[BioC] Installing beadarray

Thu Nov 1 17:33:22 CET 2007

Hello

I have just installed R 2.6.0. To save space, I usually install packages
individually rather than using biocLite().  I installed beadarray and then,
when I typed library(beadarray), I got:

Error: package 'geneplotter' could not be loaded
In addition: Warning message:
In library(pkg, character.only = TRUE, logical.return = TRUE, lib.loc =
lib.loc) :
  there is no package called 'geneplotter'

So I downloaded geneplotter and installed that.  Similarly, I got then got
errors in turn for annotate and AnnotationDbi. After I had installed these,
I got an error for DBI. But I couldn't find DBI on the Bioconductor website.

I thought maybe if I installed Bioconductor using biocLite() this would
solve my problem. But I still get an error message:

Error: package 'DBI' required by 'AnnotationDbi' could not be found

What is this DBI and where can I find it? Or is there something else I need
to do to install beadarray?

My R session is pasted below with the sessionInfo() at the bottom.

Thanks for your help.

Krys

> package.version("beadarray")
[1] "1.6.0"

> library(beadarray)
Loading required package: limma
Error: package 'limma' could not be loaded
In addition: Warning message:
In library(pkg, character.only = TRUE, logical.return = TRUE, lib.loc =
lib.loc) :
  there is no package called 'limma'
> utils:::menuInstallLocal()
package 'limma' successfully unpacked and MD5 sums checked
updating HTML package descriptions

> library(beadarray)
Loading required package: limma
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: geneplotter
Error: package 'geneplotter' could not be loaded
In addition: Warning message:
In library(pkg, character.only = TRUE, logical.return = TRUE, lib.loc =
lib.loc) :
  there is no package called 'geneplotter'
> utils:::menuInstallLocal()
package 'geneplotter' successfully unpacked and MD5 sums checked
updating HTML package descriptions

> library(beadarray)
Loading required package: geneplotter
Loading required package: annotate
Error: package 'annotate' could not be loaded
In addition: Warning message:
In library(pkg, character.only = TRUE, logical.return = TRUE, lib.loc =
lib.loc) :
  there is no package called 'annotate'
> utils:::menuInstallLocal()
package 'annotate' successfully unpacked and MD5 sums checked
updating HTML package descriptions

> library(beadarray)
Loading required package: geneplotter
Loading required package: annotate
Error: package 'AnnotationDbi' required by 'annotate' could not be found
> utils:::menuInstallLocal()
package 'AnnotationDbi' successfully unpacked and MD5 sums checked
updating HTML package descriptions

> library(beadarray)
Loading required package: geneplotter
Loading required package: annotate
Loading required package: AnnotationDbi
Error: package 'DBI' required by 'AnnotationDbi' could not be found

> source("http://bioconductor.org/biocLite.R")
> biocLite()
Running biocinstall version 2.1.8 with R version 2.6.0 
Your version of R requires version 2.1 of Bioconductor.
Will install the following packages:
 [1] "affy"         "affydata"     "affyPLM"      "annaffy"      "annotate"

 [6] "Biobase"      "Biostrings"   "DynDoc"       "gcrma"
"genefilter"  
[11] "geneplotter"  "hgu95av2"     "limma"        "marray"
"matchprobes" 
[16] "multtest"     "ROC"          "vsn"          "xtable"
"affyQCReport"
Please wait...

Warning: packages 'Biobase, limma' are in use and will not be installed
also installing the dependencies 'affyio', 'preprocessCore', 'GO', 'KEGG',
'simpleaffy', 'RColorBrewer'

trying URL
'http://bioconductor.org/packages/2.1/bioc/bin/windows/contrib/2.6/affyio_1.
6.1.zip'
Content type 'application/zip' length 129791 bytes (126 Kb)
opened URL
downloaded 126 Kb

trying URL
'http://bioconductor.org/packages/2.1/bioc/bin/windows/contrib/2.6/preproces
sCore_1.0.0.zip'
Content type 'application/zip' length 111924 bytes (109 Kb)
opened URL
downloaded 109 Kb

