Question: SOLVED: Having trouble installing Bioconductor package GEOquery
0
gravatar for daisycutter4
9 months ago by
daisycutter40 wrote:

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.

bioconductor R • 419 views
ADD COMMENTlink modified 9 months ago • written 9 months ago by daisycutter40

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).

ADD REPLYlink modified 9 months ago • written 9 months ago by genomax37k

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.

ADD REPLYlink written 9 months ago by daisycutter40
1
gravatar for genomax
9 months ago by
genomax37k
United States
genomax37k wrote:

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.

ADD COMMENTlink modified 9 months ago • written 9 months ago by genomax37k

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

I'll consider another distribution of linux!

ADD REPLYlink written 9 months ago by daisycutter40

You can go ahead and accept this answer (green check mark) to provide closure to this thread.

ADD REPLYlink written 9 months ago by genomax37k
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