Re: [Bioc-devel] Adding a lengths() method to List class

[Hervé Pagès]

On 10/15/2015 11:24 AM, Michael Lawrence wrote:

Btw, a subtle issue here is that elementLengths currently calls NROW(),
not length(), and code might be relying on DataFrameList returning row
counts. That behavior has proven convenient, so it would be nice not to
lose it. I guess nrow() already does that, but anyway, lengths() is not
the equivalent of elementLengths() there.


There is actually a big note in ?BiocGenerics::lengths about this.
This means we will need to keep elementLengths() around but the plan
is to rename it elementNROWS() (consistent with extractROWS). The
current name is clearly a misnomer and a source of confusion.

H.



On Wed, Sep 30, 2015 at 9:37 PM, Hervé Pagès > wrote:

On 09/30/2015 05:28 PM, Michael Lawrence wrote:

It wasn't a conscious choice, but it would slow things down a
bit. Not
by much though, since we're already attempting dispatch on
length(). I
can make the change.


That would be great. Thanks Michael!

H.


On Wed, Sep 30, 2015 at 1:33 PM, Hervé Pagès

>> wrote:

 Hi Michael,

 I was expecting this to just work:

base::lengths(IntegerList(1:4, 1:6))

 but it doesn't:

Error in base::lengths(IntegerList(1:4, 1:6)) :
  'x' must be a list or atomic vector

 The man page says:

   This function loops over ‘x’ and returns a compatible
vector
   containing the length of each element in ‘x’.
Effectively,
   ‘length(x[[i]])’ is called for all ‘i’, so any
methods on ‘length’
   are considered.

 If length(x[[i]]) is called for all i then it should work
on any object
 for which [[ is defined. Note that this is what happens with
 base::sapply(), base::mapply(), etc... they all use [[
internally.

 Do you know of any reason why lengths() doesn't do this?

 Thanks,
 H.


 On 09/28/2015 09:51 PM, Michael Lawrence wrote:

 That is the plan. Note that we already have
elementLengths()
 that serves
 the same purpose. It was the direct inspiration for
lengths().

 On Mon, Sep 28, 2015 at 9:41 PM, Peter Hickey
 
>>
 wrote:

 The lengths() function was added in R 3.2 to "get
the length
 of each
 element of a list or atomic vector (is.atomic) as
an integer
 or numeric
 vector." It seems useful to me to have also a
similar method
 defined for
 the S4Vectors::List class (and subclasses). What do
others
 think?

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 mailing list
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 --
 Hervé Pagès

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

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

 Fax: (206) 667-1319 




--
Hervé Pagès

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

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




--
Hervé Pagès

Re: [Bioc-devel] Adding a lengths() method to List class

[Michael Lawrence]

Btw, a subtle issue here is that elementLengths currently calls NROW(), not
length(), and code might be relying on DataFrameList returning row counts.
That behavior has proven convenient, so it would be nice not to lose it. I
guess nrow() already does that, but anyway, lengths() is not the equivalent
of elementLengths() there.

On Wed, Sep 30, 2015 at 9:37 PM, Hervé Pagès  wrote:

> On 09/30/2015 05:28 PM, Michael Lawrence wrote:
>
>> It wasn't a conscious choice, but it would slow things down a bit. Not
>> by much though, since we're already attempting dispatch on length(). I
>> can make the change.
>>
>
> That would be great. Thanks Michael!
>
> H.
>
>
>> On Wed, Sep 30, 2015 at 1:33 PM, Hervé Pagès > > wrote:
>>
>> Hi Michael,
>>
>> I was expecting this to just work:
>>
>>base::lengths(IntegerList(1:4, 1:6))
>>
>> but it doesn't:
>>
>>Error in base::lengths(IntegerList(1:4, 1:6)) :
>>  'x' must be a list or atomic vector
>>
>> The man page says:
>>
>>   This function loops over ‘x’ and returns a compatible vector
>>   containing the length of each element in ‘x’.  Effectively,
>>   ‘length(x[[i]])’ is called for all ‘i’, so any methods on
>> ‘length’
>>   are considered.
>>
>> If length(x[[i]]) is called for all i then it should work on any
>> object
>> for which [[ is defined. Note that this is what happens with
>> base::sapply(), base::mapply(), etc... they all use [[ internally.
>>
>> Do you know of any reason why lengths() doesn't do this?
>>
>> Thanks,
>> H.
>>
>>
>> On 09/28/2015 09:51 PM, Michael Lawrence wrote:
>>
>> That is the plan. Note that we already have elementLengths()
>> that serves
>> the same purpose. It was the direct inspiration for lengths().
>>
>> On Mon, Sep 28, 2015 at 9:41 PM, Peter Hickey
>> >
>> wrote:
>>
>> The lengths() function was added in R 3.2 to "get the length
>> of each
>> element of a list or atomic vector (is.atomic) as an integer
>> or numeric
>> vector." It seems useful to me to have also a similar method
>> defined for
>> the S4Vectors::List class (and subclasses). What do others
>> think?
>>
>>   [[alternative HTML version deleted]]
>>
>> ___
>> Bioc-devel@r-project.org 
>> mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>
>>
>>  [[alternative HTML version deleted]]
>>
>> ___
>> Bioc-devel@r-project.org 
>> mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>
>>
>> --
>> Hervé Pagès
>>
>> Program in Computational Biology
>> Division of Public Health Sciences
>> Fred Hutchinson Cancer Research Center
>> 1100 Fairview Ave. N, M1-B514
>> P.O. Box 19024
>> Seattle, WA 98109-1024
>>
>> E-mail: hpa...@fredhutch.org 
>> Phone: (206) 667-5791 
>> Fax: (206) 667-1319 
>>
>>
>>
> --
> Hervé Pagès
>
> Program in Computational Biology
> Division of Public Health Sciences
> Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N, M1-B514
> P.O. Box 19024
> Seattle, WA 98109-1024
>
> E-mail: hpa...@fredhutch.org
> Phone:  (206) 667-5791
> Fax:(206) 667-1319
>

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Re: [Bioc-devel] Adding a lengths() method to List class

[Peter Hickey]

Thanks, Michael!

On Fri, 2 Oct 2015 at 13:54 Michael Lawrence 
wrote:

> Change was made. Should dispatch to length and [[ methods.
>
> On Wed, Sep 30, 2015 at 9:37 PM, Hervé Pagès  wrote:
>
>> On 09/30/2015 05:28 PM, Michael Lawrence wrote:
>>
>>> It wasn't a conscious choice, but it would slow things down a bit. Not
>>> by much though, since we're already attempting dispatch on length(). I
>>> can make the change.
>>>
>>
>> That would be great. Thanks Michael!
>>
>> H.
>>
>>
>>> On Wed, Sep 30, 2015 at 1:33 PM, Hervé Pagès >> > wrote:
>>>
>>> Hi Michael,
>>>
>>> I was expecting this to just work:
>>>
>>>base::lengths(IntegerList(1:4, 1:6))
>>>
>>> but it doesn't:
>>>
>>>Error in base::lengths(IntegerList(1:4, 1:6)) :
>>>  'x' must be a list or atomic vector
>>>
>>> The man page says:
>>>
>>>   This function loops over ‘x’ and returns a compatible vector
>>>   containing the length of each element in ‘x’.  Effectively,
>>>   ‘length(x[[i]])’ is called for all ‘i’, so any methods on
>>> ‘length’
>>>   are considered.
>>>
>>> If length(x[[i]]) is called for all i then it should work on any
>>> object
>>> for which [[ is defined. Note that this is what happens with
>>> base::sapply(), base::mapply(), etc... they all use [[ internally.
>>>
>>> Do you know of any reason why lengths() doesn't do this?
>>>
>>> Thanks,
>>> H.
>>>
>>>
>>> On 09/28/2015 09:51 PM, Michael Lawrence wrote:
>>>
>>> That is the plan. Note that we already have elementLengths()
>>> that serves
>>> the same purpose. It was the direct inspiration for lengths().
>>>
>>> On Mon, Sep 28, 2015 at 9:41 PM, Peter Hickey
>>> >
>>> wrote:
>>>
>>> The lengths() function was added in R 3.2 to "get the length
>>> of each
>>> element of a list or atomic vector (is.atomic) as an integer
>>> or numeric
>>> vector." It seems useful to me to have also a similar method
>>> defined for
>>> the S4Vectors::List class (and subclasses). What do others
>>> think?
>>>
>>>   [[alternative HTML version deleted]]
>>>
>>> ___
>>> Bioc-devel@r-project.org 
>>> mailing list
>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>>
>>>
>>>  [[alternative HTML version deleted]]
>>>
>>> ___
>>> Bioc-devel@r-project.org 
>>> mailing list
>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>>
>>>
>>> --
>>> Hervé Pagès
>>>
>>> Program in Computational Biology
>>> Division of Public Health Sciences
>>> Fred Hutchinson Cancer Research Center
>>> 1100 Fairview Ave. N, M1-B514
>>> P.O. Box 19024
>>> Seattle, WA 98109-1024
>>>
>>> E-mail: hpa...@fredhutch.org 
>>> Phone: (206) 667-5791 
>>> Fax: (206) 667-1319 
>>>
>>>
>>>
>> --
>> Hervé Pagès
>>
>> Program in Computational Biology
>> Division of Public Health Sciences
>> Fred Hutchinson Cancer Research Center
>> 1100 Fairview Ave. N, M1-B514
>> P.O. Box 19024
>> Seattle, WA 98109-1024
>>
>> E-mail: hpa...@fredhutch.org
>> Phone:  (206) 667-5791
>> Fax:(206) 667-1319
>>
>
>

