[Rd] R 2.11.0 on RHEL5 / RODBC
I am compiling R 2.11.0 on a RHEL5.3 box using the following settings ./configure --with-readline=yes --enable-R-shlib=yes --with-x=yes --with-blas=-llibptf77blas -lpthread -llibatlas --prefix=/usr/local/R-2.11.0 JAVA_HOME=$JAVA_HOME CPPFLAGS=-I/usr/local/unixODBC-2.3.0/include I have compiled and installed unixODBC-2.3.0 (64-bit) in /usr/local and can connect to and query the database using isql. When I try to build RODBC, I get the following error: checking for sqlext.h... yes checking for library containing SQLTables... no configure: error: no ODBC driver manager found ERROR: configuration failed for package âRODBCâ * removing â/usr/local/R-2.11.0/lib64/R/library/RODBCâ The directory /usr/local/unixODBC-2.3.0/lib has the files libodbc.so and libodbc.la, and LD_LIBRARY_PATH has /usr/local/lib64:/usr/lib64:/usr/local/unixODBC-2.3.0/lib. Also, there is no other unixODBC version on the box. I would appreciate any help in this regard. Thanks. __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] R 2.11.0 on RHEL5
Thanks again for your note. I am now compiling using: --with-readline=yes --enable-R-shlib=yes --with-x=yes --with-blas=-llibptf77blas -lpthread -llibatlas --prefix=/usr/local/R-2.11.0 The above configuration is creating libRlapack.so as well. Do you specify --with-lapack as well? If so, what do you set that to? Section A.3.2 states -- Please do bear in mind that using --with-lapack is `definitely not recommended': it is provided only because it is necessary on some platforms. Thanks. Uwe Ligges lig...@statistik.tu-dortmund.de wrote: Why do you want shlib support, do you really need it? For the static case, A.3.1.1 ATLAS described the way to go. I have never before linked dynamically to ATLAS versions. ATL_dgemm is probably defined in one of the other libraries. I have not looked since I currently do not have any ATLAS left on my machines which I was more used to roughly 3 years ago. Uwe Ligges __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] R 2.11.0 on RHEL5
Thank you for your response. I did look in the suggested manual under A.3.1.5 Shared BLAS. Here are my steps: compiled R using --with-readline=yes --enable-R-shlib=yes --enable-BLAS-shlib=yes --with-x=yes --prefix=/usr/local/R-2.11.0 Compiled LAPACK first and then ATLAS using http://www.scipy.org/Installing_SciPy/Linux#head-89e1f6afaa3314d98a22c79b063cceee2cc6313c All the .so files have been copied to /usr/lib64 In /usr/local/R-2.11.0/lib64/R/lib, I renamed the .so files for blas and lapack and linked as libRblas.so - /usr/local/lib64/libf77blas.so libRlapack.so - /usr/local/lib64/liblapack.so R does startup OK but when I do the following: require(nlme) fm1 - nlme(height ~ SSasymp(age, Asym, R0, lrc), data = Loblolly, fixed = Asym + R0 + lrc ~ 1, random = Asym ~ 1, start = c(Asym = 103, R0 = -8.5, lrc = -3.3)) I get /usr/local/R-2.11.0/lib64/R/bin/exec/R: symbol lookup error: /usr/local/R-2.11.0/lib64/R/lib/libRblas.so: undefined symbol: ATL_dgemm This runs just fine without using the .so files which were built with R. Can you please help? Thanks. Uwe Ligges lig...@statistik.tu-dortmund.de wrote: This is explained in detail in the manual R Installation and Administration. Best, Uwe Ligges On 03.05.2010 06:02, Chuck White wrote: I have built lapack-3.2 and atlas3.8.3 for a RHEL5.3 VM. The following files have been created -- libatlas (.a .so), libcblas (.a .so), libf77blas (.a .so), liblapack (.a .so), libptcblas (.a .so), libptf77blas (.a .so) and libstatatlas.a. When building R 2.11.0, I would like to be able to specify --with-blas and --with-lapack (and not use the ones which come with R). What is the syntax for that? Which of these libraries should I specify? Thanks. __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] R 2.11.0 on RHEL5
