Re: [Bioc-devel] conflict rowRanges SummarizedExperiment/matrixStats

2017-04-10 Thread Maarten van Iterson
Thanks for the explanation and the proposed solution.
I was not aware the DelayedArray package was involved as well.
Maarten

On Fri, Apr 7, 2017 at 6:26 AM, Hervé Pagès  wrote:

> Hi Maarten, Vince,
>
> We need to fix this. The plan is to promote rowRanges to an S4 generic
> in the DelayedArray package (DelayedArray depends on matrixStats). And
> to remove the rowRanges S4 generic defined in SummarizedExperiment
> (SummarizedExperiment depends on DelayedArray). So we'll have only 1
> rowRanges generic (defined in DelayedArray). With methods defined in
> matrixStats (default method), DelayedArray (method for DelayedMatrix
> objects), and SummarizedExperiment (method for RangedSummarizedExperiment
> objects).
>
> Then there won't be anymore conflict.
>
> Will fix this ASAP.
>
> H.
>
>
>
> On 04/06/2017 03:11 AM, Vincent Carey wrote:
>
>> I am sure there are better responses to come, but here are a few initial
>> comments.
>>
>> On Thu, Apr 6, 2017 at 5:42 AM, Maarten van Iterson 
>> wrote:
>>
>> Dear all,
>>>
>>> SummarizedExperiment and matrixStats both contain a method/function
>>> called
>>> rowRanges one operates on a SummarizedExperiment-object the other on a
>>> matrix. matrixStats is required by SummarizedExperiment, or a package it
>>> is
>>> depending on, so rowRanges is masked when loading SummarizedExperiment.
>>>
>>> I thought a function/method is called depended on the type of the object;
>>>
>>>
>> There are at least two interpretations of this.  If a function that is an
>> S3 generic is called on an entity whose class corresponds to an existing
>> method, that method will be invoked.  If a function that is an S4 generic
>> is called with (a sequence of) arguments corresponding to a method with
>> signature equivalent to the sequence of classes of the arguments, that
>> method will be invoked.  In matrixStats, rowRanges is just a first level
>> function, and will be invoked directly on anything that is passed -- e.g.,
>> rowRanges(4) is just an error, when matrixStats alone is loaded.
>>
>> matrix or SummarizedExperiment-object, such that functions/methods with
>> the
>>
>>> same name can coexist. However, this doesn't seems to work for rowRanges.
>>> The only way to access rowRanges from matrixStats when
>>> SummarizedExperiment
>>> is already loaded is using the double colon operator
>>> matrixStats::rowRanges. Is this intentional or is there a other way to
>>> solve this?
>>>
>>> Regards,
>>> Maarten
>>>
>>> Here is a small example showing the issue:
>>>
>>> library(SummarizedExperiment)

>>> Loading required package: matrixStats
>>> matrixStats v0.51.0 (2016-10-08) successfully loaded. See ?matrixStats
>>> for
>>> help.
>>> Attaching package: ‘matrixStats’
>>> Attaching package: ‘SummarizedExperiment’
>>> The following object is masked from ‘package:matrixStats’:
>>> rowRanges
>>>
 nrows <- 200; ncols <- 6
 counts <- matrix(runif(nrows * ncols, 1, 1e4), nrows)
 rowRanges <- GRanges(rep(c("chr1", "chr2"), c(50, 150)),

>>> +  IRanges(floor(runif(200, 1e5, 1e6)), width=100),
>>> +  strand=sample(c("+", "-"), 200, TRUE),
>>> +  feature_id=sprintf("ID%03d", 1:200))
>>>
 colData <- DataFrame(Treatment=rep(c("ChIP", "Input"), 3),

>>> +  row.names=LETTERS[1:6])
>>>
 rse <- SummarizedExperiment(assays=SimpleList(counts=counts),

>>> + rowRanges=rowRanges, colData=colData)
>>>

 rowRanges(rse)

