Hi, thank you for your replies. I am sending full output of my R session started few minutes ago. The problem is still remaining. Best, Vojtech.
R version 3.1.1 (2014-07-10) -- "Sock it to Me" Copyright (C) 2014 The R Foundation for Statistical Computing Platform: x86_64-unknown-linux-gnu (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 3.0 (BiocInstaller 1.15.5), ?biocLite for help > BiocInstaller::biocValid() [1] TRUE > BiocInstaller::biocLite() BioC_mirror: http://bioconductor.org Using Bioconductor version 3.0 (BiocInstaller 1.15.5), R version 3.1.1. > BiocInstaller::biocLite("affycoretools") BioC_mirror: http://bioconductor.org Using Bioconductor version 3.0 (BiocInstaller 1.15.5), R version 3.1.1. Installing package(s) 'affycoretools' trying URL ' http://bioconductor.org/packages/3.0/bioc/src/contrib/affycoretools_1.37.1.tar.gz ' Content type 'application/x-gzip' length 6909574 bytes (6.6 Mb) opened URL ================================================== downloaded 6.6 Mb * installing *source* package âaffycoretoolsâ ... ** R ** inst ** preparing package for lazy loading Error : object âsymbols2indicesâ is not exported by 'namespace:limma' ERROR: lazy loading failed for package âaffycoretoolsâ * removing â/usr/local/lib/R-3.1.1/library/affycoretoolsâ The downloaded source packages are in â/tmp/RtmpjACGfx/downloaded_packagesâ Updating HTML index of packages in '.Library' Making 'packages.html' ... done Warning message: In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) : installation of package âaffycoretoolsâ had non-zero exit status > sessionInfo() R version 3.1.1 (2014-07-10) 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=en_US.UTF-8 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_1.15.5 loaded via a namespace (and not attached): [1] tools_3.1.1 > 2014-07-25 17:28 GMT+02:00 Martin Morgan <mtmor...@fhcrc.org>: > On 07/25/2014 04:32 AM, Vojtech Kulvait wrote: > >> Hello, >> when I try to install affycoretools in devel i get an error: >> >> * installing *source* package ââ¬Ëaffycoretoolsââ¬â¢ ... >> >> ** R >> ** inst >> ** preparing package for lazy loading >> Error : object ââ¬Ësymbols2indicesââ¬â¢ is not exported by >> 'namespace:limma' >> ERROR: lazy loading failed for package ââ¬Ëaffycoretoolsââ¬â¢ >> >> >> I think I have up to date instalation of all packages. >> > > Hi Vojtech -- just to add to the advice, you can use > > BiocInstaller::biocValid() > > to check your installation, > > BiocInstaller::biocLite() > > to update your current packages. > > Martin > > > Vojtech. >> >> [[alternative HTML version deleted]] >> >> >> >> _______________________________________________ >> Bioc-devel@r-project.org mailing list >> https://stat.ethz.ch/mailman/listinfo/bioc-devel >> >> > > -- > 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 > [[alternative HTML version deleted]]
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