[Bioc-devel] Update existing packages and change name

[Martin Morgan]

On 05/22/2018 05:46 AM, Sokratis Kariotis wrote:
> Hi all,
> 
> After lots of tries we decided to follow your second suggestion. How can we
> stop the support for 32-bit windows?

An obvious place to start is with a less comprehensive example data set;

 > geo_sum_data
class: SummarizedExperiment
dim: 633 393645
metadata(0):
assays(1): fingerprint
rownames(633): Glycolysis / Gluconeogenesis (KEGG) Citrate cycle (TCA
   cycle) (KEGG) ... {VCP,17} (Static Module) {VHL,12} (Static Module)
rowData names(0):
colnames(393645): GSM1000166 GSM1000167 ... GSM999842 GSM999843
colData names(7): GSM GSE ... Source Characteristics

Is it not possible to illustrate the functionality of your package with 
a much smaller example?

Martin

> 
> 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
>>
> 
> 
> 


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