dependance for conumee ‘IlluminaHumanMethylationEPICanno.ilm10b2.hg19’ package installation fails because shortage of memory
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@d97897b8
Last seen 13 days ago
France

Hello,

I was trying to install the conumee package with BiocManager, and the manager was trying to install the dependency lluminaHumanMethylationEPICanno.ilm10b2.hg19. I removed the file called 00LOCK-IlluminaHumanMethylationEPICanno.ilm10b2.hg19 from my R repository because I have red that it blocked my package installation

But now, when installing the package lluminaHumanMethylationEPICanno.ilm10b2.hg19, I get a cold killed

BiocManager::install("conumee") 

replacement repositories:
    CRAN: https://cloud.r-project.org

Bioconductor version 3.13 (BiocManager 1.30.16), R 4.1.0 (2021-05-18)
Installing package(s) 'conumee'
installation de la dépendance ‘IlluminaHumanMethylationEPICanno.ilm10b2.hg19’

essai de l'URL 'https://bioconductor.org/packages/3.13/data/annotation/src/contrib/IlluminaHumanMethylationEPICanno.ilm10b2.hg19_0.6.0.tar.gz'
Content type 'application/x-gzip' length 158636019 bytes (151.3 MB)
==================================================
downloaded 151.3 MB

essai de l'URL 'https://bioconductor.org/packages/3.13/bioc/src/contrib/conumee_1.26.0.tar.gz'
Content type 'application/x-gzip' length 1255651 bytes (1.2 MB)
==================================================
downloaded 1.2 MB

* installing *source* package ‘IlluminaHumanMethylationEPICanno.ilm10b2.hg19’ ...
* using staged installation
** data
*** moving datasets to lazyload DB
Killed
ERROR: dependency ‘IlluminaHumanMethylationEPICanno.ilm10b2.hg19’ is not available for package ‘conumee’
* removing ‘/home/diegolito/R/x86_64-pc-linux-gnu-library/4.1/conumee’

The downloaded source packages are in
    ‘/tmp/Rtmpz9kvfg/downloaded_packages’
Installation paths not writeable, unable to update packages
  path: /usr/lib/R/library
  packages:
    spatial
Messages d'avis :
1: Dans .inet_warning(msg) :
  installation of package ‘IlluminaHumanMethylationEPICanno.ilm10b2.hg19’ had non-zero exit status
2: Dans .inet_warning(msg) :
  installation of package ‘conumee’ had non-zero exit status

R version 4.1.0 (2021-05-18) -- "Camp Pontanezen"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit) )

Killed means my system is out of memory right ? I have 4 GB Ram, with 2.3 GB ocupied at rest.

I don't really know how I can resolve that

Thank you for your attention, I really hope you have any idea how to work solutions for that kind of issues

IlluminaHumanMethylationEPICanno.ilm10b2.hg19 conumee • 83 views
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Entering edit mode
@james-w-macdonald-5106
Last seen 1 day ago
United States

Usually when you run out of memory you get a message saying something like (unable to allocate a vector of XX mb). 'Killed' on the other hand sounds like a segmentation fault.

Anyway, you are almost surely not going to be able to do much with 4 Gb RAM. That is almost none at all. I mean I won't get a desktop for just regular stuff that doesn't have at least 16 Gb RAM, let alone trying to do copy number stuff.

You would probably be better off by either

  1. Adding RAM
  2. Using a different computer

Where for #2 there are options, one of which is using AWS.

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