[R] problems installing R on Linux
Rebecca Tagett
tagett at ipsogen.com
Fri Feb 9 12:14:07 CET 2007
Prof Brian Ripley <ripley <at> stats.ox.ac.uk> writes:
>
> We don't know what 'Linux' is here. What Linux distribution, what are
> your C and Fortran compilers (in detail, e.g. from gcc --version and g77
> --version)?
>
> We need to see the tail of tests/Examples/base-Ex.Rout.fail to know what
> went wrong.
>
> If you can supply those pieces of information we can begin to help.
> (But zlib is a red herring: at most it affects the png() device.)
>
> On Wed, 7 Feb 2007, Rebecca wrote:
>
> > Hi everyone,
> >
> > I am having installation problems, but this is how it all started:
> > I had some errors running the bioconductor package affyPLM that uses
> > LAPACK/Blas
> >
> > > Pset <- fitPLM(Data)
> > Background correcting PM
> > Normalizing PM
> > Fitting models
> > /usr/local/lib/R/bin/exec/R: relocation error:
> > /usr/local/lib/R/lib/libRlapack.so: undefined symbol: s_copy
> > # thrown out of R ....
> >
> > I was using R version 2.4.0, so I decided to upgrade to 2.4.1 (on
> > i686-pc-linux-gnu) and to try various configuration options : default,
> > '--with -lapack' and '--with-blas="lacml"', as described in "appendix A of
> > the Installation and Admin" manual.
> >
> > Everytime I configure and make, the message streams seem clean. But the
> > 'make check' is always a disaster (see below), and if I make install
> > regardless of the make check errors, I get the same "relocation error" from
> > fitPLM as above (of course the appropriate BioC packages were installed
> > too).
> >
> > I believe my problems are dealt with in Appendix A of the Installation and
> > Administration Guide, but I can't seem to resolve them. Indeed, I have
never
> > been able to use png() for graphics because of some unresolved issues
> > concerning access to the X11 graphics device, which I suspected had to do
> > with the libpng and zlib programs (also mentioned in Appendix A).
> >
> > Some of the postings that I have read on this forum seem to imply that
> > installation problems are sometimes due to old versions of zlib. I don't
> > understand this since the recent zlib (1.2.3) is in
> > "/usr/local/lib/R-2.4.1/src/extra/zlib". Appendix A says, referring to
zlib,
> > that "the versions in the R sources will be compiled in".
> > But just to be sure, I verified that my system's version is old :
> > rpm -q zlib
> > zlib-1.1.3-25.7
> > I downloaded and tried to install zlib-1.2.3 using tar, configure, make,
> > make test, and make install. But when I type "rpm -q zlib", I am still
> > informed that my version is "zlib-1.1.3-25.7". So, still hopeful, I thought
> > that I instead would use rpm to install zlib; I found an intermediate rpm
> > zlib version 1.2.1.2-1.2 and tried "rpm -Uhv zlib-1.2.1.2-1.2.src.rpm". No
> > diagnostics appear, but when I type "rpm -q zlib", my version is still
> > "zlib-1.1.3-25.7". I tried to uninstall the old zlib using "rpm -e zlib",
> > but rpm refuses, saying that there are too many dependencies...
> >
> > Does anyone have any suggestions?
> > Thanks!
> >
> >
> >
> > The 'make check' disaster :
> > make[1]: Entering directory `/usr/local/lib/R-2.4.1/tests'
> > make[2]: Entering directory `/usr/local/lib/R-2.4.1/tests'
> > make[3]: Entering directory `/usr/local/lib/R-2.4.1/tests/Examples'
> > make[4]: Entering directory `/usr/local/lib/R-2.4.1/tests/Examples'
> > make[4]: Leaving directory `/usr/local/lib/R-2.4.1/tests/Examples'
> > make[4]: Entering directory `/usr/local/lib/R-2.4.1/tests/Examples'
> > collecting examples for package 'base' ...
> > make[5]: Entering directory `/usr/local/lib/R-2.4.1/src/library'
> > >>> Building/Updating help pages for package 'base'
> > Formats: text html latex example
> > make[5]: Leaving directory `/usr/local/lib/R-2.4.1/src/library'
> > running code in 'base-Ex.R' ...make[4]: *** [base-Ex.Rout] Error 1
> > make[4]: Leaving directory `/usr/local/lib/R-2.4.1/tests/Examples'
> > make[3]: *** [test-Examples-Base] Error 2
> > make[3]: Leaving directory `/usr/local/lib/R-2.4.1/tests/Examples'
> > make[2]: *** [test-Examples] Error 2
> > make[2]: Leaving directory `/usr/local/lib/R-2.4.1/tests'
> > make[1]: *** [test-all-basics] Error 1
> > make[1]: Leaving directory `/usr/local/lib/R-2.4.1/tests'
> > make: *** [check] Error 2
> >
> >
> > I don't really *know* if the configure results are "clean". Here is a
subset
> > of the configure results (that may be suspect) :
> >
> > checking build system type... i686-pc-linux-gnu
> > checking host system type... i686-pc-linux-gnu
> > . . .
> > checking for cblas_cdotu_sub in vecLib framework... no
> > checking iconv.h usability... yes
> > checking iconv.h presence... yes
> > checking for iconv.h... yes
> > checking for iconv... yes
> > checking whether iconv() accepts "UTF-8", "latin1" and "UCS-*"...
> > yes
> > checking for iconvlist... no
> > . . .
> > checking for g77... g77
> > checking whether we are using the GNU Fortran 77 compiler... yes
> > checking whether g77 accepts -g... yes
> > checking for g++... g++
> > checking whether we are using the GNU C++ compiler... yes
> > checking whether g++ accepts -g... yes
> > checking how to run the C++ preprocessor... g++ -E
> > checking whether __attribute__((visibility())) is supported... no
> > checking whether gcc accepts -fvisibility... no
> > checking whether g77 accepts -fvisibility... no
> > . . .
> > checking if libtool supports shared libraries... yes
> > checking whether to build shared libraries... yes
> > checking whether to build static libraries... no
> > . . .
> > checking floatingpoint.h usability... no
> > checking floatingpoint.h presence... no
> > checking for floatingpoint.h... no
> > . . .
> > checking ieee754.h usability... yes
> > checking ieee754.h presence... yes
> > checking for ieee754.h... yes
> > checking ieeefp.h usability... no
> > checking ieeefp.h presence... no
> > checking for ieeefp.h... no
> > . . .
> > checking for dummy main to link with Fortran libraries... none
> > . . .
> > checking whether isfinite is declared... no
> > . . .
> > checking for mkdtemp... no
> > . . .
> > checking whether mkdtemp is declared... no
> > . . .
> > checking for special C compiler options needed for large files... no
> > checking for _FILE_OFFSET_BITS value needed for large files... 64
> > checking for _LARGE_FILES value needed for large files... no
> > checking for _LARGEFILE_SOURCE value needed for large files... no
> > checking for fseeko... (cached) yes
> > checking whether KERN_USRSTACK sysctl is supported... no
> > checking for visible __lib_stack_end... yes
> > . . .
> >
> > checking for g77... g77
> > checking whether we are using the GNU Fortran compiler... yes
> > checking whether g77 accepts -g... yes
> > . . .
> > checking for bison... no
> > checking for CFPreferencesCopyAppValue... (cached) no
> > checking for CFLocaleCopyCurrent... (cached) no
> > checking whether NLS is requested... yes
> > checking whether included gettext is requested... no
> > checking for GNU gettext in libc... no
> > checking for GNU gettext in libintl... no
> > . . .
> > R is now configured for i686-pc-linux-gnu
> > Source directory: .
> > Installation directory: /usr/local
> > C compiler: gcc -g -O2
> > Fortran 77 compiler: g77 -g -O2
> > C++ compiler: g++ -g -O2
> > Fortran 90/95 compiler: g77 -g -O2
> > Interfaces supported: X11, tcltk
> > External libraries: readline
> > Additional capabilities: PNG, JPEG, iconv, MBCS, NLS
> > Options enabled: shared BLAS, R profiling
> > Recommended packages: yes
> >
> > ______________________________________________
> > R-help <at> 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.
