Dear list, When compiling the R-2.3.0 on FC4 x86_64, I got the following errors: make[3]: Entering directory `/project/scratch3/ligroup/wuming/src/R-2.3.0/src/main' gcc -Wl,--export-dynamic -L/usr/local/lib64 -o R.bin Rmain.o CConverters.o CommandLineArgs.o Rdynload.o Renviron.o RNG.o apply.o arithmetic.o apse.o array.o attrib.o base.o bind.o builtin.o character.o coerce.o colors.o complex.o connections.o context.o cov.o cum.o dcf.o datetime.o debug.o deparse.o deriv.o dotcode.o dounzip.o dstruct.o duplicate.o engine.o envir.o errors.o eval.o format.o fourier.o gevents.o gram.o gram-ex.o graphics.o identical.o internet.o iosupport.o lapack.o list.o localecharset.o logic.o main.o mapply.o match.o memory.o model.o names.o objects.o optim.o optimize.o options.o par.o paste.o pcre.o platform.o plot.o plot3d.o plotmath.o print.o printarray.o printvector.o printutils.o qsort.o random.o regex.o registration.o relop.o rlocale.o saveload.o scan.o seq.o serialize.o size.o sort.o source.o split.o sprintf.o startup.o subassign.o subscript.o subset.o summary.o sysutils.o unique.o util.o version.o vfonts.o xxxpr.o ../unix/libunix.a ../appl/libappl.a ../nmath/libnmath.a -lgfortran -lm -lgcc_s ../extra/zlib/libz.a ../extra/bzip2/libbz2.a ../extra/pcre/libpcre.a -lreadline -lncurses -ldl -lm ../appl/libappl.a(cmplxblas.o)(.text+0x1100a): In function `zrotg_': /project/scratch3/ligroup/wuming/src/R-2.3.0/src/appl/cmplxblas.f:5579: undefined reference to `z_abs' ../appl/libappl.a(cmplxblas.o)(.text+0x11069):/project/scratch3/ligroup/wuming/src/R-2.3.0/src/appl/cmplxblas.f:5585: undefined reference to `z_abs' ../appl/libappl.a(cmplxblas.o)(.text+0x11079):/project/scratch3/ligroup/wuming/src/R-2.3.0/src/appl/cmplxblas.f:5585: undefined reference to `z_abs' ../appl/libappl.a(cmplxblas.o)(.text+0x110de):/project/scratch3/ligroup/wuming/src/R-2.3.0/src/appl/cmplxblas.f:5586: undefined reference to `z_abs' ../appl/libappl.a(cmplxblas.o)(.text+0x11146):/project/scratch3/ligroup/wuming/src/R-2.3.0/src/appl/cmplxblas.f:5586: undefined reference to `z_abs' ../appl/libappl.a(cmplxblas.o)(.text+0x1116e):/project/scratch3/ligroup/wuming/src/R-2.3.0/src/appl/cmplxblas.f:5588: more undefined references to `z_abs' follow collect2: ld returned 1 exit status make[3]: *** [R.bin] Error 1 make[3]: Leaving directory `/project/scratch3/ligroup/wuming/src/R-2.3.0/src/main' make[2]: *** [R] Error 2 make[2]: Leaving directory `/project/scratch3/ligroup/wuming/src/R-2.3.0/src/main' make[1]: *** [R] Error 1 make[1]: Leaving directory `/project/scratch3/ligroup/wuming/src/R-2.3.0/src' make: *** [R] Error 1 Is there any way to fix this problem? Thanks, Wuming
