On Wed, Apr 26, 2017 at 11:26 AM, Martin Morgan < martin.mor...@roswellpark.org> wrote:
> On 04/26/2017 11:23 AM, James W. MacDonald wrote: > >> >> >> On Wed, Apr 26, 2017 at 11:11 AM, Martin Morgan >> <martin.mor...@roswellpark.org <mailto:martin.mor...@roswellpark.org>> >> wrote: >> >> On 04/26/2017 10:34 AM, James W. MacDonald wrote: >> >> >> >> On Wed, Apr 26, 2017 at 10:09 AM, Martin Morgan >> <martin.mor...@roswellpark.org >> <mailto:martin.mor...@roswellpark.org> >> <mailto:martin.mor...@roswellpark.org >> >> <mailto:martin.mor...@roswellpark.org>>> >> >> 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 >> <https://bioconductor.org/packages/3.5/bioc/bin/windows/contrib> >> >> and >> >> https://bioconductor.org/packages/3.5/bioc/bin/windows/contrib >> <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 >> <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. >> > > If you're having a problem then it would be great to have your expert > insight into what is going wrong... Well, getOption("pkgType") on my Windows box returns 'both' rather than 'win.binary', so this is what I get: > contrib.url(biocinstallRepos()) [1] "https://bioconductor.org/packages/3.5/bioc/src/contrib" [2] "https://bioconductor.org/packages/3.5/data/annotation/src/contrib" [3] "https://bioconductor.org/packages/3.5/data/experiment/src/contrib" [4] "https://bioconductor.org/packages/3.5/extra/src/contrib" [5] "https://cran.rstudio.com/src/contrib" [6] "https://www.stats.ox.ac.uk/pub/RWin/src/contrib" and if I set that to win.binary, I get what you get. I don't remember ever changing that option, but maybe it gets changed when you install the Rtools toolset? I don't see any documentation to that effect, and I just re-installed Rtools just to check. Regardless, that's what the deal was. Jim > > Martin > > > >> 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 >> > > > 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]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel