Question: package affy / biobase problem with function "geneNames"
0
gravatar for Cherif Ben Hamda
5.3 years ago by
Tunisia
Cherif Ben Hamda150 wrote:
Hello, after updating all packages. I have a problem when i want normalize my data ! 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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ADD COMMENTlink modified 5.3 years ago by Martin Morgan ♦♦ 23k • written 5.3 years ago by Cherif Ben Hamda150
Answer: package affy / biobase problem with function "geneNames"
0
gravatar for Martin Morgan
5.3 years ago by
Martin Morgan ♦♦ 23k
United States
Martin Morgan ♦♦ 23k wrote:
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]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > -- 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
ADD COMMENTlink written 5.3 years ago by Martin Morgan ♦♦ 23k
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@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]] >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor@r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: http://news.gmane.org/gmane. >> science.biology.informatics.conductor >> >> > > -- > 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 > [[alternative HTML version deleted]]
ADD REPLYlink written 5.3 years ago by Cherif Ben Hamda150
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@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@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]] >>> >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor@r-project.org >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> Search the archives: http://news.gmane.org/gmane. >>> science.biology.informatics.conductor >>> >>> >> >> -- >> 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 >> > > [[alternative HTML version deleted]]
ADD REPLYlink written 5.3 years ago by Cherif Ben Hamda150
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="">: > >> 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="">: >> >> 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]] >>>> >>>> _______________________________________________ >>>> Bioconductor mailing list >>>> Bioconductor at r-project.org >>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>> Search the archives: http://news.gmane.org/gmane. >>>> science.biology.informatics.conductor >>>> >>>> >>> -- >>> 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 >>> >> > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- James W. MacDonald, M.S. Biostatistician University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way NE, # 100 Seattle WA 98105-6099
ADD REPLYlink written 5.3 years ago by James W. MacDonald50k
Hi Jim, I have no sudo privileges I will contact the administrator Monday and I will answer after that Thank you Best, Cherif 2014-04-04 16:47 GMT+01:00 James W. MacDonald <jmacdon@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@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@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]] >>>>> >>>>> _______________________________________________ >>>>> Bioconductor mailing list >>>>> Bioconductor@r-project.org >>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>>> Search the archives: http://news.gmane.org/gmane. >>>>> science.biology.informatics.conductor >>>>> >>>>> >>>>> -- >>>> 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 >>>> >>>> >>> [[alternative HTML version deleted]] >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor@r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: http://news.gmane.org/gmane. >> science.biology.informatics.conductor >> > > -- > James W. MacDonald, M.S. > Biostatistician > University of Washington > Environmental and Occupational Health Sciences > 4225 Roosevelt Way NE, # 100 > Seattle WA 98105-6099 > > [[alternative HTML version deleted]]
ADD REPLYlink written 5.3 years ago by Cherif Ben Hamda150
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]] > > _________________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org <mailto:bioconductor at="" r-project.org=""> > https://stat.ethz.ch/mailman/__listinfo/bioconductor > <https: stat.ethz.ch="" mailman="" listinfo="" bioconductor=""> > Search the archives: http://news.gmane.org/gmane. > science.biology.informatics.__conductor > > > -- > 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> > > > [[alternative HTML version deleted]] > > _________________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org <mailto:bioconductor at="" r-project.org=""> > https://stat.ethz.ch/mailman/__listinfo/bioconductor > <https: stat.ethz.ch="" mailman="" listinfo="" bioconductor=""> > Search the archives: > http://news.gmane.org/gmane.__science.biology.informatics.__conductor > <http: news.gmane.org="" gmane.science.biology.informatics.conductor=""> > > > -- > James W. MacDonald, M.S. > Biostatistician > University of Washington > Environmental and Occupational Health Sciences > 4225 Roosevelt Way NE, # 100 > Seattle WA 98105-6099 > > -- 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
ADD REPLYlink written 5.3 years ago by Martin Morgan ♦♦ 23k
Answer: package affy / biobase problem with function "geneNames"
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5.3 years ago by
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James W. MacDonald50k wrote:
Hi Cherif, The R and Bioconductor versions you are using are too old to be supported any more. Please update to R-3.0.3 and the current version of Bioconductor, and see if that helps. Best, Jim On 4/4/2014 11:08 AM, BEN HAMDA Cherif wrote: > Hello, > > after updating all packages. I have a problem when i want normalize my data > ! > > 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]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- James W. MacDonald, M.S. Biostatistician University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way NE, # 100 Seattle WA 98105-6099
ADD COMMENTlink written 5.3 years ago by James W. MacDonald50k
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