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Question: GO.db installation error
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gravatar for predeus
2.0 years ago by
predeus0
United States
predeus0 wrote:

Hello all,

I've been trying to install WGCNA on our cluster. It has module system, so I've chosen R-3.1.2 and installed bunch of libs locally (which all worked OK). Now, GO.db was the only one that failed to install. When I typed

source("https://bioconductor.org/biocLite.R")
biocLite("GO.db")

it returned
----- (download, installation logs here, no errors) ---------

** testing if installed package can be loaded
Error in sqliteSendQuery(con, statement, bind.data) : 
  error in statement: disk I/O error
Error in sqliteSendQuery(con, statement, bind.data) : 
  error in statement: disk I/O error
Error in sqliteSendQuery(con, statement, bind.data) : 
  error in statement: disk I/O error
Error : .onLoad failed in loadNamespace() for 'GO.db', details:
  call: sqliteSendQuery(con, statement, bind.data)
  error: error in statement: disk I/O error

Seems like some sort of SQL problem, but I'm really at a loss here and would appreciate any suggestions. 

All the best, 

-- Alex
ADD COMMENTlink modified 23 months ago by Daniel Lai0 • written 2.0 years ago by predeus0
2
gravatar for Peter Langfelder
2.0 years ago by
United States
Peter Langfelder1.3k wrote:

To answer the OP's question, the problem is that one of the CRAN packages that GO.db depends on (via AnnotationDBI), namely RSQLite, changed to a new API when Bioconductore released a new version, which was in the middle of R release cycle. (WGCNA got bitten by this change as well.) You should make sure that the Bioconductor version (2.14 and 3.0 were both released for R 3.1) and the RSQlite package are compatible. My impression was that BioC 2.14 worked with RSQLite 0.4 through 0.11, and BioC 3.0 and higher works with RSQLite 1.0.

ADD COMMENTlink written 2.0 years ago by Peter Langfelder1.3k
0
gravatar for James W. MacDonald
2.0 years ago by
United States
James W. MacDonald45k wrote:

Unfortunately, we are unable to provide technical help for outdated versions. Have you tried installing the current version of R and Bioconductor? If not, I would start there.

ADD COMMENTlink written 2.0 years ago by James W. MacDonald45k

Just hit this myself with a fresh install (from source) of R:

 

R version 3.3.0 (2016-05-03) -- "Supposedly Educational"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
> source('http://bioconductor.org/biocLite.R')
Bioconductor version 3.3 (BiocInstaller 1.22.2), ?biocLite for help
> biocLite()
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.3 (BiocInstaller 1.22.2), R 3.3.0 (2016-05-03).
>
> biocLite('SKAT')
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.3 (BiocInstaller 1.22.2), R 3.3.0 (2016-05-03).
Installing package(s) ‘SKAT’ [...]
** testing if installed package can be loaded
* DONE (SKAT)
> biocLite('GO.db')
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.3 (BiocInstaller 1.22.2), R 3.3.0 (2016-05-03).
Installing package(s) ‘GO.db’
trying URL 'https://bioconductor.org/packages/3.3/data/annotation/src/contrib/GO.db_3.3.0.tar.gz'

** testing if installed package can be loaded
Error in sqliteSendQuery(con, statement, bind.data) : 
  error in statement: disk I/O error
Error in sqliteSendQuery(con, statement, bind.data) : 
  error in statement: disk I/O error
Error in sqliteSendQuery(con, statement, bind.data) : 
  error in statement: disk I/O error
Error in sqliteSendQuery(con, statement, bind.data) : 
  error in statement: disk I/O error
Error : .onLoad failed in loadNamespace() for 'GO.db', details:
  call: sqliteSendQuery(con, statement, bind.data)
  error: error in statement: disk I/O error
Error: loading failed
Execution halted
ERROR: loading failed

This is with the session:

[1] RSQLite_1.0.0        DBI_0.4-1            BiocInstaller_1.22.2
ADD REPLYlink modified 17 months ago by Martin Morgan ♦♦ 20k • written 17 months ago by christopherlhartl0

Just to answer my question: this is a filesystem issue. 

 

> .libPaths('/tmp')
> biocLite('GO.db')
** testing if installed package can be loaded
* DONE (GO.db)

 

So a workaround if you're on such a filesystem: put the source .tar.gz in a central location, and you'll need to freshly install GO.db (and whatever other .dbs you need) directly from source, into a temporary library on the local (/tmp or /scratch) filesystem.

ADD REPLYlink modified 17 months ago by Martin Morgan ♦♦ 20k • written 17 months ago by christopherlhartl0

Can you provide some information about what is unique about the default location to which you were trying to install these db packages?

ADD REPLYlink written 17 months ago by Martin Morgan ♦♦ 20k
0
gravatar for Hervé Pagès
2.0 years ago by
Hervé Pagès ♦♦ 13k
United States
Hervé Pagès ♦♦ 13k wrote:

Hi Alex,

First of all why did you choose R-3.1.2? The current release of Bioconductor (BioC 3.2) only works with the R-3.2 series, which is the most current R series (the latest in that series being R-3.2.2). By installing R-3.1.2, you make the choice to use BioC 3.1, which is not supported anymore (we only suport the current release).

Second, are you sure you're actually using R-3.1.2? You're trying to source() an https URL and my understanding is that this is only supported starting with R-3.2.

Before going any further, I would strongly recommend that you update to R-3.2.2. Then start R and install BioC 3.2 with:

source("https://bioconductor.org/biocLite.R")
biocLite()

That will only install a few Bioconductor packages but it's an important test. In particular it will install the BiocInstaller package. Once you have this package installed, you don't need to source() the biocLite.R script anymore to install packages, just load the BiocInstaller package (it contains the biocLite() function). So quit R, restart it, and do:

library(BiocInstaller)
biocLite("GO.db")

Please show us the complete output of the 2 commands above.

Thanks,

H.

ADD COMMENTlink modified 2.0 years ago • written 2.0 years ago by Hervé Pagès ♦♦ 13k
0
gravatar for Daniel Lai
23 months ago by
Daniel Lai0
Canada
Daniel Lai0 wrote:

Another potential reason is that the cluster you're using doesn't fully support sqlite [1].  I have personally experienced this issue on a Lustre cluster file system.  If working off the cluster is not a possibility, potential solutions can be restricting installation (via the 'lib' option in biocLite) and analyses only to non-cluster disks (e.g. /tmp, /scratch, etc).  More drastic solutions may be reconfigure/install the cluster with proper locking mechanisms [2].

[1] https://groups.google.com/a/udel.edu/forum/#!topic/hpc-ask/K15bYR2ranc

[2] http://comments.gmane.org/gmane.comp.file-systems.lustre.user/5724

 

 

 

ADD COMMENTlink written 23 months ago by Daniel Lai0
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