I uninstalled R 2.14 and then installed R 2.15.2 instead updated R, because I wanted to remove the start up setting. When I tried to install affy, limma, and gcrma, I got warming messages "packages ???affy???, ???gcrma???, ???limma??? are not available (for R version 2.15.2)". Tried "biocLite("BiocUpgrade")" and then installed again, still the same warming message. Thank you for help. -- output of sessionInfo(): > source("http://bioconductor.org/biocLite.R") Installing package(s) into ???C:/Users/Julie Tseng-Crank/Documents/R /win-library/2.15??? (as ???lib??? is unspecified) trying URL 'http://www.bioconductor.org/packages/2.11/bioc/bin/windows /contrib/2.15/BiocInstaller_1.8.3.zip' Content type 'application/zip' length 43242 bytes (42 Kb) opened URL downloaded 42 Kb package ???BiocInstaller??? successfully unpacked and MD5 sums checked The downloaded binary packages are in C:\Users\Julie Tseng- Crank\AppData\Local\Temp\RtmpGEYYeQ\downloaded_packages Bioconductor version 2.11 (BiocInstaller 1.8.3), ?biocLite for help > biocLite() BioC_mirror: http://bioconductor.org Using Bioconductor version 2.11 (BiocInstaller 1.8.3), R version 2.15. Installing package(s) 'Biobase' 'IRanges' 'AnnotationDbi' also installing the dependencies ???BiocGenerics???, ???DBI???, ???RSQLite??? trying URL 'http://bioconductor.org/packages/2.11/bioc/bin/windows/con trib/2.15/BiocGenerics_0.4.0.zip' Content type 'application/zip' length 246934 bytes (241 Kb) opened URL downloaded 241 Kb trying URL 'http://cran.stat.sfu.ca/bin/windows/contrib/2.15/DBI_0.2-5.zip' Content type 'application/zip' length 394390 bytes (385 Kb) opened URL downloaded 385 Kb trying URL 'http://cran.stat.sfu.ca/bin/windows/contrib/2.15/RSQLite_0.11.2.zip' Content type 'application/zip' length 1129539 bytes (1.1 Mb) opened URL downloaded 1.1 Mb trying URL 'http://bioconductor.org/packages/2.11/bioc/bin/windows/con trib/2.15/Biobase_2.18.0.zip' Content type 'application/zip' length 2346708 bytes (2.2 Mb) opened URL downloaded 2.2 Mb trying URL 'http://bioconductor.org/packages/2.11/bioc/bin/windows/con trib/2.15/IRanges_1.16.4.zip' Content type 'application/zip' length 2048202 bytes (2.0 Mb) opened URL downloaded 2.0 Mb trying URL 'http://bioconductor.org/packages/2.11/bioc/bin/windows/con trib/2.15/AnnotationDbi_1.20.3.zip' Content type 'application/zip' length 4199125 bytes (4.0 Mb) opened URL downloaded 4.0 Mb package ???BiocGenerics??? successfully unpacked and MD5 sums checked package ???DBI??? successfully unpacked and MD5 sums checked package ???RSQLite??? successfully unpacked and MD5 sums checked package ???Biobase??? successfully unpacked and MD5 sums checked package ???IRanges??? successfully unpacked and MD5 sums checked package ???AnnotationDbi??? successfully unpacked and MD5 sums checked The downloaded binary packages are in C:\Users\Julie Tseng- Crank\AppData\Local\Temp\RtmpGEYYeQ\downloaded_packages Warning message: installed directory not writable, cannot update packages 'foreign', 'lattice', 'MASS', 'Matrix', 'nlme', 'rpart', 'survival' > biocLite("affy", "gcrma", "limma") Error in !suppressAutoUpdate : invalid argument type > install.packages(c("affy", "gcrma", "limma")) Installing package(s) into ???C:/Users/Julie Tseng-Crank/Documents/R /win-library/2.15??? (as ???lib??? is unspecified) Warning message: packages ???affy???, ???gcrma???, ???limma??? are not available (for R version 2.15.2) > library() > biocLite("BiocUpgrade") BioC_mirror: http://bioconductor.org Using Bioconductor version 2.11 (BiocInstaller 1.8.3), R version 2.15. Warning messages: 1: Bioconductor version 2.11 is the latest available for R version 2.15 2: installed directory not writable, cannot update packages 'foreign', 'lattice', 'MASS', 'Matrix', 'nlme', 'rpart', 'survival' > install.packages(c("affy", "gcrma", "limma")) Installing package(s) into ???C:/Users/Julie Tseng-Crank/Documents/R /win-library/2.15??? (as ???lib??? is unspecified) Warning message: packages ???affy???, ???gcrma???, ???limma??? are not available (for R version 2.15.2) > -- Sent via the guest posting facility at bioconductor.org.

On 01/22/2013 11:03 PM, Julie Tseng-Crank [guest] wrote: > > I uninstalled R 2.14 and then installed R 2.15.2 instead updated R, because I wanted to remove the start up setting. When I tried to install affy, limma, and gcrma, I got warming messages "packages ???affy???, ???gcrma???, ???limma??? are not available (for R version 2.15.2)". Tried "biocLite("BiocUpgrade")" and then installed again, still the same warming message. Thank you for help. > > -- output of sessionInfo(): > >> source("http://bioconductor.org/biocLite.R") > Installing package(s) into ???C:/Users/Julie Tseng-Crank/Documents/R /win-library/2.15??? > (as ???lib??? is unspecified) > trying URL 'http://www.bioconductor.org/packages/2.11/bioc/bin/windo ws/contrib/2.15/BiocInstaller_1.8.3.zip' > Content type 'application/zip' length 43242 bytes (42 Kb) > opened URL > downloaded 42 Kb > > package ???BiocInstaller??? successfully unpacked and MD5 sums checked > > The downloaded binary packages are in > C:\Users\Julie Tseng- Crank\AppData\Local\Temp\RtmpGEYYeQ\downloaded_packages > Bioconductor version 2.11 (BiocInstaller 1.8.3), ?biocLite for help >> biocLite() > BioC_mirror: http://bioconductor.org > Using Bioconductor version 2.11 (BiocInstaller 1.8.3), R version 2.15. > Installing package(s) 'Biobase' 'IRanges' 'AnnotationDbi' > also installing the dependencies ???BiocGenerics???, ???DBI???, ???RSQLite??? > > trying URL 'http://bioconductor.org/packages/2.11/bioc/bin/windows/c ontrib/2.15/BiocGenerics_0.4.0.zip' > Content type 'application/zip' length 246934 bytes (241 Kb) > opened URL > downloaded 241 Kb > > trying URL 'http://cran.stat.sfu.ca/bin/windows/contrib/2.15/DBI_0.2-5.zip' > Content type 'application/zip' length 394390 bytes (385 Kb) > opened URL > downloaded 385 Kb > > trying URL 'http://cran.stat.sfu.ca/bin/windows/contrib/2.15/RSQLite_0.11.2.zip' > Content type 'application/zip' length 1129539 bytes (1.1 Mb) > opened URL > downloaded 1.1 Mb > > trying URL 'http://bioconductor.org/packages/2.11/bioc/bin/windows/c ontrib/2.15/Biobase_2.18.0.zip' > Content type 'application/zip' length 2346708 bytes (2.2 Mb) > opened URL > downloaded 2.2 Mb > > trying URL 'http://bioconductor.org/packages/2.11/bioc/bin/windows/c ontrib/2.15/IRanges_1.16.4.zip' > Content type 'application/zip' length 2048202 bytes (2.0 Mb) > opened URL > downloaded 2.0 Mb > > trying URL 'http://bioconductor.org/packages/2.11/bioc/bin/windows/c ontrib/2.15/AnnotationDbi_1.20.3.zip' > Content type 'application/zip' length 4199125 bytes (4.0 Mb) > opened URL > downloaded 4.0 Mb > > package ???BiocGenerics??? successfully unpacked and MD5 sums checked > package ???DBI??? successfully unpacked and MD5 sums checked > package ???RSQLite??? successfully unpacked and MD5 sums checked > package ???Biobase??? successfully unpacked and MD5 sums checked > package ???IRanges??? successfully unpacked and MD5 sums checked > package ???AnnotationDbi??? successfully unpacked and MD5 sums checked > > The downloaded binary packages are in > C:\Users\Julie Tseng- Crank\AppData\Local\Temp\RtmpGEYYeQ\downloaded_packages > Warning message: > installed directory not writable, cannot update packages 'foreign', 'lattice', 'MASS', > 'Matrix', 'nlme', 'rpart', 'survival' >> biocLite("affy", "gcrma", "limma") > Error in !suppressAutoUpdate : invalid argument type oops, that should have been biocLite(c("affy", "gcrma", "limma")) >> install.packages(c("affy", "gcrma", "limma")) > Installing