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odd behavior

Issue #407 resolved
Jonathan Gough created an issue

I have been using bio3d without too many problems, and then today I had something weird happen. I used the same commands I have been using and now they don't work... It all falls apart at the blast step.

library(bio3d) pdb <- read.pdb("2RGP.pdb") seq <- pdbseq(pdb) blast <- blast.pdb(seq) Error in file(file, "r") : cannot open the connection

literally, I ran the same exact thing yesterday and it worked fine, today errors. Blast in a browser works, but I get the same error on my Linux box and my MacOS laptop using R on the command line.

Thanks.

Comments (15)

  1. Barry Grant

    This is likely a connection issue from the NCBI side as I get the same error from here.

    Digging in a little reveals that "NCBI is currently testing https on public web servers until 4:00 PM EDT (20:00 UTC) today. You may experience problems with NCBI services during this test".

    It also looks like they could be changing their various URLs, which would mean we would need to change those within the bio3d blast.pdb() function once we know what they are up to.

    In the mean time, as a workaround you can use the generally more sensitive HMMER service from the EBI, e.g.:

    > x <- hmmer(seq, type="phmmer", db ="pdb")
> hits <-plot(x)
> head(hits$pdb.id)
[1] "2itw_A" "2ity_A" "2j5e_A" "3poz_A" "2j6m_A" "2j5f_A"
  2. Jonathan Gough reporter

    Thanks Barry,

    Glad to know I'm not going crazy. I really appreciate the quick reply.

    Best, Jonathan

  4. Lars Skjærven

    Looks like substituting http with https in blast.pdb.R fixes this issue. I'll try to commit this later today

  7. Barry Grant

    I have made the fix now (on the releases branch, which I then merged into master). To get this fixed development version you can use the following commands within your R session:

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

    This will build from source - let us know if you have any problems.

  8. Jonathan Gough reporter

    I'm not sure what the problem is. I guess I don't have devtools?

    bio3d works. ( I could load a pdb)

    [jgough@localhost-2 pdb_files]$ R

    R version 3.2.3 (2015-12-10) -- "Wooden Christmas-Tree" Copyright (C) 2015 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu (64-bit)

    R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details.

    Natural language support but running in an English locale

    R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications.

    Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R.

    [Previously saved workspace restored]

    HEADER TRANSFERASE 04-OCT-07 2RGP

    Error in library(devtools) : there is no package called ‘devtools’ Error: could not find function "install_bitbucket"

  9. Lars Skjærven

    can you install the package?

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

> aa <- get.seq("1rx2")
> blast <- blast.pdb(aa) 
 Searching ... please wait (updates every 5 seconds) RID = 24GMZS0E01R 
 .
 Reporting 578 hits
  10. Jonathan Gough reporter

    I finally got it installed. There was some weird issue with git2r

    But.. now I have an error with bio3d

    [jgough@localhost-2 pdb_files]$ R

    R version 3.2.3 (2015-12-10) -- "Wooden Christmas-Tree" Copyright (C) 2015 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu (64-bit)

    R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details.

    Natural language support but running in an English locale

    R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications.

    Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R.

    [Previously saved workspace restored]

    Error in file(file, "r") : https:// URLs are not supported

  11. Lars Skjærven

    Do you get that error message only by starting R? If so, this might be related to the "[Previously saved workspace restored]" message. Try to launch R from a different (clean) directory, or delete the .RData file in your working dir. Let us know if that helps or not.

  12. Jonathan Gough reporter

    I still haven't figured out what the deal is with my linux desktop.

    I was able to install the dev version on my mac laptop with out a problem. However, I then got another error when using the pdbsplit function in the Dev version. I was going to report the error, but blast stopped working again yetserday afternoon.

    I had a temporary workaround whereby I would grab the files on the laptop (dev version), in dropbox, and then process them on my desktop (bio3d_2.2-2.tar.gz).

    However, I had to install the tar.gz version and load it each time. 1. Is there a way within R to determine what version of bio3d is loaded or installed? 2. How do you uninstall/reinstalll a library? 3. The workaround seemed to have stopped working.... I'm guessing it has something to do with blast again.

