Can't load the arabidopsis.db annotation package created in AnnotationDbi
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@groot-philip-de-1307
Last seen 8.2 years ago
Hello all, I created an arabidopsis library based on the MBNI custom CDF version 10 (TAIR), see http://nugo-r.bioinformatics.nl/NuGO_R.html. In BioC 2.2 all works very well. However, when trying to load the package in R-2.8.0/BioC 2.3, I get the following error message: > library(ath1attair.db) Loading required package: DBI Error in sqliteExecStatement(con, statement, bind.data) : RS-DBI driver: (error in statement: no such table: chrlengths) Error : .onLoad failed in 'loadNamespace' for 'ath1attair.db' Error: package/namespace load failed for 'ath1attair.db' Rebuilding the library with the "makeARABIDOPSISCHIP_DB" function did not solve the problem. The library installs without error message, but fails to load. The error message is obvious (no chrlengths table), but how can I solve this problem? Regards, Dr. Philip de Groot Ph.D. Bioinformatics Researcher Wageningen University / TIFN Nutrigenomics Consortium Nutrition, Metabolism & Genomics Group Division of Human Nutrition PO Box 8129, 6700 EV Wageningen Visiting Address: "De Valk" ("Erfelijkheidsleer"), Building 304 Verbindingsweg 4, 6703 HC Wageningen Room: 0052a T: 0317 485786 F: 0317 483342 E-mail: Philip.deGroot at wur.nl Internet: http://www.nutrigenomicsconsortium.nl <http: www.nutrigenomicsconsortium.nl=""/> http://humannutrition.wur.nl <http: humannutrition.wur.nl=""/>
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@sean-davis-490
Last seen 3 months ago
United States
On Mon, Nov 3, 2008 at 11:10 AM, Groot, Philip de <philip.degroot@wur.nl>wrote: > Hello all, > > I created an arabidopsis library based on the MBNI custom CDF version 10 > (TAIR), see http://nugo-r.bioinformatics.nl/NuGO_R.html. In BioC 2.2 all > works very well. However, when trying to load the package in R-2.8.0/BioC > 2.3, I get the following error message: > > > library(ath1attair.db) > Loading required package: DBI > Error in sqliteExecStatement(con, statement, bind.data) : > RS-DBI driver: (error in statement: no such table: chrlengths) > Error : .onLoad failed in 'loadNamespace' for 'ath1attair.db' > Error: package/namespace load failed for 'ath1attair.db' > > > Rebuilding the library with the "makeARABIDOPSISCHIP_DB" function did not > solve the problem. The library installs without error message, but fails to > load. > > The error message is obvious (no chrlengths table), but how can I solve > this problem? > Hi, Philip. I think you will need to include your sessionInfo() so that folks can see versions of AnnotationDbi, RSQLite, etc. Sean [[alternative HTML version deleted]]
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