Re: [R] g++ verfsion
Hi, Li, Thanks for reply. It is strange that I used RBGL_1.6.0 successfully on the same linux system with R 2.3.1 before! After trying to install R 2.5.1, the RBGL_1.12.0 failed to be installed. Then, I uninstalled R. Delete the directory R/lib/. Installed R.2.3.1 again. And run getBioC1.8.5 for R 2.3.1 to download the three packages graph_1.10.6, RBGL_1.12.0 and Ruuid_1.10.0. But still failed as: .. boost::vec_adj_list_vertex_id_mapboost::propertyboost::vertex_color_t, boost::default_color_type, boost::no_property, size_t)' make: *** [interfaces.o] Error 1 chmod: failed to get attributes of `/usr/local/lib/R/library/RBGL/libs/*': No such file or directory ERROR: compilation failed for package 'RBGL' ** Removing '/usr/local/lib/R/library/RBGL' % Is it maybe because I use redhat9 with libxml2-2.5.4-1, which doesn't neet the not meets the requirment of RBGL_1.12.0 ? But I do not know how to updata them, even after downloading the file libxml2-2.5.4-3.rh9.i386.rpm, I failed to install it: [EMAIL PROTECTED] software]# rpm -i libxml2-2.5.4-3.rh9.i386.rpm file /usr/bin/xmlcatalog from install of libxml2-2.5.4-3.rh9 conflicts with file from package libxml2-2.5.4-1 file /usr/bin/xmllint from install of libxml2-2.5.4-3.rh9 conflicts with file from package libxml2-2.5.4-1 file /usr/lib/libxml2.so.2.5.4 from install of libxml2-2.5.4-3.rh9 conflicts with file from package libxml2-2.5.4-1 file /usr/share/man/man1/xmlcatalog.1.gz from install of libxml2-2.5.4-3.rh9 conflicts with file from package libxml2-2.5.4-1 file /usr/share/man/man1/xmllint.1.gz from install of libxml2-2.5.4-3.rh9 conflicts with file from package libxml2-2.5.4-1 file /usr/share/man/man3/libxml.3.gz from install of libxml2-2.5.4-3.rh9 conflicts with file from package libxml2-2.5.4-1 % FOr redhat9, Is it possible to updat gcc? Thanks, Xinan [EMAIL PROTECTED] wrote: This gcc is VERY old, we saw some problems in template handling with different version of g++. I would suggest to try a newer version of g++ and see what happens. Li and, [EMAIL PROTECTED] getBioC2.5-R2.5.1]# g++ --version g++ (GCC) 3.2.2 20030222 (Red Hat Linux 3.2.2-5) Copyright (C) 2002 Free Software Foundation, Inc. tks, xinan __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] install error for RBGL_1.12.0 on linux
Dear all, I meet error when installing the newest Bioconductor packages 2.0 for R 2.5.1. the enviroments are as bellow: sessionInfo() R version 2.5.1 (2007-06-27) i686-pc-linux-gnu locale: LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=en_US.UTF-8;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods [7] base The error messages are partly as: . boost::vec_adj_list_vertex_id_mapboost::propertyboost::vertex_color_t, boost::default_color_type, boost::no_property, size_t)' make: *** [interfaces.o] Error 1 chmod: failed to get attributes of `/usr/local/lib/R/library/RBGL/libs/*': No such file or directory ERROR: compilation failed for package 'RBGL' but, there exists such directory /usr/local/lib/R/library/RBGL/libs/ in my computer: [EMAIL PROTECTED] getBioC2.5-R2.5.1]# ls -al /usr/local/lib/R/library/RBGL/libs/ total 17364 drwxr-xr-x2 root root 4096 Dec 23 2005 . drwxr-xr-x 17 root root 4096 Dec 23 2005 .. -rwxr-xr-x1 root root 17743886 Dec 23 2005 RBGL.so Please help me to fix it. THanks, xinan __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] install error for RBGL_1.12.0 on linux ---2
Hi, Li and all lists, More, I have searched the web, and found one solution as described in: https://stat.ethz.ch/pipermail/bioc-devel/2007-June/001168.html But, My condition is some how different: 1) my g++ version is: g++ (GCC) 3.2.2 20030222 (Red Hat Linux 3.2.2-5) 2) the SHLIB file is the same, but some difference in /usr/local/lib/R/etc/Makeconf: SHELL = /bin/sh SHLIB_CFLAGS = SHLIB_CXXFLAGS = SHLIB_CXXLD = g++ SHLIB_CXXLDFLAGS = -shared SHLIB_EXT = .so SHLIB_FCLD = g77 SHLIB_FCLDFLAGS = -shared SHLIB_FFLAGS = SHLIB_LD = gcc -std=gnu99 SHLIB_LDFLAGS = -shared SHLIB_LIBADD = SHLIB_LINK = $(SHLIB_LD) $(SHLIB_LDFLAGS) $(LDFLAGS) what should I do? thanks, xinan __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] question about hierclust {multiv}
my major is bioinformatics, and i'm trying to cluster ( agglomerate the closest pari of observations ) in R. i have already got my own similarities metric, but do not know how to clust it based on similarities instead of dissimilarities. since the help document of hierclust mentions the parameter sim, which seems good to me, but it doesn't appear in the code of hierclust() function again? and no sample about it. so could anybody please help me as author? thanks in advance xinan yang [EMAIL PROTECTED] __ [EMAIL PROTECTED] mailing list https://www.stat.math.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