>>> GRanges object with 200 ranges and 1 metadata column:
>>> seqnames   ranges strand |  feature_id
>>>   | 
>>> [1] chr1 [858613, 858712]  - |   ID001
>>>

 rowRanges(counts)

>>> Error in (function (classes, fdef, mtable)  :
>>>   unable to find an inherited method for function ‘rowRanges’ for
>>> signature
>>> ‘"matrix"’
>>>

 library(matrixStats) ##it is already loading so this doesn't alter the

>>>
>>>
>> Actually in this case matrixStats is loaded and attached.  Sometimes the
>> difference is significant.
>>
>>
>> search path
>>>

 rowRanges(rse)

>>> GRanges object with 200 ranges and 1 metadata column:
>>> seqnames   ranges strand |  feature_id
>>>   | 
>>> [1] chr1 [858613, 858712]  - |   ID001
>>>
 rowRanges(counts)

>>> Error in (function (classes, fdef, mtable)  :
>>>   unable to find an inherited method for function ‘rowRanges’ for
>>> signature
>>> ‘"matrix"’
>>>
>>>
>> So -- we got a warning when there was a collision in namespaces, when
>> SummarizedExperiment was attached, and an indication that rowRanges is an
>> S4 generic when we encountered the error.  When should we introduce
>> the method
>>
>> setMethod("rowRanges", "matrix", function(x, ...)
>> matrixStats::rowRanges(x,
>> ...))
>>
>> that would foster the behavior I think you are 

Re: [Bioc-devel] conflict rowRanges SummarizedExperiment/matrixStats

2017-04-06 Thread Hervé Pagès

Hi Maarten, Vince,

We need to fix this. The plan is to promote rowRanges to an S4 generic
in the DelayedArray package (DelayedArray depends on matrixStats). And
to remove the rowRanges S4 generic defined in SummarizedExperiment
(SummarizedExperiment depends on DelayedArray). So we'll have only 1
rowRanges generic (defined in DelayedArray). With methods defined in
matrixStats (default method), DelayedArray (method for DelayedMatrix
objects), and SummarizedExperiment (method for 
RangedSummarizedExperiment objects).


Then there won't be anymore conflict.

Will fix this ASAP.

H.


On 04/06/2017 03:11 AM, Vincent Carey wrote:

I am sure there are better responses to come, but here are a few initial
comments.

On Thu, Apr 6, 2017 at 5:42 AM, Maarten van Iterson 
wrote:


Dear all,

SummarizedExperiment and matrixStats both contain a method/function called
rowRanges one operates on a SummarizedExperiment-object the other on a
matrix. matrixStats is required by SummarizedExperiment, or a package it is
depending on, so rowRanges is masked when loading SummarizedExperiment.

I thought a function/method is called depended on the type of the object;



There are at least two interpretations of this.  If a function that is an
S3 generic is called on an entity whose class corresponds to an existing
method, that method will be invoked.  If a function that is an S4 generic
is called with (a sequence of) arguments corresponding to a method with
signature equivalent to the sequence of classes of the arguments, that
method will be invoked.  In matrixStats, rowRanges is just a first level
function, and will be invoked directly on anything that is passed -- e.g.,
rowRanges(4) is just an error, when matrixStats alone is loaded.

matrix or SummarizedExperiment-object, such that functions/methods with the

same name can coexist. However, this doesn't seems to work for rowRanges.
The only way to access rowRanges from matrixStats when SummarizedExperiment
is already loaded is using the double colon operator
matrixStats::rowRanges. Is this intentional or is there a other way to
solve this?