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Re: [Bioc-devel] Adding a lengths() method to List class

[Michael Lawrence]

Change was made. Should dispatch to length and [[ methods.

On Wed, Sep 30, 2015 at 9:37 PM, Hervé Pagès  wrote:

> On 09/30/2015 05:28 PM, Michael Lawrence wrote:
>
>> It wasn't a conscious choice, but it would slow things down a bit. Not
>> by much though, since we're already attempting dispatch on length(). I
>> can make the change.
>>
>
> That would be great. Thanks Michael!
>
> H.
>
>
>> On Wed, Sep 30, 2015 at 1:33 PM, Hervé Pagès > > wrote:
>>
>> Hi Michael,
>>
>> I was expecting this to just work:
>>
>>base::lengths(IntegerList(1:4, 1:6))
>>
>> but it doesn't:
>>
>>Error in base::lengths(IntegerList(1:4, 1:6)) :
>>  'x' must be a list or atomic vector
>>
>> The man page says:
>>
>>   This function loops over ‘x’ and returns a compatible vector
>>   containing the length of each element in ‘x’.  Effectively,
>>   ‘length(x[[i]])’ is called for all ‘i’, so any methods on
>> ‘length’
>>   are considered.
>>
>> If length(x[[i]]) is called for all i then it should work on any
>> object
>> for which [[ is defined. Note that this is what happens with
>> base::sapply(), base::mapply(), etc... they all use [[ internally.
>>
>> Do you know of any reason why lengths() doesn't do this?
>>
>> Thanks,
>> H.
>>
>>
>> On 09/28/2015 09:51 PM, Michael Lawrence wrote:
>>
>> That is the plan. Note that we already have elementLengths()
>> that serves
>> the same purpose. It was the direct inspiration for lengths().
>>
>> On Mon, Sep 28, 2015 at 9:41 PM, Peter Hickey
>> >
>> wrote:
>>
>> The lengths() function was added in R 3.2 to "get the length
>> of each
>> element of a list or atomic vector (is.atomic) as an integer
>> or numeric
>> vector." It seems useful to me to have also a similar method
>> defined for
>> the S4Vectors::List class (and subclasses). What do others
>> think?
>>
>>   [[alternative HTML version deleted]]
>>
>> ___
>> Bioc-devel@r-project.org 
>> mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>
>>
>>  [[alternative HTML version deleted]]
>>
>> ___
>> Bioc-devel@r-project.org 
>> mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>
>>
>> --
>> Hervé Pagès
>>
>> Program in Computational Biology
>> Division of Public Health Sciences
>> Fred Hutchinson Cancer Research Center
>> 1100 Fairview Ave. N, M1-B514
>> P.O. Box 19024
>> Seattle, WA 98109-1024
>>
>> E-mail: hpa...@fredhutch.org 
>> Phone: (206) 667-5791 
>> Fax: (206) 667-1319 
>>
>>
>>
> --
> Hervé Pagès
>
> Program in Computational Biology
> Division of Public Health Sciences
> Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N, M1-B514
> P.O. Box 19024
> Seattle, WA 98109-1024
>
> E-mail: hpa...@fredhutch.org
> Phone:  (206) 667-5791
> Fax:(206) 667-1319
>

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Re: [Bioc-devel] Adding a lengths() method to List class

[Hervé Pagès]

Hi Michael,

I was expecting this to just work:

  base::lengths(IntegerList(1:4, 1:6))

but it doesn't:

  Error in base::lengths(IntegerList(1:4, 1:6)) :
'x' must be a list or atomic vector

The man page says:

 This function loops over ‘x’ and returns a compatible vector
 containing the length of each element in ‘x’.  Effectively,
 ‘length(x[[i]])’ is called for all ‘i’, so any methods on ‘length’
 are considered.

