[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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>
>                 --
>                 Computational Biology / Fred Hutchinson Cancer Research Center
>                 1100 Fairview Ave. N.
>                 PO Box 19024 Seattle, WA 98109
>
>                 Location: Arnold Building M1 B861
>                 Phone: (206) 667-2793 <tel:%28206%29%20667-2793>
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>     --
>     James W. MacDonald, M.S.
>     Biostatistician
>     University of Washington
>     Environmental and Occupational Health Sciences
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