Regards,
Maarten

Here is a small example showing the issue:


library(SummarizedExperiment)

Loading required package: matrixStats
matrixStats v0.51.0 (2016-10-08) successfully loaded. See ?matrixStats for
help.
Attaching package: ‘matrixStats’
Attaching package: ‘SummarizedExperiment’
The following object is masked from ‘package:matrixStats’:
rowRanges

nrows <- 200; ncols <- 6
counts <- matrix(runif(nrows * ncols, 1, 1e4), nrows)
rowRanges <- GRanges(rep(c("chr1", "chr2"), c(50, 150)),

+  IRanges(floor(runif(200, 1e5, 1e6)), width=100),
+  strand=sample(c("+", "-"), 200, TRUE),
+  feature_id=sprintf("ID%03d", 1:200))

colData <- DataFrame(Treatment=rep(c("ChIP", "Input"), 3),

+  row.names=LETTERS[1:6])

rse <- SummarizedExperiment(assays=SimpleList(counts=counts),

+ rowRanges=rowRanges, colData=colData)


rowRanges(rse)

GRanges object with 200 ranges and 1 metadata column:
seqnames   ranges strand |  feature_id
  | 
[1] chr1 [858613, 858712]  - |   ID001


rowRanges(counts)

Error in (function (classes, fdef, mtable)  :
  unable to find an inherited method for function ‘rowRanges’ for signature
‘"matrix"’


library(matrixStats) ##it is already loading so this doesn't alter the




Actually in this case matrixStats is loaded and attached.  Sometimes the
difference is significant.



search path


rowRanges(rse)

GRanges object with 200 ranges and 1 metadata column:
seqnames   ranges strand |  feature_id
  | 
[1] chr1 [858613, 858712]  - |   ID001

rowRanges(counts)

Error in (function (classes, fdef, mtable)  :
  unable to find an inherited method for function ‘rowRanges’ for signature
‘"matrix"’



So -- we got a warning when there was a collision in namespaces, when
SummarizedExperiment was attached, and an indication that rowRanges is an
S4 generic when we encountered the error.  When should we introduce
the method

setMethod("rowRanges", "matrix", function(x, ...) matrixStats::rowRanges(x,
...))

that would foster the behavior I think you are looking for?





head(matrixStats::rowRanges(counts))

   [,1] [,2]
[1,]   51.27791 9350.048
[2,] 1417.41010 8272.040

sessionInfo()

R Under development (unstable) (2016-08-25 r71150)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 14.04.5 LTS

locale:
 [1] LC_CTYPE=en_US.UTF-8   LC_NUMERIC=C
 [3] LC_TIME=en_US.UTF-8LC_COLLATE=en_US.UTF-8
 [5] LC_MONETARY=en_US.UTF-8LC_MESSAGES=en_US.UTF-8
 [7] LC_PAPER=en_US.UTF-8   LC_NAME=C
 [9] LC_ADDRESS=C   LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] parallel  stats4stats graphics  grDevices utils 

Re: [Bioc-devel] conflict rowRanges SummarizedExperiment/matrixStats

2017-04-06 Thread Vincent Carey
I am sure there are better responses to come, but here are a few initial
comments.

On Thu, Apr 6, 2017 at 5:42 AM, Maarten van Iterson 
wrote:

> Dear all,
>
> SummarizedExperiment and matrixStats both contain a method/function called
> rowRanges one operates on a SummarizedExperiment-object the other on a
> matrix. matrixStats is required by SummarizedExperiment, or a package it is
> depending on, so rowRanges is masked when loading SummarizedExperiment.
>
> I thought a function/method is called depended on the type of the object;
>

There are at least two interpretations of this.  If a function that is an
S3 generic is called on an entity whose class corresponds to an existing
method, that method will be invoked.  If a function that is an S4 generic
is called with (a sequence of) arguments corresponding to a method with
signature equivalent to the sequence of classes of the arguments, that
method will be invoked.  In matrixStats, rowRanges is just a first level
function, and will be invoked directly on anything that is passed -- e.g.,
rowRanges(4) is just an error, when matrixStats alone is loaded.

