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Korbinian Strimmer

2004-Feb-15 21:09 UTC

[Rd] build problems on Fedora Core 1

Hello...

   I tried to build R-devel today on Fedora Core 1 (with gcc 3.3.2)
but I am running into a couple of errors.  On the same system R-1.8.1
compiles just fine, as did a previous version of R-devel.

This is what I did:

  # change LANG as default in FC1 is UTF-8
  export LANG=en_US.ISO8859-1
  export LANGVAR=en_US.ISO8859-1

  # get fresh sources and configure
  mkdir R-devel
  rsync -vrC rsync.r-project.org::r-devel R-devel
  cd R-devel
  ./tools/rsync-recommended
  ./configure


This results in the following configuration:


#####################################################################
R is now configured for i686-pc-linux-gnu

   Source directory:          .
   Installation directory:    /usr/local

   C compiler:                gcc -D__NO_MATH_INLINES -mieee-fp -g -O2
   C++ compiler:              g++ -mieee-fp -g -O2
   Fortran compiler:          g77 -mieee-fp -g -O2

   Interfaces supported:      X11, tcltk
   External libraries:        readline
   Additional capabilities:   PNG, JPEG
   Options enabled:           R profiling

   Recommended packages:      yes
#####################################################################


After typing "make" the build process started and everything look ok
until an error message in the directory /library/stats4 occurs
(see full make log file below):

  Error in get(x, envir, mode, inherits) : variable ".getGenerics" was
not found

Later the make process aborts with a string of messages

   Error: couldn't find function ".installPackageNamespaceInfo"


Any idea what could be going on?

Thanks,

    Korbinian


Korbinian Strimmer           http://www.stat.uni-muenchen.de/~strimmer
Dept. of Statistics, University of Munich, Ludwigstr. 33, 80539 Munich
+49 89 2180-3225 (phone), -5041 (fax), strimmer@stat.uni-muenchen.de




