[R] installing problems repeated.tgz linux

Liaw, Andy andy_liaw at merck.com
Mon Jul 26 21:16:45 CEST 2004 

I downloaded repeated.tgz and tried it myself on one of our AMD Opterons
running SLES8, and it worked (R-1.9.1 compiled as 64-bit).  Notice that I do
get a couple of warnings from gcc about labels, and from g77 about the use
of `sum' function.

Andy

[andy at leo:lindsey]% R CMD INSTALL -l ~/rlibs repeated
* Installing *source* package 'repeated' ...
** libs
g77   -fPIC  -O2 -m64 -msse2 -march=k8 -mcpu=k8 -g -c chidden.f -o chidden.o
g77   -fPIC  -O2 -m64 -msse2 -march=k8 -mcpu=k8 -g -c cphidden.f -o
cphidden.o
gcc -I/usr/local/lib/R/include  -I/usr/local/include   -fPIC  -O7 -m64
-msse2 -march=k8 -mcpu=k8 -g -c cutil.c -o cutil.o
gcc -I/usr/local/lib/R/include  -I/usr/local/include   -fPIC  -O7 -m64
-msse2 -march=k8 -mcpu=k8 -g -c dist.c -o dist.o
gcc -I/usr/local/lib/R/include  -I/usr/local/include   -fPIC  -O7 -m64
-msse2 -march=k8 -mcpu=k8 -g -c gar.c -o gar.o
g77   -fPIC  -O2 -m64 -msse2 -march=k8 -mcpu=k8 -g -c hidden.f -o hidden.o
gcc -I/usr/local/lib/R/include  -I/usr/local/include   -fPIC  -O7 -m64
-msse2 -march=k8 -mcpu=k8 -g -c kcountb.c -o kcountb.o
kcountb.c: In function `kcountb':
kcountb.c:263: warning: deprecated use of label at end of compound statement
kcountb.c:270: warning: deprecated use of label at end of compound statement
gcc -I/usr/local/lib/R/include  -I/usr/local/include   -fPIC  -O7 -m64
-msse2 -march=k8 -mcpu=k8 -g -c kserieb.c -o kserieb.o
g77   -fPIC  -O2 -m64 -msse2 -march=k8 -mcpu=k8 -g -c logitord.f -o
logitord.o
g77   -fPIC  -O2 -m64 -msse2 -march=k8 -mcpu=k8 -g -c binnest.f -o binnest.o
binnest.f: In subroutine `calcbn':
binnest.f:537: warning:
                    J_Prod = J_Prod * Sum(H2,uph2) ! Calculate the product
of J
                                      ^
Reference to unimplemented intrinsic `SUM' at (^) (assumed EXTERNAL)
binnest.f: In subroutine `calcbn2':
binnest.f:1255: warning:
                    J_Prod = J_Prod * Sum(H2,uph2) ! Calculate the product
of J
                                      ^
Reference to unimplemented intrinsic `SUM' at (^) (assumed EXTERNAL)
g77   -fPIC  -O2 -m64 -msse2 -march=k8 -mcpu=k8 -g -c gausscop.f -o
gausscop.o
gcc -I/usr/local/lib/R/include  -I/usr/local/include   -fPIC  -O7 -m64
-msse2 -march=k8 -mcpu=k8 -g -c gaps.c -o gaps.o
gcc -I/usr/local/lib/R/include  -I/usr/local/include   -fPIC  -O7 -m64
-msse2 -march=k8 -mcpu=k8 -g -c calcs.c -o calcs.o
gcc -I/usr/local/lib/R/include  -I/usr/local/include   -fPIC  -O7 -m64
-msse2 -march=k8 -mcpu=k8 -g -c calcs1.c -o calcs1.o
gcc -I/usr/local/lib/R/include  -I/usr/local/include   -fPIC  -O7 -m64
-msse2 -march=k8 -mcpu=k8 -g -c calcs2.c -o calcs2.o
gcc -I/usr/local/lib/R/include  -I/usr/local/include   -fPIC  -O7 -m64
-msse2 -march=k8 -mcpu=k8 -g -c calcs3.c -o calcs3.o
gcc -I/usr/local/lib/R/include  -I/usr/local/include   -fPIC  -O7 -m64
-msse2 -march=k8 -mcpu=k8 -g -c calcs4.c -o calcs4.o
gcc -shared -o repeated.so chidden.o cphidden.o cutil.o dist.o gar.o
hidden.o kcountb.o kserieb.o logitord.o binnest.o gausscop.o gaps.o calcs.o
calcs1.o calcs2.o calcs3.o calcs4.o -L/usr/local/lib
-L/opt/gcc33/lib64/gcc-lib/x86_64-suse-linux/3.3
-L/opt/gcc33/lib64/gcc-lib/x86_64-suse-linux/3.3/../../../../lib64
-L/opt/gcc33/lib64/gcc-lib/x86_64-suse-linux/3.3/../../.. -L/lib/../lib64
-L/usr/lib/../lib64 -lfrtbegin -lg2c -lm -lgcc_s
** R
** help
 >>> Building/Updating help pages for package 'repeated'
     Formats: text html latex example 
[snipped.  I think you get the idea...]