"Wuming Gong" <wuming.gong at gmail.com> writes:> Dear list, > > When compiling the R-2.3.0 on FC4 x86_64, I got the following errors: > > make[3]: Entering directory > `/project/scratch3/ligroup/wuming/src/R-2.3.0/src/main' > gcc -Wl,--export-dynamic -L/usr/local/lib64 -o R.bin Rmain.o > CConverters.o CommandLineArgs.o Rdynload.o Renviron.o RNG.o apply.o > arithmetic.o apse.o array.o attrib.o base.o bind.o builtin.o > character.o coerce.o colors.o complex.o connections.o context.o cov.o > cum.o dcf.o datetime.o debug.o deparse.o deriv.o dotcode.o dounzip.o > dstruct.o duplicate.o engine.o envir.o errors.o eval.o format.o > fourier.o gevents.o gram.o gram-ex.o graphics.o identical.o internet.o > iosupport.o lapack.o list.o localecharset.o logic.o main.o mapply.o > match.o memory.o model.o names.o objects.o optim.o optimize.o > options.o par.o paste.o pcre.o platform.o plot.o plot3d.o plotmath.o > print.o printarray.o printvector.o printutils.o qsort.o random.o > regex.o registration.o relop.o rlocale.o saveload.o scan.o seq.o > serialize.o size.o sort.o source.o split.o sprintf.o startup.o > subassign.o subscript.o subset.o summary.o sysutils.o unique.o util.o > version.o vfonts.o xxxpr.o ../unix/libunix.a ../appl/libappl.a > ../nmath/libnmath.a -lgfortran -lm -lgcc_s ../extra/zlib/libz.a > ../extra/bzip2/libbz2.a ../extra/pcre/libpcre.a -lreadline -lncurses > -ldl -lm > ../appl/libappl.a(cmplxblas.o)(.text+0x1100a): In function `zrotg_': > /project/scratch3/ligroup/wuming/src/R-2.3.0/src/appl/cmplxblas.f:5579: > undefined reference to `z_abs' > ../appl/libappl.a(cmplxblas.o)(.text+0x11069):/project/scratch3/ligroup/wuming/src/R-2.3.0/src/appl/cmplxblas.f:5585: > undefined reference to `z_abs' > ../appl/libappl.a(cmplxblas.o)(.text+0x11079):/project/scratch3/ligroup/wuming/src/R-2.3.0/src/appl/cmplxblas.f:5585: > undefined reference to `z_abs' > ../appl/libappl.a(cmplxblas.o)(.text+0x110de):/project/scratch3/ligroup/wuming/src/R-2.3.0/src/appl/cmplxblas.f:5586: > undefined reference to `z_abs' > ../appl/libappl.a(cmplxblas.o)(.text+0x11146):/project/scratch3/ligroup/wuming/src/R-2.3.0/src/appl/cmplxblas.f:5586: > undefined reference to `z_abs' > ../appl/libappl.a(cmplxblas.o)(.text+0x1116e):/project/scratch3/ligroup/wuming/src/R-2.3.0/src/appl/cmplxblas.f:5588: > more undefined references to `z_abs' follow > collect2: ld returned 1 exit status > make[3]: *** [R.bin] Error 1 > make[3]: Leaving directory > `/project/scratch3/ligroup/wuming/src/R-2.3.0/src/main' > make[2]: *** [R] Error 2 > make[2]: Leaving directory > `/project/scratch3/ligroup/wuming/src/R-2.3.0/src/main' > make[1]: *** [R] Error 1 > make[1]: Leaving directory `/project/scratch3/ligroup/wuming/src/R-2.3.0/src' > make: *** [R] Error 1 > > Is there any way to fix this problem?Hmm... It's not happening to me on a similar setup $ uname -a Linux janus 2.6.16-1.2096_FC4smp #1 SMP Wed Apr 19 16:01:54 EDT 2006 x86_64 x86_64 x86_64 GNU/Linux gcc -Wl,--export-dynamic -L/usr/local/lib64 -o R.bin Rmain.o CConverters.o CommandLineArgs.o Rdynload.o Renviron.o RNG.o apply.o arithmetic.o apse.o array.o attrib.o base.o bind.o builtin.o character.o coerce.o colors.o complex.o connections.o context.o cov.o cum.o dcf.o datetime.o debug.o deparse.o deriv.o dotcode.o dounzip.o dstruct.o duplicate.o engine.o envir.o errors.o eval.o format.o fourier.o gevents.o gram.o gram-ex.o graphics.o identical.o internet.o iosupport.o lapack.o list.o localecharset.o logic.o main.o mapply.o match.o memory.o model.o names.o objects.o optim.o optimize.o options.o par.o paste.o pcre.o platform.o