[BioC] package affy / biobase problem with function "geneNames"
Martin Morgan
mtmorgan at fhcrc.org
Fri Apr 4 18:51:03 CEST 2014
On 04/04/2014 09:20 AM, BEN HAMDA Cherif wrote:
> Hi Jim,
> I have no sudo privileges
> I will contact the administrator Monday
> and I will answer after that
From the command line
R --vanilla
> library(BiocInstaller)
> biocLite("BiocUpgrade")
R 3.0.3 and Bioconductor are both available for linux, Windows, and Mac.
Martin
> Thank you
>
> Best,
> Cherif
>
>
> 2014-04-04 16:47 GMT+01:00 James W. MacDonald <jmacdon at uw.edu
> <mailto:jmacdon at uw.edu>>:
>
> Hi Cherif,
>
> You don't want to upgrade when you have a bunch of packages already loaded.
> Restart R and then perform the upgrade.
>
> In addition, you won't be able to upgrade the base packages noted in the
> second warning. For that you will want to use apt-get, if you have sudo
> privileges. If not, see if your sysadmin will upgrade for you.
>
> Best,
>
> Jim
>
>
>
> On 4/4/2014 11:32 AM, BEN HAMDA Cherif wrote:
>
> and right now when i try to upgrade one more
>
> i have this message
> * DONE (BiocInstaller)
>
> The downloaded source packages are in
> '/tmp/Rtmp9PxG1j/downloaded___packages'
> BiocInstaller version 1.4.9, ?biocLite for help
> A newer version of Bioconductor is available for this version of R,
> ?BiocUpgrade for help
> 'BiocInstaller' changed to version 1.4.9
> BioC_mirror: http://bioconductor.org
> Using R version 2.15, BiocInstaller version 1.4.9.
> Warning messages:
> 1: 'BiocInstaller' namespace cannot be unloaded:
> namespace 'BiocInstaller' is imported by 'gcrma', 'affy' so cannot be
> unloaded
> 2: installed directory not writable, cannot update packages 'bit',
> 'mvtnorm',
> 'xtable', 'cluster', 'KernSmooth', 'lattice', 'mgcv', 'nnet', 'rpart',
> 'survival
>
>
> thanks
>
>
> 2014-04-04 16:27 GMT+01:00 BEN HAMDA Cherif <cherifbenhamda at gmail.com
> <mailto:cherifbenhamda at gmail.com>>:
>
> Hi,
> Thank you Martin and Jim for all your response.
> R 3.0.3 and bioconductor 2.13 it's for windows !
> I work with debian and the latest version for this distribution its
> mine .
>
> it works very well but after the update for bioconductor packages
> (today)
> he released this kind of error .
>
> so there is other solution ?
> thank you
>
>
> 2014-04-04 16:18 GMT+01:00 Martin Morgan <mtmorgan at fhcrc.org
> <mailto:mtmorgan at fhcrc.org>>:
>
> On 04/04/2014 08:08 AM, BEN HAMDA Cherif wrote:
>
> Hello,
>
> after updating all packages. I have a problem when i want
> normalize my
> data
> !
>
> This is a package version mismatch. Biobase is from Bioconductor
> version
> 2.11, affy and BiocInstaller from version 2.10. I think
>
> library(BiocInstaller)
> biocLite("BiocUpgrade")
>
> will update all packages to version 2.11.
>
> Really you should update to the current R (3.0.3) and
> Bioconductor (2.13)
> or wait until after April 15 and update to R 3.1.0 and
> Bioconductor 2.14.
>
> Martin
>
>
> and the error message is :
>
> eset <- rma(rawdata)
> Error in rma(rawdata) : could not find function "geneNames"
>
> Someone can help me Please , Thank you very much
>
> Best
> Cherif
>
> sessionInfo()
> R version 2.15.1 (2012-06-22)
> Platform: x86_64-pc-linux-gnu (64-bit)
>
> locale:
> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
> LC_TIME=C
> [4] LC_COLLATE=en_US.UTF-8 LC_MONETARY=C
> LC_MESSAGES=en_US.UTF-8
> [7] LC_PAPER=C LC_NAME=C
> LC_ADDRESS=C
> [10] LC_TELEPHONE=C LC_MEASUREMENT=C
> LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats graphics grDevices utils datasets
> methods base
>
> other attached packages:
> [1] hgu133plus2cdf_2.11.0 AnnotationDbi_1.18.4
> simpleaffy_2.34.0
> [4] gcrma_2.30.0 genefilter_1.38.0 affy_1.34.0
> [7] Biobase_2.18.0 BiocGenerics_0.4.0 limma_3.12.3
>
> loaded via a namespace (and not attached):
> [1] affyio_1.24.0 annotate_1.34.1
> BiocInstaller_1.4.9
> [4] Biostrings_2.24.1 DBI_0.2-7
> IRanges_1.14.4
> [7] preprocessCore_1.18.0 RSQLite_0.11.4
> splines_2.15.1
> [10] stats4_2.15.1 survival_2.37-7 tools_2.15.1
> [13] XML_3.98-1.1 xtable_1.7-1 zlibbioc_1.2.0
>
> [[alternative HTML version deleted]]
>
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> James W. MacDonald, M.S.
> Biostatistician
> University of Washington
> Environmental and Occupational Health Sciences
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