package(s) into ???C:/Users/Julie Tseng-Crank/Documents/R /win-library/2.15??? > (as ???lib??? is unspecified) > Warning message: > packages ???affy???, ???gcrma???, ???limma??? are not available (for R version 2.15.2) >> library() >> biocLite("BiocUpgrade") > BioC_mirror: http://bioconductor.org > Using Bioconductor version 2.11 (BiocInstaller 1.8.3), R version 2.15. > Warning messages: > 1: Bioconductor version 2.11 is the latest available for R version 2.15 > 2: installed directory not writable, cannot update packages 'foreign', 'lattice', 'MASS', > 'Matrix', 'nlme', 'rpart', 'survival' >> install.packages(c("affy", "gcrma", "limma")) > Installing package(s) into ???C:/Users/Julie Tseng-Crank/Documents/R /win-library/2.15??? > (as ???lib??? is unspecified) > Warning message: > packages ???affy???, ???gcrma???, ???limma??? are not available (for R version 2.15.2) using install.packages by default means that you are looking on CRAN for Bioconductor packages, so the Bioconductor packages are not found. Just biocLite(c("affy", "gcrma", "limma")) Martin >> > > > -- > Sent via the guest posting facility at bioconductor.org. > > _______________________________________________ > 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 > -- Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M1 B861 Phone: (206) 667-2793

I think the problem is related to: ------------------------- 2: installed directory not writable, cannot update packages 'foreign', 'lattice', 'MASS', 'Matrix', 'nlme', 'rpart', 'survival' -------------- perhaps you have installed R as sudo or superuser so the core 'foreign', 'lattice', 'MASS', 'Matrix', 'nlme', 'rpart', 'survival' packages are in a directory where "/Users/Julie Tseng-Crank" can't write to. BioC wants to update these but not have permission to do so. If you start R as sudo OR give user "/Users/Julie Tseng-Crank" permission to write to the directory where 'foreign', 'lattice', 'MASS', 'Matrix', 'nlme', 'rpart', 'survival' is located (and can modify files there too) you shoudl be ok. Cheers Paul Dr Paul Leo Senior Bioinformatician The University of Queensland Diamantina Institute --------------------------------------------------------------------- TRI, level , 37 Kent Street, Woolloongabba QLD 4102 Tel: +61 7 3443 7072 Mob: 041 303 8691 Fax: +61 7 3443 6966 -----Original Message----- From: Julie Tseng-Crank [guest] <guest@bioconductor.org> To: bioconductor at r-project.org, jtsengcr at yahoo.com Cc: affy Maintainer <rafa at="" jhu.edu=""> Subject: [BioC] R 2.15.2 trouble Date: Tue, 22 Jan 2013 23:03:04 -0800 I uninstalled R 2.14 and then installed R 2.15.2 instead updated R, because I wanted to remove the start up setting. When I tried to install affy, limma, and gcrma, I got warming messages "packages ??~affy??T, ??~gcrma??T, ??~limma??T are not available (for R version 2.15.2)". Tried "biocLite("BiocUpgrade")" and then installed again, still the same warming message. Thank you for help. -- output of sessionInfo(): > source("http://bioconductor.org/biocLite.R") Installing package(s) into ??~C:/Users/Julie Tseng-Crank/Documents/R /win-library/2.15??T (as ??~lib??T is unspecified) trying URL 'http://www.bioconductor.org/packages/2.11/bioc/bin/windows /contrib/2.15/BiocInstaller_1.8.3.zip' Content type 'application/zip' length 43242 bytes (42 Kb) opened URL downloaded 42 Kb package ??