search for: mkimpel

...of my system. I did download and install the latest curl 7.18.1 on top of the other one, put /usr/local/ to the start of my PATH, reinstalled RCurl, and still the same erro message comes up. So, what does it mean that the output of nm is different on our systems and is it important? Thanks, Mark mkimpel-m90 ~/bin/curl-7.18.1: nm /home/mkimpel/R_HOME/site-library-2.7.0/RCurl/libs/RCurl.so | grep base64_encode U Curl_base64_encode 0000000000003910 T R_base64_encode mkimpel-m90 ~/bin/curl-7.18.1: nm /home/mkimpel/R_HOME/site-library-2.7.0/RCurl/libs/RCurl.so | grep Curl_base64_encode...

...of my system. I did download and install the latest curl 7.18.1 on top of the other one, put /usr/local/ to the start of my PATH, reinstalled RCurl, and still the same erro message comes up. So, what does it mean that the output of nm is different on our systems and is it important? Thanks, Mark mkimpel-m90 ~/bin/curl-7.18.1: nm /home/mkimpel/R_HOME/site-library-2.7.0/RCurl/libs/RCurl.so | grep base64_encode U Curl_base64_encode 0000000000003910 T R_base64_encode mkimpel-m90 ~/bin/curl-7.18.1: nm /home/mkimpel/R_HOME/site-library-2.7.0/RCurl/libs/RCurl.so | grep Curl_base64_encode...

...can provide, but before deluging the list with unnecessary output, I thought I would ask first what would be helpfu. Mark #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...

...;, package "Category" may be out of date 2: In .updateMethodsInTable(fdef, where, attach) : Methods list for generic "conditional" not found > require(RSPython) Loading required package: RSPython Error in dyn.load(file, ...) : unable to load shared library '/home/mkimpel/R_HOME/site-library/RSPython/libs/RSPython.so': /home/mkimpel/R_HOME/site-library/RSPython/libs/RSPython.so: undefined symbol: Rf_initEmbeddedR > sessionInfo() R version 2.6.0 Under development (unstable) (2007-08-01 r42387) i686-pc-linux-gnu locale: LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;L...

...ing mpi.h presence... no checking for mpi.h... no Try to find libmpi.so or libmpich.a checking for main in -lmpi... yes checking for openpty in -lutil... yes checking for main in -lpthread... yes configure: creating ./config.status config.status: creating src/Makevars ** libs gcc -std=gnu99 -I/home/mkimpel/R_HOME/R-patched/R-build/lib64/R/include -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -...

...HOME/R-devel/library ~/RCurl_0.8-0.tar.gz I received no errors during this install 3. when I go back to R and require(RCurl), I get > require(RCurl) Loading required package: RCurl Error in dyn.load(x, as.logical(local), as.logical(now)) : unable to load shared library '/N/u/mkimpel/BigRed/R_HOME/R-devel/library/RCurl/libs/RCurl.so': libcurl.so.4: cannot open shared object file: No such file or directory ?1? FALSE Outside of R I get mkimpel?BigRed:?/R_HOME/R-devel/library/RCurl/libs> ls RCurl.so I can cat into RCurl and I have even done chmod a+x RCurl.so in case...

...HOME/R-devel/library ~/RCurl_0.8-0.tar.gz I received no errors during this install 3. when I go back to R and require(RCurl), I get > require(RCurl) Loading required package: RCurl Error in dyn.load(x, as.logical(local), as.logical(now)) : unable to load shared library '/N/u/mkimpel/BigRed/R_HOME/R-devel/library/RCurl/libs/RCurl.so': libcurl.so.4: cannot open shared object file: No such file or directory ?1? FALSE Outside of R I get mkimpel?BigRed:?/R_HOME/R-devel/library/RCurl/libs> ls RCurl.so I can cat into RCurl and I have even done chmod a+x RCurl.so in case...

...ions will break. Finally, does anyone know where to find the development version tarballs of packages (probably a better ? for R-devel but I"m trying to avoid multiple postings). Thanks, Mark * Installing *source* package 'RBGL' ... untarring boost include tree... ** libs g++ -I/home/mkimpel/R_HOME/R-devel/R-build/lib64/R/include -I/usr/local/include -IboostIncl -fpic -g -O2 -c bbc.cpp -o bbc.o In file included from /usr/include/c++/4.3/ext/hash_set:64, from boostIncl/boost/graph/adjacency_list.hpp:22, from RBGL.hpp:26, from bbc.cp...

...ng whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed checking how to run the C preprocessor... gcc -E checking for sed... /bin/sed checking for xml2-config... no Cannot find xml2-config ERROR: configuration failed for package 'XML' ** Removing '/home/mkimpel/R_HOME/site-library-2.8.0/XML' ------------------------------------------------------------ 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...

