hmmer no data

[Former user]

Good afternoon,

I´ve just recently been using bio3d and its great! I´ve been tring to use hmmer to get all sequences of a domain. Following the example in http://thegrantlab.org/bio3d/html/hmmer.html

seq <- get.seq("2abl_A", outfile=tempfile())
res <- hmmer(seq, db="pdb")

i´ve got this error, i think, with no data downloaded:

• Adding handle: conn: 0x1291a7800
• Adding handle: send: 0
• Adding handle: recv: 0
• Curl_addHandleToPipeline: length: 1
• • Conn 12 (0x1291a7800) send_pipe: 1, recv_pipe: 0
• About to connect() to hmmer.janelia.org port 80 (#12)
• Trying 206.241.0.22...

• Connected to hmmer.janelia.org (206.241.0.22) port 80 (#12)

  POST /search/phmmer HTTP/1.1 Host: hmmer.janelia.org Accept:text/xml Content-Length: 184 Content-Type: application/x-www-form-urlencoded

• upload completely sent off: 184 out of 184 bytes < HTTP/1.1 301 Moved Permanently < Date: Tue, 28 Jul 2015 10:51:17 GMT

• Server Apache/2.2.3 (Scientific Linux) is not blacklisted < Server: Apache/2.2.3 (Scientific Linux) < Location: http://www.ebi.ac.uk/Tools/hmmer/search/phmmer < Content-Length: 346 < Connection: close < Content-Type: text/html; charset=iso-8859-1 <
• Closing connection 12
• Issue another request to this URL: 'http://www.ebi.ac.uk/Tools/hmmer/search/phmmer'
• Violate RFC 2616/10.3.2 and switch from POST to GET
• Adding handle: conn: 0x10f80d000
• Adding handle: send: 0
• Adding handle: recv: 0
• Curl_addHandleToPipeline: length: 1
• • Conn 13 (0x10f80d000) send_pipe: 1, recv_pipe: 0
• About to connect() to www.ebi.ac.uk port 80 (#13)
• Trying 193.62.193.80...
• Connected to www.ebi.ac.uk (193.62.193.80) port 80 (#13)

  GET /Tools/hmmer/search/phmmer HTTP/1.1 Host: www.ebi.ac.uk Accept:text/xml

< HTTP/1.1 200 OK * Server Apache/2.2.15 (Red Hat) is not blacklisted < Server: Apache/2.2.15 (Red Hat) < Vary: Content-Type < Content-Type: text/xml < Date: Tue, 28 Jul 2015 10:51:17 GMT < Connection: Keep-Alive < Set-Cookie: hmmerserver_session=343ac165a5eec53d406c5a69f90683740f21d10f; path=/; expires=Wed, 27-Jul-2016 16:40:03 GMT; HttpOnly < Content-Length: 16 < * Connection #13 to host www.ebi.ac.uk left intact Error in tmpi : subscript out of bounds

i don´t know if i´m making some mistake... thank you for your time and the great work (don´t know if this is the correct place to do this, if not sorry)

tiago

[Lars Skjærven]

Hi Tiago, can you try to install the latest release of bio3d (not through CRAN)? I think the hmmer URL has changed, and this causes the problem. You can install the latest version with these commands:

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

Hope it helps. Lars

[Barry Grant]

This change might be worth a CRAN patch update before the new version. Thanks for posting Tiago! Barry

[Tiago Lopes]

Updated to the devel version. It game me the same error. thanks tiago

[Lars Skjærven]

Ah, the bugfix is in the master branch, and not merged with releases yet.

Use this command:

install_bitbucket("Grantlab/bio3d", subdir = "ver_devel/bio3d/")

Sorry about that L

[Tiago Lopes]

when tring to load it gives me this error:

Error in get(Info[i, 1], envir = env) : lazy-load database '/Library/Frameworks/R.framework/Versions/3.2/Resources/library/bio3d/R/bio3d.rdb' is corrupt In addition: Warning message: In get(Info[i, 1], envir = env) : internal error -3 in R_decompress1 Error: package or namespace load failed for ‘bio3d’

thanks

[Lars Skjærven]

close and restart R first

[Tiago Lopes]

Did it after updating (i`m using rstudio). Gave same mistake. thanks

[Lars Skjærven]

Are you sure you loaded a clean R session? check with typing sessionInfo() in the R shell to see that you don't have a previous bio3d version loaded. If it doesn't work in Rstudio, see if it works in Terminal. (looks like you're on OSX?)

[Tiago Lopes]

Did that before also. yes mac osx. sessionInfo gives bio3d_2.2-3 (the latest one i think) In terminal its the same error. thank you

[Lars Skjærven]

Strange. Perhaps try removing bio3d first with remove.packages?

[Tiago Lopes]

Ok it worked after remove.packages. Now reseted to bio3d_2.2-2.9000 devtools_1.8.0, and seems to be working. thank you