[Bioc-devel] Update existing packages and change name

[Sokratis Kariotis]

Hi all,

After lots of tries we decided to follow your second suggestion. How can we
stop the support for 32-bit windows?

Cheers,
Sokratis

On 22 March 2018 at 15:14, Hervé Pagès <hpages at fredhutch.org> wrote:

> Hi Sokratis,
>
> On 03/22/2018 06:13 AM, Sokratis Kariotis wrote:
>
>>   Hey all,
>>
>> I have been updating my pathprint and pathprintGeoData packages (in 3.7)
>> and I encountered the following error in one of them (only on windows
>> server):
>>
>> Error: cannot allocate vector of size 237.3 Mb
>>
>> Here is the report: https://urldefense.proofpoint.
>> com/v2/url?u=https-3A__bioconductor.org_checkResults_3.7_
>> bioc-2DLATEST_&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAv
>> imeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=vq6ajmYLDu1OVYL9MQ4KO2q
>> mc3ypMSQdmMTd3m4ygxY&s=kFbj_KW3LgfOmlyR4Pi4-ewT1wzqjOKnhdVUOB7u9xE&e=
>> pathprint/tokay2-checksrc.html
>>
>> How can I fix this? Thanks in advance.
>>
>
> Note that this error happens only when running the examples in 32-bit
> mode (arch i386) but not in 64-bit mode (arch x64). 32-bit Windows
> doesn't allow a process to use more than 2 Gb of RAM. There is no such
> limit with 64-bit Windows.
>
> You have 2 options: (1) reduce the memory footprint of the examples,
> or (2) give up on supporting your package for 32-bit Windows users.
>
> (2) should be the last resort.
>
> Cheers,
> H.
>
>
>
>> Cheers,
>> Sokratis
>>
>>
>> On 21 February 2018 at 20:37, Obenchain, Valerie <
>> Valerie.Obenchain at roswellpark.org> wrote:
>>
>> Hi Sokratis,
>>>
>>> Unfortunately you can't rename a package ... and there is no such thing
>>> as
>>> a 'sub package'. Maybe you meant sub-package terms of dependencies. If
>>> you
>>> have new data to add that's independent of what's in pathprintGEOData you
>>> can create a new data package.
>>>
>>> I'm not sure what you mean by 'considerably more data'. The
>>> pathprintGEOData package is currently 22MG:
>>>
>>> ~ >du -h pathprintGEOData_1.4.0.tar.gz
>>> 22M    pathprintGEOData_1.4.0.tar.gz
>>>
>>> We don't support git LFS yet in the experimental data repo. If you plan
>>> on
>>> making the package(s) very large we should consider making a
>>> ExperimentHub
>>> package where the data can be stored in S3.
>>>
>>> Valerie
>>>
>>>
>>>
>>> On 02/21/2018 05:16 AM, Sokratis Kariotis wrote:
>>>
>>> Hey all, I am updating 2 of my packages (pathprint & pathprintGEOData)
>>> with
>>> considerably more data and a few code updates. I also want to change the
>>> name of the data package to reflect the new content. Can the package name
>>> be changed or do I have to create new sub-packages? Thanks in advance.
>>>
>>> Cheers
>>>
>>>
>>>
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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: hpages at fredhutch.org
> Phone:  (206) 667-5791
> Fax:    (206) 667-1319
>



-- 
Sokratis Kariotis
Scientific Programmer
Hidelab
Sheffield Institute for Translational Neuroscience
385a Glossop Rd, Sheffield, S10 2HQ

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