[Rd] X11 and vfonts modules on AIX 5.2
I am trying to get R-2.2.1 to pass make check on an AIX 5.2 at work (I know
R-2.2.1 is not the latest release, but I encountered make errors in my attempts
to install either R-2.3.0 or the R-patched_2006-05-10 on the version of AIX I
am on. I will post those errors in a separate posting from this.)
So far, configure and make finish without error for R-2.2.1 using gnu make,
gcc-4.1.0, and
CC=/usr/local/bin/gcc
F77=/usr/local/bin/gfortran
CXX=/usr/local/bin/g++
MAIN_LDFLAGS=-Wl,-brtl
SHLIB_LDFLAGS=-Wl,-G
CFLAGS='-g -O'
FFLAGS='-O'
CXXFLAGS='-g -O'
bash-3.00$ ./configure --disable-nls
...
R is now configured for powerpc-ibm-aix5.2.0.0
Source directory: .
Installation directory:/usr/local
C compiler:/usr/local/bin/gcc -mno-fp-in-toc -g -O
C++ compiler: /usr/local/bin/g++ -g -O
Fortran compiler: /usr/local/bin/gfortran -O
Interfaces supported: X11
External libraries:readline
Additional capabilities: MBCS
Options enabled: R profiling
Recommended packages: yes
After make, I can run R-2.2.1 from its build directory but I get the following
X11 module loading error when trying to plot
> plot(1:10)
Error in X11() : X11 module cannot be loaded
In addition: Warning message:
unable to load shared library '/home/js36954/src/R-2.2.1/modules/R_X11.so':
rtld: 0712-001 Symbol log10 was referenced
from module /home/js36954/src/R-2.2.1/modules/R_X11.so(), but a runtime
definition of the symbol was not found.
rtld: 0712-001 Symbol floor was referenced
from module /home/js36954/src/R-2.2.1/modules/R_X11.so(), but a runtime
definition of the symbol was not found.
rtld: 0712-001 Symbol pow was referenced
from module /home/js36954/src/R-2.2.1/modules/R_X11.so(), but a runtime
definition of the symbol was not found.
rtld: 0712-001 Symbol sin was referenced
from module /home/js36954/src/R-2.2.1/modules/R_X11.so(), but a runtime
definition of the symbol was not found.
rtld: 0712-001 Symbol cos was referenced
from module /home/js36954/src/R-2.2.1/modules/R_X11.so(), but a runtime
definition of the symbol was not found.
rtld: 0712-001 Symbol tan was referenced
from module /home/js36954/src/R-2.2.1/modules
This error didn't occur for R-2.0.1 which passes make check using the above
config.site settings on the same AIX 5.2.
Searching the archives on R-devel for similar AIX problems, I tried a diff
between the X11 makefiles for R-2.0.1 and R-2.2.1
diff ~/src/R-2.0.1/src/modules/X11/Makefile
~/src/R-2.2.1/src/modules/X11/Makefile
54c54
< $(SHLIB_LINK) -o $@ $(R_X11_la_LDFLAGS) $(R_X11_la_OBJECTS)
$(R_X11_la_LIBADD) $(LIBS)
---
> $(SHLIB_LINK) -o $@ $(R_X11_la_LDFLAGS) $(R_X11_la_OBJECTS)
> $(R_X11_la_LIBADD)
...
Adding $(LIBS) at the end of line 54 in the R-2.2.1 X11 makefile caused the
loading error above to go away, but I don't know if this is what I should be
doing ...
After editing that makefile, I was able to plot in R-2.2.1 but eventually
encountered a similar error on the vfonts module during make check
> Vf <- c("serif", "plain")
> text(4, 2, "\\#J2438\\#J2421\\#J2451\\#J2473", vfont = Vf)
Warning: unable to load shared library
'/home/js36954/src/R-2.2.1/modules/vfonts.so':
rtld: 0712-001 Symbol cos was referenced
from module /home/js36954/src/R-2.2.1/modules/vfonts.so(), but a runtime
definition
of the symbol was not found.
rtld: 0712-001 Symbol sin was referenced
from module /home/js36954/src/R-2.2.1/modules/vfonts.so(), but a runtime
definition
of the symbol was not found.
