Below is my .Rprofile and the my.update.packages function that it calls (which is in the right place and has not caused problems before). As I was writing this, R just finished compiling using gcc-4.3. R once again crashes as it did with the 4.4 compile. Just for completeness, immediately below is my build script, the followed by .Rprofile. Thanks guys!
#############################################################3 # build R-devel cd ~/R_HOME wget ftp://ftp.stat.math.ethz.ch/Software/R/R-devel.tar.gz tar -xzf R-devel.tar.gz cd ~/R_HOME/R-devel mkdir R-build cd R-build ../configure --prefix=/home/mkimpel/R_HOME/R-devel/R-build CC=/usr/bin/gcc-4.3 CXX=/usr/bin/g++-4.3 F77=/usr/bin/gfortran-4.3 make all make install # end build script ##################################### # .Rprofile #tell R where site-library is ver <- getRversion() options(editor="emacs") if (ver == "2.9.1"){.libPaths(new= "~/R_HOME/site-library-2.9.0")} if (ver == "2.10.0"){.libPaths(new= "~/R_HOME/site-library-2.10.0")} options(htmlhelp=TRUE) options(browser="firefox newTab") #update packages source("~/R.functions/General_Functions/my.update.packages.func.R") if (interactive()) { #needed to keep R from looping as it calls R for install scripts my.update.packages.func(force = FALSE) ################################################## # source function loader function and execute it source("~/R.functions/General_Functions/UtilityFunctions/load.R.func.files.R") get.and.load.functions.func() ###################################################################### # set error recovery option options(error=utils::recover) } ################################################# # end .Rprofile ################################################ # ~/R.functions/General_Functions/UtilityFunctions/load.R.func.files.R my.update.packages.func <- function(update.interveral.days = 7, force = TRUE){ require(utils) old.wd <- getwd() setwd("~/") last.update.error <- try(load(file = ".Rupdate.date"), TRUE) if(inherits(last.update.error, "try-error")) {last.update <- as.POSIXct("2007-01-01")} else { load(file = ".Rupdate.date")} #if .Rupdate.date does not exist or can't load, update if(force) {last.update <- as.POSIXct("2007-01-01")} #allow to force updates current.time <- Sys.time() time.diff <- current.time - last.update if( ( (units(time.diff) == "days") && (time.diff[[1]][1] >= update.interveral.days) ) || inherits(last.update.error, "try-error") ){ #then update ############################################################################ ##From Jim McDonald: I just have the above in my .Rprofile file, so biocLite() is always there for me. source("http://www.bioconductor.org/biocLite.R";) biocLite("Biobase") library("Biobase") repos <- biocReposList() update.packages(repos=repos, ask=FALSE)################################################### update.packages(repos="http://www.omegahat.org/R";, ask = FALSE) last.update <- current.time local(save(last.update, file = ".Rupdate.date")) print("packages updated") } else {print("packages do not need updated")} setwd(old.wd) } ############################################### # End file ######################################## Mark W. Kimpel MD ** Neuroinformatics ** Dept. of Psychiatry Indiana University School of Medicine 15032 Hunter Court, Westfield, IN 46074 (317) 490-5129 Work, & Mobile & VoiceMail (317) 399-1219 Skype No Voicemail please On Wed, Sep 16, 2009 at 8:10 PM, Simon Urbanek <simon.urba...@r-project.org>wrote: > > On Sep 16, 2009, at 7:48 PM, Mark Kimpel wrote: > > Peter, >> >> I have not yet tried Simon's suggestion of using gcc 4.3 (just got back >> from >> a meeting), but running your commands produces the output below. As you >> can >> see, R --vanilla works, but just plain "R" doesn't. >> > > Please send us you .Rprofile because that's likely what's causing the crash > ... (reading a profile causes the crash, so unless you have a custom site > profile the .Rprofile is the one to blame). > > Thanks, > S > > > > > See the results of gdb >> far below. >> >> I do not have a saved workspace in my R_HOME or any of its subdirectories. >> >> Will report back on what I get with gcc 4.3 just as soon as I read the >> R-admin manual and figure out how to get configure configured.... >> >> Mark >> >> >> mkimpel-XPS ~/sshfs: R --vanilla >> >> R version 2.10.0 Under development (unstable) (2009-09-15 r49711) >> Copyright (C) 2009 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. >> >> q() >>> >> mkimpel-XPS ~/sshfs: R >> >> R version 2.10.0 Under development (unstable) (2009-09-15 r49711) >> Copyright (C) 2009 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. >> >> >> *** caught segfault *** >> address (nil), cause 'memory not mapped' >> >> 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: 4 >> mkimpel-XPS ~/sshfs: R -d gdb >> GNU gdb (GDB) 6.8.50.20090628-cvs-debian >> Copyright (C) 2009 Free Software Foundation, Inc. >> License GPLv3+: GNU GPL version 3 or later < >> http://gnu.org/licenses/gpl.html >> >>> >>> This is free