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,lim No > 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 > NOTICE: This email message is for the sole use of the intended recipient(s) and may contain confidential and privileged information. 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