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Question: NOISeq installation error
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gravatar for Fatemehsadat Seyednasrollah
5.2 years ago by
Hi all, I am trying to install NOISeq package from Bioconductor using commands : source("http://bioconductor.org/biocLite.R") biocLite("NOISeq") But there is an error when installing: Warning message: package ?NOISeq? is not available (for R version 2.15.1) But in the manual it is mentioned that NOISeq is available for R (>=2.0.3) so why is that? Thanks in advance
ADD COMMENTlink modified 5.2 years ago by Sean Davis21k • written 5.2 years ago by Fatemehsadat Seyednasrollah260
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gravatar for Sean Davis
5.2 years ago by
Sean Davis21k
United States
Sean Davis21k wrote:
On Mon, Oct 8, 2012 at 8:04 AM, Fatemehsadat Seyednasrollah <fatsey at="" utu.fi=""> wrote: > Hi all, > I am trying to install NOISeq package from Bioconductor using commands : > source("http://bioconductor.org/biocLite.R") > biocLite("NOISeq") > > But there is an error when installing: Warning message: package ?NOISeq? is not available (for R version 2.15.1) > When reporting errors, be sure to post the output of sessionInfo(). Without that, we are all guessing a bit as to what your R setup is. Sean > But in the manual it is mentioned that NOISeq is available for R (>=2.0.3) so why is that? > Thanks in advance > _______________________________________________ > 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
ADD COMMENTlink written 5.2 years ago by Sean Davis21k
Sorry for that, this is my sessionInfo() output: > sessionInfo() R version 2.15.1 (2012-06-22) Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) locale: [1] C/UTF-8/C/C/C/C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] BiocInstaller_1.4.8 loaded via a namespace (and not attached): [1] tools_2.15.1 ________________________________________ From: seandavi@gmail.com [seandavi@gmail.com] on behalf of Sean Davis [sdavis2@mail.nih.gov] Sent: Monday, October 08, 2012 3:11 PM To: Fatemehsadat Seyednasrollah Cc: bioconductor at r-project.org Subject: Re: [BioC] NOISeq installation error On Mon, Oct 8, 2012 at 8:04 AM, Fatemehsadat Seyednasrollah <fatsey at="" utu.fi=""> wrote: > Hi all, > I am trying to install NOISeq package from Bioconductor using commands : > source("http://bioconductor.org/biocLite.R") > biocLite("NOISeq") > > But there is an error when installing: Warning message: package ?NOISeq? is not available (for R version 2.15.1) > When reporting errors, be sure to post the output of sessionInfo(). Without that, we are all guessing a bit as to what your R setup is. Sean > But in the manual it is mentioned that NOISeq is available for R (>=2.0.3) so why is that? > Thanks in advance > _______________________________________________ > 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
ADD REPLYlink written 5.2 years ago by Fatemehsadat Seyednasrollah260
On Mon, Oct 8, 2012 at 8:14 AM, Fatemehsadat Seyednasrollah <fatsey at="" utu.fi=""> wrote: > Sorry for that, this is my sessionInfo() output: > >> sessionInfo() > > R version 2.15.1 (2012-06-22) > Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) > > locale: > [1] C/UTF-8/C/C/C/C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] BiocInstaller_1.4.8 It looks like your BiocInstaller package is out-of-date. In a new R session, try: > source('http://bioconductor.org/biocLite.R') > biocLite('NOISeq') This worked fine for me with this sessionInfo(). > sessionInfo() R version 2.15.1 Patched (2012-08-09 r60221) Platform: i386-apple-darwin9.8.0/i386 (32-bit) locale: [1] C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] BiocInstaller_1.8.1 loaded via a namespace (and not attached): [1] tools_2.15.1 > loaded via a namespace (and not attached): > [1] tools_2.15.1 > > ________________________________________ > From: seandavi at gmail.com [seandavi at gmail.com] on behalf of Sean Davis [sdavis2 at mail.nih.gov] > Sent: Monday, October 08, 2012 3:11 PM > To: Fatemehsadat Seyednasrollah > Cc: bioconductor at r-project.org > Subject: Re: [BioC] NOISeq installation error > > On Mon, Oct 8, 2012 at 8:04 AM, Fatemehsadat Seyednasrollah > <fatsey at="" utu.fi=""> wrote: >> Hi all, >> I am trying to install NOISeq package from Bioconductor using commands : >> source("http://bioconductor.org/biocLite.R") >> biocLite("NOISeq") >> >> But there is an error when installing: Warning message: package ?NOISeq? is not available (for R version 2.15.1) >> > > When reporting errors, be sure to post the output of sessionInfo(). > Without that, we are all guessing a bit as to what your R setup is. > > Sean > >> But in the manual it is mentioned that NOISeq is available for R (>=2.0.3) so why is that? >> Thanks in advance >> _______________________________________________ >> 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 > > _______________________________________________ > 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
ADD REPLYlink written 5.2 years ago by Sean Davis21k
On 10/08/2012 05:32 AM, Sean Davis wrote: > On Mon, Oct 8, 2012 at 8:14 AM, Fatemehsadat Seyednasrollah > <fatsey at="" utu.fi=""> wrote: >> Sorry for that, this is my sessionInfo() output: >> >>> sessionInfo() >> >> R version 2.15.1 (2012-06-22) >> Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit) >> >> locale: >> [1] C/UTF-8/C/C/C/C >> >> attached base packages: >> [1] stats graphics grDevices utils datasets methods base >> >> other attached packages: >> [1] BiocInstaller_1.4.8 > > It looks like your BiocInstaller package is out-of-date. In a new R > session, try: Actually, BiocInstaller is a sentinel for Bioconductor version; the original poster is using BiocInstaller 1.4.x, which corresponds to Bioconductor version 1.10. Sean is using BiocInstaller 1.8.x, which corresponds to Bioconductor version 1.11. NOISeq is available only in Bioconductor version 1.11, so the original poster needs to upgrade to Bioconductor version 1.11, for instance source("http://bioconductor.org/biocLite.R") biocLite("BiocUpgrade") Since this is an _upgrade_, the original poster should be prepared for many packages to be re-installed, and perhaps some complications from that. Martin > >> source('http://bioconductor.org/biocLite.R') >> biocLite('NOISeq') > > This worked fine for me with this sessionInfo(). > >> sessionInfo() > R version 2.15.1 Patched (2012-08-09 r60221) > Platform: i386-apple-darwin9.8.0/i386 (32-bit) > > locale: > [1] C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] BiocInstaller_1.8.1 > > loaded via a namespace (and not attached): > [1] tools_2.15.1 > >> loaded via a namespace (and not attached): >> [1] tools_2.15.1 >> >> ________________________________________ >> From: seandavi at gmail.com [seandavi at gmail.com] on behalf of Sean Davis [sdavis2 at mail.nih.gov] >> Sent: Monday, October 08, 2012 3:11 PM >> To: Fatemehsadat Seyednasrollah >> Cc: bioconductor at r-project.org >> Subject: Re: [BioC] NOISeq installation error >> >> On Mon, Oct 8, 2012 at 8:04 AM, Fatemehsadat Seyednasrollah >> <fatsey at="" utu.fi=""> wrote: >>> Hi all, >>> I am trying to install NOISeq package from Bioconductor using commands : >>> source("http://bioconductor.org/biocLite.R") >>> biocLite("NOISeq") >>> >>> But there is an error when installing: Warning message: package ?NOISeq? is not available (for R version 2.15.1) >>> >> >> When reporting errors, be sure to post the output of sessionInfo(). >> Without that, we are all guessing a bit as to what your R setup is. >> >> Sean >> >>> But in the manual it is mentioned that NOISeq is available for R (>=2.0.3) so why is that? >>> Thanks in advance >>> _______________________________________________ >>> 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 >> >> _______________________________________________ >> 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 > > _______________________________________________ > 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 REPLYlink written 5.2 years ago by Martin Morgan ♦♦ 21k
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