[BioC] RMySQL

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
http://dev.mysql.com/downloads/mysql/5.0.html

Cheers,
Alex

--------------------------------------------
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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
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

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