<p>It depends of course on your available RAM on your computer.</p>

<p>Under Windows you can increase the available RAM in R with memory limit:</p>

<pre><code>&gt; memory.limit()
[1] 8070
&gt; memory.limit(size=10000)
[1] 10000
&gt; memory.limit()
[1] 10000
</code></pre>

<p>But that is not necessary on linux/unix.</p>

CC BY-SA 4.0
2018-05-20T12:39:34.923Z
**This only works** (and is only required) **on Windows.** OP is using Linux. Not sure why he accepted this answer.
Konrad Rudolph
CC BY-SA 4.0
2018-05-21T00:17:36.673Z
Indeed, memory.limit()
[1] Inf
Warning message:
'memory.limit()' is Windows-specific. I understood this as 'no memory limit' on Linux, so only limited by available RAM?
Biomagician
CC BY-SA 4.0
2018-05-19T22:10:49.897Z
2018-05-21T08:09:36.823Z
2018-05-21T08:09:36.823Z
benn
<p>I want to load a GFF (annotation) file into an R data frame in order to extract some information from it, e.g. the location of transposons in the genome.</p>

<p>I used the following code:</p>

<pre><code>library(rtracklayer)
gff &lt;- rtracklayer::import('c_elegans.PRJNA13758.WS263.annotations.gff3.gz')
Error: cannot allocate vector of size 210.2 Mb
</code></pre>

<p>It seems that the GFF3 file is too big for loading into R. Do you know if this is limited by R or by my computer's memory?</p>

<p>I ran this on a GNU/Linux computer.</p>

<r><bioconductor><sequence-annotation><errors>
GFF file too big to load into R
# GFF file too big to load into R

(Asked by: username_0 on 2018-05-19)

I want to load a GFF (annotation) file into an R data frame in order to extract some information from it, e.g. the location of transposons in the genome.
I used the following code:
library(rtracklayer)
gff <- rtracklayer::import('c_elegans.PRJNA13758.WS263.annotations.gff3.gz')
Error: cannot allocate vector of size 210.2 Mb

It seems that the GFF3 file is too big for loading into R. Do you know if this is limited by R or by my computer's memory?
I ran this on a GNU/Linux computer.

**Tags:** r, bioconductor, sequence-annotation, errors

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## 1 answers

### Answer by username_1 on 2018-05-19. Score: 3 | Accepted answer

It depends of course on your available RAM on your computer.
Under Windows you can increase the available RAM in R with memory limit:
> memory.limit()
[1] 8070
> memory.limit(size=10000)
[1] 10000
> memory.limit()
[1] 10000

But that is not necessary on linux/unix.

> **Comments:**
> **username_2**: **This only works** (and is only required) **on Windows.** OP is using Linux. Not sure why he accepted this answer.  
> **username_0**: Indeed, memory.limit() [1] Inf Warning message: 'memory.limit()' is Windows-specific. I understood this as 'no memory limit' on Linux, so only limited by available RAM?  

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