...r in new("dgCMatrix") : trying to generate an object from a virtual class ("dgCMatrix") Calls: <Anonymous> ... eval.parent -> eval -> eval -> eval -> eval -> new -> .Call Execution halted ERROR: installing package indices failed ** Removing '/home/mkimpel/R_HOME/site-library/Matrix' ** Restoring previous '/home/mkimpel/R_HOME/site-library/Matrix' The downloaded packages are in /tmp/RtmpJviXfF/downloaded_packages Warning message: In install.packages("Matrix") : installation of package 'Matrix' had non-zero e...

...es contain? Mark ------------------------------------------------------------ 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 Home Skype: mkimpel "The real problem is not whether machines think but whether men do." -- B. F. Skinner ****************************************************************** [[alternative HTML version deleted]]

...ing) } new.vec } ------------------------------------------------------------ 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 Home Skype: mkimpel ****************************************************************** [[alternative HTML version deleted]]

I have identical R.profiles and R_HOME directories set up on both my local machine and a remote linux cluster. To keep my libraries and R install separate, I use a site-library on both machines. The first line of my .Rprofile is: '.libPaths(new= "~/R_HOME/site-library") #tell R where site-library is' Until R-2.6.0 this was working fine on both machines, but since I have been

...C cluster) started about 3 weeks ago and is present whether I used R-devel or R-2.6.0 or R-2.5.1. Also, of course I manually remove the 00LOCK folder after each failed attempt. Below is my error output, my .Rprofile, and sessionInfo(). Thanks, Mark ERROR: failed to lock directory '/N/hd03/mkimpel/BigRed/R_HOME/site-library' for modifying Try removing '/N/hd03/mkimpel/BigRed/R_HOME/site-library/00LOCK' > sessionInfo() R version 2.7.0 Under development (unstable) (2007-10-07 r43113) powerpc64-unknown-linux-gnu locale: LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_...

...ns? I'd be happy to share more of my R and C code if that is helpful, but I wanted to avoid a very long post at this point. Thanks, Mark > dyn.load(x = c.code, local = TRUE, now = TRUE) Error in dyn.load(x = c.code, local = TRUE, now = TRUE) : unable to load shared library '/N/u/mkimpel/BigRed/my_C/R.shared.so/cocite.mat.true.parallel.so': /N/u/mkimpel/BigRed/my_C/R.shared.so/cocite.mat.true.parallel.so: undefined symbol: ompi_mpi_comm_world > sessionInfo() R version 2.7.0 Under development (unstable) (2008-01-05 r43880) powerpc64-unknown-linux-gnu locale: LC_CTYPE=e...

...lt;- 5.5 res.lst ------------------------------------------------------------ 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 Home Skype: mkimpel ****************************************************************** [[alternative HTML version deleted]]

...e answer. Nevertheless, I'd like to make my usage decisions on something rather than anedotal claims. So, does anyone know of a good benchmarking script or would be willing to contribute one? And here are the settings we used to compile R with Intel 10.1 compilers: ../configure --prefix=/N/u/mkimpel/R_HOME/R-patched/R-build \ --with-system-zlib=/usr/lib64 --with-system-bzlib=/usr/lib64 \ --with-mpi=/N/soft/linux-rhel4-x86_64/openmpi/1.2.5/intel-64 --with-tcltk \ --with-tcl-config=/N/soft/linux-rhel4-x86_64/tcl8.4.16/lib64/tclConfig.sh \ --with-tk-config=/N/soft/linux-rhel4-x86_64/tk8.4.16/lib6...

...viola, successful install. I immediately exited out of R-2.7.1 and started R-2.9.1 as root and compilation fails. The file The output is voluminous, but is included below. I had originally thought that my problem had to do with setting environmental variables, but now it seems not. Thanks, Mark mkimpel-debian-xps /usr/lib/jvm/java-6-sun/include: su root Password: mkimpel-debian-xps:/usr/lib/jvm/java-6-sun/include# /home/mkimpel/R_HOME/R-2.9.1/R-build/bin/R WARNING: ignoring environment value of R_HOME R version 2.9.1 (2009-06-26) Copyright (C) 2009 The R Foundation for Statistical Computing ISBN...

...methods base ------------------------------------------------------------ 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 Home Skype: mkimpel "The real problem is not whether machines think but whether men do." -- B. F. Skinner ****************************************************************** [[alternative HTML version deleted]]

...the error seen at the end of the output below. Don't know what to make of this but thought I should report it. In general, when installing the latest version of R, should one use R-latest or R-patched? R-latest is stable, but one would assume that R-patched includes the latest bug fixes. Mark mkimpel-m90 ~/R_HOME/R-patched/R-build/bin: ./R R version 2.7.0 Patched (2008-05-02 r45591) Copyright (C) 2008 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 'lic...