[BioC] Error in loading "IRanges" package (version 1.6.1)

[Hervé Pagès]

Hi Lilyana, Patrick,

Patrick Aboyoun wrote:
> I found a candidate replacement:
> 
>  > format(Sys.time(), "%Y-%m-%d %X %z (%a, %d %b %Y)")
> [1] "2010-05-12 21:19:17 -0700 (Wed, 12 May 2010)"
> 
> The author of the original C code, Herve Pages, is currently on holiday 
> and I don't know if he had a reason not to use the built in Sys.time 
> function.

I was not aware of the format method for POSIXct objects
(format.POSIXct). It's good to know about it. Unfortunately the
conversion specification %z is not portable. It seems to work
fine on Mac OS X but it produces "+0000" on my Ubuntu 9.04 instead
of "-0700" (I'm in Seattle):

   > format(Sys.time(), "%z")
   [1] "+0000"

I just committed a new version of svn.time() that compiles and behaves
consistently on Linux, Windows and Mac OS X (Leopard and Tiger).
It will be available in IRanges 1.6.3 (release) and 1.7.4 (devel) thru
biocLite() in the next 24 hours.

Cheers,
H.


> If there are not objections within the next 24 hours by the 
> user community, I'll check in this this fix.
> 
> 
> Cheers,
> Patrick
> 
> 
> 
> On 5/12/10 9:10 PM, Patrick Aboyoun wrote:
>> Lilyana,
>> Steve is right. We added an svn.time function to IRanges that produces 
>> a time/date stamp in the same format as the BioC Subversion server, 
>> e.g. "2007-12-07 10:03:15 -0800 (Fri, 07 Dec 2007)", for use by the 
>> GenomicFeatures package. We implemented a method in C that builds on 
>> Linux, Windows 32bit&  64bit, and Mac OS X 10.5&  10.6, but not on Mac 
>> OS X 10.4 (Tiger). Since we dropped support for Mac OS X 10.4, we felt 
>> comfortable with this decision at the time. We'll explore alternatives 
>> to see if we can come up with an svn.time solution that doesn't 
>> preclude building on Mac OS X 10.4. Suggestions by the user community 
>> is welcome to speed this process along.
>>
>>
>> Cheers,
>>
>> Patrick
>>
>>
>> On 5/12/10 6:48 PM, Steve Lianoglou wrote:
>>> Hi,
>>>
>>> On Wed, May 12, 2010 at 6:28 PM, Lilyana Margaretha<lilyanam at uw.edu>  
>>> wrote:
>>>> Hi,
>>>>
>>>> I am a beginner user of R and trying to install "IRanges" package.
>>>> I have R version 2.11 and running it on Mac OS X 10.4.11.
>>>> It always gives out this error:
>>>>
>>>> gcc -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include
>>>>   -I/sw/include -I/usr/local/include    -fPIC  -g -O2 -c strutils.c -o
>>>> strutils.o
>>>> strutils.c: In function ‘get_svn_time’:
>>>> strutils.c:167:27: error: invalid operands to binary / (have ‘char *
>>>> (*)(int,  int)’ and ‘int’)
>>>> make: *** [strutils.o] Error 1
>>>> ERROR: compilation failed for package ‘IRanges’
>>>> * removing ‘/Users/lilyanamargaretha/Desktop/IRanges.Rcheck/IRanges’
>>>>
>>>> Any suggestion on how to solve this will be very much appreciated.
>>> I guess I shouldn't really respond since I don't know this for a fact,
>>> but maybe you need a minimum OS X version of 10.5 (leopard) for
>>> everything to work?
>>>
>>> (I see the that binaries provided online are for Leopard, which is why
>>> I'm guessing so)
>>>
>>> -steve
>>>
>>>
>>
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> 
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-- 
Hervé Pagès

Program in Computational Biology
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