Error in text.default(4, 2, "\\#J2438\\#J2421\\#J2451\\#J2473", vfont = Vf) :
Hershey fonts cannot be loaded
A diff on the R-2.0.1 and R-2.2.1 vfonts module makefiles,
diff ~/src/R-2.0.1/src/modules/vfonts/Makefile
~/src/R-2.2.1/src/modules/vfonts/Makefile
51c51
< $(SHLIB_LINK) -o $@ $(vfonts_la_LDFLAGS) $(vfonts_la_OBJECTS)
$(vfonts_la_LIBADD) $(LIBS)
---
> $(SHLIB_LINK) -o $@ $(vfonts_la_LDFLAGS) $(vfonts_la_OBJECTS)
> $(vfonts_la_LIBADD)
...
I added $(LIBS) at the end of the R-2.2.1 vfonts makefile, and the above error
went away the next time I ran make check.
So, where I am currently at is that I can get R-2.2.1 to pass make check on my
AIX 5.2 with the above two makefile edits, but I am not sure how harmful that
may be overall ...
E.g. the plots I now get in R-2.2.1, after editing the X11 and vfonts
makefiles, appear with darker axis labels and tick marks than in R-2.0.1, say.
Any advice to help clean things up would be greatly appreciated. I would be
happy to provide any additional details.
Thanks,
Jagat
Jagat K. Sheth 1000 Technology Drive
> Mortgage AnalyticsThird Floor, Mail Station 55
> CitiMortgage, Inc.O'Fallon, MO 63368-2240
> Tel:(636)261-1407 FAX:(636)261-1312
>
> Email: [EMAIL PROTECTED]
>
>
>
>
>
>
__
[Rd] R-2.3.0 make error on AIX 5.2
I am encountering a make error on an AIX 5.2 with R-2.3.0 and R-patched_2006-05-10 after successfully configuring them using gcc-4.1.0, gnu make, and the following configure options CC=/usr/local/bin/gcc F77=/usr/local/bin/gfortran CXX=/usr/local/bin/g++ MAIN_LDFLAGS=-Wl,-brtl SHLIB_LDFLAGS=-Wl,-G CFLAGS='-g -O' FFLAGS='-O' CXXFLAGS='-g -O' bash-3.00$ ./configure --disable-nls The gcc specs on this machine are bash-3.00$ /usr/local/bin/gcc -v Using built-in specs. Target: powerpc-ibm-aix5.2.0.0 Configured with: ../gcc-4.1.0/configure --disable-aix64 --disable-nls Thread model: aix gcc version 4.1.0 The make error from R-patched_2006-05-10 is make[4]: Entering directory `/sas/data/cmi/ma/data/js36954/src/R-patched/src/mod ules/internet' /usr/local/bin/gcc -I. -I../../../src/include -I../../../src/include -I/usr/loca l/include -DHAVE_CONFIG_H -mno-fp-in-toc -g -O -c internet.c -o internet.o internet.c: In function 'in_R_newurl': internet.c:174: error: 'struct Rconn' has no member named 'open64' make[4]: *** [internet.o] Error 1 make[4]: Leaving directory `/sas/data/cmi/ma/data/js36954/src/R-patched/src/modu les/internet' make[3]: *** [R] Error 2 make[3]: Leaving directory `/sas/data/cmi/ma/data/js36954/src/R-patched/src/modu les/internet' make[2]: *** [R] Error 1 make[2]: Leaving directory `/sas/data/cmi/ma/data/js36954/src/R-patched/src/modu les' make[1]: *** [R] Error 1 make[1]: Leaving directory `/sas/data/cmi/ma/data/js36954/src/R-patched/src' make: *** [R] Error 1 I haven't encountered any make errors on this machine when building R-2.0.1 or R-2.2.1 (although the latter failed make check and didn't load the X11 and vfonts modules unless $(LIBS) was added to their makefiles as mentioned in a separate posting from this). Any advice on the above would be greatly appreciated. I will be happy to provide other additional details. Thanks, Jagat Jagat K. Sheth 1000 Technology Drive > Mortgage AnalyticsThird Floor, Mail Station 55 > CitiMortgage, Inc.O'Fallon, MO 63368-2240 > Tel:(636)261-1407 FAX:(636)261-1312 > > Email: [EMAIL PROTECTED] > > > > > > __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] Dropping dimnames doesn't matter (anymore)?