trying URL
'http://bioconductor.org/packages/2.1/data/annotation/bin/windows/contrib/2.
6/GO_2.0.1.zip'
Content type 'application/zip' length 19689821 bytes (18.8 Mb)
opened URL
downloaded 18.8 Mb

trying URL
'http://bioconductor.org/packages/2.1/data/annotation/bin/windows/contrib/2.
6/KEGG_2.0.1.zip'
Content type 'application/zip' length 304136 bytes (297 Kb)
opened URL
downloaded 297 Kb

trying URL
'http://bioconductor.org/packages/2.1/bioc/bin/windows/contrib/2.6/simpleaff
y_2.14.05.zip'
Content type 'application/zip' length 835024 bytes (815 Kb)
opened URL
downloaded 815 Kb

trying URL
'http://cran.fhcrc.org/bin/windows/contrib/2.6/RColorBrewer_1.0-2.zip'
Content type 'application/zip' length 40461 bytes (39 Kb)
opened URL
downloaded 39 Kb

trying URL
'http://bioconductor.org/packages/2.1/bioc/bin/windows/contrib/2.6/affy_1.16
.0.zip'
Content type 'application/zip' length 2166988 bytes (2.1 Mb)
opened URL
downloaded 2.1 Mb

trying URL
'http://bioconductor.org/packages/2.1/data/experiment/bin/windows/contrib/2.
6/affydata_1.11.3.zip'
Content type 'application/zip' length 9902440 bytes (9.4 Mb)
opened URL
downloaded 9.4 Mb

trying URL
'http://bioconductor.org/packages/2.1/bioc/bin/windows/contrib/2.6/affyPLM_1
.14.0.zip'
Content type 'application/zip' length 6969077 bytes (6.6 Mb)
opened URL
downloaded 6.6 Mb

trying URL
'http://bioconductor.org/packages/2.1/bioc/bin/windows/contrib/2.6/annaffy_1
.10.0.zip'
Content type 'application/zip' length 392470 bytes (383 Kb)
opened URL
downloaded 383 Kb

trying URL
'http://bioconductor.org/packages/2.1/bioc/bin/windows/contrib/2.6/annotate_
1.16.1.zip'
Content type 'application/zip' length 1889235 bytes (1.8 Mb)
opened URL
downloaded 1.8 Mb

trying URL
'http://bioconductor.org/packages/2.1/bioc/bin/windows/contrib/2.6/Biostring
s_2.6.3.zip'
Content type 'application/zip' length 779408 bytes (761 Kb)
opened URL
downloaded 761 Kb

trying URL
'http://bioconductor.org/packages/2.1/bioc/bin/windows/contrib/2.6/DynDoc_1.
16.0.zip'
Content type 'application/zip' length 130515 bytes (127 Kb)
opened URL
downloaded 127 Kb

trying URL
'http://bioconductor.org/packages/2.1/bioc/bin/windows/contrib/2.6/gcrma_2.1
0.0.zip'
Content type 'application/zip' length 199643 bytes (194 Kb)
opened URL
downloaded 194 Kb

trying URL
'http://bioconductor.org/packages/2.1/bioc/bin/windows/contrib/2.6/genefilte
r_1.16.0.zip'
Content type 'application/zip' length 466940 bytes (455 Kb)
opened URL
downloaded 455 Kb

trying URL
'http://bioconductor.org/packages/2.1/bioc/bin/windows/contrib/2.6/geneplott
er_1.16.0.zip'
Content type 'application/zip' length 1760486 bytes (1.7 Mb)
opened URL
downloaded 1.7 Mb

trying URL
'http://bioconductor.org/packages/2.1/data/annotation/bin/windows/contrib/2.
6/hgu95av2_2.0.1.zip'
Content type 'application/zip' length 8322091 bytes (7.9 Mb)
opened URL
downloaded 7.9 Mb

trying URL
'http://bioconductor.org/packages/2.1/bioc/bin/windows/contrib/2.6/marray_1.
16.0.zip'
Content type 'application/zip' length 5041209 bytes (4.8 Mb)
opened URL
downloaded 4.8 Mb