If length(x[[i]]) is called for all i then it should work on any object
for which [[ is defined. Note that this is what happens with
base::sapply(), base::mapply(), etc... they all use [[ internally.

Do you know of any reason why lengths() doesn't do this?

Thanks,
H.

On 09/28/2015 09:51 PM, Michael Lawrence wrote:

That is the plan. Note that we already have elementLengths() that serves
the same purpose. It was the direct inspiration for lengths().

On Mon, Sep 28, 2015 at 9:41 PM, Peter Hickey 
wrote:


The lengths() function was added in R 3.2 to "get the length of each
element of a list or atomic vector (is.atomic) as an integer or numeric
vector." It seems useful to me to have also a similar method defined for
the S4Vectors::List class (and subclasses). What do others think?

 [[alternative HTML version deleted]]

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--
Hervé Pagès

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

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

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Re: [Bioc-devel] Adding a lengths() method to List class

[Michael Lawrence]

It wasn't a conscious choice, but it would slow things down a bit. Not by
much though, since we're already attempting dispatch on length(). I can
make the change.

On Wed, Sep 30, 2015 at 1:33 PM, Hervé Pagès  wrote:

> Hi Michael,
>
> I was expecting this to just work:
>
>   base::lengths(IntegerList(1:4, 1:6))
>
> but it doesn't:
>
>   Error in base::lengths(IntegerList(1:4, 1:6)) :
> 'x' must be a list or atomic vector
>
> The man page says:
>
>  This function loops over ‘x’ and returns a compatible vector
>  containing the length of each element in ‘x’.  Effectively,
>  ‘length(x[[i]])’ is called for all ‘i’, so any methods on ‘length’
>  are considered.
>
> If length(x[[i]]) is called for all i then it should work on any object
> for which [[ is defined. Note that this is what happens with
> base::sapply(), base::mapply(), etc... they all use [[ internally.
>
> Do you know of any reason why lengths() doesn't do this?
>
> Thanks,
> H.
>
>
> On 09/28/2015 09:51 PM, Michael Lawrence wrote:
>
>> That is the plan. Note that we already have elementLengths() that serves
>> the same purpose. It was the direct inspiration for lengths().
>>
>> On Mon, Sep 28, 2015 at 9:41 PM, Peter Hickey 
>> wrote:
>>
>> The lengths() function was added in R 3.2 to "get the length of each
>>> element of a list or atomic vector (is.atomic) as an integer or numeric
>>> vector." It seems useful to me to have also a similar method defined for
>>> the S4Vectors::List class (and subclasses). What do others think?
>>>
>>>  [[alternative HTML version deleted]]
>>>
>>> ___
>>> Bioc-devel@r-project.org mailing list
>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>>
>>>
>> [[alternative HTML version deleted]]
>>
>> ___
>> Bioc-devel@r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>
>>
> --
> Hervé Pagès
>
> Program in Computational Biology
> Division of Public Health Sciences
> Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N, M1-B514
> P.O. Box 19024
> Seattle, WA 98109-1024
>
> E-mail: hpa...@fredhutch.org
> Phone:  (206) 667-5791
> Fax:(206) 667-1319
>

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Re: [Bioc-devel] Adding a lengths() method to List class

[Hervé Pagès]

On 09/30/2015 05:28 PM, Michael Lawrence wrote:

It wasn't a conscious choice, but it would slow things down a bit. Not
by much though, since we're already attempting dispatch on length(). I
can make the change.


That would be great. Thanks Michael!

H.



On Wed, Sep 30, 2015 at 1:33 PM, Hervé Pagès > wrote:

Hi Michael,

I was expecting this to just work:

   base::lengths(IntegerList(1:4, 1:6))

but it doesn't:

   Error in base::lengths(IntegerList(1:4, 1:6)) :
 'x' must be a list or atomic vector

The man page says:

  This function loops over ‘x’ and returns a compatible vector
  containing the length of each element in ‘x’.  Effectively,
  ‘length(x[[i]])’ is called for all ‘i’, so any methods on ‘length’
  are considered.