In the "old days", one way of speeding up matrix calculations was to drop the dimnames of the matrices prior to the calculations, i.e., dimnames(X) <- NULL. I distinctly remember that this could have a great impact at least in Splus 3.x (under UNIX/Linux). I just did a small, informal test of this with a couple of functions I use to fit plsr models, in R 2.3.0 (Linux). It didn't seem to have any effect at all (the functions actually ran a tiny bit slower, probably due to the "dimnames(X) <- NULL" command). Is the "general rule-of-thumb" with current R versions that the overhead of keeping the dimnames through calculations is negligible? -- Bjørn-Helge Mevik __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] R-2.3.0 make error on AIX 5.2
We've seen something almost identical before. Looks like fcntl is redefining open (and not open()). At the top of the file is #ifdef HAVE_FCNTL_H # include #endif Insert #undef open in there. On Fri, 12 May 2006, Sheth, Jagat K wrote: > I am encountering a make error on an AIX 5.2 with R-2.3.0 and > R-patched_2006-05-10 after successfully configuring them using gcc-4.1.0, gnu > make, and the following configure options > > CC=/usr/local/bin/gcc > F77=/usr/local/bin/gfortran > CXX=/usr/local/bin/g++ > MAIN_LDFLAGS=-Wl,-brtl > SHLIB_LDFLAGS=-Wl,-G > CFLAGS='-g -O' > FFLAGS='-O' > CXXFLAGS='-g -O' > > bash-3.00$ ./configure --disable-nls > > The gcc specs on this machine are > > bash-3.00$ /usr/local/bin/gcc -v > Using built-in specs. > Target: powerpc-ibm-aix5.2.0.0 > Configured with: ../gcc-4.1.0/configure --disable-aix64 --disable-nls > Thread model: aix > gcc version 4.1.0 > > The make error from R-patched_2006-05-10 is > > make[4]: Entering directory > `/sas/data/cmi/ma/data/js36954/src/R-patched/src/mod > ules/internet' > /usr/local/bin/gcc -I. -I../../../src/include -I../../../src/include > -I/usr/loca > l/include -DHAVE_CONFIG_H -mno-fp-in-toc -g -O -c internet.c -o internet.o > internet.c: In function 'in_R_newurl': > internet.c:174: error: 'struct Rconn' has no member named 'open64' > make[4]: *** [internet.o] Error 1 > make[4]: Leaving directory > `/sas/data/cmi/ma/data/js36954/src/R-patched/src/modu > les/internet' > make[3]: *** [R] Error 2 > make[3]: Leaving directory > `/sas/data/cmi/ma/data/js36954/src/R-patched/src/modu > les/internet' > make[2]: *** [R] Error 1 > make[2]: Leaving directory > `/sas/data/cmi/ma/data/js36954/src/R-patched/src/modu > les' > make[1]: *** [R] Error 1 > make[1]: Leaving directory `/sas/data/cmi/ma/data/js36954/src/R-patched/src' > make: *** [R] Error 1 > > I haven't encountered any make errors on this machine when building R-2.0.1 > or R-2.2.1 (although the latter failed make check and didn't load the X11 and > vfonts modules unless $(LIBS) was added to their makefiles as mentioned in a > separate posting from this). > > Any advice on the above would be greatly appreciated. I will be happy to > provide other additional details. > > Thanks, > Jagat > > Jagat K. Sheth 1000 Technology Drive >> Mortgage AnalyticsThird Floor, Mail Station 55 >> CitiMortgage, Inc.O'Fallon, MO 63368-2240 >> Tel:(636)261-1407 FAX:(636)261-1312 >> >> Email: [EMAIL PROTECTED] >> >> >> >> >> >> > > __ > R-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-devel > > -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] X11 and vfonts modules on AIX 5.2
I think rather you want to add $(LIBM) to the end of ...la_LIBADD.
We've seen things like this before, but OTOH people have succeeded in
building R-2.2.1 on AIX 5.2/3.
