search for: commandlineargs

...f the things I'd really like to do is find a way to load an R library I've developed, and call one function with arguments. Currently, I achieve that by building a separate R client file, which reads in the command line arguments, loads the library, and calls the main function. The commandLineArgs function below uses commandArgs(), and searches the vector for the keys/values to make life easier. (code available at inside "birdsuite executables" at http://www.broad.mit.edu/science/programs/medical-and-population-genetics/birdsuite/birdsuite-downloads-0) Example: --- library (bro...

...rpc-unknown-linux-gnu" CFLAGS="-O2 -mcpu=G4 -mtune=G4 -fno-strict-aliasing -pipe -maltivec -mabi=altivec" CHOST="powerpc-unknown-linux-gnu" Fault log gfortran -fpic -g -O2 -c xxxpr.f -o xxxpr.o powerpc-unknown-linux-gnu-gcc -shared -o libR.so Rembedded.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...

...ome OK bits of output, to help show where the problem is>> ... making vfonts.d from vfonts.c gcc -O2 -Wall -pedantic -DLEA_MALLOC -I../include -DHAVE_CONFIG_H -DR_DLL_BUILD -c CConverters.c -o CConverters.o gcc -O2 -Wall -pedantic -DLEA_MALLOC -I../include -DHAVE_CONFIG_H -DR_DLL_BUILD -c CommandLineArgs.c -o CommandLineArg s.o gcc -O2 -Wall -pedantic -DLEA_MALLOC -I../include -DHAVE_CONFIG_H -DR_DLL_BUILD -c Rdynload.c -o Rdynload.o gcc -O2 -Wall -pedantic -DLEA_MALLOC -I../include -DHAVE_CONFIG_H -DR_DLL_BUILD -c Renviron.c -o Renviron.o gcc -O2 -Wall -pedantic -DLEA_MALLOC -I../include -DHA...

...on RHEL6. The version of R in the 6 repos is 3.0, and rpy2 does not work with that version. I installed R 3.3.3 following the directions here: https://oguya.ch/posts/2017-03-18-building-R-on-rhel-6/. But even with 3.3.3 it's still failing. Using pip it fails with: /usr/local/lib64/R/lib/libR.a(CommandLineArgs.o): could not read symbols: Bad value and installing from source it fails with: /usr/bin/ld: cannot find -lr_utils Anyone know how I can get rpy2 working on RHEL6? (I did post to the rpy mailing list and also on SO, but did not get any answers.)

...src/library/Recommended' make: *** [stamp-recommended] Error 2 $ cd ../R-packages; R CMD INSTALL MASS succeeds, though $ make still fails on MASS, as above $ cd $R_HOME; ./configure --enable-R-shlib returns ... gcc -std=gnu99 -shared -fopenmp -L/usr/local/lib64 -o libR.so CommandLineArgs.o Rdynload.o Renviron.o RNG.o agrep.o apply.o arithmetic.o array.o attrib.o bind.o builtin.o character.o coerce.o colors.o complex.o connections.o context.o cum.o dcf.o datetime.o debug.o deparse.o devices.o dotcode.o dounzip.o dstruct.o duplicate.o edit.o engine.o envir.o errors.o eval.o forma...

I would like to simulate the effect of the command-line option --quiet from user-level scripts and startup code. From src/main/CommandLineArgs.c I learn that Rp->R_Quiet is set, and I see how that is used in main/main.c. I would use this from code in Rprofile.site. In other words, I want to be silent when --quiet is used (as e.g. by littler or Rscript) but not by R itself in normal interactive mode or from ESS. But it seems that I ca...

Hi, Cosmetic. Starting R with e.g. --max-ppsize=-10 produces the following warning: WARNING: '-max-ppsize' value is negative: ignored The name of the option displayed in the warning is incorrect. Could that be fixed? See src/main/CommandLineArgs.c (there are 3 places in that file where the name of this option needs to be adjusted). This is with current R-alpha. Thanks! H. -- Herv? Pag?s Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M2-B876 P.O. Box 1902...

..., when I did make, I got below. Maybe I need to do the make with options also. But, if so, I couldn't figure out where to look for them. Thanks. # part where I got the error when running make #====================================== gcc -std=gnu99 -shared -fopenmp -L/usr/local/lib64 -o libR.so CommandLineArgs.o Rdynload.o Renviron.o RNG.o agrep.o apply.o arithmetic.o array.o attrib.o bind.o builtin.o character.o coerce.o colors.o complex.o connections.o context.o cum.o dcf.o datetime.o debug.o deparse.o devices.o dotcode.o dounzip.o dstruct.o duplicate.o edit.o engine.o envir.o errors.o eval.o format.o...

...the 6 repos is > 3.0, and rpy2 does not work with that version. I installed R 3.3.3 > following the directions here: > https://oguya.ch/posts/2017-03-18-building-R-on-rhel-6/. But even with > 3.3.3 it's still failing. Using pip it fails with: > > /usr/local/lib64/R/lib/libR.a(CommandLineArgs.o): could not read > symbols: Bad value > > and installing from source it fails with: > > /usr/bin/ld: cannot find -lr_utils > > Anyone know how I can get rpy2 working on RHEL6? > > (I did post to the rpy mailing list and also on SO, but did not get > any answers.)...