I have built lapack-3.2 and atlas3.8.3 for a RHEL5.3 VM. The following files have been created -- libatlas (.a .so), libcblas (.a .so), libf77blas (.a .so), liblapack (.a .so), libptcblas (.a .so), libptf77blas (.a .so) and libstatatlas.a. When building R 2.11.0, I would like to be able to specify --with-blas and --with-lapack (and not use the ones which come with R). What is the syntax for that? Which of these libraries should I specify? Thanks. __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] R 2.11.0 on RHEL5
I have built lapack-3.2 and atlas3.8.3 for a RHEL5.3 VM. The following files have been created -- libatlas (.a .so), libcblas (.a .so), libf77blas (.a .so), liblapack (.a .so), libptcblas (.a .so), libptf77blas (.a .so) and libstatatlas.a. When building R 2.11.0, I would like to be able to specify --with-blas and --with-lapack (and not use the ones which come with R). What is the syntax for that? Which of these libraries should I specify? Thanks. __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] R292 and tcl/tk
BACKGROUND R2.9.2 built on power5 aix5.3 using gcc 4.2.4 (also installed: tcl and tk 8.5.7) Access from a Windows XP machine using Exceed v9.0, aixterm (DISPLAY etc. setup) export LDFLAGS=-L/usr/lib64 -L/opt/freeware/lib64 -L/opt/freeware/64/lib -L/usr/X11R6/lib -L/opt/freeware/lib export CPPFLAGS=-I/opt/freeware/include -I/usr/lpp/X11/include/X11 CONFIGURATION 1 (with tcl/tk) ../R-2.9.2/configure --enable-R-shlib --enable-BLAS-shlib --with-tcl-config=/opt/freeware/lib64/tclConfig.sh --with-tk-config=/opt/freeware/lib64/tkConfig.sh --prefix=/usr/local/R-2.9.2 config_292.log 21 update.packages() --- Please select a CRAN mirror for use in this session --- Loading Tcl/Tk interface ... *** caught segfault *** address 21188073e, cause 'memory not mapped' Traceback: 1: .C(tcltk_init, PACKAGE = tcltk) 2: fun(...) 3: doTryCatch(return(expr), name, parentenv, handler) ... 19: tryCatch(asNamespace(pkg), hasNoNamespaceError = function(e) NULL) 20: tcltk::tk_select.list 21: menu(m[, 1L], graphics, CRAN mirror) 22: chooseCRANmirror() 23: contrib.url(repos, type) 24: available.packages(contriburl = contriburl, method = method) 25: update.packages() CONFIGURATION 2 (without tcl/tk) ../R-2.9.2/configure --enable-R-shlib --enable-BLAS-shlib --with-tcltk=no --prefix=/usr/local/R-2.9.2 config_292.log 21 ; make make_292.log 21 update.packages() --- Please select a CRAN mirror for use in this session --- CRAN mirror 1: Argentina (Buenos Aires)2: Australia 3: Austria 4: Belarus 5: Belgium 6: Brazil (PR) QUESTION 1. Are there any known issues with tcl/tk? Should I be doing anything different in the configuration? 2. When I try a simple plot command in either configuration (eg. plot(sin, -pi, pi)), the plot window shows up immediately on my machine but the plot itself takes all of two minutes to draw. I am not sure if the two issues are related. I would appreciate any help with this. Thanks. __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] unable to compile RODBC (R 2.9.2, AIX)
I could compile RODBC on AIX 5.3/R-2.9.2. I set LDFLAGS to: export LDFLAGS=-L/usr/lib64 -L/opt/freeware/lib64 -L/usr/X11R6/lib Earlier, I had some other paths which had 32-bit libraries as well. Obviously, I re-compiled R and all the other libraries using this flag. Prof. Ripley and Marc, thanks for your response. Marc Schwartz marc_schwa...@me.com wrote: On Oct 31, 2009, at 1:13 PM, Chuck White wrote: Hello -- I am trying to compile (linker error, not compiler error) RODBC for R 2.9.2 on AIX 5.3 using gcc. I get the following error: __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] unable to compile mgcv
I have been able to compile mgcv 1.5-6 *successfully* on the AIX box with gcc. I replaced all the TRUE/FALSE in magic.c and gdi.c with mgcvTRUE/mgcvFALSE. Thanks to William Dunlap for his help. __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] unable to compile RODBC (R 2.9.2, AIX)
