Hi all- In effort to follow vignettes I have run into an package issue. I have been trying to understand the latest posts on errors in the RMySQL for Windows package. And I think my lack of knowledge in the computer language department is rising up an keeping me from solving the problem. As far as I can tell the RMySQL package cannot load because I need to install MySQL (whether into R which is what I am unclear on and from where do I download, www.mysql.com not very clear what is appropriate product that I need) and have the libmysql.dll in the path for the RMySQL library (please see code below). I would appreciate any assistance that can be provided. Sincerely Louisa "If we knew what we were doing, it wouldn't be called Research." - Albert Einstein Louisa Rispoli, Ph.D. Reproductive Physiology Department of Animal Science University of Tennessee, Knoxville A105 Johnson Animal Research and Teaching Unit 1750 Alcoa Highway Knoxville, TN 37920 phone:(865) 946-1874 fax:(865) 946-1010 email: lrispoli at utk.edu > library(affycoretools) Loading required package: affy 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: preprocessCore Loading required package: limma Loading required package: GOstats Loading required package: graph Loading required package: GO.db Loading required package: AnnotationDbi Loading required package: DBI Loading required package: RSQLite Loading required package: annotate Loading required package: xtable Loading required package: RBGL Loading required package: Category Loading required package: genefilter Loading required package: survival Loading required package: splines Loading required package: biomaRt Loading required package: RCurl Attaching package: 'biomaRt' The following object(s) are masked from package:annotate : getGO Loading required package: gcrma Loading required package: matchprobes Loading required package: annaffy Loading required package: KEGG.db Attaching package: 'annaffy' The following object(s) are masked from package:RCurl : getURL > load("exprSet2.Rdata") > library(limma) > design <- model.matrix(~0 + factor(rep(1:4, each = 3))) > colnames(design) <- LETTERS[1:4] > contrast <- makeContrasts(A-B, C-D, levels=design) > fit <-lmFit(eset, design) > fit2 <- contrasts.fit(fit, contrast) > fit3 <- eBayes(fit2) > dt <- decideTests(fit3, method="nestedF") > rslt <- vennCounts2(dt) > vennDiagram(rslt) > vennSelectBM(eset, design, rslt, contrast, fit3, species="hsampiens") Loading required package: RMySQL Error in inDL(x, as.logical(local), as.logical(now), ...) : unable to load shared library 'C:/PROGRA~1/R/R-27~1.1/library/RMySQL/libs/RMySQL.dll': LoadLibrary failure: The specified module could not be found. Error in do.call(as.character(drvName), list(...)) : could not find function "MySQL" > sessionInfo() R version 2.7.1 (2008-06-23) i386-pc-mingw32 locale: LC_COLLATE=English_United States.1252;LC_CTYPE=English_United States.1252;LC_MONETARY=English_United States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 attached base packages: [1] splines tools stats graphics grDevices utils datasets methods base other attached packages: [1] affycoretools_1.12.0 annaffy_1.12.1 KEGG.db_2.2.0 gcrma_2.12.1 [5] matchprobes_1.12.0 biomaRt_1.14.0 RCurl_0.9-3 GOstats_2.6.0 [9] Category_2.6.0 genefilter_1.20.0 survival_2.34-1 RBGL_1.16.0 [13] annotate_1.18.0 xtable_1.5-2 GO.db_2.2.0 AnnotationDbi_1.2.2 [17] RSQLite_0.6-9 DBI_0.2-4 graph_1.18.1 limma_2.14.5 [21] affy_1.18.2 preprocessCore_1.2.0 affyio_1.8.0 Biobase_2.0.1 loaded via a namespace (and not attached): [1] cluster_1.11.11 XML_1.94-0.1

Dear Louisa, If you haven't got MySQL on your PC then you need to install it. Try the free version on http://dev.mysql.com/downloads/mysql/5.0.html Cheers, Alex -------------------------------------------- Alex C. Lam Roslin Institute (Edinburgh) Midlothian EH25 9PS United Kingdom Tel: +44 131 5274471 Former email address: alex.lam at bbsrc.ac.uk New email address: alex.lam at roslin.ed.ac.uk Both addresses are functional Roslin Institute is a company limited by guarantee, registered in Scotland (registered number SC157100) and a Scottish Charity (registered number SC023592). Our registered office is at Roslin, Midlothian, EH25 9PS. VAT registration number 847380013. The information contained in this e-mail (including any attachments) is confidential and is intended for the use of the addressee only. The opinions expressed within this e-mail (including any attachments) are the opinions of the sender and do not necessarily constitute those of Roslin Institute (Edinburgh) ("the Institute") unless specifically stated by a sender who is duly authorised to do so on behalf of the Institute -----Original Message----- From: bioconductor-bounces@stat.math.ethz.ch [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Louisa A Rispoli/AS/EXP/UTIA Sent: 11 July 2008 19:39 To: bioconductor at stat.math.ethz.ch Subject: [BioC] RMySQL Hi all- In effort to follow vignettes I have run into an package issue. I have been trying to understand the latest posts on errors in the RMySQL for Windows package. And I think my lack of knowledge in the computer language department is rising up an keeping me from solving the problem. As far as I can tell the RMySQL package cannot load because I need to install MySQL (whether into R which is what I am unclear on and from where do I download, www.mysql.com not very clear what is appropriate product that I need) and have the libmysql.dll in the path for the RMySQL library (please see code below). I would appreciate any assistance that can be provided. Sincerely Louisa "If we knew what we were doing, it wouldn't be called Research." - Albert Einstein Louisa Rispoli, Ph.D. Reproductive Physiology Department of Animal Science University of Tennessee, Knoxville A105 Johnson Animal Research and Teaching Unit 1750 Alcoa Highway Knoxville, TN 37920 phone:(865) 946-1874 fax:(865) 946-1010 email: lrispoli at utk.edu > library(affycoretools) Loading required package: affy 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: preprocessCore Loading required package: limma Loading required package: GOstats Loading required package: graph Loading required package: GO.db Loading required package: AnnotationDbi Loading required package: DBI Loading required package: RSQLite Loading required package: annotate Loading required package: xtable Loading required package: RBGL Loading required package: Category Loading required package: genefilter Loading required package: survival Loading required package: splines Loading required package: biomaRt Loading required package: RCurl Attaching package: 'biomaRt' The following object(s) are masked from package:annotate : getGO Loading required package: gcrma Loading required package: matchprobes Loading required package: annaffy Loading required package: KEGG.db Attaching package: 'annaffy' The following object(s) are masked from package:RCurl : getURL > load("exprSet2.Rdata") > library(limma) > design <- model.matrix(~0 + factor(rep(1:4, each = 3))) > colnames(design) <- LETTERS[1:4] > contrast <- makeContrasts(A-B, C-D, levels=design) fit <-lmFit(eset, > design) > fit2 <- contrasts.fit(fit, contrast) > fit3 <- eBayes(fit2) > dt <- decideTests(fit3, method="nestedF") rslt <- vennCounts2(dt) > vennDiagram(rslt) > vennSelectBM(eset, design, rslt, contrast, fit3, species="hsampiens") Loading required package: RMySQL Error in inDL(x, as.logical(local), as.logical(now), ...) : unable to load shared library 'C:/PROGRA~1/R/R-27~1.1/library/RMySQL/libs/RMySQL.dll': LoadLibrary failure: The specified module could not be found. Error in do.call(as.character(drvName), list(...)) : could not find function "MySQL" > sessionInfo() R version 2.7.1 (2008-06-23) i386-pc-mingw32 locale: LC_COLLATE=English_United States.1252;LC_CTYPE=English_United States.1252;LC_MONETARY=English_United States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 attached base packages: [1] splines tools stats graphics grDevices utils datasets methods base other attached packages: [1] affycoretools_1.12.0 annaffy_1.12.1 KEGG.db_2.2.0 gcrma_2.12.1 [5] matchprobes_1.12.0 biomaRt_1.14.0 RCurl_0.9-3 GOstats_2.6.0 [9] Category_2.6.0 genefilter_1.20.0 survival_2.34-1 RBGL_1.16.0 [13] annotate_1.18.0 xtable_1.5-2 GO.db_2.2.0 AnnotationDbi_1.2.2 [17] RSQLite_0.6-9 DBI_0.2-4 graph_1.18.1 limma_2.14.5 [21] affy_1.18.2 preprocessCore_1.2.0 affyio_1.8.0 Biobase_2.0.1 loaded via a namespace (and not attached): [1] cluster_1.11.11 XML_1.94-0.1 _______________________________________________ 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