...R install as non-root with source packages: after downloading the latest tarball and unzipping: ./configure --prefix=/opt --enable-R-shlib make make[3]: Entering directory `/ifs/data/columbia/tm_lab/so2346/R-2.12.1/src/main' gcc -std=gnu99 -shared -L/usr/local/lib64 -o libR.so CConverters.o CommandLineArgs.o Rdynload.o Renviron.o RNG.o agrep.o apply.o arithmetic.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 devices.o dotcode.o dounzip.o dstruct.o duplicate.o engine.o envir.o errors.o ev...

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...

...prevented configure from inserting -L /usr/local/lib, so linked /usr/lib/libreadline.dylib, which is the Apple-supplied one, which possibly is really libedit... -p > On 18 May 2016, at 22:01 , peter dalgaard <pdalgd at gmail.com> wrote: > > gcc -L/usr/X11R6/lib -o R.bin Rmain.o CommandLineArgs.o Rdynload.o Renviron.o RNG.o agrep.o apply.o arithmetic.o array.o attrib.o bind.o builtin.o character.o coerce.o colors.o complex.o connections.o context.o cum.o dcf.o datetime.o debug.o deparse.o devices.o dotcode.o dounzip.o dstruct.o duplicate.o edit.o engine.o envir.o errors.o eval.o format.o...

...R-users, is there anyone else with problems to get R-2.1.0 compiled on FreeBSD6-CURRENT? After typing '.configure' and then 'make' I get the following output: ------------------------------------- [...snip...] gcc -export-dynamic -L/usr/local/lib -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...

...R-users, is there anyone else with problems to get R-2.1.0 compiled on FreeBSD6-CURRENT? After typing '.configure' and then 'make' I get the following output: ------------------------------------- [...snip...] gcc -export-dynamic -L/usr/local/lib -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...

...on -g -O2 - std=gnu99 -c vfonts.c -o vfonts.o g77 -fPIC -fno-common -g -O2 -c xxxpr.f -o xxxpr.o gcc -dynamiclib -L/usr/local/lib -dynamiclib -install_name libR.dylib -compatibility_version 2.3.0 -current_version 2.3.0 - headerpad_max_install_names -o libR.dylib Rembedded.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....

...G: you cannot build PDF versions of the R manuals and output for make command make[3]: Leaving directory `/datos/java/temp/R-2.4.0/src/main' make[3]: Entering directory `/datos/java/temp/R-2.4.0/src/main' gcc -L/opt/SUNWmlib/lib -L/opt/SUNWmlib/lib/sparcv9 -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...

...R-2.1.0 OS: FreeBSD6-CURRENT from May 19 2005 Submission from: (NULL) (213.54.77.26) /configure does well in FreeBSD6-CURRENT. When typing 'make' after a while I get: ------------------------------------- [...snip...] gcc -export-dynamic -L/usr/local/lib -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...

...number. It does keep fixing the bug on my platform (Fedora 22 Linux, readline 6.3) and it may help in Keith' setup. Please do check it, Keith. (svn rev >= 70631) Martin > -pd > ..... > ranlib: file: libR.a(printf.o) has no symbols > gcc -L/usr/X11R6/lib -o R.bin Rmain.o CommandLineArgs.o Rdynload.o Renviron.o RNG.o agrep.o apply.o arithmetic.o array.o attrib.o bind.o builtin.o character.o coerce.o colors.o complex.o connections.o context.o cum.o dcf.o datetime.o debug.o deparse.o devices.o dotcode.o dounzip.o dstruct.o duplicate.o edit.o engine.o envir.o errors.o eval.o format.o...

...9 -I../../src/extra/zlib -I../../src/extra/bzip2 -I../../src/extra/pcre -I../../src/extra? -I../../src/extra/xz/api -I. -I../../src/include -I../../src/include -I/usr/local/include -DHAVE_CONFIG_H???? -g -O2 -c vfonts.c -o vfonts.o gfortran??? -g -O2 -c xxxpr.f -o xxxpr.o ar cr libR.a CConverters.o CommandLineArgs.o Rdynload.o Renviron.o RNG.o agrep.o apply.o arithmetic.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 devices.o dotcode.o dounzip.o dstruct.o duplicate.o engine.o envir.o errors.o ev...

...include -I/usr/local/include -DHAVE_CONFIG_H -D__NO_MATH_INLINES -xO5 -xlibmil -xc99=%all -xlibmieee -c mkdtemp.c -o mkdtemp.o /opt/SUNWspro/bin/cc -xarch=amd64 -L/usr/local/lib/64 -L/usr/sfw/lib/64 -L/lib/amd64 -R/usr/local/lib/64 -R/usr/sfw/lib/64 -R/lib/amd64 -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 fo...