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 chris at linux:/space/downs> R CMD INSTALL - l /usr/lib/R/library repeated WARNING: invalid package '-' WARNING: invalid package 'l' WARNING: invalid package '/usr/lib/R/library' * Installing *source* package 'repeated' ... ** libs /usr/lib/R/share/make/shlib.mk:5: *** Target-Muster enth??lt kein ??%??. Schluss. ERROR: compilation failed for package 'repeated' ** Removing '/usr/lib/R/library/repeated'
On Mon, 2004-07-26 at 09:34, Christian Schulz wrote:> 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 > > > chris at linux:/space/downs> R CMD INSTALL - l /usr/lib/R/library repeated > WARNING: invalid package '-' > WARNING: invalid package 'l' > WARNING: invalid package '/usr/lib/R/library' > * Installing *source* package 'repeated' ... > ** libs > /usr/lib/R/share/make/shlib.mk:5: *** Target-Muster enth伱仱lt kein 伮伝%伮伀. > Schluss. > ERROR: compilation failed for package 'repeated' > ** Removing '/usr/lib/R/library/repeated'Christian, There is a space (' ') between the '-' and the 'l', which will be parsed as two separate arguments. Hence the initial WARNING messages. You need to use: R CMD INSTALL -l /usr/lib/R/library repeated Also note that you need to have 'root' privileges in order to install the packages into the /usr/lib/R tree. Thus, you should 'su' to root before running the command. You should verify that your R tree is in /usr/lib, as the default is /usr/local/lib, for which you would not require the '-l /usr/lib/R/library' argument. Presumably Windows worked fine because you typically do not require administrator privileges to install the package locally on Windows or your account has administrative privileges, which is typical (and bad) on Windows NT/XP. HTH, Marc Schwartz
> 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
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??lt 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??lt 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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New
> Jersey, USA 08889), and/or its affiliates (which may be known outside the
> United States as Merck Frosst, Merck Sharp & Dohme or MSD and in Japan,
as
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> privileged. It is intended solely for the use of the individual or entity
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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??lt > 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??lt > 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 > > > > > > > > > -------------------------------------------------------------- > ------------- > >--- Notice: This e-mail message, together with any > attachments, contains > > information of Merck & Co., Inc. (One Merck Drive, > Whitehouse Station, New > > Jersey, USA 08889), and/or its affiliates (which may be > known outside the > > United States as Merck Frosst, Merck Sharp & Dohme or MSD > and in Japan, as > > Banyu) that may be confidential, proprietary copyrighted > and/or legally > > privileged. It is intended solely for the use of the > individual or entity > > named on this message. If you are not the intended > recipient, and have > > received this message in error, please notify us > immediately by reply > > e-mail and then delete it from your system. > > > -------------------------------------------------------------- > ------------- > >--- > >
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??lt
> > 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??lt
> > 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
> > >
> > >
> > >
> > >
> > --------------------------------------------------------------
> > -------------
> > >--- Notice: This e-mail message, together with any
> > attachments, contains
> > > information of Merck & Co., Inc. (One Merck Drive,
> > Whitehouse Station, New
> > > Jersey, USA 08889), and/or its affiliates (which may be
> > known outside the
> > > United States as Merck Frosst, Merck Sharp & Dohme or MSD
> > and in Japan, as
> > > Banyu) that may be confidential, proprietary copyrighted
> > and/or legally
> > > privileged. It is intended solely for the use of the
> > individual or entity
> > > named on this message. If you are not the intended
> > recipient, and have
> > > received this message in error, please notify us
> > immediately by reply
> > > e-mail and then delete it from your system.
> > >
> > --------------------------------------------------------------
> > -------------
> > >---
> >
> >
>
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> Notice: This e-mail message, together with any attachments,
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> Whitehouse Station, New Jersey, USA 08889), and/or its
> affiliates (which may be known outside the United States as
> Merck Frosst, Merck Sharp & Dohme or MSD and in Japan, as
> Banyu) that may be confidential, proprietary copyrighted
> and/or legally privileged. It is intended solely for the use
> of the individual or entity named on this message. If you
> are not the intended recipient, and have received this
> message in error, please notify us immediately by reply
> e-mail and then delete it from your system.
> --------------------------------------------------------------
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