Answers.Body: <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>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2018-05-20T12:39:34.923Z
Answers.Text: **This only works** (and is only required) **on Windows.** OP is using Linux. Not sure why he accepted this answer.
Answers.UserDisplayName: Konrad Rudolph
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2018-05-21T00:17:36.673Z
Answers.Text: 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?
Answers.UserDisplayName: Biomagician
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2018-05-19T22:10:49.897Z
Answers.LastActivityDate: 2018-05-21T08:09:36.823Z
Answers.LastEditDate: 2018-05-21T08:09:36.823Z
Answers.UserDisplayName: benn
Body: <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>
  
Tags: <r><bioconductor><sequence-annotation><errors>
Title: GFF file too big to load into R
ThreadText: # 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
  
  
  ---
  
  ## 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?  
  
  ---
  
  