On Wed, Apr 26, 2017 at 11:11 AM, Martin Morgan < [email protected]> wrote:
> On 04/26/2017 10:34 AM, James W. MacDonald wrote: > >> >> >> On Wed, Apr 26, 2017 at 10:09 AM, Martin Morgan >> <[email protected] <mailto:[email protected]>> >> >> wrote: >> >> On 04/26/2017 10:00 AM, James W. MacDonald wrote: >> >> I see the binaries on the respective web pages, but biocLite >> seems not to: >> >> >> I'm not 100% sure but can you try again in a new R session? I think >> you have a cached version of the repository index. >> >> >> At a command prompt, using --vanilla: >> >> C:\Users\jmacdon> C:\Progra~1\R\R-3.4.0\bin\x64\R --vanilla >> >> R version 3.4.0 (2017-04-21) -- "You Stupid Darkness" >> Copyright (C) 2017 The R Foundation for Statistical Computing >> Platform: x86_64-w64-mingw32/x64 (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. >> >> library(BiocInstaller) >>> >> Bioconductor version 3.5 (BiocInstaller 1.26.0), ?biocLite for help >> >>> biocLite() >>> >> BioC_mirror: https://bioconductor.org >> Using Bioconductor 3.5 (BiocInstaller 1.26.0), R 3.4.0 (2017-04-21). >> installation path not writeable, unable to update packages: foreign >> Old packages: 'Biobase', 'IRanges', 'S4Vectors' >> Update all/some/none? [a/s/n]: a >> >> There are binary versions available but the source versions are later: >> binary source needs_compilation >> Biobase 2.35.1 2.36.0 TRUE >> IRanges 2.9.19 2.10.0 TRUE >> S4Vectors 0.13.17 0.14.0 TRUE >> >> Do you want to install from sources the packages which need compilation? >> y/n: >> >> Is there a way to remove the cache manually? I have already uninstalled >> and re-installed BiocInstaller. >> > > contrib.url(BiocInstaller::biocinstallRepos()) > > should be pointing to > > https://bioconductor.org/packages/3.5/bioc/bin/windows/contrib > > and > > https://bioconductor.org/packages/3.5/bioc/bin/windows/contrib > /3.4/PACKAGES > > has the current information > > Package: Biobase > Version: 2.36.0 > Depends: R (>= 2.10), BiocGenerics (>= 0.3.2), utils > Imports: methods > Suggests: tools, tkWidgets, ALL, RUnit, golubEsets > License: Artistic-2.0 > Archs: i386, x64 > > as well as in R > > > fl = "https://bioconductor.org/packages/3.5/bioc/bin/windows/cont > rib/3.4/PACKAGES.rds" > > xx = readRDS(url(fl)) > > xx['Biobase', , drop=FALSE] Package Version Priority > Biobase "Biobase" "2.36.0" NA > Depends Imports LinkingTo > Biobase "R (>= 2.10), BiocGenerics (>= 0.3.2), utils" "methods" NA > Suggests Enhances License > Biobase "tools, tkWidgets, ALL, RUnit, golubEsets" NA "Artistic-2.0" > License_is_FOSS License_restricts_use OS_type Archs MD5sum > Biobase NA NA NA "i386, x64" NA > > should be pointing to the current .zip files. > > biocLite() delegates to available.packages(), which should be checking the > session temporary directory and, since you're in a new session, retrieving > the rds file above. You could > > debug(available.packages) > > and try and figure out where the issue is? > > FWIW with a new R installation I could not reproduce your problem. OK. If it's just weirdness on my end I don't really care. I was just concerned that this would be a problem for regular end users. Thanks, Jim > > > > sessionInfo() > R version 3.4.0 (2017-04-21) > Platform: i386-w64-mingw32/i386 (32-bit) > Running under: Windows Server 2012 R2 x64 (build 9600) > > Matrix products: default > > locale: > [1] LC_COLLATE=English_United States.1252 > [2] LC_CTYPE=English_United States.1252 > [3] LC_MONETARY=English_United States.1252 > [4] LC_NUMERIC=C > [5] LC_TIME=English_United States.1252 > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] BiocInstaller_1.26.0 > > loaded via a namespace (and not attached): > [1] compiler_3.4.0 tools_3.4.0 > > Martin > > > >> Jim >> >> >> >> >> Martin >> >> >> biocLite() >> >> BioC_mirror: https://bioconductor.org >> Using Bioconductor 3.5 (BiocInstaller 1.26.0), R 3.4.0 >> (2017-04-21). >> installation path not writeable, unable to update packages: >> foreign >> Old packages: 'AnnotationDbi', 'Biobase', 'BiocGenerics', >> 'biomaRt', >> 'IRanges', >> 'S4Vectors' >> Update all/some/none? [a/s/n]: a >> >> There are binary versions available but the source versions >> are later: >> binary source needs_compilation >> AnnotationDbi 1.37.4 1.38.0 FALSE >> Biobase 2.35.1 2.36.0 TRUE >> BiocGenerics 0.21.3 0.22.0 FALSE >> biomaRt 2.31.10 2.32.0 FALSE >> IRanges 2.9.19 2.10.0 TRUE >> S4Vectors 0.13.17 0.14.0 TRUE >> >> Do you want to install from sources the packages which need >> compilation? >> y/n: >> >> sessionInfo() >> >> R version 3.4.0 (2017-04-21) >> Platform: x86_64-w64-mingw32/x64 (64-bit) >> Running under: Windows 10 x64 (build 14393) >> >> Matrix products: default >> >> locale: >> [1] LC_COLLATE=English_United States.1252 >> [2] LC_CTYPE=English_United States.1252 >> [3] LC_MONETARY=English_United States.1252 >> [4] LC_NUMERIC=C >> [5] LC_TIME=English_United States.1252 >> >> attached base packages: >> [1] stats graphics grDevices utils datasets methods >> base >> >> other attached packages: >> [1] BiocInstaller_1.26.0 >> >> loaded via a namespace (and not attached): >> [1] compiler_3.4.0 tools_3.4.0 >> >> >> >> This email message may contain legally privileged and/or >> confidential information. If you are not the intended recipient(s), >> or the employee or agent responsible for the delivery of this >> message to the intended recipient(s), you are hereby notified that >> any disclosure, copying, distribution, or use of this email message >> is prohibited. If you have received this message in error, please >> notify the sender immediately by e-mail and delete this email >> message from your computer. Thank you. >> >> >> >> >> -- >> James W. MacDonald, M.S. >> Biostatistician >> University of Washington >> Environmental and Occupational Health Sciences >> 4225 Roosevelt Way NE, # 100 >> Seattle WA 98105-6099 >> > > > This email message may contain legally privileged and/or confidential > information. If you are not the intended recipient(s), or the employee or > agent responsible for the delivery of this message to the intended > recipient(s), you are hereby notified that any disclosure, copying, > distribution, or use of this email message is prohibited. If you have > received this message in error, please notify the sender immediately by > e-mail and delete this email message from your computer. Thank you. > -- 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]] _______________________________________________ [email protected] mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
