RobinHankin
commented
4 years ago Hi there, this is a frequently asked question, I should make it more prominent in the docs. You need to upgrade GSL to version 2, it looks like you have version 1.15, which will give the errors you report.
let me know how you get on Robin hankin.robin@gmail.com hankin.robin@gmail.com
On Wed, Nov 27, 2019 at 5:17 PM Guillermo Cardenas notifications@github.com wrote:
Hi Robin I have detected an issue with the packae install for R I have read the documentation of CRAN for install this package for unix/ linux
I check the path gsl config libs and cflags (-L) # gsl-config --libs -lgsl -lgslcblas -lm (-I) # gsl-config --cflags -I/usr/include
I Change Makevars in gsl/src: • Add -L/usr/lib -lgsl -lgslcblas -lm to PKG_LIBS • Add (new) line: PKG_CPPFLAGS=-I/usr/include
- Install gsl via LDFLAGS=-L/usr/lib -lgsl -lgslcblas -lm; export LDFLAGS CPPFLAGS=-I/usr/include;export CPPFLAGS R CMD INSTALL gsl
Packages installed [root@ektrh7 src]# rpm -qa |grep -iE "gsl" gsl-1.15-13.el7.x86_64 gsl-devel-1.15-13.el7.x86_64
SO RHEL version [root@ektrh7cdhrtd src]# cat /etc/redhat-release Red Hat Enterprise Linux Server release 7.2 (Maipo)
[root@ektrh7 src]# pwd /rtd/src/gsl/gsl/src [root@ektrh7 src]# ls airy.c clausen.c coupling.c debye.c ellint.c fermi_dirac.c init.c log.c poly.c rng.c vector.c airy.o clausen.o coupling.o debye.o elljac.c gamma.c laguerre.c Makevars pow_int.c synchrotron.c vector.h bessel.c coulomb.c dawson.c dilog.c error.c gegenbauer.c lambert.c Makevars.in psi.c transport.c zeta.c bessel.o coulomb.o dawson.o dilog.o expint.c hyperg.c legendre.c Makevars.win qrng.c trig.c [root@ektrh7cdhrtd src]#
The Makevars looks like... Kindly supplied by Dirk Eddelbuettel set by configure
GSL_CFLAGS = -I/usr/include GSL_LIBS = -lgsl -lgslcblas -lm combine to standard arguments for R
PKG_CPPFLAGS = $(GSL_CFLAGS) -I. PKG_LIBS = $(GSL_LIBS)
But the error show
[root@ektrh7cdhrtd gsl]# R CMD INSTALL gsl
- installing to library ‘/usr/lib64/R/library’
- installing source package ‘gsl’ ... checking for gsl-config... /bin/gsl-config checking if GSL version >= 2.1... checking for gcc... gcc checking whether the C compiler works... yes checking for C compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C compiler... yes checking whether gcc accepts -g... yes checking for gcc option to accept ISO C89... none needed yes configure: creating ./config.status config.status: creating src/Makevars libs gcc -m64 -std=gnu99 -I/usr/include/R -DNDEBUG -I/usr/include -I. -I/usr/local/include -fpic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64 -mtune=generic -c ellint.c -o ellint.o ellint.c: In function ‘ellint_D_e’: ellint.c:82:5: warning: passing argument 4 of ‘gsl_sf_ellint_D_e’ makes integer from pointer without a cast [enabled by default] status[i] = gsl_sf_ellint_D_e(phi[i], k[i], sf_mode[mode], &result) ; ^ In file included from ellint.c:1:0: /usr/include/gsl/gsl_sf_ellint.h:84:5: note: expected ‘gsl_mode_t’ but argument is of type ‘struct gsl_sf_result ’ int gsl_sf_ellint_D_e(double phi, double k, double n, gsl_mode_t mode, gsl_sf_result result); ^ ellint.c:82:5: error: too few arguments to function ‘gsl_sf_ellint_D_e’ status[i] = gsl_sf_ellint_D_e(phi[i], k[i], sf_mode[mode], &result) ; ^ In file included from ellint.c:1:0: /usr/include/gsl/gsl_sf_ellint.h:84:5: note: declared here int gsl_sf_ellint_D_e(double phi, double k, double n, gsl_mode_t mode, gsl_sf_result result); ^ make: [ellint.o] Error 1 ERROR: compilation failed for package ‘gsl’
- removing ‘/usr/lib64/R/library/gsl’
I have tried install from install package from RStudio Pro but the same error still show. Have any one adittional step for install this gsl package for rhel7?
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AliceeDiaz
Hi Robin I have detected an issue with the package install for R I have read the documentation of CRAN for install this package for unix/ linux I check the path gsl config libs and cflags
(-L) # gsl-config --libs
-lgsl -lgslcblas -lm
(-I) # gsl-config --cflags
-I/usr/include
I Change Makevars in gsl/src: • Add -L/usr/lib -lgsl -lgslcblas -lm to PKG_LIBS • Add (new) line: PKG_CPPFLAGS=-I/usr/include
Install gsl via LDFLAGS=-L/usr/lib -lgsl -lgslcblas -lm; export LDFLAGS CPPFLAGS=-I/usr/include;export CPPFLAGS R CMD INSTALL gsl
Packages installed [root@ektrh7 src]# rpm -qa |grep -iE "gsl" gsl-1.15-13.el7.x86_64 gsl-devel-1.15-13.el7.x86_64
SO RHEL version [root@ektrh7cdhrtd src]# cat /etc/redhat-release Red Hat Enterprise Linux Server release 7.2 (Maipo)
[root@ektrh7 src]# pwd /rtd/src/gsl/gsl/src [root@ektrh7 src]# ls airy.c clausen.c coupling.c debye.c ellint.c fermi_dirac.c init.c log.c poly.c rng.c vector.c airy.o clausen.o coupling.o debye.o elljac.c gamma.c laguerre.c Makevars pow_int.c synchrotron.c vector.h bessel.c coulomb.c dawson.c dilog.c error.c gegenbauer.c lambert.c Makevars.in psi.c transport.c zeta.c bessel.o coulomb.o dawson.o dilog.o expint.c hyperg.c legendre.c Makevars.win qrng.c trig.c [root@ektrh7cdhrtd src]#
# The Makevars looks like...
But the error show
I have tried install from install package from RStudio Pro but the same error still show. Have any one adittional step for install this gsl package for rhel7?