On Fri, 12 May 2006, Sheth, Jagat K wrote:
>
> I am trying to get R-2.2.1 to pass make check on an AIX 5.2 at work (I know
> R-2.2.1 is not the latest release, but I encountered make errors in my
> attempts to install either R-2.3.0 or the R-patched_2006-05-10 on the version
> of AIX I am on. I will post those errors in a separate posting from this.)
>
> So far, configure and make finish without error for R-2.2.1 using gnu make,
> gcc-4.1.0, and
>
> CC=/usr/local/bin/gcc
> F77=/usr/local/bin/gfortran
> CXX=/usr/local/bin/g++
> MAIN_LDFLAGS=-Wl,-brtl
> SHLIB_LDFLAGS=-Wl,-G
> CFLAGS='-g -O'
> FFLAGS='-O'
> CXXFLAGS='-g -O'
>
> bash-3.00$ ./configure --disable-nls
>
> ...
>
> R is now configured for powerpc-ibm-aix5.2.0.0
>
> Source directory: .
> Installation directory:/usr/local
>
> C compiler:/usr/local/bin/gcc -mno-fp-in-toc -g -O
> C++ compiler: /usr/local/bin/g++ -g -O
> Fortran compiler: /usr/local/bin/gfortran -O
>
> Interfaces supported: X11
> External libraries:readline
> Additional capabilities: MBCS
> Options enabled: R profiling
>
> Recommended packages: yes
>
>
> After make, I can run R-2.2.1 from its build directory but I get the
> following X11 module loading error when trying to plot
>
>
>> plot(1:10)
>
> Error in X11() : X11 module cannot be loaded
> In addition: Warning message:
> unable to load shared library '/home/js36954/src/R-2.2.1/modules/R_X11.so':
> rtld: 0712-001 Symbol log10 was referenced
> from module /home/js36954/src/R-2.2.1/modules/R_X11.so(), but a runtime
> definition of the symbol was not found.
> rtld: 0712-001 Symbol floor was referenced
> from module /home/js36954/src/R-2.2.1/modules/R_X11.so(), but a runtime
> definition of the symbol was not found.
> rtld: 0712-001 Symbol pow was referenced
> from module /home/js36954/src/R-2.2.1/modules/R_X11.so(), but a runtime
> definition of the symbol was not found.
> rtld: 0712-001 Symbol sin was referenced
> from module /home/js36954/src/R-2.2.1/modules/R_X11.so(), but a runtime
> definition of the symbol was not found.
> rtld: 0712-001 Symbol cos was referenced
> from module /home/js36954/src/R-2.2.1/modules/R_X11.so(), but a runtime
> definition of the symbol was not found.
> rtld: 0712-001 Symbol tan was referenced
> from module /home/js36954/src/R-2.2.1/modules
>
> This error didn't occur for R-2.0.1 which passes make check using the above
> config.site settings on the same AIX 5.2.
>
> Searching the archives on R-devel for similar AIX problems, I tried a diff
> between the X11 makefiles for R-2.0.1 and R-2.2.1
>
> diff ~/src/R-2.0.1/src/modules/X11/Makefile
> ~/src/R-2.2.1/src/modules/X11/Makefile
> 54c54
> < $(SHLIB_LINK) -o $@ $(R_X11_la_LDFLAGS) $(R_X11_la_OBJECTS)
> $(R_X11_la_LIBADD) $(LIBS)
> ---
>
>> $(SHLIB_LINK) -o $@ $(R_X11_la_LDFLAGS) $(R_X11_la_OBJECTS)
>> $(R_X11_la_LIBADD)
>
>
> ...
>
> Adding $(LIBS) at the end of line 54 in the R-2.2.1 X11 makefile caused the
> loading error above to go away, but I don't know if this is what I should be
> doing ...
>
> After editing that makefile, I was able to plot in R-2.2.1 but eventually
> encountered a similar error on the vfonts module during make check
>
>
>> Vf <- c("serif", "plain")
>> text(4, 2, "\\#J2438\\#J2421\\#J2451\\#J2473", vfont = Vf)
>
> Warning: unable to load shared library
> '/home/js36954/src/R-2.2.1/modules/vfonts.so':
> rtld: 0712-001 Symbol cos was referenced
> from module /home/js36954/src/R-2.2.1/modules/vfonts.so(), but a runtime
> definition
> of the symbol was not found.
