Issue: When trying to execute filter.probes the following error occurs: >ddFILT=filter.probes(ddNORM,control,wellaboveBG,isfound,wellaboveNEG, sa 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. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply email and destroy all copies of the original message. [[alternative HTML version deleted]]

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 at="" njhealth.org=""> wrote: > Issue: > > When trying to execute filter.probes the following error occurs: > >>ddFILT=filter.probes(ddNORM,control,wellaboveBG,isfound,wellaboveNEG ,sa > t,PopnOL,NonUnifOL,nas,limWellAbove,limISF,limNEG,limSAT,limPopnOL,l imNo > 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. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply email and destroy all copies of the original message. > > ? ? ? ?[[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >