Question: Cannot upgrade bioconductor from 2.12 to 2.13
0
gravatar for A M Torres, Hugo
5.8 years ago by
A M Torres, Hugo10 wrote:
Hi, I am following the upgrade instructions here: http://master.bioconductor.org/install/#update-bioconductor-packages But I keep getting biocLite 2.12 instead of 2.13 **no matter which mirror I choose.** Any clues? R R version 3.0.2 (2013-09-25) -- "Frisbee Sailing" Copyright (C) 2013 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu (64-bit) R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. Natural language support but running in an English locale R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. R » source("http://bioconductor.org/biocLite.R") Your Bioconductor is out-of-date, upgrade to version 2.13 by following instructions at http://bioconductor.org/install. R » biocLite() BioC_mirror: http://www.bioconductor.org Using Bioconductor version 2.12 (BiocInstaller 1.10.4), R version 3.0.2. [[alternative HTML version deleted]]
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ADD COMMENTlink modified 5.8 years ago by Julie Zhu4.0k • written 5.8 years ago by A M Torres, Hugo10
Answer: Cannot upgrade bioconductor from 2.12 to 2.13
0
gravatar for Levi Waldron
5.8 years ago by
Levi Waldron950
CUNY Graduate School of Public Health and Health Policy, New York, NY
Levi Waldron950 wrote:
Dear Hugo, try: biocLite("BiocUpgrade") On Thu, Oct 24, 2013 at 9:32 AM, A M Torres, Hugo <hugo.am.torres@usp.br>wrote: > Hi, > > I am following the upgrade instructions here: > http://master.bioconductor.org/install/#update-bioconductor-packages > > But I keep getting biocLite 2.12 instead of 2.13 **no matter which mirror > I choose.** > > > Any clues? > > R > > R version 3.0.2 (2013-09-25) -- "Frisbee Sailing" > Copyright (C) 2013 The R Foundation for Statistical Computing > Platform: x86_64-pc-linux-gnu (64-bit) > > R is free software and comes with ABSOLUTELY NO WARRANTY. > You are welcome to redistribute it under certain conditions. > Type 'license()' or 'licence()' for distribution details. > > Natural language support but running in an English locale > > R is a collaborative project with many contributors. > Type 'contributors()' for more information and > 'citation()' on how to cite R or R packages in publications. > > Type 'demo()' for some demos, 'help()' for on-line help, or > 'help.start()' for an HTML browser interface to help. > Type 'q()' to quit R. > > R » source("http://bioconductor.org/biocLite.R") > Your Bioconductor is out-of-date, upgrade to version 2.13 by following > instructions > at http://bioconductor.org/install. > R » biocLite() > BioC_mirror: http://www.bioconductor.org > Using Bioconductor version 2.12 (BiocInstaller 1.10.4), R version 3.0.2. > > [[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 > -- Levi Waldron Assistant Professor Epidemiology and Biostatistics Program CUNY School of Public Health at Hunter College 2180 3rd Ave Rm 538 New York NY 10035-4003 [[alternative HTML version deleted]]
ADD COMMENTlink written 5.8 years ago by Levi Waldron950
Answer: Cannot upgrade bioconductor from 2.12 to 2.13
0
gravatar for Julie Zhu
5.8 years ago by
Julie Zhu4.0k
United States
Julie Zhu4.0k wrote:
Hugo, I had similar problem a week ago. Here is my work around. First download the latest version of the BiocInstaller package, then upgrades all currently installed packages to the latest repositories using the following commands. source("http://bioconductor.org/biocLite.R") biocLite("BiocUpgrade") Hope this helps. Best regards, Julie On 10/24/13 9:32 AM, "A M Torres, Hugo" <hugo.am.torres at="" usp.br=""> wrote: > Hi, > > I am following the upgrade instructions here: > http://master.bioconductor.org/install/#update-bioconductor-packages > > But I keep getting biocLite 2.12 instead of 2.13 **no matter which mirror > I choose.** > > > Any clues? > > R > > R version 3.0.2 (2013-09-25) -- "Frisbee Sailing" > Copyright (C) 2013 The R Foundation for Statistical Computing > Platform: x86_64-pc-linux-gnu (64-bit) > > R is free software and comes with ABSOLUTELY NO WARRANTY. > You are welcome to redistribute it under certain conditions. > Type 'license()' or 'licence()' for distribution details. > > Natural language support but running in an English locale > > R is a collaborative project with many contributors. > Type 'contributors()' for more information and > 'citation()' on how to cite R or R packages in publications. > > Type 'demo()' for some demos, 'help()' for on-line help, or > 'help.start()' for an HTML browser interface to help. > Type 'q()' to quit R. > > R ?? source("http://bioconductor.org/biocLite.R") > Your Bioconductor is out-of-date, upgrade to version 2.13 by following > instructions > at http://bioconductor.org/install. > R ?? biocLite() > BioC_mirror: http://www.bioconductor.org > Using Bioconductor version 2.12 (BiocInstaller 1.10.4), R version 3.0.2. > > [[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
ADD COMMENTlink written 5.8 years ago by Julie Zhu4.0k
Thank you Levi and Julie, I had the same problem last week also but it did not seem to get in the way of my work. Per your suggestion, I tried biocLite("BiocUpgrade") and it worked fine just now on Linux Ubuntu 13.04. The upgrade, however, removed the arrayQualityMetrics package I have been working with and I got a "Non-zero exit status" message. To fix that, I started R as root user, re-installed biocLite("arrayQualityMetrics"). The package and everything else is working fine now. Lisa On Thu, Oct 24, 2013 at 10:03 AM, Zhu, Lihua (Julie) <julie.zhu@umassmed.edu> wrote: > Hugo, > > I had similar problem a week ago. Here is my work around. > > First download the latest version of the BiocInstaller package, then > upgrades all currently installed packages to the latest repositories using > the following commands. > source("http://bioconductor.org/biocLite.R") > biocLite("BiocUpgrade") > > Hope this helps. > > Best regards, > > Julie > > > On 10/24/13 9:32 AM, "A M Torres, Hugo" <hugo.am.torres@usp.br> wrote: > > > Hi, > > > > I am following the upgrade instructions here: > > http://master.bioconductor.org/install/#update-bioconductor- packages > > > > But I keep getting biocLite 2.12 instead of 2.13 **no matter which > mirror > > I choose.** > > > > > > Any clues? > > > > R > > > > R version 3.0.2 (2013-09-25) -- "Frisbee Sailing" > > Copyright (C) 2013 The R Foundation for Statistical Computing > > Platform: x86_64-pc-linux-gnu (64-bit) > > > > R is free software and comes with ABSOLUTELY NO WARRANTY. > > You are welcome to redistribute it under certain conditions. > > Type 'license()' or 'licence()' for distribution details. > > > > Natural language support but running in an English locale > > > > R is a collaborative project with many contributors. > > Type 'contributors()' for more information and > > 'citation()' on how to cite R or R packages in publications. > > > > Type 'demo()' for some demos, 'help()' for on-line help, or > > 'help.start()' for an HTML browser interface to help. > > Type 'q()' to quit R. > > > > R » source("http://bioconductor.org/biocLite.R") > > Your Bioconductor is out-of-date, upgrade to version 2.13 by following > > instructions > > at http://bioconductor.org/install. > > R » biocLite() > > BioC_mirror: http://www.bioconductor.org > > Using Bioconductor version 2.12 (BiocInstaller 1.10.4), R version 3.0.2. > > > > [[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 > > _______________________________________________ > 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 > [[alternative HTML version deleted]]
ADD REPLYlink written 5.8 years ago by Lisa Cohen50
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