matrix or SummarizedExperiment-object, such that functions/methods with the
> same name can coexist. However, this doesn't seems to work for rowRanges.
> The only way to access rowRanges from matrixStats when SummarizedExperiment
> is already loaded is using the double colon operator
> matrixStats::rowRanges. Is this intentional or is there a other way to
> solve this?
>
> Regards,
> Maarten
>
> Here is a small example showing the issue:
>
> > library(SummarizedExperiment)
> Loading required package: matrixStats
> matrixStats v0.51.0 (2016-10-08) successfully loaded. See ?matrixStats for
> help.
> Attaching package: ‘matrixStats’
> Attaching package: ‘SummarizedExperiment’
> The following object is masked from ‘package:matrixStats’:
> rowRanges
> > nrows <- 200; ncols <- 6
> > counts <- matrix(runif(nrows * ncols, 1, 1e4), nrows)
> > rowRanges <- GRanges(rep(c("chr1", "chr2"), c(50, 150)),
> +  IRanges(floor(runif(200, 1e5, 1e6)), width=100),
> +  strand=sample(c("+", "-"), 200, TRUE),
> +  feature_id=sprintf("ID%03d", 1:200))
> > colData <- DataFrame(Treatment=rep(c("ChIP", "Input"), 3),
> +  row.names=LETTERS[1:6])
> > rse <- SummarizedExperiment(assays=SimpleList(counts=counts),
> + rowRanges=rowRanges, colData=colData)
> >
> > rowRanges(rse)
> GRanges object with 200 ranges and 1 metadata column:
> seqnames   ranges strand |  feature_id
>   | 
> [1] chr1 [858613, 858712]  - |   ID001
> >
> > rowRanges(counts)
> Error in (function (classes, fdef, mtable)  :
>   unable to find an inherited method for function ‘rowRanges’ for signature
> ‘"matrix"’
> >
> > library(matrixStats) ##it is already loading so this doesn't alter the
>

Actually in this case matrixStats is loaded and attached.  Sometimes the
difference is significant.


> search path
> >
> > rowRanges(rse)
> GRanges object with 200 ranges and 1 metadata column:
> seqnames   ranges strand |  feature_id
>   | 
> [1] chr1 [858613, 858712]  - |   ID001
> > rowRanges(counts)
> Error in (function (classes, fdef, mtable)  :
>   unable to find an inherited method for function ‘rowRanges’ for signature
> ‘"matrix"’
>

So -- we got a warning when there was a collision in namespaces, when
SummarizedExperiment was attached, and an indication that rowRanges is an
S4 generic when we encountered the error.  When should we introduce
the method

setMethod("rowRanges", "matrix", function(x, ...) matrixStats::rowRanges(x,
...))

that would foster the behavior I think you are looking for?


>
> > head(matrixStats::rowRanges(counts))
>[,1] [,2]
> [1,]   51.27791 9350.048
> [2,] 1417.41010 8272.040
> > sessionInfo()
> R Under development (unstable) (2016-08-25 r71150)
> Platform: x86_64-pc-linux-gnu (64-bit)
> Running under: Ubuntu 14.04.5 LTS
>
> locale:
>  [1] LC_CTYPE=en_US.UTF-8   LC_NUMERIC=C
>  [3] LC_TIME=en_US.UTF-8LC_COLLATE=en_US.UTF-8
>  [5] LC_MONETARY=en_US.UTF-8LC_MESSAGES=en_US.UTF-8
>  [7] LC_PAPER=en_US.UTF-8   LC_NAME=C
>  [9] LC_ADDRESS=C   LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] parallel  stats4stats graphics  grDevices utils datasets
> [8] methods   base
>
> other attached packages:
> [1] SummarizedExperiment_1.5.7 DelayedArray_0.1.7
> [3] matrixStats_0.51.0 Biobase_2.35.1
> [5] GenomicRanges_1.27.23  GenomeInfoDb_1.11.10
> [7] IRanges_2.9.19 S4Vectors_0.13.15
> [9] BiocGenerics_0.21.3
>
> loaded via a namespace (and not attached):
> [1] lattice_0.20-34 bitops_1.0-6grid_3.4.0
> [4] zlibbioc_1.21.0 XVector_0.15.2  Matrix_1.2-8
> [7] 

[Bioc-devel] conflict rowRanges SummarizedExperiment/matrixStats

2017-04-06 Thread Maarten van Iterson
Dear all,

SummarizedExperiment and matrixStats both contain a method/function called
rowRanges one operates on a SummarizedExperiment-object the other on a
matrix. matrixStats is required by SummarizedExperiment, or a package it is
depending on, so rowRanges is masked when loading SummarizedExperiment.

