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 <hpa...@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.obench...@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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