Search
Question: Upgrading Bioconductor using BiocUpgrade
0
gravatar for Lavinia Gordon
5.1 years ago by
Lavinia Gordon480 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. > 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]]
ADD COMMENTlink modified 5.1 years ago by Dan Tenenbaum ♦♦ 8.2k • written 5.1 years ago by Lavinia Gordon480
0
gravatar for Dan Tenenbaum
5.1 years ago by
Dan Tenenbaum ♦♦ 8.2k
United States
Dan Tenenbaum ♦♦ 8.2k wrote:
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
ADD COMMENTlink written 5.1 years ago by Dan Tenenbaum ♦♦ 8.2k
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 ______________________________________________________________________
ADD REPLYlink written 5.1 years ago by Lavinia Gordon480
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 118 users visited in the last hour