If length(x[[i]]) is called for all i then it should work on any object
for which [[ is defined. Note that this is what happens with
base::sapply(), base::mapply(), etc... they all use [[ internally.

Do you know of any reason why lengths() doesn't do this?

Thanks,
H.


On 09/28/2015 09:51 PM, Michael Lawrence wrote:

That is the plan. Note that we already have elementLengths()
that serves
the same purpose. It was the direct inspiration for lengths().

On Mon, Sep 28, 2015 at 9:41 PM, Peter Hickey
>
wrote:

The lengths() function was added in R 3.2 to "get the length
of each
element of a list or atomic vector (is.atomic) as an integer
or numeric
vector." It seems useful to me to have also a similar method
defined for
the S4Vectors::List class (and subclasses). What do others
think?

  [[alternative HTML version deleted]]

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--
Hervé Pagès

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

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




--
Hervé Pagès

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

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

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Re: [Bioc-devel] Adding a lengths() method to List class

[Cook, Malcolm]

Yay m- thx

From: Michael Lawrence [mailto:lawrence.mich...@gene.com]
Sent: Tuesday, September 29, 2015 11:16 AM
To: Cook, Malcolm <m...@stowers.org>
Cc: Michael Lawrence <lawrence.mich...@gene.com>; Peter Hickey 
<peter.hic...@gmail.com>; bioc-devel@r-project.org
Subject: Re: [Bioc-devel] Adding a lengths() method to List class

The plan is to move to only having lengths().

On Tue, Sep 29, 2015 at 9:02 AM, Cook, Malcolm 
<m...@stowers.org<mailto:m...@stowers.org>> wrote:
Dumb question (?) follows in line:

> That is the plan. Note that we already have elementLengths() that serves the
 > same purpose. It was the direct inspiration for lengths().

Why have both?

 >
 > On Mon, Sep 28, 2015 at 9:41 PM, Peter Hickey 
 > <peter.hic...@gmail.com<mailto:peter.hic...@gmail.com>>
 > wrote:
 >
 > > The lengths() function was added in R 3.2 to "get the length of each
 > > element of a list or atomic vector (is.atomic) as an integer or
 > > numeric vector." It seems useful to me to have also a similar method
 > > defined for the S4Vectors::List class (and subclasses). What do others 
 > > think?



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Re: [Bioc-devel] Adding a lengths() method to List class

[Cook, Malcolm]

Dumb question (?) follows in line:

> That is the plan. Note that we already have elementLengths() that serves the
 > same purpose. It was the direct inspiration for lengths().

Why have both?

 > 
 > On Mon, Sep 28, 2015 at 9:41 PM, Peter Hickey 
 > wrote:
 > 
 > > The lengths() function was added in R 3.2 to "get the length of each
 > > element of a list or atomic vector (is.atomic) as an integer or
 > > numeric vector." It seems useful to me to have also a similar method
 > > defined for the S4Vectors::List class (and subclasses). What do others 
 > > think?

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Re: [Bioc-devel] Adding a lengths() method to List class

[Michael Lawrence]

The plan is to move to only having lengths().

On Tue, Sep 29, 2015 at 9:02 AM, Cook, Malcolm  wrote:

> Dumb question (?) follows in line:
>
> > That is the plan. Note that we already have elementLengths() that serves
> the
>  > same purpose. It was the direct inspiration for lengths().
>
> Why have both?
>
>  >
>  > On Mon, Sep 28, 2015 at 9:41 PM, Peter Hickey 
>  > wrote:
>  >
>  > > The lengths() function was added in R 3.2 to "get the length of each
>  > > element of a list or atomic vector (is.atomic) as an integer or
>  > > numeric vector." It seems useful to me to have also a similar method
>  > > defined for the S4Vectors::List class (and subclasses). What do
> others think?
>
>
>

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Re: [Bioc-devel] Adding a lengths() method to List class

[Michael Lawrence]

That is the plan. Note that we already have elementLengths() that serves
the same purpose. It was the direct inspiration for lengths().

On Mon, Sep 28, 2015 at 9:41 PM, Peter Hickey 
wrote:

> The lengths() function was added in R 3.2 to "get the length of each
> element of a list or atomic vector (is.atomic) as an integer or numeric
> vector." It seems useful to me to have also a similar method defined for
> the S4Vectors::List class (and subclasses). What do others think?
>
> [[alternative HTML version deleted]]
>
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>

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