Question: GenomicFeatures: Unable to save TranscriptDb object
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gravatar for KORIR, PAUL
8.0 years ago by
KORIR, PAUL20
KORIR, PAUL20 wrote:
Hi, I've created a TranscriptDb object and would like to save it. I get an error that I'm unable to decode as shown below: > saveFeatures(txdb,file="../txdb.sqlite") Error in sqliteCopyDatabase(txdbConn(x), file) : RS-DBI driver: (database is locked) Here's my sessionInfo() output: > sessionInfo() R version 2.11.0 (2010-04-22) x86_64-redhat-linux-gnu locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 LC_PAPER=en_US.UTF-8 [8] LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] GenomicFeatures_1.0.10 Rsamtools_1.0.8 Biostrings_2.16.9 GenomicRanges_1.0.9 IRanges_1.6.17 data.table_1.5.3 loaded via a namespace (and not attached): [1] Biobase_2.8.0 biomaRt_2.4.0 BSgenome_1.16.5 DBI_0.2-5 RCurl_1.4-3 RSQLite_0.9-2 rtracklayer_1.8.1 tools_2.11.0 XML_3.1-1 Could someone please help? P. Kibet Korir Bioinformatics (PhD Student), NUI Galway +353 86 224 19 66 [[alternative HTML version deleted]]
transcriptdb • 578 views
ADD COMMENTlink modified 8.0 years ago by Hervé Pagès ♦♦ 13k • written 8.0 years ago by KORIR, PAUL20
Answer: GenomicFeatures: Unable to save TranscriptDb object
0
gravatar for Marc Carlson
8.0 years ago by
Marc Carlson7.2k
United States
Marc Carlson7.2k wrote:
Hi Paul, I am having trouble reproducing this error. But when a SQLite database is locked it normally means that some other process is actively writing to it. Can you update RSQLite using biocLite() and try again? There are instructions on our website: http://www.bioconductor.org/install/ Also, you version of R and Bioconductor is really pretty long in the tooth for using the GenomicFeatures (and related) packages. You might want to update soon (R-2-13 will release imminently. Hope this helps, Marc On 04/08/2011 05:37 AM, KORIR, PAUL wrote: > Hi, > > I've created a TranscriptDb object and would like to save it. I get an error that I'm unable to decode as shown below: > >> saveFeatures(txdb,file="../txdb.sqlite") > Error in sqliteCopyDatabase(txdbConn(x), file) : > RS-DBI driver: (database is locked) > > Here's my sessionInfo() output: >> sessionInfo() > R version 2.11.0 (2010-04-22) > x86_64-redhat-linux-gnu > > locale: > [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 LC_PAPER=en_US.UTF-8 > [8] LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] GenomicFeatures_1.0.10 Rsamtools_1.0.8 Biostrings_2.16.9 GenomicRanges_1.0.9 IRanges_1.6.17 data.table_1.5.3 > > loaded via a namespace (and not attached): > [1] Biobase_2.8.0 biomaRt_2.4.0 BSgenome_1.16.5 DBI_0.2-5 RCurl_1.4-3 RSQLite_0.9-2 rtracklayer_1.8.1 tools_2.11.0 XML_3.1-1 > Could someone please help? > > P. Kibet Korir > Bioinformatics (PhD Student), > NUI Galway > +353 86 224 19 66 > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
ADD COMMENTlink written 8.0 years ago by Marc Carlson7.2k
Answer: GenomicFeatures: Unable to save TranscriptDb object
0
gravatar for Hervé Pagès
8.0 years ago by
Hervé Pagès ♦♦ 13k
United States
Hervé Pagès ♦♦ 13k wrote:
Hi Paul, Maybe you are trying to overwrite an SQLite file that is currently in use? Something like: > saveFeatures(txdb1, "txdb1.sqlite") > txdb2 <- loadFeatures("txdb1.sqlite") > saveFeatures(txdb2, "txdb1.sqlite") Error in sqliteCopyDatabase(txdbConn(x), file) : RS-DBI driver: (database is locked) Cheers, H. On 11-04-08 05:37 AM, KORIR, PAUL wrote: > Hi, > > I've created a TranscriptDb object and would like to save it. I get an error that I'm unable to decode as shown below: > >> saveFeatures(txdb,file="../txdb.sqlite") > Error in sqliteCopyDatabase(txdbConn(x), file) : > RS-DBI driver: (database is locked) > > Here's my sessionInfo() output: >> sessionInfo() > R version 2.11.0 (2010-04-22) > x86_64-redhat-linux-gnu > > locale: > [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 LC_PAPER=en_US.UTF-8 > [8] LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] GenomicFeatures_1.0.10 Rsamtools_1.0.8 Biostrings_2.16.9 GenomicRanges_1.0.9 IRanges_1.6.17 data.table_1.5.3 > > loaded via a namespace (and not attached): > [1] Biobase_2.8.0 biomaRt_2.4.0 BSgenome_1.16.5 DBI_0.2-5 RCurl_1.4-3 RSQLite_0.9-2 rtracklayer_1.8.1 tools_2.11.0 XML_3.1-1 > Could someone please help? > > P. Kibet Korir > Bioinformatics (PhD Student), > NUI Galway > +353 86 224 19 66 > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M2-B876 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: hpages at fhcrc.org Phone: (206) 667-5791 Fax: (206) 667-1319
ADD COMMENTlink written 8.0 years ago by Hervé Pagès ♦♦ 13k
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