[Bioc-devel] BiocCheck failing

2015-09-30 Thread Samuel E Zimmerman 
Hi everyone,

I just submitted a package to Bioconductor. All the tests passed except for the 
BiocCheck step in the "Mac OS X Mavericks (10.9.5)/x86_64" OS. The version of 
BiocCheck used was 1.5.9 and the error is below.


Error in curl::curl_fetch_memory(url, handle = handle) :
  Timeout was reached
Calls:  ... request_fetch -> request_fetch.write_memory -> 
 -> .Call
Execution halted

This error only occurs in the Mavericks OS. All the tests pass Snow Leopard, 
Linux, and Windows Server. Does anyone know what could account for this error?

Thank you very much.

Best,
Sam

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Re: [Bioc-devel] BiocCheck failing

2015-09-30 Thread Dan Tenenbaum 


- Original Message -
> From: "Samuel E Zimmerman" 
> To: bioc-devel@r-project.org
> Sent: Wednesday, September 30, 2015 2:02:06 PM
> Subject: [Bioc-devel] BiocCheck failing
> 
> Hi everyone,
> 
> I just submitted a package to Bioconductor. All the tests passed
> except for the BiocCheck step in the "Mac OS X Mavericks
> (10.9.5)/x86_64" OS. The version of BiocCheck used was 1.5.9 and the
> error is below.
> 
> 
> Error in curl::curl_fetch_memory(url, handle = handle) :
>   Timeout was reached
> Calls:  ... request_fetch -> request_fetch.write_memory ->
>  -> .Call
> Execution halted
> 
> This error only occurs in the Mavericks OS. All the tests pass Snow
> Leopard, Linux, and Windows Server. Does anyone know what could
> account for this error?
> 

It's an internal issue with BiocCheck on that machine. We will 
investigate/resolve it and you can ignore that error.

Dan


> Thank you very much.
> 
> Best,
> Sam
> 
>   [[alternative HTML version deleted]]
> 
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Re: [Bioc-devel] Adding a lengths() method to List class

2015-09-30 Thread 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?

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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

2015-09-30 Thread 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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[Bioc-devel] packages marked as deprecated in the upcoming release

2015-09-30 Thread Dan Tenenbaum 
Hi all,

In accordance with our package end-of-life policy 
(http://www.bioconductor.org/developers/package-end-of-life/) we have marked 
the following packages as deprecated:

 CausalR
 DAVIDQuery
 eisa
 GenoView
 NGScopy

Two packages (R3CPET and IdMappingRetrieval) depend on DAVIDQuery and one 
(ExpressionView) depends on eisa (no packages in turn depend on these three 
packages).  The maintainers of these packages have been notified. 

Let us know if you have questions about this.
Dan

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

2015-09-30 Thread 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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