> rtld: 0712-001 Symbol sin was referenced
> from module /home/js36954/src/R-2.2.1/modules/vfonts.so(), but a runtime
> definition
> of the symbol was not found.
> Error in text.default(4, 2, "\\#J2438\\#J2421\\#J2451\\#J2473", vfont = Vf) :
>Hershey fonts cannot be loaded
>
> A diff on the R-2.0.1 and R-2.2.1 vfonts module makefiles,
>
> diff ~/src/R-2.0.1/src/modules/vfonts/Makefile
> ~/src/R-2.2.1/src/modules/vfonts/Makefile
> 51c51
> < $(SHLIB_LINK) -o $@ $(vfonts_la_LDFLAGS) $(vfonts_la_OBJECTS)
> $(vfonts_la_LIBADD) $(LIBS)
> ---
>
>> $(SHLIB_LINK) -o $@ $(vfonts_la_LDFLAGS) $(vfonts_la_OBJECTS)
>> $(vfonts_la_LIBADD)
>
>
> ...
>
> I added $(LIBS) at the end of the R-2.2.1 vfonts makefile, and the above
> error went away the next time I ran make check.
>
> So, where I am currently at is that I can get R-2.2.1 to pass make check on
> my AIX 5.2 with the above two makefile edits, but I am not sure how harmful
> that may be overall ...
>
> E.g. the plots I now get in R-2.2.1, after editing the X11 and vfonts
> makefiles, appear with darker axis labels and tick marks than in R-2.0.1, say.
>
> Any advice to help
Re: [Rd] Dropping dimnames doesn't matter (anymore)?
On Fri, 12 May 2006, Bjørn-Helge Mevik wrote: In the "old days", one way of speeding up matrix calculations was to drop the dimnames of the matrices prior to the calculations, i.e., dimnames(X) <- NULL. I distinctly remember that this could have a great impact at least in Splus 3.x (under UNIX/Linux). I just did a small, informal test of this with a couple of functions I use to fit plsr models, in R 2.3.0 (Linux). It didn't seem to have any effect at all (the functions actually ran a tiny bit slower, probably due to the "dimnames(X) <- NULL" command). Is the "general rule-of-thumb" with current R versions that the overhead of keeping the dimnames through calculations is negligible? It depends on whether the dimnames are an appreciable part of the size of the object. If they are (e.g. a nx1 array for large n) then manipulating them will add an appeciable overhead. (BTW, character vectors such as dimnames are faster in R for some operations but take much more memory.) -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595__ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] wilcox.exact function (PR#8856)
Full_Name: Patrick Hodgson Version: 2.0 OS: solaris 2.9 Submission from: (NULL) (65.94.128.161) The value reported for the parameter W in the function wilcox.exact appears to be incorrect. I have checked the reference in the help file for this function (Myles & Hollander 1973, as well as 2nd ed. 1999 by same authors) and it is clear that W is the sum of the ranks of the data set with the smaller number of members. Here is sample input/output: > x<-c(1,2,3,4,5,6,7,8,9,10) > y<-c(11,12,13,14,15) > library(exactRankTests) > wil<-wilcox.exact(x,y) > wil Exact Wilcoxon rank sum test data: x and y W = 0, p-value = 0.000666 alternative hypothesis: true mu is not equal to 0 In this case W should be the sum of the ranks of y (coincidentally also the values of the y data)= 11+12+13+14+15 = 65. W of zero is ridiculous. Similarly, in this case W should be 2+4+6+8 = 20, not 10 as reported. > x<-c(1,3,5,7,9) > y<-c(2,4,6,8) > wil<-wilcox.exact(x,y) > wil Exact Wilcoxon rank sum test data: x and y W = 10, p-value = 1 alternative hypothesis: true mu is not equal to 0 __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] wilcox.exact function (PR#8856)
