's function assays()

[Bioc-devel] Using LaTeX packages in vignettes

Re: [Bioc-devel] Cannot find SummarizedExperiment's function assays()

Re: [Bioc-devel] Trouble checking out svn with username and password

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