    1. Another random question/error/hiccup I encountered... within my workflow, I am: reading in a seed pdb. running blast, finding all proteins within a certain tolerance, downloading all of those pdbs, using reduce to protonate the pdb (because I want/need H's on both the ligands and the protein and reduce uses the connect records which get lost if chains are split by bio3d), splitting the new protonated files into separate pdbs, aligning them and then spitting them all back out (aligned). One of the hiccups I encountered was if and when other proteins are in the files, when one goes to align them it dies (because the sequences have almost no homology, is my guess). Do you have any thoughts on how to get over that hiccup? Can one re-read in the split files and cull those that don't match a certain homology?

    Thanks again for all your help patience with a newbie. Jonathan

  13. Lars Skjærven

    Use sessionInfo() for Q1: 

    > sessionInfo()
R version 3.3.2 (2016-10-31)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X Yosemite 10.10.5

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] bio3d_2.3-1.9000 devtools_1.12.0 

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.7    roxygen2_5.0.1 XML_3.98-1.4   crayon_1.3.2   digest_0.6.10 
 [6] withr_1.0.2    bitops_1.0-6   grid_3.3.2     R6_2.2.0       magrittr_1.5  
[11] stringi_1.1.2  testthat_1.0.2 tools_3.3.2    stringr_1.1.0  RCurl_1.95-4.8
[16] parallel_3.3.2 memoise_1.0.0

    for Q2:

    > remove.packages("bio3d")
Removing package from ‘/Library/Frameworks/R.framework/Versions/3.3/Resources/library’
(as ‘lib’ is unspecified)

    Re-install with 

    install.packages("bio3d")

    (new version on CRAN now)

  14. Jonathan Gough reporter

    Thank you. Blast is working on the Laptop(Mac OSX) and now on the Desktop (Linux).

    The versions of R between the two were different, so I updated R on the LINUX desktop and that fixed the blast error. R version 3.2.3 updated to R version 3.3.1

    I have now been able to re-create the error I found in the devel version. Should I open a new thread?

    If not, here is what I have: | | 0%Error in eval(substitute(expr), envir, enclos) : basic_string::substr

    For completeness and future trouble shooting, Below are the specifications for both machines.

    Laptop: Warning message: package ‘bio3d’ was built under R version 3.3.2 R version 3.3.1 (2016-06-21) Platform: x86_64-apple-darwin13.4.0 (64-bit) Running under: OS X 10.12.1 (Sierra)

    locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

    attached base packages: [1] stats graphics grDevices utils datasets methods base

    other attached packages: [1] bio3d_2.3-1

    loaded via a namespace (and not attached): [1] parallel_3.3.1 Rcpp_0.12.7 grid_3.3.1

    Blast Not working on the Desktop (linux): R version 3.2.3 (2015-12-10) Platform: x86_64-pc-linux-gnu (64-bit) Running under: CentOS Linux 7 (Core)

    locale: [1] LC_CTYPE=en_US.utf8 LC_NUMERIC=C [3] LC_TIME=en_US.utf8 LC_COLLATE=en_US.utf8 [5] LC_MONETARY=en_US.utf8 LC_MESSAGES=en_US.utf8 [7] LC_PAPER=en_US.utf8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.utf8 LC_IDENTIFICATION=C

    attached base packages: [1] stats graphics grDevices utils datasets base

    other attached packages: [1] bio3d_2.3-1

    loaded via a namespace (and not attached): [1] parallel_3.2.3 Rcpp_0.12.7 grid_3.2.3 methods_3.2.3

    Blast now working Desktop: R version 3.3.1 (2016-06-21) Platform: x86_64-redhat-linux-gnu (64-bit) Running under: CentOS Linux 7 (Core)

    locale: [1] LC_CTYPE=en_US.utf8 LC_NUMERIC=C [3] LC_TIME=en_US.utf8 LC_COLLATE=en_US.utf8 [5] LC_MONETARY=en_US.utf8 LC_MESSAGES=en_US.utf8 [7] LC_PAPER=en_US.utf8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.utf8 LC_IDENTIFICATION=C

    attached base packages: [1] stats graphics grDevices utils datasets methods base

    other attached packages: [1] bio3d_2.3-1

    loaded via a namespace (and not attached): [1] parallel_3.3.1 grid_3.3.1

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Assignee
Bio3D Project
Type
bug
Priority
major
Status
resolved
Component
Q&A
Version
v2.2
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0
Watchers
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