Hello -- I am trying to compile (linker error, not compiler error) RODBC for R 2.9.2 on AIX 5.3 using gcc. I get the following error: gcc -maix64 -pthread -std=gnu99 -shared -Wl,-brtl -Wl,-G -Wl,-bexpall -Wl,-bnoentry -lc -L/usr/lib -L/usr/X 11R6/lib -L/usr/local/lib -L/opt/freeware/lib -L/opt/freeware/lib64 -o RODBC.so RODBC.o -lodbc -lm -L/usr/l ocal/builddir/lib -lR ld: 0711-738 ERROR: Input file /usr/lib/libodbc.so: XCOFF32 object files are not allowed in 64-bit mode. collect2: ld returned 8 exit status gmake: *** [RODBC.so] Error 1 ERROR: compilation failed for package 'RODBC' I would appreciate any help I can get in this regard. Thanks. __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] unable to compile mgcv
Thanks for your response. In the past I have build R for RHEL and it was very simple. I did not have to do anything specific for certain libraries. I do see the .tgz file (actually it is a link to the original file which has version number too). Questions [1] do I need to unzip the tgz file, make changes, and zip it back again? Or would the makefile be able to handle the unzipped directory? [2] is there a way to just compile that library only? [3] what do I do to resume the compilation of the rest of the libraries. Re-running make would likely try to build the original version of mgcv again. Thanks -- I would appreciate any document/instructions you can point me to. William Dunlap wdun...@tibco.com wrote: -Original Message- From: Chuck White [mailto:chuckwhi...@charter.net] Sent: Wednesday, October 28, 2009 3:47 PM To: r-devel@r-project.org; William Dunlap Subject: RE: [Rd] unable to compile mgcv Thanks for your response. Can you please point me to the make file where I would make this change. Thanks. If you untar src/library/Recommended/mgcv.tgz (sp?) this file will be in mgcv/src. I'm not sure of the best way to take care of it on AIX. It may be possible to #undef TRUE in include/R.h. The AIX system includes define it in many places, the most prominent of which is in types.h. If you cannot generally #undef TRUE in a global R include file then you will have to edit the C or h files in mgcv. __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] unable to compile mgcv
Hello -- I am trying to compile R-2.9.2 on IBM Power5 machine with AIX 5.3. I
have posted three previous posts. Over time I have made significant progress
towards getting a successful build. I am now getting the following error:
==
begin installing recommended package mgcv
* Installing *source* package 'mgcv' ...
** libs
gmake[2]: Entering directory `/tmp/RtmpOtsRnd/R.INSTALL2781446b/mgcv/src'
gcc -maix64 -pthread -std=gnu99 -I/usr/local/builddir/include
-I/usr/local/include -O2 -g -mcpu=power5 -c gcv.c -o gcv.o
gcc -maix64 -pthread -std=gnu99 -I/usr/local/builddir/include
-I/usr/local/include -O2 -g -mcpu=power5 -c gdi.c -o gdi.o
gdi.c: In function 'qr_ldet_inv':
gdi.c:294: error: expected identifier or '(' before numeric constant
gdi.c:308: error: lvalue required as unary '' operand
gdi.c:308: error: lvalue required as unary '' operand
gdi.c:316: error: 'j' undeclared (first use in this function)
gdi.c:316: error: (Each undeclared identifier is reported only once
gdi.c:316: error: for each function it appears in.)
gdi.c: In function 'get_detS2a':
gdi.c:617: error: expected identifier or '(' before numeric constant
gdi.c:620: error: 'Mf' undeclared (first use in this function)
gdi.c:636: error: 'max_col' undeclared (first use in this function)
.
ERROR: compilation failed for package 'mgcv'
* Removing '/usr/local/builddir/library/mgcv'
gmake[1]: *** [mgcv.ts] Error 1
gmake[1]: Leaving directory `/usr/local/builddir/src/library/Recommended'
gmake: *** [recommended-packages] Error 2
make: The error code from the last command is 2.
Stop.
==
Initially I had mgcv 1.5-5 and I downloaded mgcv 1.5-6 and tried again. I get
the same error.
I would really appreciate any help with this.
Thanks.
