Question: SOLVED: Having trouble installing Bioconductor package GEOquery
0
gravatar for daisycutter4
10 days 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 • 113 views
ADD COMMENTlink modified 9 days ago • written 10 days 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 10 days ago • written 10 days ago by genomax223k

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 10 days ago by daisycutter40
1
gravatar for genomax2
9 days ago by
genomax223k
United States
genomax223k 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 days ago • written 9 days ago by genomax223k

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

I'll consider another distribution of linux!

ADD REPLYlink written 9 days ago by daisycutter40

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

ADD REPLYlink written 9 days ago by genomax223k
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