Upgrading Bioconductor using BiocUpgrade
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@lavinia-gordon-2959
Last seen 6.6 years ago
Dear all, I am trying to upgrade Bioconductor from 2.10 to 2.11 on a machine running R.2.15.0. Unfortunately this fails, unable to find function 'globalVariables'. Any advice greatly appreciated. > source("http://bioconductor.org/biocLite.R") BiocInstaller version 1.4.9, ?biocLite for help A newer version of Bioconductor is available for this version of R, ?BiocUpgrade for help > biocLite("BiocUpgrade") Upgrade all packages to Bioconductor version 2.11? [y/n]: y trying URL 'http://bioconductor.org/packages/2.11/bioc/src/contrib/Bio cInstaller_1.8.2.tar.gz' Content type 'application/x-gzip' length 12006 bytes (11 Kb) opened URL ================================================== downloaded 11 Kb * installing *source* package âBiocInstallerâ ... ** R ** inst ** preparing package for lazy loading Error in eval(expr, envir, enclos) : could not find function "globalVariables" Error : unable to load R code in package âBiocInstallerâ ERROR: lazy loading failed for package âBiocInstallerâ * removing â/usr/local/lib64/R/library/BiocInstallerâ * restoring previous â/usr/local/lib64/R/library/BiocInstallerâ The downloaded source packages are in â/tmp/RtmpnPmRq7/downloaded_packagesâ Updating HTML index of packages in '.Library' Making packages.html ... done 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. > sessionInfo() R version 2.15.0 (2012-03-30) Platform: x86_64-unknown-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=C LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] BiocInstaller_1.4.9 loaded via a namespace (and not attached): [1] tools_2.15.0 Lavinia Gordon Senior Research Officer Quantitative Sciences Core, Bioinformatics Murdoch Childrens Research Institute The Royal Children's Hospital Flemington Road Parkville Victoria 3052 Australia T 03 8341 6221 www.mcri.edu.au <http: www.mcri.edu.au=""/> ______________________________________________________________________ This email has been scanned by the Symantec Email Security.cloud service. For more information please visit http://www.symanteccloud.com ______________________________________________________________________ [[alternative HTML version deleted]]
BiocInstaller BiocInstaller • 21k views
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Dan Tenenbaum ★ 8.2k
@dan-tenenbaum-4256
Last seen 9 weeks ago
United States
Hi Lavinia, On Tue, Oct 23, 2012 at 2:14 PM, Lavinia Gordon <lavinia.gordon at="" mcri.edu.au=""> wrote: > Dear all, > > I am trying to upgrade Bioconductor from 2.10 to 2.11 on a machine running R.2.15.0. Unfortunately this fails, unable to find function 'globalVariables'. Any advice greatly appreciated. > It looks like older versions of R-2.15 did not have the globalVariables() function. We just pushed a new version of BiocInstaller (1.8.3) for Bioc 2.11 that checks to make sure this function exists before calling it. Start a fresh R session and try the upgrade instructions again. Thanks, Dan > > >> source("http://bioconductor.org/biocLite.R") > > BiocInstaller version 1.4.9, ?biocLite for help > > A newer version of Bioconductor is available for this version of R, > > ?BiocUpgrade for help > >> biocLite("BiocUpgrade") > > Upgrade all packages to Bioconductor version 2.11? [y/n]: y > > trying URL 'http://bioconductor.org/packages/2.11/bioc/src/contrib/B iocInstaller_1.8.2.tar.gz' > > Content type 'application/x-gzip' length 12006 bytes (11 Kb) > > opened URL > > ================================================== > > downloaded 11 Kb > > > > * installing *source* package ?BiocInstaller? ... > > ** R > > ** inst > > ** preparing package for lazy loading > > Error in eval(expr, envir, enclos) : > > could not find function "globalVariables" > > Error : unable to load R code in package ?BiocInstaller? > > ERROR: lazy loading failed for package ?BiocInstaller? > > * removing ?/usr/local/lib64/R/library/BiocInstaller? > > * restoring previous ?/usr/local/lib64/R/library/BiocInstaller? > > > > The downloaded source packages are in > > ?/tmp/RtmpnPmRq7/downloaded_packages? > > Updating HTML index of packages in '.Library' > > Making packages.html ... done > > 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. > >> sessionInfo() > > R version 2.15.0 (2012-03-30) > > Platform: x86_64-unknown-linux-gnu (64-bit) > > > > locale: > > [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C > > [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 > > [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 > > [7] LC_PAPER=C LC_NAME=C > > [9] LC_ADDRESS=C LC_TELEPHONE=C > > [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C > > > > attached base packages: > > [1] stats graphics grDevices utils datasets methods base > > > > other attached packages: > > [1] BiocInstaller_1.4.9 > > > > loaded via a namespace (and not attached): > > [1] tools_2.15.0 > > > > > > Lavinia Gordon > > Senior Research Officer > > Quantitative Sciences Core, Bioinformatics > > > > Murdoch Childrens Research Institute > > The Royal Children's Hospital > > Flemington Road Parkville Victoria 3052 Australia > > T 03 8341 6221 > > www.mcri.edu.au <http: www.mcri.edu.au=""/> > > > > > ______________________________________________________________________ > This email has been scanned by the Symantec Email Security.cloud service. > For more information please visit http://www.symanteccloud.com > ______________________________________________________________________ > [[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
