[Bioc-devel] Update existing packages and change name

Hervé Pagès hpages at fredhutch.org
Thu Mar 22 16:14:01 CET 2018

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=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=vq6ajmYLDu1OVYL9MQ4KO2qmc3ypMSQdmMTd3m4ygxY&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,
> 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

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