I thought a function/method is called depended on the type of the object;
matrix or SummarizedExperiment-object, such that functions/methods with the
same name can coexist. However, this doesn't seems to work for rowRanges.
The only way to access rowRanges from matrixStats when SummarizedExperiment
is already loaded is using the double colon operator
matrixStats::rowRanges. Is this intentional or is there a other way to
solve this?

Regards,
Maarten

Here is a small example showing the issue:

> library(SummarizedExperiment)
Loading required package: matrixStats
matrixStats v0.51.0 (2016-10-08) successfully loaded. See ?matrixStats for
help.
Attaching package: ‘matrixStats’
Attaching package: ‘SummarizedExperiment’
The following object is masked from ‘package:matrixStats’:
rowRanges
> nrows <- 200; ncols <- 6
> counts <- matrix(runif(nrows * ncols, 1, 1e4), nrows)
> rowRanges <- GRanges(rep(c("chr1", "chr2"), c(50, 150)),
+  IRanges(floor(runif(200, 1e5, 1e6)), width=100),
+  strand=sample(c("+", "-"), 200, TRUE),
+  feature_id=sprintf("ID%03d", 1:200))
> colData <- DataFrame(Treatment=rep(c("ChIP", "Input"), 3),
+  row.names=LETTERS[1:6])
> rse <- SummarizedExperiment(assays=SimpleList(counts=counts),
+ rowRanges=rowRanges, colData=colData)
>
> rowRanges(rse)
GRanges object with 200 ranges and 1 metadata column:
seqnames   ranges strand |  feature_id
  | 
[1] chr1 [858613, 858712]  - |   ID001
>
> rowRanges(counts)
Error in (function (classes, fdef, mtable)  :
  unable to find an inherited method for function ‘rowRanges’ for signature
‘"matrix"’
>
> library(matrixStats) ##it is already loading so this doesn't alter the
search path
>
> rowRanges(rse)
GRanges object with 200 ranges and 1 metadata column:
seqnames   ranges strand |  feature_id
  | 
[1] chr1 [858613, 858712]  - |   ID001
> rowRanges(counts)
Error in (function (classes, fdef, mtable)  :
  unable to find an inherited method for function ‘rowRanges’ for signature
‘"matrix"’
>
> head(matrixStats::rowRanges(counts))
   [,1] [,2]
[1,]   51.27791 9350.048
[2,] 1417.41010 8272.040
> sessionInfo()
R Under development (unstable) (2016-08-25 r71150)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 14.04.5 LTS

locale:
 [1] LC_CTYPE=en_US.UTF-8   LC_NUMERIC=C
 [3] LC_TIME=en_US.UTF-8LC_COLLATE=en_US.UTF-8
 [5] LC_MONETARY=en_US.UTF-8LC_MESSAGES=en_US.UTF-8
 [7] LC_PAPER=en_US.UTF-8   LC_NAME=C
 [9] LC_ADDRESS=C   LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] parallel  stats4stats graphics  grDevices utils datasets
[8] methods   base

other attached packages:
[1] SummarizedExperiment_1.5.7 DelayedArray_0.1.7
[3] matrixStats_0.51.0 Biobase_2.35.1
[5] GenomicRanges_1.27.23  GenomeInfoDb_1.11.10
[7] IRanges_2.9.19 S4Vectors_0.13.15
[9] BiocGenerics_0.21.3

loaded via a namespace (and not attached):
[1] lattice_0.20-34 bitops_1.0-6grid_3.4.0
[4] zlibbioc_1.21.0 XVector_0.15.2  Matrix_1.2-8
[7] RCurl_1.95-4.8  GenomeInfoDbData_0.99.0

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