[EMAIL PROTECTED] writes: > Full_Name: Patrick Hodgson > Version: 2.0 > OS: solaris 2.9 > Submission from: (NULL) (65.94.128.161) > > > The value reported for the parameter W in the function wilcox.exact appears to > be incorrect. I have checked the reference in the help file for this function > (Myles & Hollander 1973, as well as 2nd ed. 1999 by same authors) and it is > clear that W is the sum of the ranks of the data set with the smaller number > of > members. You should not use the bug repository to report on a (non-core) package. However, it is the same W used by wilcox.test and help(wilcox.test) has the explanation. > Here is sample input/output: > > x<-c(1,2,3,4,5,6,7,8,9,10) > > y<-c(11,12,13,14,15) > > library(exactRankTests) > > wil<-wilcox.exact(x,y) > > wil > > Exact Wilcoxon rank sum test > > data: x and y > W = 0, p-value = 0.000666 > alternative hypothesis: true mu is not equal to 0 > > In this case W should be the sum of the ranks of y (coincidentally also the > values of the y data)= 11+12+13+14+15 = 65. > W of zero is ridiculous. > > Similarly, in this case W should be 2+4+6+8 = 20, not 10 as reported. > > x<-c(1,3,5,7,9) > > y<-c(2,4,6,8) > > wil<-wilcox.exact(x,y) > > wil > > Exact Wilcoxon rank sum test > > data: x and y > W = 10, p-value = 1 > alternative hypothesis: true mu is not equal to 0 > > __ > R-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-devel > -- O__ Peter Dalgaard Øster Farimagsgade 5, Entr.B c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~ - ([EMAIL PROTECTED]) FAX: (+45) 35327907 __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] R-2.3.0 make error on AIX 5.2
Thanks, that worked. Make finished without any errors on the R-patched_2006-05-10. To get R-patched_2006-05-10 to pass make check on the AIX 5.2 here I added $(LIBM) as you suggested in the other posting for R-2.2.1 to the end of R_X11_la_LIBADD and vfonts_la_LIBADD in the X11 and vfonts modules makefiles respectively before running make. So those makefiles, namely .../src/modules/X11/Makefile and .../src/modules/vfonts/Makefile, have R_X11_la_LIBADD = $(ALL_X_LIBS) $(BITMAP_LIBS) $(LIBR) $(LIBM) vfonts_la_LIBADD = $(LIBR) $(LIBM) Similar editing for the R-2.2.1 version over here allows it to pass make check. Although for some reason the axis labels and tick marks for both R-2.2.1 and R-2.3.0 still seem darker and bold-faced on the x11 device compared to R-2.0.1. Don't know what to make of that, but looks like I can live with everything so far. Thanks, Jagat -Original Message- From: Prof Brian Ripley [mailto:[EMAIL PROTECTED] Sent: Friday, May 12, 2006 8:06 AM To: Sheth, Jagat K Cc: r-devel@stat.math.ethz.ch Subject: Re: [Rd] R-2.3.0 make error on AIX 5.2 We've seen something almost identical before. Looks like fcntl is redefining open (and not open()). At the top of the file is #ifdef HAVE_FCNTL_H # include #endif Insert #undef open in there. On Fri, 12 May 2006, Sheth, Jagat K wrote: > I am encountering a make error on an AIX 5.2 with R-2.3.0 and > R-patched_2006-05-10 after successfully configuring them using gcc-4.1.0, gnu > make, and the following configure options > > CC=/usr/local/bin/gcc > F77=/usr/local/bin/gfortran > CXX=/usr/local/bin/g++ > MAIN_LDFLAGS=-Wl,-brtl > SHLIB_LDFLAGS=-Wl,-G > CFLAGS='-g -O' > FFLAGS='-O' > CXXFLAGS='-g -O' > > bash-3.00$ ./configure --disable-nls > > The gcc specs on this machine are > > bash-3.00$ /usr/local/bin/gcc -v > Using built-in specs. > Target: powerpc-ibm-aix5.2.0.0 > Configured with: ../gcc-4.1.0/configure --disable-aix64 --disable-nls > Thread model: aix > gcc version 4.1.0 > > The make error from R-patched_2006-05-10 is > > make[4]: Entering directory > `/sas/data/cmi/ma/data/js36954/src/R-patched/src/mod > ules/internet' > /usr/local/bin/gcc -I. -I../../../src/include -I../../../src/include > -I/usr/loca > l/include -DHAVE_CONFIG_H -mno-fp-in-toc -g -O -c internet.c -o internet.o > internet.c: In function 'in_R_newurl': > internet.c:174: error: 'struct Rconn' has no member named 'open64' > make[4]: *** [internet.o] Error 1 > make[4]: Leaving directory > `/sas/data/cmi/ma/data/js36954/src/R-patched/src/modu > les/internet' > make[3]: *** [R] Error 2 > make[3]: Leaving directory > `/sas/data/cmi/ma/data/js36954/src/R-patched/src/modu > les/internet' > make[2]: *** [R] Error 1 > make[2]: Leaving directory > `/sas/data/cmi/ma/data/js36954/src/R-patched/src/modu > les' > make[1]: *** [R] Error 1 > make[1]: Leaving directory `/sas/data/cmi/ma/data/js36954/src/R-patched/src' > make: *** [R] Error 1 > > I haven't encountered any make errors on this machine when building R-2.0.1 > or R-2.2.1 (although the latter failed make check and didn't load the X11 and > vfonts modules unless $(LIBS) was added to their makefiles as mentioned in a > separate posting from this). > > Any advice on the above would be greatly appreciated. I will be happy to > provide other additional details. > > Thanks, > Jagat > > Jagat K. Sheth 1000 Technology Drive >> Mortgage AnalyticsThird Floor, Mail Station 55 >> CitiMortgage, Inc.O'Fallon, MO 63368-2240 >> Tel:(636)261-1407 FAX:(636)261-1312 >> >> Email: [EMAIL PROTECTED] >> >> >> >> >> >> > > __ > R-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-devel > > -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] R-2.3.0 make error on AIX 5.2
On Fri, 12 May 2006, Sheth, Jagat K wrote: > Thanks, that worked. Make finished without any errors on the > R-patched_2006-05-10. > > To get R-patched_2006-05-10 to pass make check on the AIX 5.2 here I added > $(LIBM) as you suggested in the other posting for R-2.2.1 to the end of > R_X11_la_LIBADD and vfonts_la_LIBADD in the X11 and vfonts modules makefiles > respectively before running make. So those makefiles, namely > .../src/modules/X11/Makefile and .../src/modules/vfonts/Makefile, have > > R_X11_la_LIBADD = $(ALL_X_LIBS) $(BITMAP_LIBS) $(LIBR) $(LIBM) > vfonts_la_LIBADD = $(LIBR) $(LIBM) > > Similar editing for the R-2.2.1 version over here allows it to pass make > check. Thanks for the confirmation. I have now committed those changes to R-patched and R-devel. > Although for some reason the axis labels and tick marks for both > R-2.2.1 and R-2.3.0 still seem darker and bold-faced on the x11 device > compared to R-2.0.1. Don't know what to make of that, but looks like I > can live with everything so far. 2.0.1 was choosing the wrong fonts on devices far from 75dpi except 100+/-0.5dpi. So this should be an improvement, and is for most people and most X servers. > > Thanks, > Jagat > > > -Original Message- > From: Prof Brian Ripley [mailto:[EMAIL PROTECTED] > Sent: Friday, May 12, 2006 8:06 AM > To: Sheth, Jagat K > Cc: r-devel@stat.math.ethz.ch > Subject: Re: [Rd] R-2.3.0 make error on AIX 5.2 > > > We've seen something almost identical before. Looks like fcntl is > redefining open (and not open()). At the top of the file is > > #ifdef HAVE_FCNTL_H > # include > #endif > > Insert > > #undef open > > in there. > > > On Fri, 12 May 2006, Sheth, Jagat K wrote: > >> I am encountering a make error on an AIX 5.2 with R-2.3.0 and >> R-patched_2006-05-10 after successfully configuring them using gcc-4.1.0, >> gnu make, and the following configure options >> >> CC=/usr/local/bin/gcc >> F77=/usr/local/bin/gfortran >> CXX=/usr/local/bin/g++ >> MAIN_LDFLAGS=-Wl,-brtl >> SHLIB_LDFLAGS=-Wl,-G >> CFLAGS='-g -O' >> FFLAGS='-O' >> CXXFLAGS='-g -O' >> >> bash-3.00$ ./configure --disable-nls >> >> The gcc specs on this machine are >> >> bash-3.00$ /usr/local/bin/gcc -v >> Using built-in specs. >> Target: powerpc-ibm-aix5.2.0.0 >> Configured with: ../gcc-4.1.0/configure --disable-aix64 --disable-nls >> Thread model: aix >> gcc version 4.1.0 >> >> The make error from R-patched_2006-05-10 is >> >> make[4]: Entering directory >> `/sas/data/cmi/ma/data/js36954/src/R-patched/src/mod >> ules/internet' >> /usr/local/bin/gcc -I. -I../../../src/include -I../../../src/include >> -I/usr/loca >> l/include -DHAVE_CONFIG_H -mno-fp-in-toc -g -O -c internet.c -o internet.o >> internet.c: In function 'in_R_newurl': >> internet.c:174: error: 'struct Rconn' has no member named 'open64' >> make[4]: *** [internet.o] Error 1 >> make[4]: Leaving directory >> `/sas/data/cmi/ma/data/js36954/src/R-patched/src/modu >> les/internet' >> make[3]: *** [R] Error 2 >> make[3]: Leaving directory >> `/sas/data/cmi/ma/data/js36954/src/R-patched/src/modu >> les/internet' >> make[2]: *** [R] Error 1 >> make[2]: Leaving directory >> `/sas/data/cmi/ma/data/js36954/src/R-patched/src/modu >> les' >> make[1]: *** [R] Error 1 >> make[1]: Leaving directory `/sas/data/cmi/ma/data/js36954/src/R-patched/src' >> make: *** [R] Error 1 >> >> I haven't encountered any make errors on this machine when building R-2.0.1 >> or R-2.2.1 (although the latter failed make check and didn't load the X11 >> and vfonts modules unless $(LIBS) was added to their makefiles as mentioned >> in a separate posting from this). >> >> Any advice on the above would be greatly appreciated. I will be happy to >> provide other additional details. >> >> Thanks, >> Jagat >> >> Jagat K. Sheth 1000 Technology Drive >>> Mortgage AnalyticsThird Floor, Mail Station 55 >>> CitiMortgage, Inc.O'Fallon, MO 63368-2240 >>> Tel:(636)261-1407 FAX:(636)261-1312 >>> >>> Email: [EMAIL PROTECTED] >>> >>> >>> >>> >>> >>> >> >> __ >> R-devel@r-project.org mailing list >> https://stat.ethz.ch/mailman/listinfo/r-devel >> >> > > -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UKFax: +44 1865 272595 __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] reusing routines
I've created some Splus code for a microarray problem that - needed to be in C, to take advantage of some sparse matrix properties - uses a cholesky decompostion as part of the computation For the cholesky, I used the cholesky2 routine, which is a part of the survival library. It does just what I want and I'm familiar with it (after all, I wrote it). In Splus, this all works fine. A colleague working on the same problem prefers R; things don't work there. The dyn.load command complains that the routine is not found, even when the survival library is already loaded. I looked at the manual page for dyn.load, but don't see anything. What are we missing? Please reply via email, as I don't read this list. (But I likely will start to later this summer, when I port the newest mixed-effects Cox model code over from S). Terry Therneau Mayo Clinic [EMAIL PROTECTED] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] reusing routines
R has a sparse matrix package called Matrix. Maybe with that you don't need any C? On 5/12/06, Terry Therneau <[EMAIL PROTECTED]> wrote: > I've created some Splus code for a microarray problem that >- needed to be in C, to take advantage of some sparse matrix > properties >- uses a cholesky decompostion as part of the computation > > For the cholesky, I used the cholesky2 routine, which is a part of the > survival library. It does just what I want and I'm familiar with it (after > all, I wrote it). > > In Splus, this all works fine. A colleague working on the same problem > prefers R; things don't work there. The dyn.load command complains that > the routine is not found, even when the survival library is already loaded. > > I looked at the manual page for dyn.load, but don't see anything. What > are we missing? > > Please reply via email, as I don't read this list. (But I likely will start > to later this summer, when I port the newest mixed-effects Cox model code > over from S). > >Terry Therneau >Mayo Clinic >[EMAIL PROTECTED] > > __ > 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