trying URL
'http://bioconductor.org/packages/2.1/bioc/bin/windows/contrib/2.6/matchprob
es_1.10.0.zip'
Content type 'application/zip' length 8143988 bytes (7.8 Mb)
opened URL
downloaded 7.8 Mb

trying URL
'http://bioconductor.org/packages/2.1/bioc/bin/windows/contrib/2.6/multtest_
1.18.0.zip'
Content type 'application/zip' length 1654333 bytes (1.6 Mb)
opened URL
downloaded 1.6 Mb

trying URL
'http://bioconductor.org/packages/2.1/bioc/bin/windows/contrib/2.6/ROC_1.12.
0.zip'
Content type 'application/zip' length 144305 bytes (140 Kb)
opened URL
downloaded 140 Kb

trying URL
'http://bioconductor.org/packages/2.1/bioc/bin/windows/contrib/2.6/vsn_3.2.1
.zip'
Content type 'application/zip' length 1989028 bytes (1.9 Mb)
opened URL
downloaded 1.9 Mb

trying URL 'http://cran.fhcrc.org/bin/windows/contrib/2.6/xtable_1.5-2.zip'
Content type 'application/zip' length 232057 bytes (226 Kb)
opened URL
downloaded 226 Kb

trying URL
'http://bioconductor.org/packages/2.1/bioc/bin/windows/contrib/2.6/affyQCRep
ort_1.16.0.zip'
Content type 'application/zip' length 182289 bytes (178 Kb)
opened URL
downloaded 178 Kb

package 'affyio' successfully unpacked and MD5 sums checked
package 'preprocessCore' successfully unpacked and MD5 sums checked
package 'GO' successfully unpacked and MD5 sums checked
package 'KEGG' successfully unpacked and MD5 sums checked
package 'simpleaffy' successfully unpacked and MD5 sums checked
package 'RColorBrewer' successfully unpacked and MD5 sums checked
package 'affy' successfully unpacked and MD5 sums checked
package 'affydata' successfully unpacked and MD5 sums checked
package 'affyPLM' successfully unpacked and MD5 sums checked
package 'annaffy' successfully unpacked and MD5 sums checked
package 'annotate' successfully unpacked and MD5 sums checked
package 'Biostrings' successfully unpacked and MD5 sums checked
package 'DynDoc' successfully unpacked and MD5 sums checked
package 'gcrma' successfully unpacked and MD5 sums checked
package 'genefilter' successfully unpacked and MD5 sums checked
package 'geneplotter' successfully unpacked and MD5 sums checked
package 'hgu95av2' successfully unpacked and MD5 sums checked
package 'marray' successfully unpacked and MD5 sums checked
package 'matchprobes' successfully unpacked and MD5 sums checked
package 'multtest' successfully unpacked and MD5 sums checked
package 'ROC' successfully unpacked and MD5 sums checked
package 'vsn' successfully unpacked and MD5 sums checked
package 'xtable' successfully unpacked and MD5 sums checked
package 'affyQCReport' successfully unpacked and MD5 sums checked

The downloaded packages are in
        C:\Documents and Settings\Krys\Local
Settings\Temp\RtmpgBjmPH\downloaded_packages
updating HTML package descriptions
> library(beadarray)
Loading required package: geneplotter
Loading required package: annotate
Loading required package: AnnotationDbi
Error: package 'DBI' required by 'AnnotationDbi' could not be found

> sessionInfo()
R version 2.6.0 (2007-10-03) 
i386-pc-mingw32 

locale:
LC_COLLATE=English_United Kingdom.1252;LC_CTYPE=English_United
Kingdom.1252;LC_MONETARY=English_United
Kingdom.1252;LC_NUMERIC=C;LC_TIME=English_United Kingdom.1252

attached base packages:
[1] tools     stats     graphics  grDevices utils     datasets  methods
base     

other attached packages:
[1] Biobase_1.16.1 limma_2.12.0  
>

Dr Krystyna A Kelly (Krys)

Department of Pathology
University of Cambridge, Tennis Court Road, Cambridge CB2 1QP
Tel: 01223 333331

and

MRC Biostatistics Unit
Institute of Public Health, Robinson Way, Cambridge CB2 0SR
Tel: 01223 767408

Email: kak28 at cam.ac.uk