############## here are the final bits of the make output 
###################


make[5]: Entering directory `/home/strimmer/R-devel/src/library/splines/src'
gcc -I../../../../include  -I/usr/local/include -D__NO_MATH_INLINES 
-mieee-fp  -fPIC  -g -O2 -c splines.c -o splines.o
gcc -shared -L/usr/local/lib -o splines.so splines.o
mkdir -p -- ../../../../library/splines/libs
make[5]: Leaving directory `/home/strimmer/R-devel/src/library/splines/src'
make[4]: Leaving directory `/home/strimmer/R-devel/src/library/splines/src'
make[3]: Leaving directory `/home/strimmer/R-devel/src/library/splines'
make[3]: Entering directory `/home/strimmer/R-devel/src/library/stats4'
building package 'stats4'
mkdir -p -- ../../../library/stats4/R
mkdir -p -- ../../../library/stats4/man
make[4]: Entering directory `/home/strimmer/R-devel/src/library/stats4'
dumping R code in package 'stats4'
Loading required package: methods
Error in get(x, envir, mode, inherits) : variable ".getGenerics" was
not
found
Error in eval(expr, envir, enclos) : couldn't find function
"setGeneric"
Execution halted
make[4]: Leaving directory `/home/strimmer/R-devel/src/library/stats4'
make[3]: Leaving directory `/home/strimmer/R-devel/src/library/stats4'
make[3]: Entering directory `/home/strimmer/R-devel/src/library/tcltk'
building package 'tcltk'
mkdir -p -- ../../../library/tcltk/R
mkdir -p -- ../../../library/tcltk/demo
mkdir -p -- ../../../library/tcltk/exec
mkdir -p -- ../../../library/tcltk/man
make[4]: Entering directory `/home/strimmer/R-devel/src/library/tcltk/src'
making init.d from init.c
making tcltk.d from tcltk.c
make[5]: Entering directory `/home/strimmer/R-devel/src/library/tcltk/src'
make[5]: `Makedeps' is up to date.
make[5]: Leaving directory `/home/strimmer/R-devel/src/library/tcltk/src'
make[5]: Entering directory `/home/strimmer/R-devel/src/library/tcltk/src'
gcc -I../../../../include -I/usr/include -I/usr/include 
-I/usr/X11R6/include -I/usr/local/include -D__NO_MATH_INLINES -mieee-fp 
  -fPIC  -g -O2 -c init.c -o init.ogcc -I../../../../include 
-I/usr/include -I/usr/include -I/usr/X11R6/include -I/usr/local/include 
-D__NO_MATH_INLINES -mieee-fp  -fPIC  -g -O2 -c tcltk.c -o tcltk.o
gcc -shared -L/usr/local/lib -o tcltk.so init.o tcltk.o  -L/usr/lib 
-ltcl8.3 -L/usr/lib -ltk8.3 -L/usr/X11R6/lib -lX11 -ldl  -lieee -lm -lm
mkdir -p -- ../../../../library/tcltk/libs
make[5]: Leaving directory `/home/strimmer/R-devel/src/library/tcltk/src'
make[4]: Leaving directory `/home/strimmer/R-devel/src/library/tcltk/src'
make[3]: Leaving directory `/home/strimmer/R-devel/src/library/tcltk'
make[3]: Entering directory `/home/strimmer/R-devel/src/library/ctest'
building package 'ctest'
mkdir -p -- ../../../library/ctest/R
make[3]: Leaving directory `/home/strimmer/R-devel/src/library/ctest'
make[3]: Entering directory `/home/strimmer/R-devel/src/library/eda'
building package 'eda'
mkdir -p -- ../../../library/eda/R
make[3]: Leaving directory `/home/strimmer/R-devel/src/library/eda'
make[3]: Entering directory `/home/strimmer/R-devel/src/library/lqs'
building package 'lqs'
mkdir -p -- ../../../library/lqs/R
make[3]: Leaving directory `/home/strimmer/R-devel/src/library/lqs'
make[3]: Entering directory `/home/strimmer/R-devel/src/library/mle'
building package 'mle'
mkdir -p -- ../../../library/mle/R
make[3]: Leaving directory `/home/strimmer/R-devel/src/library/mle'
make[3]: Entering directory `/home/strimmer/R-devel/src/library/modreg'
building package 'modreg'
mkdir -p -- ../../../library/modreg/R
make[3]: Leaving directory `/home/strimmer/R-devel/src/library/modreg'
make[3]: Entering directory `/home/strimmer/R-devel/src/library/mva'
building package 'mva'
mkdir -p -- ../../../library/mva/R
make[3]: Leaving directory `/home/strimmer/R-devel/src/library/mva'
make[3]: Entering directory `/home/strimmer/R-devel/src/library/nls'
building package 'nls'
mkdir -p -- ../../../library/nls/R
make[3]: Leaving directory `/home/strimmer/R-devel/src/library/nls'
make[3]: Entering directory `/home/strimmer/R-devel/src/library/stepfun'
building package 'stepfun'
mkdir -p -- ../../../library/stepfun/R
make[3]: Leaving directory `/home/strimmer/R-devel/src/library/stepfun'
make[3]: Entering directory `/home/strimmer/R-devel/src/library/ts'
building package 'ts'
mkdir -p -- ../../../library/ts/R
make[3]: Leaving directory `/home/strimmer/R-devel/src/library/ts'
installing parsed NAMESPACE files
Error: couldn't find function ".installPackageNamespaceInfo"
Execution halted
Error: couldn't find function ".installPackageNamespaceInfo"
Execution halted
Error: couldn't find function ".installPackageNamespaceInfo"
Execution halted
Error: couldn't find function ".installPackageNamespaceInfo"
Execution halted
Error: couldn't find function ".installPackageNamespaceInfo"
Execution halted
Error: couldn't find function ".installPackageNamespaceInfo"
Execution halted
Error: couldn't find function ".installPackageNamespaceInfo"
Execution halted
Error: couldn't find function ".installPackageNamespaceInfo"
Execution halted
Error: couldn't find function ".installPackageNamespaceInfo"
Execution halted
make[2]: *** [R] Error 1
make[2]: Leaving directory `/home/strimmer/R-devel/src/library'
make[1]: *** [R] Error 1
make[1]: Leaving directory `/home/strimmer/R-devel/src'
make: *** [R] Error 1
[strimmer@amoeba R-devel]$

Peter Dalgaard

2004-Feb-15 21:37 UTC

head link

[Rd] build problems on Fedora Core 1

Korbinian Strimmer <strimmer@stat.uni-muenchen.de> writes:
> Hello...
> 
>    I tried to build R-devel today on Fedora Core 1 (with gcc 3.3.2)
> but I am running into a couple of errors.  On the same system R-1.8.1
> compiles just fine, as did a previous version of R-devel.
...> Any idea what could be going on?
Not really, but a build from the current CVS on SuSE9 seems to work
fine... 

-- 
   O__  ---- Peter Dalgaard             Blegdamsvej 3  
  c/ /'_ --- Dept. of Biostatistics     2200 Cph. N   
 (*) \(*) -- University of Copenhagen   Denmark      Ph: (+45) 35327918
~~~~~~~~~~ - (p.dalgaard@biostat.ku.dk)             FAX: (+45) 35327907

Korbinian Strimmer

2004-Feb-16 09:53 UTC

head link

[Rd] build problems on Fedora Core 1

Robert Gentleman wrote:> Hi,
>   looks like the R-devel build might be picking up R 1.8.1 somehow
>   (maybe R_HOME or some such thing is set, or set to the wrong value).
> Robert
> 
That's it! In our system we have a system wide setting of the R_LIBS 
variable - which of course points to the stable version of R...

If I switch this variable off, everything works.

Many thanks!

   Korbinian


-- 
Korbinian Strimmer           http://www.stat.uni-muenchen.de/~strimmer
Dept. of Statistics, University of Munich, Ludwigstr. 33, 80539 Munich
+49 89 2180-3225 (phone), -5041 (fax), strimmer@stat.uni-muenchen.de

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