plot.o plot3d.o plotmath.o print.o printarray.o printvector.o printutils.o qsort.o random.o regex.o registration.o relop.o rlocale.o saveload.o scan.o seq.o serialize.o size.o sort.o source.o split.o sprintf.o startup.o subassign.o subscript.o subset.o summary.o sysutils.o unique.o util.o version.o vfonts.o xxxpr.o ../unix/libunix.a ../appl/libappl.a ../nmath/libnmath.a -lblas -lgfortran -lm -lgcc_s ../extra/zlib/libz.a ../extra/bzip2/libbz2.a ../extra/pcre/libpcre.a -lreadline -lncurses -ldl -lm Apparently, you are configuring without a BLAS library, but it is not like I get into trouble by removing them from my setup. I'm puzzled. You might check whether you need to upgrade something in your system. -- O__ ---- Peter Dalgaard ?ster Farimagsgade 5, Entr.B c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 ~~~~~~~~~~ - (p.dalgaard at biostat.ku.dk) FAX: (+45) 35327907
Hi Peter, This is mine: AR = ar BLAS_LIBS C_VISIBILITY = -fvisibility=hidden CC = gcc CFLAGS = -g -O2 -std=gnu99 CPICFLAGS = -fpic CPPFLAGS = -I/usr/local/include CXX = g++ CXXCPP = g++ -E CXXFLAGS = -g -O2 CXXPICFLAGS = -fpic DYLIB_EXT = .so DYLIB_LD = gcc DYLIB_LDFLAGS = -shared DYLIB_LINK = $(DYLIB_LD) $(DYLIB_LDFLAGS) $(LDFLAGS) ECHO_C ECHO_N = -n ECHO_T F77 = gfortran F77_VISIBILITY = -fvisibility=hidden FC = f95 FCFLAGS = -g -O2 FFLAGS = -g -O2 FLIBS = -lgfortran -lm -lgcc_s FCPICFLAGS = -fpic FPICFLAGS = -fpic JAVA = /usr/bin/java JAVA_HOME = /usr/lib/jvm/java-1.4.2-gcj-1.4.2.0/jre JAVA_LD_LIBRARY_PATH JAVA_LIBS = -L -ljvm LAPACK_LIBS = -L$(R_HOME)/lib$(R_ARCH) -lRlapack LIBM = -lm LIBR LIBS = -ldl -lm LIBTOOL = $(SHELL) $(R_HOME)/bin/libtool LDFLAGS = -L/usr/local/lib64 R_ARCH RANLIB = ranlib SAFE_FFLAGS = -g -O2 -ffloat-store SED = /bin/sed SHELL = /bin/sh SHLIB_CFLAGS SHLIB_CXXFLAGS SHLIB_CXXLD = g++ SHLIB_CXXLDFLAGS = -shared SHLIB_EXT = .so SHLIB_FCLD = f95 SHLIB_FCLDFLAGS = -shared SHLIB_FFLAGS SHLIB_LD = gcc SHLIB_LDFLAGS = -shared SHLIB_LIBADD SHLIB_LINK = $(SHLIB_LD) $(SHLIB_LDFLAGS) $(LDFLAGS) TCLTK_CPPFLAGS TCLTK_LIBS On 02 May 2006 08:51:21 +0200, Peter Dalgaard <p.dalgaard at biostat.ku.dk> wrote:> "Wuming Gong" <wuming.gong at gmail.com> writes: > > > Dear Peter, > > > > $ uname -a > > Linux bl3 2.6.15-1.1833_FC4smp #1 SMP Wed Mar 1 23:55:52 EST 2006 > > x86_64 x86_64 x86_64 GNU/Linux > > > > When ./configure, I did not claim any options... > > > > Wuming > > Hm. Which are your compilers? I have (in etc/Makeconf). > > AR = ar > BLAS_LIBS > C_VISIBILITY = -fvisibility=hidden > CC = gcc > CFLAGS = -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m64 > -mtune=nocona > CPICFLAGS = -fpic > CPPFLAGS = -I/usr/local/include > CXX = g++ > CXXCPP = g++ -E > CXXFLAGS = -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m64 > -mtune=nocona > CXXPICFLAGS = -fpic > DYLIB_EXT = .so > DYLIB_LD = gcc > DYLIB_LDFLAGS = -shared > DYLIB_LINK = $(DYLIB_LD) $(DYLIB_LDFLAGS) $(LDFLAGS) > ECHO_C > ECHO_N = -n > ECHO_T > F77 = gfortran > F77_VISIBILITY = -fvisibility=hidden > FC = f95 > FCFLAGS = -g -O2 > FFLAGS = -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m64 > -mtune=nocona > FLIBS = -lgfortran -lm -lgcc_s > FCPICFLAGS = -fpic > FPICFLAGS = -fpic > JAVA = /usr/bin/java > JAVA_HOME = /usr/lib/jvm/java-1.4.2-gcj-1.4.2.0/jre > JAVA_LD_LIBRARY_PATH > JAVA_LIBS = -L -ljvm > LAPACK_LIBS = -L$(R_HOME)/lib$(R_ARCH) -lRlapack > LIBM = -lm > LIBR > LIBS = -ldl -lm > LIBTOOL = $(SHELL) $(R_HOME)/bin/libtool > LDFLAGS = -L/usr/local/lib64 > R_ARCH > RANLIB = ranlib > SAFE_FFLAGS = -O2 -g -pipe -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -m64 > -mtune=nocona -ffloat-store > SED = /bin/sed > SHELL = /bin/sh > SHLIB_CFLAGS > SHLIB_CXXFLAGS > SHLIB_CXXLD = g++ > SHLIB_CXXLDFLAGS = -shared > SHLIB_EXT = .so > SHLIB_FCLD = f95 > SHLIB_FCLDFLAGS = -shared > SHLIB_FFLAGS > SHLIB_LD = gcc > SHLIB_LDFLAGS = -shared > SHLIB_LIBADD > SHLIB_LINK = $(SHLIB_LD) $(SHLIB_LDFLAGS) $(LDFLAGS) > TCLTK_CPPFLAGS = -I/usr/include -I/usr/include -I/usr/X11R6/include > TCLTK_LIBS = -L/usr/lib64 -ltcl8.4 -L/usr/lib64 -ltk8.4 > -L/usr/X11R6/lib64 -lX11 > > > > On 01 May 2006 19:30:48 +0200, Peter Dalgaard <p.dalgaard at biostat.ku.dk> wrote: > > > "Wuming Gong" <wuming.gong at gmail.com> writes: > > > > > > > Dear list, > > > > > > > > When compiling the R-2.3.0 on FC4 x86_64, I got the following errors: > > > > > > > > make[3]: Entering directory > > > > `/project/scratch3/ligroup/wuming/src/R-2.3.0/src/main' > > > > gcc -Wl,--export-dynamic -L/usr/local/lib64 -o R.bin Rmain.o > > > > CConverters.o CommandLineArgs.o Rdynload.o Renviron.o RNG.o apply.o > > > > arithmetic.o apse.o array.o attrib.o base.o bind.o builtin.o > > > > character.o coerce.o colors.o complex.o connections.o context.o cov.o > > > > cum.o dcf.o datetime.o debug.o deparse.o deriv.o dotcode.o dounzip.o > > > > dstruct.o duplicate.o engine.o envir.o errors.o eval.o format.o > > > > fourier.o gevents.o gram.o gram-ex.o graphics.o identical.o internet.o > > > > iosupport.o lapack.o list.o localecharset.o logic.o main.o mapply.o > > > > match.o memory.o model.o names.o objects.o optim.o optimize.o > > > > options.o par.o paste.o pcre.o platform.o plot.o plot3d.o plotmath.o > > > > print.o printarray.o printvector.o printutils.o qsort.o random.o > > > > regex.o registration.o relop.o rlocale.o saveload.o scan.o seq.o > > > > serialize.o size.o sort.o source.o split.o sprintf.o startup.o > > > > subassign.o subscript.o subset.o summary.o sysutils.o unique.o util.o > > > > version.o vfonts.o xxxpr.o ../unix/libunix.a ../appl/libappl.a > > > > ../nmath/libnmath.a -lgfortran -lm -lgcc_s ../extra/zlib/libz.a > > > > ../extra/bzip2/libbz2.a ../extra/pcre/libpcre.a -lreadline -lncurses > > > > -ldl -lm > > > > ../appl/libappl.a(cmplxblas.o)(.text+0x1100a): In function `zrotg_': > > > > /project/scratch3/ligroup/wuming/src/R-2.3.0/src/appl/cmplxblas.f:5579: > > > > undefined reference to `z_abs' > > > > ../appl/libappl.a(cmplxblas.o)(.text+0x11069):/project/scratch3/ligroup/wuming/src/R-2.3.0/src/appl/cmplxblas.f:5585: > > > > undefined reference to `z_abs' > > > > ../appl/libappl.a(cmplxblas.o)(.text+0x11079):/project/scratch3/ligroup/wuming/src/R-2.3.0/src/appl/cmplxblas.f:5585: > > > > undefined reference to `z_abs' > > > > ../appl/libappl.a(cmplxblas.o)(.text+0x110de):/project/scratch3/ligroup/wuming/src/R-2.3.0/src/appl/cmplxblas.f:5586: > > > > undefined reference to `z_abs' > > > > ../appl/libappl.a(cmplxblas.o)(.text+0x11146):/project/scratch3/ligroup/wuming/src/R-2.3.0/src/appl/cmplxblas.f:5586: > > > > undefined reference to `z_abs' > > > > ../appl/libappl.a(cmplxblas.o)(.text+0x1116e):/project/scratch3/ligroup/wuming/src/R-2.3.0/src/appl/cmplxblas.f:5588: > > > > more undefined references to `z_abs' follow > > > > collect2: ld returned 1 exit status > > > > make[3]: *** [R.bin] Error 1 > > > > make[3]: Leaving directory > > > > `/project/scratch3/ligroup/wuming/src/R-2.3.0/src/main' > > > > make[2]: *** [R] Error 2 > > > > make[2]: Leaving directory > > > > `/project/scratch3/ligroup/wuming/src/R-2.3.0/src/main' > > > > make[1]: *** [R] Error 1 > > > > make[1]: Leaving directory `/project/scratch3/ligroup/wuming/src/R-2.3.0/src' > > > > make: *** [R] Error 1 > > > > > > > > Is there any way to fix this problem? > > > > > > Hmm... It's not happening to me on a similar setup > > > > > > $ uname -a > > > Linux janus 2.6.16-1.2096_FC4smp #1 SMP Wed Apr 19 16:01:54 EDT 2006 > > > x86_64 x86_64 x86_64 GNU/Linux > > > > > > gcc -Wl,--export-dynamic -L/usr/local/lib64 -o R.bin Rmain.o > > > CConverters.o CommandLineArgs.o Rdynload.o Renviron.o RNG.o apply.o > > > arithmetic.o apse.o array.o attrib.o base.o bind.o builtin.o > > > character.o coerce.o colors.o complex.o connections.o context.o cov.o > > > cum.o dcf.o datetime.o debug.o deparse.o deriv.o dotcode.o dounzip.o > > > dstruct.o duplicate.o engine.o envir.o errors.o eval.o format.o > > > fourier.o gevents.o gram.o gram-ex.o graphics.o identical.o internet.o > > > iosupport.o lapack.o list.o localecharset.o logic.o main.o mapply.o > > > match.o memory.o model.o names.o objects.o optim.o optimize.o > > > options.o par.o paste.o pcre.o platform.o plot.o plot3d.o plotmath.o > > > print.o printarray.o printvector.o printutils.o qsort.o random.o > > > regex.o registration.o relop.o rlocale.o saveload.o scan.o seq.o > > > serialize.o size.o sort.o source.o split.o sprintf.o startup.o > > > subassign.o subscript.o subset.o summary.o sysutils.o unique.o util.o > > > version.o vfonts.o xxxpr.o ../unix/libunix.a ../appl/libappl.a > > > ../nmath/libnmath.a -lblas -lgfortran -lm -lgcc_s > > > ../extra/zlib/libz.a ../extra/bzip2/libbz2.a ../extra/pcre/libpcre.a > > > -lreadline -lncurses -ldl -lm > > > > > > Apparently, you are configuring without a BLAS library, but it is not > > > like I get into trouble by removing them from my setup. I'm puzzled. > > > > > > You might check whether you need to upgrade something in your system. > > > > > > > > > -- > > > O__ ---- Peter Dalgaard ?ster Farimagsgade 5, Entr.B > > > c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K > > > (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 > > > ~~~~~~~~~~ - (p.dalgaard at biostat.ku.dk) FAX: (+45) 35327907 > > > > > > > -- > O__ ---- Peter Dalgaard ?ster Farimagsgade 5, Entr.B > c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K > (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918 > ~~~~~~~~~~ - (p.dalgaard at biostat.ku.dk) FAX: (+45) 35327907 >
