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Hi Tae-Hoon, It's a bit hard to say what might be the problem. Can you send us the sessionInfo() output? In particular, can you make sure that DBI and RSQLite are up to date? I just tried installing pd.mapping50k.hind240 using R 2.6.0 (devel) and BioC devel packages and it worked fine... > biocLite("pd.mapping50k.hind240") [snip] > library("pd.mapping50k.hind240") [snip] > sessionInfo() R version 2.6.0 Under development (unstable) (--) x86_64-unknown-linux-gnu locale: LC_CTYPE=en_US;LC_NUMERIC=C;LC_TIME=en_US;LC_COLLATE=en_US;LC_MONETARY =en_US;LC_MESSAGES=en_US;LC_PAPER=en_US;LC_NAME=C;LC_ADDRESS=C;LC_TELE PHONE=C;LC_MEASUREMENT=en_US;LC_IDENTIFICATION=C attached base packages: [1] splines tools stats graphics grDevices datasets utils [8] methods base other attached packages: [1] pd.mapping50k.hind240_0.3.2 oligo_1.1.5 [3] preprocessCore_0.99.8 BufferedMatrixMethods_1.1.2 [5] BufferedMatrix_1.1.3 affyio_1.5.6 [7] Biobase_1.15.19 RSQLite_0.6-3 [9] DBI_0.2-3 loaded via a namespace (and not attached): [1] rcompgen_0.1-15 -- Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center BioC: http://bioconductor.org/ Blog: http://userprimary.net/user/

Hi, All; The sessionInfo() was like this: R version 2.5.1 (2007-06-27) x86_64-unknown-linux-gnu locale: LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US .UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US. UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8 ;LC_IDENTIFICATION=C attached base packages: [1] "splines" "tools" "stats" "graphics" "grDevices" "utils" [7] "datasets" "methods" "base" other attached packages: oligo affyio Biobase "1.0.2-6" "1.4.1" "1.14.0" BufferedMatrixMethods BufferedMatrix RSQLite "1.0.0" "1.0.1" "0.5-4" DBI "0.2-3" I've used three different methods to install the annotation package: getBioC, biocLite, and R CMD INSTALL. But all failed. One catch: I've been trying to install it in a server into one of my local folder called "~/Library/R64" using either getBioC("pd.mapping50k.hind240", lib="~/Library/R64") or biocLite("pd.mapping50k.hind240", lib="~/Library/R64") or R CMD INSTALL -l ~/Library/R64 pd.mapping50k.hind240_0.2.8.tar.gz. -----Original Message----- From: Seth Falcon [mailto:sfalcon@fhcrc.org] Sent: Mon 8/6/2007 10:18 PM To: Tae-Hoon Chung Cc: Bioconductor list list Subject: Re: [BioC] oligo package locked database question Hi Tae-Hoon, It's a bit hard to say what might be the problem. Can you send us the sessionInfo() output? In particular, can you make sure that DBI and RSQLite are up to date? I just tried installing pd.mapping50k.hind240 using R 2.6.0 (devel) and BioC devel packages and it worked fine... > biocLite("pd.mapping50k.hind240") [snip] > library("pd.mapping50k.hind240") [snip] > sessionInfo() R version 2.6.0 Under development (unstable) (--) x86_64-unknown-linux-gnu locale: LC_CTYPE=en_US;LC_NUMERIC=C;LC_TIME=en_US;LC_COLLATE=en_US;LC_MONETARY =en_US;LC_MESSAGES=en_US;LC_PAPER=en_US;LC_NAME=C;LC_ADDRESS=C;LC_TELE PHONE=C;LC_MEASUREMENT=en_US;LC_IDENTIFICATION=C attached base packages: [1] splines tools stats graphics grDevices datasets utils [8] methods base other attached packages: [1] pd.mapping50k.hind240_0.3.2 oligo_1.1.5 [3] preprocessCore_0.99.8 BufferedMatrixMethods_1.1.2 [5] BufferedMatrix_1.1.3 affyio_1.5.6 [7] Biobase_1.15.19 RSQLite_0.6-3 [9] DBI_0.2-3 loaded via a namespace (and not attached): [1] rcompgen_0.1-15 -- Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center BioC: http://bioconductor.org/ Blog: http://userprimary.net/user/

I wonder what the sessionInfo() is... and what exactly you used to install the package so I can try to reproduce it here. b On Aug 6, 2007, at 9:00 PM, Tae-Hoon Chung wrote: > Hi, All; > > I tried to install pd.mapping50k.hind240 package but got an error: > > * Installing *source* package 'pd.mapping50k.hind240' ... > ** R > ** inst > ** preparing package for lazy loading > Loading required package: RSQLite > Loading required package: DBI > Loading required package: oligo > Loading required package: Biobase > Loading required package: tools > > Welcome to Bioconductor > > Vignettes contain introductory material. To view, type > 'openVignette()'. To cite Bioconductor, see > 'citation("Biobase")' and for packages 'citation(pkgname)'. > > Loading required package: affyio > Loading required package: splines > Loading required package: BufferedMatrix > Loading required package: BufferedMatrixMethods > This is the oligo package > Error in sqliteExecStatement(con, statement, bind.data) : > RS-DBI driver: (error in statement: database is locked) > Error: unable to load R code in package 'pd.mapping50k.hind240' > Execution halted > ERROR: lazy loading failed for package 'pd.mapping50k.hind240' > ** Removing '/users04/tchung/Library/R64/pd.mapping50k.hind240' > > Anyone knows how to unlock the locked database? > > Tae-Hoon Chung > > Post-Doctoral Researcher > Computational Biology Division, TGEN > 445 N 5th St. Phoenix, AZ 85004 USA > O: 1-602-343-8724 > F: 1-602-343-8840 > > > > [[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

Hi, <thchung at="" tgen.org=""> writes: > The sessionInfo() was like this: > > R version 2.5.1 (2007-06-27) > x86_64-unknown-linux-gnu > > locale: > LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_ US.UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_U S.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF -8;LC_IDENTIFICATION=C > > attached base packages: > [1] "splines" "tools" "stats" "graphics" "grDevices" "utils" > [7] "datasets" "methods" "base" > > other attached packages: > oligo affyio Biobase > "1.0.2-6" "1.4.1" "1.14.0" > BufferedMatrixMethods BufferedMatrix RSQLite > "1.0.0" "1.0.1" "0.5-4" > DBI > "0.2-3" You're RSQLite is out of date, the current version is 0.5-6, so I would recommend updating and then seeing if the problem persists. If it does, can you also provide the output of: library("RSQLite") dbGetInfo(SQLite())$clientVersion + seth -- Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center BioC: http://bioconductor.org/ Blog: http://userprimary.net/user/