> From: Liaw, Andy
> 
> Sorry, Christian.  I have no idea what those error messages 
> in German say.
> 
> Andy
> 
> > From: ozric at web.de 
> > 
> > Hello,
> > 
> >  thanks for your and Marc's hint, but it seems not the probleme!?
> > Is there any  probleme with my make?
> > 
> > many thanks and regards, 
> > christian
> > 
> > 
> > chris at linux:/usr/lib/R> R CMD INSTALL 
> > -l /usr/lib/R/library  /space/downs/repeated.tgz
> > * Installing *source* package 'repeated' ...
> > ** libs
> > /usr/lib/R/share/make/shlib.mk:5: *** Target-Muster enthält 
> > kein »%«.  
> > Schluss.
> > ERROR: compilation failed for package 'repeated'
> > ** Removing '/usr/lib/R/library/repeated'
> > 
> > chris at linux:/usr/lib/R> R CMD INSTALL 
> > -l /usr/lib/R/library  /space/downs/repeated
> > * Installing *source* package 'repeated' ...
> > ** libs
> > /usr/lib/R/share/make/shlib.mk:5: *** Target-Muster enthält 
> > kein »%«.  
> > Schluss.
> > ERROR: compilation failed for package 'repeated'
> > ** Removing '/usr/lib/R/library/repeated'
> > 
> > ...with your great RandomForest and other packages 
> > it works!
> > 
> > chris at linux:/usr/lib/R> R CMD INSTALL 
> > -l /usr/lib/R/library  /space/downs/randomForest*.tar.gz
> > * Installing *source* package 'randomForest' ...
> > ** libs
> > gcc -I/usr/lib/R/include  -I/usr/local/include -I/opt/gnome/include 
> > -D__NO_MATH_INLINES -mieee-fp  -fPIC   -c regrf.c -o regrf.o
> > g77 -mieee-fp  -fPIC   -c regrfsub.f -o regrfsub.o
> > gcc -I/usr/lib/R/include  -I/usr/local/include -I/opt/gnome/include 
> > -D__NO_MATH_INLINES -mieee-fp  -fPIC   -c rf.c -o rf.o
> > g77 -mieee-fp  -fPIC   -c rfsub.f -o rfsub.o
> > gcc -shared -L/usr/local/lib -L/opt/gnome/lib -o 
> > randomForest.so regrf.o 
> > regrfsub.o rf.o rfsub.o  -L/usr/local/lib -L/opt/gnome/lib 
> > -L/usr/lib/gcc-lib/i586-suse-linux/3.3.1 
> > -L/usr/lib/gcc-lib/i586-suse-linux/3.3.1/../../../../i586-suse
> > -linux/lib 
> > -L/usr/lib/gcc-lib/i586-suse-linux/3.3.1/../../.. -lfrtbegin 
> > -lg2c -lm 
> > -lgcc_s -L/usr/lib/R/bin -lR
> > ** R
> > ** inst
> > ** help
> >  >>> Building/Updating help pages for package 'randomForest'
> >      Formats: text html latex example
> >   MDSplot                           text    html    latex   example
> >   combine                           text    html    latex   example
> >   getTree                           text    html    latex   example
> >   grow                              text    html    latex   example
> >   importance                        text    html    latex
> >   margin                            text    html    latex   example
> >   na.roughfix                       text    html    latex   example
> >   partialPlot                       text    html    latex   example
> >   plot.randomForest                 text    html    latex   example
> >   predict.randomForest              text    html    latex   example
> >   randomForest                      text    html    latex   example
> >   rfImpute                          text    html    latex   example
> >   treesize                          text    html    latex   example
> >   tuneRF                            text    html    latex   example
> >   varImpPlot                        text    html    latex   example
> >   varUsed                           text    html    latex   example
> > * DONE (randomForest)
> > 
> > 
> > 
> > 
> > 
> > 
> > Am Montag, 26. Juli 2004 18:56 schrieb Liaw, Andy:
> > > > From: Christian Schulz
> > > >
> > > > Hi,
> > > >
> > > > i try several possibilities adn looking in the archive,
> > > >  but didn't getting success to install  j.lindsey's  
> > usefuel "library
> > > > repeated" on my linux (suse9.0 with kernel 2.6.7,R.1.9.1)
> > > >
> > > > P.S. Windows, works  fine
> > > >
> > > > Many thanks for help
> > > > Christian
> > > >
> > > > > R CMD INSTALL - l /usr/lib/R/library   repeated
> > >
> > >                    ^
> > > Try again without that space.
> > >
> > > Andy
> > >
> > >
> > >
> > > 
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