> >
>
Thank you both Pr. Ripley and Dr. Skyler for taking the time to help. I got
your further responses in my email here at work. I really think that Dr.
Ripley is correct : "The symptoms look like a very old Linux distro and a
missing/damaged/incompatible libg2c".
# gcc --version
2.96
# g77 --version
GNU Fortran 0.5.26 20000731 (Red Hat Linux 7.3 2.96-110)
(embarrassingly old?)
My collegues and I are going to try to update it to the most recent free
version (9.something).
Since you asked, the tail of tests/Examples/base-Ex.Rout.fail are below. I'll
come back to the list if, after upgrading Linux, R still does not configure
correctly. But do let me know if the errors below are nothing to do with old
Linux-ness.
In the meantime, in your opinion, will I need to use any configure options for
BLAS and LAPACK described in Appendix A of the Installation and Administration
Manual? I hope that "simple compliation" will be sufficient.
base-Ex.Rout.fail
--- ### Name: bindenv
--- ### Title: Binding and Environment Adjustments
--- ### Aliases: bindenv lockEnvironment environmentIsLocked lockBinding
--- ### unlockBinding makeActiveBinding bindingIsLocked bindingIsActive
--- ### Keywords: internal
. . .
--- assign("x", 2, env = e)
--- try(assign("y", 2, env = e)) # error
Error in assign("y", 2, env = e) : cannot add bindings to a locked environment
. . .
--- try(assign("x", 2, env = e)) # error
Error in assign("x", 2, env = e) : cannot change value of locked binding
for 'x'
+++++++++++++++++++++++++
--- ### Name: chartr
--- ### Title: Character Translation and Casefolding
--- ### Aliases: chartr tolower toupper casefold
--- ### Keywords: character
. . .
--- ## now for a non-positive-definite matrix
--- ( m <- matrix(c(5,-5,-5,3),2,2) )
[,1] [,2]
[1,] 5 -5
[2,] -5 3
--- try(chol(m)) # fails
Error in chol(m) : the leading minor of order 2 is not positive definite
--- try(chol(m, LINPACK=TRUE)) # fails
Error in chol(m, LINPACK = TRUE) : non-positive definite matrix in 'chol'
--- (Q <- chol(m, pivot = TRUE)) # warning
Warning in chol(m, pivot = TRUE) : matrix not positive definite
[,1] [,2]
[1,] 2.236068 -2.236068
[2,] 0.000000 -2.000000
attr(,"pivot")
[1] 1 2
attr(,"rank")
[1] 1
--- crossprod(Q) # not equal to m
[,1] [,2]
[1,] 5 -5
[2,] -5 9
+++++++++++++++++++++++++
--- ### Name: match
--- ### Title: Value Matching
--- ### Aliases: match \%in\%
--- ### Keywords: manip logic
. . .
--- try(center(x, "m")) # Error
Error in match.arg(type) : 'arg' should be one of mean, median, trimmed
+++++++++++++++++++++++++
--- ### Name: NotYet
--- ### Title: Not Yet Implemented Functions and Unused Arguments
--- ### Aliases: NotYetImplemented .NotYetImplemented
NotYetUsed .NotYetUsed
--- ### Keywords: documentation utilities
---
. . .
--- try(plot.mlm())
Error: 'plot.mlm' is not implemented yet
---
--- barplot(1:5, inside = TRUE) # 'inside' is not yet used
Warning: argument 'inside' is not used (yet)
+++++++++++++++++++++++++
--- ### Name: sample
--- ### Title: Random Samples and Permutations
--- ### Aliases: sample
--- ### Keywords: distribution
. . .
--- try(sample(x[x --- 10]))# error!
Error in sample(length(x), size, replace, prob) :
invalid 'x' argument
+++++++++++++++++++++++++
--- ### Name: seq.Date
--- ### Title: Generate Regular Sequences of Dates
--- ### Aliases: seq.Date
--- ### Keywords: manip chron
---
--- ### ** Examples
---
--- ## first days of years
--- seq(as.Date("1910/1/1"), as.Date("1999/1/1"), "years")
Error in fromchar(x) : character string is not in a standard unambiguous format
Execution halted
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