Regarding: RSQLite driver: (RS_SQLite_fetch: failed first step: disk I/O
error)

 

We successfully diagnosed and solved this problem. We tried the

suggestions of installing the R packages on a local disk and ran

RSQLite-specific commands which indicated the RSQLite-package was
installed

and working but the error persisted. The problem manifested in a call

to the lookUp() function of the 'annotate' package which uses

RSQLite. It appeared that for the version installed on the server,

there was some hard-coded limit in the underlying (non-R) SQLite that

caused calls to lookUp() with > 24814 items to throw the error. 

 

In particular, sqlite 3.3.6-2 was installed on our server that

demonstrated the error, while on a separate server running 3.3.6-5,

the function ran properly. Thus, we installed sqlite with the newest

date on the src tree under 3.3.6 from

http://www.sqlite.org/src/info/715cecb8c7 on our server and we no

longer see this error.

 

For future reference, this snippet of code was enough to pinpoint the

problem (we noticed that could use lookUp for subsets of all PROBE_ID
but

not for the full vector of PROBE_ID):

-----------------------

library(annotate)

library(mgug4112a.db)

 

PROBE_ID = <list of probe ids>

 

# This returns ACCNUM without error for first PROBE_ID

GENE_ID= lookUp(PROBE_ID[1], 'mgug4112a.db', "ACCNUM")

 

# This gets RSQLite error and any subsequent calls to lookUp show

# error, have to restart R session to reset -> dislikes whole vector as
input

GENE_ID= lookUp(PROBE_ID, 'mgug4112a.db', "ACCNUM") # has RSQLite error

 

# This displays ACCNUM for each PROBE_ID individually, without error

# so problem isn't a specific PROBE_ID[i]

for (i in 0:length(PROBE_ID)) { 

   GENE_ID= lookUp(PROBE_ID[i], 'mgug4112a.db', "ACCNUM");

   cat(i, " ", GENE_ID,"\n")

}

 

# This displays i-th ACCNUM when lookUp 1:i but get error for

# i=24815, reproducibly and any subsequent call to lookUp displays

# RSQLite error - seems to be hard-coded size limit in SQLite

for (i in 0:length(PROBE_ID)) { 

   GENE_ID= lookUp(PROBE_ID[1:i], 'mgug4112a.db', "ACCNUM");

   cat(i, " ", GENE_ID[i],"\n")

}

 

 

--------- Previous Posts -----------------------------

From: Benilton Carvalho [mailto:beniltoncarvalho@gmail.com]

Sent: Wednesday, August 25, 2010 2:44 PM

To: Brown, Joseph

Cc: bioconductor@stat.math.ethz.ch

Subject: Re: [BioC] Agi4x44PreProcess- RSQLite driver: (RS_SQLite_fetch:
failed first step: disk I/O error)

 

I have seen something similar (with RSQLite alone)... and, back in the

day, it appeared to have an association with the fact that the library

directory was on a network drive (and the connection of the machine

with the storage system was not that great)...

 

Installing the RSQLite-dependent package on a local disk always solved

the problem for me...

 

b

 

On 25 August 2010 21:10, Brown, Joseph <BrownJo@njhealth.org> wrote:

> Issue:

> 

> When trying to execute filter.probes the following error occurs:

> 

>>ddFILT=filter.probes(ddNORM,control,wellaboveBG,isfound,wellaboveNEG,s
a

>
t,PopnOL,NonUnifOL,nas,limWellAbove,limISF,limNEG,limSAT,limPopnOL,limNo

> nUnifOL,limNAS,makePLOT=FALSE, annotation.package,flag.counts,targets)

> 

> FILTERING PROBES BY FLAGS

> 

> 

> 

> 

> 

> FILTERING BY ControlType FLAG

> 

> Error in sqliteFetch(rs, n = -1, ...) :

> 

>  RSQLite driver: (RS_SQLite_fetch: failed first step: disk I/O error)

> 

> 

> 

> 

> 

> This issue is reproducible on this particular Linux installation only

> (craps out on all data sets, including sets known to work), so I've

> tried uninstalling and reinstalling R, as well as the packages,
several

> times.  Utilizing the same data, I have been able to get results using

> Windows installations and other Linux installs.

> 

> 

> 

> Has anyone seen this error before and/or have ideas to remedy the

> problem?

> 

> 

> 

> My session info:

> 

>> sessionInfo()

> 

> R version 2.11.1 (2010-05-31)

> 

> x86_64-unknown-linux-gnu

> 

> 

> 

> locale:

> 

>  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C

> 

>  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8

> 

>  [5] LC_MONETARY=C              LC_MESSAGES=en_US.UTF-8

> 

>  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C

> 

>  [9] LC_ADDRESS=C               LC_TELEPHONE=C

> 

> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

> 

> 

> 

> attached base packages:

> 

> [1] stats     graphics  grDevices utils     datasets  methods   base

> 

> 

> 

> other attached packages:

> 

>  [1] vsn_3.16.0              mgug4122a.db_2.4.1
org.Mm.eg.db_2.4.1

> 

>  [4] RSQLite_0.9-2           DBI_0.2-5

> Agi4x44PreProcess_1.8.0

> 

>  [7] genefilter_1.30.0       annotate_1.26.1

> AnnotationDbi_1.10.2

> 

> [10] limma_3.4.4             Biobase_2.8.0

> 

> 

> 

> loaded via a namespace (and not attached):

> 

> [1] affy_1.26.1           affyio_1.16.0         grid_2.11.1

> 

> [4] lattice_0.18-8        preprocessCore_1.10.0 splines_2.11.1

> 

> [7] survival_2.35-8       xtable_1.5-6

> 


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