Answers.Body: <p>You could use the <code>tryCatch</code> <a href="http://127.0.0.1:30714/library/base/html/conditions.html" rel="nofollow noreferrer">function</a> to handle inputs that throw an error. A good example on how to write them can be found <a href="https://stackoverflow.com/questions/12193779/how-to-write-trycatch-in-r">here</a>. Though the message indicates it's a warning, so does the function stop running when you get this message?</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2023-11-02T09:47:51.477Z
Answers.LastActivityDate: 2023-11-02T09:47:51.477Z
Answers.UserDisplayName: dthorbur
Body: <p>I have developed an R function to download the &quot;organism&quot; name of the numerous NCBI accession numbers which are already saved in an object.
  The function:</p>
  <pre><code>get_organism_names &lt;- function(accession_numbers) {
    organism_names &lt;- sapply(accession_numbers, function(accession) {
      record &lt;- entrez_summary(db = &quot;nucleotide&quot;, id = accession)
      return(record$organism)
    }, USE.NAMES = FALSE)
    names(organism_names) &lt;- accession_numbers
    return(organism_names)
  }
  </code></pre>
  <p>Although it works for some accession numbers, for others it encounters an error stating for example:</p>
  <pre><code>Warning: Esummary includes error message: Invalid uid KU253616.1 at position= 0Error: No esummary records found in file
  </code></pre>
  <p>How can I either solve this error or ask R to skip the problematic accession and keep downloading the rest?</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2023-10-25T12:53:30.697Z
Comments.Text: Have you tried running it in a loop with a single accession each time instead of giving it all of them?
Comments.UserDisplayName: terdon
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2023-10-25T12:56:07.410Z
Comments.Text: Also, please give us all of the code. Presumably, you are loading some libraries, which ones? We need example code that we can use to reproduce the problem. See https://stackoverflow.com/help/minimal-reproducible-example. We need example input, and then code that we can run locally that reproduces the error.
Comments.UserDisplayName: terdon
Tags: <r><ncbi>
Title: error in downloading the annotation of sequences on NCBI
ThreadText: # error in downloading the annotation of sequences on NCBI
  
  (Asked by: username_0 on 2023-10-25)
  
  I have developed an R function to download the "organism" name of the numerous NCBI accession numbers which are already saved in an object.
  The function:
  
  ```
  get_organism_names <- function(accession_numbers) {
    organism_names <- sapply(accession_numbers, function(accession) {
      record <- entrez_summary(db = "nucleotide", id = accession)
      return(record$organism)
    }, USE.NAMES = FALSE)
    names(organism_names) <- accession_numbers
    return(organism_names)
  }
  
  ```
  
  Although it works for some accession numbers, for others it encounters an error stating for example:
  
  ```
  Warning: Esummary includes error message: Invalid uid KU253616.1 at position= 0Error: No esummary records found in file
  
  ```
  
  How can I either solve this error or ask R to skip the problematic accession and keep downloading the rest?
  
  **Tags:** r, ncbi
  
  > **Comments:**
  > **username_1**: Have you tried running it in a loop with a single accession each time instead of giving it all of them?  
  > **username_1**: Also, please give us all of the code. Presumably, you are loading some libraries, which ones? We need example code that we can use to reproduce the problem. See https://stackoverflow.com/help/minimal-reproducible-example. We need example input, and then code that we can run locally that reproduces the error.  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_2 on 2023-11-02. Score: 1
  
  You could use the `tryCatch` [function](http://127.0.0.1:30714/library/base/html/conditions.html) to handle inputs that throw an error. A good example on how to write them can be found [here](https://stackoverflow.com/questions/12193779/how-to-write-trycatch-in-r). Though the message indicates it's a warning, so does the function stop running when you get this message?
  
  
  ---
  
  