On 5/7/06, Alexander Nervedi <alexnerdy at hotmail.com> wrote:> Hi > > is there an R equivalent of the Stata collpase command? > > suppose i have: > > classes <- 1:5 > schools <- letters[1:5] > stud <- 1:10 > > dat <- expand.grid(School = schools, Grade = classes, Student.ID = stud) > with(dat, table(Student.ID, School)) > dat$marks <- rnorm(nrow(dat), 50, 25) > > > I want to get the mean score by school and class while the data is at the > school-class-student level. I could write something up but I was wondering > if there is already something otu there. >library(doBy) summaryBy(marks ~ School + Grade, dat) # by school/Grade combo # or library(Hmisc) with(dat, summarize(marks, dat[,1:2], mean)) # same # or (not quite the same) library(Hmisc) summary(marks ~ School + Grade, dat) # by School and separately by Grade Also see ?tapply, ?by, colMeans?
Dear R-users, are there pre-programmed packages that implement integer maximization? A preliminary google search didnt uncover anything that seemed to match. I want to solve something like Max{U(x) + beta*U(x+y)} with respect to y, where y can take only integer values. thanks. Alnuddy
On Sun, 2006-05-14 at 19:29 +0000, Alexander Nervedi wrote:> Hi All, > > I would like to control the order in which my boxplots are drawn. When i > issue the lines below I find that group "a" get plotted lowest, while the > highest letter grade is plotted on the top. I want to plot the letter grades > in descending order and I was wondering if tere is a quick way to do that. > > thanks. > Alex. > > > play <- data.frame(code = letters[round(runif(100)*10+1)], income = > runif(100)) > with(play, boxplot(income~code, horizontal = TRUE, boxwex = 0.1))The boxplot group order is based upon the factor levels for the RHS of the formula. By default, the levels are done with an alpha sort. So, to change the order, you can use the reorder() function, which has a factor method: with(play, boxplot(income ~ reorder(code, rev(levels(code))), horizontal = TRUE, boxwex = 0.1)) or you could break out the reorder() component into a separate line of code if you find that easier to read. See ?reorder for more information and an example. HTH, Marc Schwartz
Change the order of the levels in the factor: with(play, boxplot(income~factor(code, levels = rev(levels(code))), horizontal = TRUE, boxwex = 0.1)) On 5/14/06, Alexander Nervedi <alexnerdy at hotmail.com> wrote:> Hi All, > > I would like to control the order in which my boxplots are drawn. When i > issue the lines below I find that group "a" get plotted lowest, while the > highest letter grade is plotted on the top. I want to plot the letter grades > in descending order and I was wondering if tere is a quick way to do that. > > thanks. > Alex. > > > play <- data.frame(code = letters[round(runif(100)*10+1)], income > runif(100)) > with(play, boxplot(income~code, horizontal = TRUE, boxwex = 0.1)) > > ______________________________________________ > 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 >