software: you are free to change and redistribute it. >> There is NO WARRANTY, to the extent permitted by law. Type "show copying" >> and "show warranty" for details. >> This GDB was configured as "x86_64-linux-gnu". >> For bug reporting instructions, please see: >> <http://www.gnu.org/software/gdb/bugs/>... >> (gdb) run >> Starting program: /home/mkimpel/R_HOME/R-devel/R-build/lib64/R/bin/exec/R >> >> R version 2.10.0 Under development (unstable) (2009-09-15 r49711) >> Copyright (C) 2009 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. >> >> >> Program received signal SIGSEGV, Segmentation fault. >> Rf_setAttrib (vec=0x12e3d68, name=0x94d450, val=0x0) at >> ../../../src/main/attrib.c:226 >> 226 if (NAMED(val)) val = duplicate(val); >> (gdb) bt >> #0 Rf_setAttrib (vec=0x12e3d68, name=0x94d450, val=0x0) at >> ../../../src/main/attrib.c:226 >> #1 0x000000000056264f in xxexprlist1 () at gram.y:574 >> #2 Rf_yyparse () at gram.y:337 >> #3 0x0000000000563469 in R_Parse1 (status=0x94d450) at gram.y:1126 >> #4 0x0000000000563cfb in R_Parse1File (fp=0x1200920, gencode=1, >> status=0x7fffffffcd94, first=<value optimized out>) at gram.y:1164 >> #5 0x0000000000416cb2 in R_ReplFile (fp=0x1200920, rho=0x973338, >> savestack=0, browselevel=<value optimized out>) at >> ../../../src/main/main.c:87 >> #6 0x0000000000416e08 in R_LoadProfile (fparg=<value optimized out>, >> env=0x973338) at ../../../src/main/main.c:651 >> #7 0x00000000004172c2 in setup_Rmainloop () at >> ../../../src/main/main.c:875 >> #8 0x00000000004185c9 in Rf_mainloop () at ../../../src/main/main.c:967 >> #9 0x0000000000415c38 in main (ac=<value optimized out>, av=<value >> optimized out>) at ../../../src/main/Rmain.c:33 >> #10 0x00007ffff6ed05c6 in __libc_start_main () from /lib/libc.so.6 >> #11 0x0000000000415b29 in _start () at ../sysdeps/x86_64/elf/start.S:113 >> (gdb) >> >> Mark W. Kimpel MD ** Neuroinformatics ** Dept. of Psychiatry >> Indiana University School of Medicine >> >> 15032 Hunter Court, Westfield, IN 46074 >> >> (317) 490-5129 Work, & Mobile & VoiceMail >> (317) 399-1219 Skype No Voicemail please >> >> >> On Wed, Sep 16, 2009 at 4:45 PM, Peter Dalgaard <p.dalga...@biostat.ku.dk >> >wrote: >> >> Mark Kimpel wrote: >>> >>> I just downloaded R-devel and when loaded it immediately segfaults. I'm >>>> not >>>> sure how much or what sort of diagnostic info and can provide, but below >>>> is >>>> my build script, my console output, and the output of uname -r. I am >>>> currently dependent on the development version of a package, so I'd like >>>> to >>>> get R-devel up and running if possible. I am sure there is more info I >>>> can >>>> provide, but before deluging the list with unnecessary output, I thought >>>> I >>>> would ask first what would be helpfu. Mark >>>> >>>> >>> Not happening for me with 49727 (SUSE 64bit). >>> >>> Do you have a saved workspace in that dir by any chance? >>> >>> Could you try >>> >>> R --vanilla >>> >>> and >>> >>> R -d gdb >>> followed by "run" and "bt" on the segfault >>> >>> #Make R >>> >>>> cd ~/R_HOME >>>> wget ftp://ftp.stat.math.ethz.ch/Software/R/R-devel.tar.gz >>>> tar -xzf R-devel.tar.gz >>>> cd ~/R_HOME/R-devel >>>> mkdir R-build >>>> cd R-build >>>> ../configure --prefix=/home/mkimpel/R_HOME/R-devel/R-build >>>> make all >>>> make install >>>> >>>> #####################################33 >>>> # console output >>>> mkimpel-XPS ~/R_HOME/R-devel/R-build/bin: ./R >>>> >>>> R version 2.10.0 Under development (unstable) (2009-09-15 r49711) >>>> Copyright (C) 2009 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. >>>> >>>> >>>> *** caught segfault *** >>>> address (nil), cause 'memory not mapped' >>>> >>>> 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: 2 >>>> Save workspace image? [y/n/c]: n >>>> >>>> ###################################### >>>> # kernel version >>>> mkimpel-XPS ~/R_HOME/R-devel/R-build/bin: uname -r >>>> 2.6.30-1-amd64 >>>> mkimpel-XPS ~/R_HOME/R-devel/R-build/bin: >>>> >>>> >>>> Mark W. Kimpel MD ** Neuroinformatics ** Dept. of Psychiatry >>>> Indiana University School of Medicine >>>> >>>> 15032 Hunter Court, Westfield, IN 46074 >>>> >>>> (317) 490-5129 Work, & Mobile & VoiceMail >>>> (317) 399-1219 Skype No Voicemail please >>>> >>>> [[alternative HTML version deleted]] >>>> >>>> ______________________________________________ >>>> R-devel@r-project.org mailing list >>>> https://stat.ethz.ch/mailman/listinfo/r-devel >>>> >>>> >>> >>> -- >>> O__ ---- Peter Dalgaard Øster Farimagsgade 5, Entr.B >>> c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K >>> (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 >>> ~~~~~~~~~~ - (p.dalga...@biostat.ku.dk) FAX: (+45) 35327907 >>> >>> >> [[alternative HTML version deleted]] >> >> ______________________________________________ >> R-devel@r-project.org mailing list >> https://stat.ethz.ch/mailman/listinfo/r-devel >> > > [[alternative HTML version deleted]]
______________________________________________ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