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Thanks Dan, works perfectly, greatly appreciate your prompt response. Lavinia Gordon Senior Research Officer Quantitative Sciences Core, Bioinformatics Murdoch Childrens Research Institute The Royal Children?s Hospital Flemington Road Parkville Victoria 3052 Australia T 03 8341 6221 www.mcri.edu.au -----Original Message----- From: Dan Tenenbaum [mailto:dtenenba@fhcrc.org] Sent: Wednesday, 24 October 2012 8:44 AM To: Lavinia Gordon Cc: bioconductor at r-project.org Subject: Re: [BioC] Upgrading Bioconductor using BiocUpgrade Hi Lavinia, On Tue, Oct 23, 2012 at 2:14 PM, Lavinia Gordon <lavinia.gordon at="" mcri.edu.au=""> wrote: > Dear all, > > I am trying to upgrade Bioconductor from 2.10 to 2.11 on a machine running R.2.15.0. Unfortunately this fails, unable to find function 'globalVariables'. Any advice greatly appreciated. > It looks like older versions of R-2.15 did not have the globalVariables() function. We just pushed a new version of BiocInstaller (1.8.3) for Bioc 2.11 that checks to make sure this function exists before calling it. Start a fresh R session and try the upgrade instructions again. Thanks, Dan > > >> source("http://bioconductor.org/biocLite.R") > > BiocInstaller version 1.4.9, ?biocLite for help > > A newer version of Bioconductor is available for this version of R, > > ?BiocUpgrade for help > >> biocLite("BiocUpgrade") > > Upgrade all packages to Bioconductor version 2.11? [y/n]: y > > trying URL 'http://bioconductor.org/packages/2.11/bioc/src/contrib/B iocInstaller_1.8.2.tar.gz' > > Content type 'application/x-gzip' length 12006 bytes (11 Kb) > > opened URL > > ================================================== > > downloaded 11 Kb > > > > * installing *source* package ?BiocInstaller? ... > > ** R > > ** inst > > ** preparing package for lazy loading > > Error in eval(expr, envir, enclos) : > > could not find function "globalVariables" > > Error : unable to load R code in package ?BiocInstaller? > > ERROR: lazy loading failed for package ?BiocInstaller? > > * removing ?/usr/local/lib64/R/library/BiocInstaller? > > * restoring previous ?/usr/local/lib64/R/library/BiocInstaller? > > > > The downloaded source packages are in > > ?/tmp/RtmpnPmRq7/downloaded_packages? > > Updating HTML index of packages in '.Library' > > Making packages.html ... done > > 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. > >> sessionInfo() > > R version 2.15.0 (2012-03-30) > > Platform: x86_64-unknown-linux-gnu (64-bit) > > > > locale: > > [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C > > [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 > > [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 > > [7] LC_PAPER=C LC_NAME=C > > [9] LC_ADDRESS=C LC_TELEPHONE=C > > [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C > > > > attached base packages: > > [1] stats graphics grDevices utils datasets methods base > > > > other attached packages: > > [1] BiocInstaller_1.4.9 > > > > loaded via a namespace (and not attached): > > [1] tools_2.15.0 > > > > > > Lavinia Gordon > > Senior Research Officer > > Quantitative Sciences Core, Bioinformatics > > > > Murdoch Childrens Research Institute > > The Royal Children's Hospital > > Flemington Road Parkville Victoria 3052 Australia > > T 03 8341 6221 > > www.mcri.edu.au <http: www.mcri.edu.au=""/> > > > > > ______________________________________________________________________ > This email has been scanned by the Symantec Email Security.cloud service. > For more information please visit http://www.symanteccloud.com > ______________________________________________________________________ > [[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 ______________________________________________________________________ This email has been scanned by the Symantec Email Security.cloud service. For more information please visit http://www.symanteccloud.com If you have any question, please contact MCRI IT Helpdesk for further assistance. ______________________________________________________________________ ______________________________________________________________________ This email has been scanned by the Symantec Email Security.cloud service. For more information please visit http://www.symanteccloud.com ______________________________________________________________________
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