Greetings, I've just installed R-2.6.1 from the R for Mac OS X site http://cran.r-project.org/bin/macosx/ R-2.6.1.dmg
When I attempt to update bioconductor packages R crashes on attempting to install http://bioconductor.org/packages/2.1/bioc/bin/macosx/universal/contrib/2.6/oligo_1.2.2.tgz Is anyone else having this problem? Is this an issue with Mac OS X R, or with the oligo mac binary? Any opinions/advice would be appreciated. I can reproduce this running R.app (see output from R.app that I posted to Bioconductor at end of this email) and also running R from the command line in a Mac 'terminal' shell as follows: Dapple:~ stevenmckinney$ R R version 2.6.1 (2007-11-26) Copyright (C) 2007 The R Foundation for Statistical Computing ISBN 3-900051-07-0 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. [Previously saved workspace restored] Making links in per-session dir ... If '/usr/bin/open' is already running, it is *not* restarted, and you must switch to its window. Otherwise, be patient ... > sessionInfo() R version 2.6.1 (2007-11-26) powerpc-apple-darwin8.10.1 locale: C attached base packages: [1] stats graphics grDevices utils datasets methods base loaded via a namespace (and not attached): [1] rcompgen_0.1-17 > source("http://bioconductor.org/biocLite.R";) > update.packages(repos=biocinstallRepos(), ask=FALSE) trying URL 'http://bioconductor.org/packages/2.1/bioc/bin/macosx/universal/contrib/2.6/cellHTS2_2.2.3.tgz' Content type 'application/x-gzip' length 4448886 bytes (4.2 Mb) opened URL ================================================== downloaded 4.2 Mb trying URL 'http://bioconductor.org/packages/2.1/bioc/bin/macosx/universal/contrib/2.6/oligo_1.2.2.tgz' Content type 'application/x-gzip' length 532702 bytes (520 Kb) opened URL ================================================== downloaded 520 Kb *** caught bus error *** address 0x18, cause 'invalid alignment' Traceback: 1: unlink(instPath, recursive = TRUE) 2: unpackPkg(foundpkgs[okp, 2], foundpkgs[okp, 1], lib, installWithVers) 3: .install.macbinary(pkgs = pkgs, lib = lib, contriburl = contriburl, method = method, available = available, destdir = destdir, installWithVers = installWithVers, dependencies = dependencies) 4: install.packages(update[instlib == l, "Package"], l, contriburl = contriburl, method = method, available = available, ..., type = type) 5: update.packages(repos = biocinstallRepos(), ask = FALSE) Possible actions: 1: abort (with core dump, if enabled) 2: normal R exit 3: exit R without saving workspace 4: exit R saving workspace Selection: -----Original Message----- From: Steven McKinney Sent: Tue 11/27/2007 12:34 PM To: [EMAIL PROTECTED] Subject: update.packages() for bioconductor packages generates bus error in R.app for R-2.6.1 on Mac OS X Greetings, I just installed the latest Mac upgrade version of R R-2.6.1 When I attempt to update bioconductor packages, R catches a bus to crashville. I'm using the recommended approach from http://www.bioconductor.org/docs/install-howto.html i.e. source("http://bioconductor.org/biocLite.R";) update.packages(repos=biocinstallRepos(), ask=FALSE) Session info and error report are below. I'm not seeing this issue in R news groups yet. Anyone else having this problem? Steve McKinney Mac info: System Version: Mac OS X 10.4.11 (8S165) Kernel Version: Darwin 8.11.0 Boot Volume: Macintosh HD Machine Name: Power Mac G5 Quad Machine Model: PowerMac11,2 CPU Type: PowerPC G5 (1.1) Number Of CPUs: 4 CPU Speed: 2.5 GHz L2 Cache (per CPU): 1 MB Memory: 16 GB Bus Speed: 1.25 GHz R info: R version 2.6.1 (2007-11-26) Copyright (C) 2007 The R Foundation for Statistical Computing ISBN 3-900051-07-0 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. [Workspace restored from /Users/stevenmckinney/.RData] > sessionInfo() R version 2.6.1 (2007-11-26) powerpc-apple-darwin8.10.1 locale: en_CA.UTF-8/en_CA.UTF-8/en_CA.UTF-8/C/en_CA.UTF-8/en_CA.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base > help.start() Making links in per-session dir ... If '/usr/bin/open' is already running, it is *not* restarted, and you must switch to its window. Otherwise, be patient ... > source("http://bioconductor.org/biocLite.R";) > update.packages(repos=biocinstallRepos(), ask=FALSE) trying URL 'http://bioconductor.org/packages/2.1/bioc/bin/macosx/universal/contrib/2.6/annaffy_1.10.1.tgz' Content type 'application/x-gzip' length 277396 bytes (270 Kb) opened URL ================================================== downloaded 270 Kb trying URL 'http://bioconductor.org/packages/2.1/bioc/bin/macosx/universal/contrib/2.6/biomaRt_1.12.2.tgz' Content type 'application/x-gzip' length 398253 bytes (388 Kb) opened URL ================================================== downloaded 388 Kb trying URL 'http://bioconductor.org/packages/2.1/bioc/bin/macosx/universal/contrib/2.6/cellHTS2_2.2.3.tgz' Content type 'application/x-gzip' length 4448886 bytes (4.2 Mb) opened URL ================================================== downloaded 4.2 Mb trying URL 'http://bioconductor.org/packages/2.1/bioc/bin/macosx/universal/contrib/2.6/oligo_1.2.2.tgz' Content type 'application/x-gzip' length 532702 bytes (520 Kb) opened URL ================================================== downloaded 520 Kb *** caught bus error *** address 0x20, cause 'invalid alignment' Traceback: 1: unlink(instPath, recursive = TRUE) 2: unpackPkg(foundpkgs[okp, 2], foundpkgs[okp, 1], lib, installWithVers) 3: .install.macbinary(pkgs = pkgs, lib = lib, contriburl = contriburl, method = method, available = available, destdir = destdir, installWithVers = installWithVers, dependencies = dependencies) 4: install.packages(update[instlib == l, "Package"], l, contriburl = contriburl, method = method, available = available, ..., type = type) 5: update.packages(repos = biocinstallRepos(), ask = FALSE) Possible actions: 1: abort (with core dump, if enabled) 2: normal R exit 3: exit R without saving workspace 4: exit R saving workspace Selection: _______________________________________________ R-SIG-Mac mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/r-sig-mac