__
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Re: [Rd] unable to compile mgcv
Thanks for your response. Can you please point me to the make file where I would make this change. Thanks. William Dunlap wdun...@tibco.com wrote: The first offending line in gdc.c is 294 int *pivot,i,TRUE=1,j; and TRUE must be #defined in some AIX include file. Change it to true or add #undef TRUE prior to its use and it may compile. Bill Dunlap Spotfire, TIBCO Software wdunlap tibco.com __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] R292 on AIX53 using gcc
Hello -- I haven't received any respones to my previous post on compiling R2.9.2 for AIX 5.3. Meanwhile, I have looked at the following post by Ei-ji Nakama [http://tolstoy.newcastle.edu.au/R/e4/devel/08/07/2171.html] and it appears that all the changes suggested in the patch are already in R2.9.2 Makefiles. I have also looked at the documentation under R-Forge/AIX page [http://r-forge.r-project.org/projects/aix/]. That does not seem to help either. Bottomline, I am trying to compile R2.9.2 on a AIX 5.3 Power5 box with gcc 4.3 and get the following error: gcc -maix64 -pthread -std=gnu99 -Wl,-brtl -Wl,-bexpall -Wl,-bpT:0x1 -Wl,-bpD:0x11000 -lc -L/usr/local/lib -o R.bin Rmain.o -L../../lib -lR -lRblas ld: 0711-224 WARNING: Duplicate symbol: .memcpy, memcpy, .bcopy, bcopy, .memmove, .memset, memset, .fres, fres ld: 0711-345 Use the -bloadmap or -bnoquiet option to obtain more information. ld: 0711-317 ERROR: Undefined symbol: R_running_as_main_program Command used: ./configure --enable-R-shlib --enable-BLAS-shlib --without-iconv ; make make.log 21 I would really appreciate any help. Thanks in advance. __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] R292 on AIX53 using gcc
Hello -- after my previous post, I tried to compile R 2.9.2 using xlc. The config.site changes are: == OBJECT_MODE=64 AR=ar -X64 R_SHELL=/usr/bin/bash CONFIG_SHELL=/usr/bin/bash CC=xlc_r -q64 CFLAGS=-O -qstrict CPPFLAGS=-I/usr/include -I/usr/local/include -I/opt/freeware/include -I/usr/X11R6/include CXX=xlC_r -q64 CXXFLAGS=-O -qstrict LDFLAGS=-L/opt/freeware/lib64 -L/opt/freeware/64/lib -L/opt/freeware/lib -L/usr/local/lib -L/usr/lib F77=xlf_r -q64 FFLAGS=-O -qstrict FC=xlf95 -q64 FCFLAGS=-O -qstrict MAKE=/opt/freeware/bin/make == Error -- mkdir ../../../../library/grDevices/libs Warning in solve.default(rgb) : unable to load shared library '/usr/local/R-2.9.2/modules//lapack.so': rtld: 0712-001 Symbol idamax was referenced from module /usr/local/R-2.9.2/lib/libRlapack.so(), but a runtime definition of the symbol was not found. rtld: 0712-001 Symbol dger was referenced from module /usr/local/R-2.9.2/lib/libRlapack.so(), but a runtime definition of the symbol was not found. .. Error in solve.default(rgb) : lapack routines cannot be loaded Error: unable to load R code in package 'grDevices' Execution halted make: The error code from the last command is 1. Thanks in advance. I would really appreciate any help. __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] R292 on AIX53 using gcc
I apologize for cross posting this message in the R-help group as well. Having posted it there a couple of hours ago, I felt this may be a more appropriate forum for a question of this type. Hello -- I am unable to build R 2.9.2 on IBM PowerPC AIX5.3. I would appreciate any help in this matter. ===details== Machine: IBM PowerPC_POWER5 / 4 proc, 1499 MHz 64-bit / AIX 5.3.0.0 Building R 2.9.2 using gcc/g++/gfortran 4.2.4 Config.site changes are: OBJECT_MODE=64 CONFIG_SHELL=/usr/bin/bash LIBICONV=/opt/freeware/lib AR=ar -X64 CC=gcc -maix64 F77=gfortran -maix64 LDFLAGS=-L/opt/freeware/lib64 -L/opt/freeware/64/lib -L/opt/freeware/lib -L/usr/local/lib CXX=g++ -maix64 FC=gfortran -maix64 R_BROWSER=/opt/freeware/bin/firefox MAKE=/opt/freeware/bin/make Command for configure: ./configure --enable-R-shlib Looks like I have to set OBJECT_MODE explicitly on the command line. So, I enter: set OBJECT_MODE=64. It does not seem to help that I have it in config.site. make stops with the following error: gcc -maix64 -std=gnu99 -Wl,-brtl -Wl,-bexpall -Wl,-bpT:0x1 -Wl,-bpD:0x11000 -lc -L/opt/freeware/lib64 -L/opt/freeware/64/lib -L/opt/freeware/lib -L/usr/local/lib -o R.bin Rmain.o -L../../lib -lR ld: 0711-224 WARNING: Duplicate symbol: .memcpy ...duplicate symbol warning for: memcpy,bcopy,memset,fres ld: 0711-317 ERROR: Undefined symbol: R_running_as_main_program collect2: ld returned 8 exit status make: The error code from the last command is 1. __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
