problem of sequence analysis

[B Albert]

Hello:

I am running the following command:

seq <- get.seq("1rx2_A") pfam <- hmmer(seq, type="hmmscan", db="pfam")

but it failed with messages:

*   Trying 206.241.0.22...
* Connected to hmmer.janelia.org (206.241.0.22) port 80 (#0)
> POST /search/hmmscan HTTP/1.1
Host: hmmer.janelia.org
Accept:text/xml
Content-Length: 181
Content-Type: application/x-www-form-urlencoded

* upload completely sent off: 181 out of 181 bytes
< HTTP/1.1 301 Moved Permanently
< Date: Thu, 03 Sep 2015 19:38:10 GMT
< Server: Apache/2.2.3 (Scientific Linux)
< Location: http://www.ebi.ac.uk/Tools/hmmer/search/hmmscan
< Content-Length: 347
< Connection: close
< Content-Type: text/html; charset=iso-8859-1
< 
* Closing connection 0
* Issue another request to this URL: 'http://www.ebi.ac.uk/Tools/hmmer/search/hmmscan'
* Switch from POST to GET
*   Trying 193.62.193.80...
* Connected to www.ebi.ac.uk (193.62.193.80) port 80 (#1)
> GET /Tools/hmmer/search/hmmscan HTTP/1.1
Host: www.ebi.ac.uk
Accept:text/xml

< HTTP/1.1 200 OK
< Server: Apache/2.2.15 (Red Hat)
< Vary: Content-Type
< Content-Type: text/xml
< Date: Thu, 03 Sep 2015 19:38:16 GMT
< Connection: Keep-Alive
< Set-Cookie: hmmerserver_session=85d74452648bac559aff16d53b90c4f3b902d5d6; path=/; expires=Sat, 03-Sep-2016 01:27:02 GMT; HttpOnly
< Content-Length: 84
< 
* Connection #1 to host www.ebi.ac.uk left intact
Error in .subset2(x, i, exact = exact) : 
  attempt to select less than one element

[Barry Grant]

This movement of the HMMER web services was noted in some previously discussed issues here and can be fixed by updating to the latest development version from our bitbucket site.

Do let us know if you still have problems please.

Side-note for developers: we need to update the CRAN package version to fix this issue there also.

[Xinqiu Yao]

That is an important note. We have had a patched version (2.2-3) ready on releases with all recent bugfixes included. It should be fine to just submit it to CRAN. Any other comment, Lars?

[Barry Grant]

Lets update with this patched version...

[Lars Skjærven]

bug has previously been fixed and the fix should be available through CRAN. otherwise the development version can be installed using the devtools package:

install.packages("devtools")
library(devtools)
install_bitbucket("Grantlab/bio3d", subdir = "ver_devel/bio3d/")