blastSequences queries failing due to BLAST switch to https?
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@arielhecht-11631
Last seen 5.6 years ago

I was using blastSequences in the annotate package to run BLAST queries from R. At first I was getting the following error message:

Error: failed to load external entity "http://www.ncbi.nlm.nih.gov/blast/Blast.cgi?QUERY=AGCCGGTATACACGAA&DATABASE=nr&HITLIST_SIZE=10&FILTER=L&EXPECT=10&PROGRAM=blastn&CMD=Put" ​

I assumed that this was because NCBI switched over to requiring https on Sep. 30, 2016: https://www.ncbi.nlm.nih.gov/news/06-10-2016-ncbi-https/. I tried modifying the blastSequences code using trace(blastSequences,edit=T) and changing editing the url to use https. I then got the following error message:

Error in Sys.sleep(time) : invalid 'time' value

In addition: Warning message: XML content does not seem to be XML: 'https://www.ncbi.nlm.nih.gov/blast/Blast.cgi?QUERY=AGCCGGTATACACGAA&DATABASE=nr&HITLIST_SIZE=10&FILTER=L&EXPECT=10&PROGRAM=blastn&CMD=Put' ​

Does anyone know how to address this issue? Is there an update of blastSequences forthcoming to address this issue?

Thanks!

annotate blastSequences BLAST https • 1.5k views
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@martin-morgan-1513
Last seen 6 days ago
United States

Changing the url is not enough, https:// needs to be retrieved via RCurl::getURL() and then parsed by XML.This has been fixed in the 'devel' branch for a while, but I neglected to port it to release. It should appear as 1.50.1 at about this time tomorrow. Thanks for the report!

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Awesome, thanks for responding so quickly! I'll download the update and see if it works!