alex lam (RI) alex.lam at roslin.ed.ac.uk
Mon Jul 14 10:46:15 CEST 2008

Dear Louisa,

If you haven't got MySQL on your PC then you need to install it. Try the
free version on


Alex C. Lam
Roslin Institute (Edinburgh)
EH25 9PS
United Kingdom
Tel: +44 131 5274471

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New email address: alex.lam at roslin.ed.ac.uk
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-----Original Message-----
From: bioconductor-bounces at stat.math.ethz.ch
[mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Louisa A
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.



"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 :


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 :


> 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
  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)

LC_COLLATE=English_United States.1252;LC_CTYPE=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
 [5] matchprobes_1.12.0   biomaRt_1.14.0       RCurl_0.9-3
 [9] Category_2.6.0       genefilter_1.20.0    survival_2.34-1
[13] annotate_1.18.0      xtable_1.5-2         GO.db_2.2.0
[17] RSQLite_0.6-9        DBI_0.2-4            graph_1.18.1
[21] affy_1.18.2          preprocessCore_1.2.0 affyio_1.8.0

loaded via a namespace (and not attached):
[1] cluster_1.11.11 XML_1.94-0.1

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