~BiocInstaller??T successfully unpacked and MD5 sums checked The downloaded binary packages are in C:\Users\Julie Tseng- Crank\AppData\Local\Temp\RtmpGEYYeQ\downloaded_packages Bioconductor version 2.11 (BiocInstaller 1.8.3), ?biocLite for help > biocLite() BioC_mirror: http://bioconductor.org Using Bioconductor version 2.11 (BiocInstaller 1.8.3), R version 2.15. Installing package(s) 'Biobase' 'IRanges' 'AnnotationDbi' also installing the dependencies ??~BiocGenerics??T, ??~DBI??T, ??~RSQLite??T trying URL 'http://bioconductor.org/packages/2.11/bioc/bin/windows/con trib/2.15/BiocGenerics_0.4.0.zip' Content type 'application/zip' length 246934 bytes (241 Kb) opened URL downloaded 241 Kb trying URL 'http://cran.stat.sfu.ca/bin/windows/contrib/2.15/DBI_0.2-5.zip' Content type 'application/zip' length 394390 bytes (385 Kb) opened URL downloaded 385 Kb trying URL 'http://cran.stat.sfu.ca/bin/windows/contrib/2.15/RSQLite_0.11.2.zip' Content type 'application/zip' length 1129539 bytes (1.1 Mb) opened URL downloaded 1.1 Mb trying URL 'http://bioconductor.org/packages/2.11/bioc/bin/windows/con trib/2.15/Biobase_2.18.0.zip' Content type 'application/zip' length 2346708 bytes (2.2 Mb) opened URL downloaded 2.2 Mb trying URL 'http://bioconductor.org/packages/2.11/bioc/bin/windows/con trib/2.15/IRanges_1.16.4.zip' Content type 'application/zip' length 2048202 bytes (2.0 Mb) opened URL downloaded 2.0 Mb trying URL 'http://bioconductor.org/packages/2.11/bioc/bin/windows/con trib/2.15/AnnotationDbi_1.20.3.zip' Content type 'application/zip' length 4199125 bytes (4.0 Mb) opened URL downloaded 4.0 Mb package ??~BiocGenerics??T successfully unpacked and MD5 sums checked package ??~DBI??T successfully unpacked and MD5 sums checked package ??~RSQLite??T successfully unpacked and MD5 sums checked package ??~Biobase??T successfully unpacked and MD5 sums checked package ??~IRanges??T successfully unpacked and MD5 sums checked package ??~AnnotationDbi??T successfully unpacked and MD5 sums checked The downloaded binary packages are in C:\Users\Julie Tseng- Crank\AppData\Local\Temp\RtmpGEYYeQ\downloaded_packages Warning message: installed directory not writable, cannot update packages 'foreign', 'lattice', 'MASS', 'Matrix', 'nlme', 'rpart', 'survival' > biocLite("affy", "gcrma", "limma") Error in !suppressAutoUpdate : invalid argument type > install.packages(c("affy", "gcrma", "limma")) Installing package(s) into ??~C:/Users/Julie Tseng-Crank/Documents/R /win-library/2.15??T (as ??~lib??T is unspecified) Warning message: packages ??~affy??T, ??~gcrma??T, ??~limma??T are not available (for R version 2.15.2) > library() > biocLite("BiocUpgrade") BioC_mirror: http://bioconductor.org Using Bioconductor version 2.11 (BiocInstaller 1.8.3), R version 2.15. Warning messages: 1: Bioconductor version 2.11 is the latest available for R version 2.15 2: installed directory not writable, cannot update packages 'foreign', 'lattice', 'MASS', 'Matrix', 'nlme', 'rpart', 'survival' > install.packages(c("affy", "gcrma", "limma")) Installing package(s) into ??~C:/Users/Julie Tseng-Crank/Documents/R /win-library/2.15??T (as ??~lib??T is unspecified) Warning message: packages ??~affy??T, ??~gcrma??T, ??~limma??T are not available (for R version 2.15.2) > -- Sent via the guest posting facility at bioconductor.org. _______________________________________________ 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