date:20170330

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,
>>
>>
>>

[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
> > > 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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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 Hervé Pagès

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=DwIGaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=ILfV0tHrE_BxAkWYlvUUwWcBdBdtVD7BlEljGiO3WbY=zUahQYlBHRwNf6lPnSA1515Rm-iL5ffQI7hUcDW-JkE=

one of them is

https://urldefense.proofpoint.com/v2/url?u=https-3A__www.r-2Dproject.org_nosvn_R.check_r-2Ddevel-2Dmacos-2Dx86-5F64-2Dclang_FastImputation-2D00check.html=DwIGaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=ILfV0tHrE_BxAkWYlvUUwWcBdBdtVD7BlEljGiO3WbY=Z7LkVlUzmdmhqxGNFl4LuMVxYwQQGHSV7KdpKCJu12k=

I strongly suspect this is the same bug as yours, but for a case
where the correct behavior is *not* giving an error.

I have also written and shown  Herve's example  to the R-core team.

Unfortunately, I have no platform where I can trigger the bug.
Martin

> Cheers,
> Andrzej

> On Wed, Mar 22, 2017 at 1:28 AM, Martin Morgan <
> martin.mor...@roswellpark.org> wrote:

>> On

Re: [Bioc-devel] Problem for Biostrings?

2017-03-30 Thread Hai Fang

Thanks Herve for resolving it. Best, Hai

Sent from my iPhone

> On 30 Mar 2017, at 06:42, Hervé Pagès  wrote:
> 
> Hi Hai,
> 
> Looks you added CRAN ggforce recently (in February) to the Suggests
> field of Pi. ggforce depends on CRAN package udunits2, which itself
> requires system library libudunits2 in order to compile on Linux,
> which itself can be installed with
> 
>  sudo apt-get install libudunits2-dev
> 
> on Debian/Ubuntu.
> 
> We didn't have libudunits2-dev on malbec2 yet so I just installed it.
> The fact that we didn't have it indicates that Pi is the first
> Bioconductor package to (indirectly) require it.
> 
> If everything goes as expected, Pi should turn all green on Friday.
> 
> Cheers,
> H.
> 
> 
>> On 03/29/2017 09:08 PM, hfang.shanghai wrote:
>> Thanks for the clarification. Now everything is ok except the check in Linux 
>> (https://urldefense.proofpoint.com/v2/url?u=http-3A__bioconductor.org_checkResults_devel_bioc-2DLATEST_Pi_malbec2-2Dchecksrc.html=DwIFaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=q6QK4JMsHgaqD9x6avyUhERn3LtF6NIbMxmXc_omuXE=0Y-86XDQL67bMUlLmRJOg3cEWekH9GHDJNrc5ZEStPg=
>>  ). The package 'ggforce' is not preinstalled in Linux (others seem fine).
>> 
>> Best, Hai
>> 
>> Sent from my iPhone
>> 
>>> On 29 Mar 2017, at 17:17, Michael Lawrence  
>>> wrote:
>>> 
>>> It's actually an error in rtracklayer.
>>> 
>>> On Wed, Mar 29, 2017 at 8:28 AM, Shepherd, Lori
>>>  wrote:
 That is correct.  When the Biostrings package is corrected this ERROR in 
 your package should resolve automatically.

 Lori Shepherd

 Bioconductor Core Team

 Roswell Park Cancer Institute

 Department of Biostatistics & Bioinformatics

 Elm & Carlton Streets

 Buffalo, New York 14263

 From: Bioc-devel  on behalf of Hai Fang 

 Sent: Wednesday, March 29, 2017 10:28:39 AM
 To: bioc-devel@r-project.org
 Subject: [Bioc-devel] Problem for Biostrings?

 Hi,

 I got the error ��object ��inverted�� is not exported by 
 'namespace:Biostrings�� at 
 https://urldefense.proofpoint.com/v2/url?u=http-3A__bioconductor.org_checkResults_devel_bioc-2DLATEST_Pi_=DwIFaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=q6QK4JMsHgaqD9x6avyUhERn3LtF6NIbMxmXc_omuXE=2bhT9aV6mJhSUF8Iq3BZHB_Y2EVt0wNFx6ZcylnnUaE=
  . It  seems due to the package ��Biostrings�� which failed to pass the 
 check 
 (https://urldefense.proofpoint.com/v2/url?u=http-3A__bioconductor.org_checkResults_devel_bioc-2DLATEST_Biostrings_=DwIFaQ=eRAMFD45gAfqt84VtBcfhQ=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA=q6QK4JMsHgaqD9x6avyUhERn3LtF6NIbMxmXc_omuXE=COIN8OGj-Nd6NzWJEoBq6sXBbJLSqHoZpwPKuGe8DH8=
  ). Is it right or something else?

 Thanks,

 Hai

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Re: [Bioc-devel] Problem with champ.load ( wateRmelon::beadcount function )

2017-03-30 Thread Mohammad Tanvir Ahamed via Bioc-devel

Dear Yuan Tian, 

Thank you very much for your mail . 

I have already add a session info with the previous mail. 

Problem arise in your script "champ.load.R" line  70 ( bc=beadcount(rgSet) ). 
"beadcount" belongs to package "wateRmelon". 
In "beadcount" function  from line 3 (nb <- assayDataElement(x, "NBeads")) 
problem arise !!

I am using : 
R version 3.4.0 alpha (2017-03-28 r72427) 
Platform: x86_64-w64-mingw32/x64 (64-bit) 
Biobase (2.35.1), minfi (1.21.5), wateRmelon (1.19.3) 

Yes you are right. minfi has change their class definition for 
"RGChannelSetExtended" 

In my current version of R, 

> getClass("RGChannelSetExtended") 
Class "RGChannelSetExtended" [package "minfi"] 

Slots: 

Name:  annotation  colData  assays NAMES   elementMetadata  
metadata 
Class:  characterDataFrame  Assays character_OR_NULL   DataFrame  
list 

Extends: 
Class "RGChannelSet", directly 
Class "SummarizedExperiment", by class "RGChannelSet", distance 2 
Class "Vector", by class "RGChannelSet", distance 3 
Class "Annotated", by class "RGChannelSet", distance 4 

but in 
R version 3.3.3 (2017-03-06) 
Platform: x86_64-w64-mingw32/x64 (64-bit) 
Running under: Windows 10 x64 (build 14393) 

minfi (1.20.2) 

> getClass("RGChannelSetExtended") 
Class "RGChannelSetExtended" [package "minfi"] 

Slots: 

Name:  assayData  phenoData featureData experimentData  
annotationprotocolData  .__classVersion__ 
Class:  AssayData AnnotatedDataFrame  AnnotatedDataFrame  MIAxE 
  character  AnnotatedDataFrame  Versions 

Extends: 
Class "RGChannelSet", directly 
Class "eSet", by class "RGChannelSet", distance 2 
Class "VersionedBiobase", by class "RGChannelSet", distance 3 
Class "Versioned", by class "RGChannelSet", distance 4 
> 

No "assayData" is present in present version of minfi !!

Can anybody suggest how to solve the problem ? 

Tanvir Ahamed 
Göteborg, Sweden  |  mashra...@yahoo.com 

From: Tian Yuan 

Sent: Thursday, 30 March 2017, 7:35
Subject: Re: Problem with champ.load

Below is my Test Code:

> testDir=system.file("extdata",package="ChAMPdata")
> myLoad <- champ.load(testDir,arraytype="450K")
[===]
[ ChAMP.LOAD START >]
-
Loading data from 
/home/tianyuan/R/x86_64-pc-linux-gnu-library/3.3/ChAMPdata/extdata
[read.metharray.sheet] Found the following CSV files:

[1] 
"/home/tianyuan/R/x86_64-pc-linux-gnu-library/3.3/ChAMPdata/extdata/lung_test_set.csv"
Loading required package: IlluminaHumanMethylation450kmanifest
<< Read DataSet Success. >>

The fraction of failed positions per sample

(You may need to delete samples with high proportion of failed 
probes
):
   Failed CpG Fraction.
C1 0.0013429122
C2 0.0022162171
C3 0.0003563249
C4 0.0002842360
T1 0.0003831007
T2 0.0011946152
T3 0.0014953286
T4 0.0015447610
Filtering probes with a detection p-value above 0.01 in one or more samples has 
removed 2728 probes from the analysis. If a large number of probes have been 
removed, ChAMP suggests you to identify potentially bad samples.
<< Filter DetP Done. >>

Filtering probes with a beadcount <3 in at least 5% of samples, has removed 
9291 from the analysis.
<< Filter Beads Done. >>

Filtering non-cg probes, has removed 2959 from the analysis.
<< Filter NoCG Done. >>

Using general 450K SNP list for filtering.
Filtering probes with SNPs as identified in Zhou's Nucleic Acids Research 
Paper, 2016, has removed 49231 from the analysis.
<< Filter SNP Done. >>

Filtering probes that align to multiple locations as identified in Nordlund et 
al, has removed 7003 from the analysis.
<< Filter MultiHit Done. >>

Filtering probes on the X or Y chromosome has removed 9917 from the analysis.
<< Filter XY chromosome Done. >>

[Beta value is selected as output.]

Zeros in your dataset have been replaced with 0.01

The analysis will be proceed with 404383 probes and 8 samples.

[< ChAMP.LOAD END >>]
[===]
[You may want to process champ.QC() next.]

Best
Yuan Tian

On Thu, 30 Mar 2017 at 12:02 Tian Yuan  wrote:

Hello Tanvir:
>
>
>The error looks wired because seems no one reported that before, I guess it's 
>a problem caused by version of Bioba, whihc is a bug in minfi, which is used 
>by ChAMP. The problem is the latest version minfi is conflict with old version 
>Biobase. The solution is replace your current Biobase package with the latest 
>version (2.34), then it should be OK.
>
>Please try it see if it works. You are using Demo data, which should be 
>correct as I tried now.
>
>
>Best
>Yuan Tian
>

wrote:
>
>Hi,
>>I am writing the following commend

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 '$<-'

[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

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] Problem for Biostrings?

Re: [Bioc-devel] Problem with champ.load ( wateRmelon::beadcount function )

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