SOLVED: Having trouble installing Bioconductor package GEOquery
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4.2 years ago

Hello everyone,

when trying to install GEOquery, a bioconductor package for R, appears 12 warnings, so the install has not been completed. (I'm using a Raspbian OS)

Warning messages:

1: In system2(cmd0, args, env = env, stdout = outfile, stderr = outfile) :
  system call failed: Cannot allocate memory

2: In install.packages(pkgs = pkgs, lib = lib, repos = repos,  ... :
  installation of package 'BiocGenerics' had non-zero exit status

3: In system2(cmd0, args, env = env, stdout = outfile, stderr = outfile) :
  system call failed: Cannot allocate memory

4: In install.packages(pkgs = pkgs, lib = lib, repos = repos,  ... :
  installation of package 'bitops' had non-zero exit status

5: In system2(cmd0, args, env = env, stdout = outfile, stderr = outfile) :
  system call failed: Cannot allocate memory

6: In install.packages(pkgs = pkgs, lib = lib, repos = repos,  ... :
  installation of package 'XML' had non-zero exit status

7: In system2(cmd0, args, env = env, stdout = outfile, stderr = outfile) :
  system call failed: Cannot allocate memory

8: In install.packages(pkgs = pkgs, lib = lib, repos = repos,  ... :
  installation of package 'Biobase' had non-zero exit status

9: In system2(cmd0, args, env = env, stdout = outfile, stderr = outfile) :
  system call failed: Cannot allocate memory

10: In install.packages(pkgs = pkgs, lib = lib, repos = repos,  ... :
  installation of package 'RCurl' had non-zero exit status

11: In system2(cmd0, args, env = env, stdout = outfile, stderr = outfile) :
  system call failed: Cannot allocate memory

12: In install.packages(pkgs = pkgs, lib = lib, repos = repos,  ... :
  installation of package 'GEOquery' had non-zero exit status

How could i solve it?

Thanks!

Solved: I've followed the steps of this post : https://www.raspberrypi.org/forums/viewtopic.php?t=111375&p=767299 And if you have problems with dphys-swapfile, try to install it: http://manpages.ubuntu.com/manpages/trusty/man8/dphys-swapfile.8.html

sudo apt-get install dphys-swapfile

and then restart the previous steps.

R bioconductor • 2.6k views
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Are you trying to do this on a raspberry Pi? I doubt there is enough RAM on the Pi to do useful bioinformatics (or install packages).

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No, I'm using an old laptop with this OS, probably it's not the best OS to do bioinformatics. And the RAM(1gb) is enough to try to do basic things.

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4.2 years ago
GenoMax 99k

See if this helps? You may still be better off using another lightweight linux distro instead of one meant for use on Pi on this laptop.

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Thank very much for sharing that post, it has been really useful!!

I'll consider another distribution of linux!

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