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RobinHankin / gsl

an R wrapper for the Gnu Scientific Library
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What happened to 2.1 on CRAN? #1

Closed QuLogic closed 5 years ago

QuLogic commented 5 years ago

Metacran seems to have thought that 2.1-1 existed about 2.5 years ago, but it doesn't appear to be the latest version on CRAN. This is confusing downstream monitoring of releases (or at least, me anyway).

Did something go wrong with 2.1?

RobinHankin commented 5 years ago

yes, I released gsl_2.1 a couple of years ago, and Brian Ripley pointed out that it required a version of the GSL library which was too recent for most distros, and he strongly suggested that this was a problem. So I archived gsl_2.1-1 on CRAN. It is available under the archive section, but it's not "current". IIRC he pointed to April 2019 as the soonest I could rely on GSL 2, but I don't have the email exchange to hand. When that comes I'll upload 2.1-1, but it is a nontrivial task as the package has many reverse dependencies. Best wishes, Robin

sahilseth commented 5 years ago

Is this a related issue?

** package ‘gsl’ successfully unpacked and MD5 sums checked
checking for gsl-config... /risapps/rhel6/gsl/1.16/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
/risapps/rhel6/gcc/7.1.0/bin/gcc -I"/risapps/rhel6/R/3.5.2-shlib/lib64/R/include" -DNDEBUG -I/risapps/rhel6/gsl/1.16/include -I.  -fPIC -fopenmp -O3 -I/risapps/rhel6/bzip2/1.0.6/include -I/risapps/rhel6/xz/5.2.2/include            -I/risapps/rhel6/zlib/1.2.8/include -I/risapps/rhel6/pcre/8.38/include -I/risapps/rhel6/curl/7.47.1/include   -fpic  -fPIC -fopenmp -O3   -c airy.c -o airy.o
/risapps/rhel6/gcc/7.1.0/bin/gcc -I"/risapps/rhel6/R/3.5.2-shlib/lib64/R/include" -DNDEBUG -I/risapps/rhel6/gsl/1.16/include -I.  -fPIC -fopenmp -O3 -I/risapps/rhel6/bzip2/1.0.6/include -I/risapps/rhel6/xz/5.2.2/include            -I/risapps/rhel6/zlib/1.2.8/include -I/risapps/rhel6/pcre/8.38/include -I/risapps/rhel6/curl/7.47.1/include   -fpic  -fPIC -fopenmp -O3   -c bessel.c -o bessel.o
/risapps/rhel6/gcc/7.1.0/bin/gcc -I"/risapps/rhel6/R/3.5.2-shlib/lib64/R/include" -DNDEBUG -I/risapps/rhel6/gsl/1.16/include -I.  -fPIC -fopenmp -O3 -I/risapps/rhel6/bzip2/1.0.6/include -I/risapps/rhel6/xz/5.2.2/include            -I/risapps/rhel6/zlib/1.2.8/include -I/risapps/rhel6/pcre/8.38/include -I/risapps/rhel6/curl/7.47.1/include   -fpic  -fPIC -fopenmp -O3   -c clausen.c -o clausen.o
/risapps/rhel6/gcc/7.1.0/bin/gcc -I"/risapps/rhel6/R/3.5.2-shlib/lib64/R/include" -DNDEBUG -I/risapps/rhel6/gsl/1.16/include -I.  -fPIC -fopenmp -O3 -I/risapps/rhel6/bzip2/1.0.6/include -I/risapps/rhel6/xz/5.2.2/include            -I/risapps/rhel6/zlib/1.2.8/include -I/risapps/rhel6/pcre/8.38/include -I/risapps/rhel6/curl/7.47.1/include   -fpic  -fPIC -fopenmp -O3   -c coulomb.c -o coulomb.o
/risapps/rhel6/gcc/7.1.0/bin/gcc -I"/risapps/rhel6/R/3.5.2-shlib/lib64/R/include" -DNDEBUG -I/risapps/rhel6/gsl/1.16/include -I.  -fPIC -fopenmp -O3 -I/risapps/rhel6/bzip2/1.0.6/include -I/risapps/rhel6/xz/5.2.2/include            -I/risapps/rhel6/zlib/1.2.8/include -I/risapps/rhel6/pcre/8.38/include -I/risapps/rhel6/curl/7.47.1/include   -fpic  -fPIC -fopenmp -O3   -c coupling.c -o coupling.o
/risapps/rhel6/gcc/7.1.0/bin/gcc -I"/risapps/rhel6/R/3.5.2-shlib/lib64/R/include" -DNDEBUG -I/risapps/rhel6/gsl/1.16/include -I.  -fPIC -fopenmp -O3 -I/risapps/rhel6/bzip2/1.0.6/include -I/risapps/rhel6/xz/5.2.2/include            -I/risapps/rhel6/zlib/1.2.8/include -I/risapps/rhel6/pcre/8.38/include -I/risapps/rhel6/curl/7.47.1/include   -fpic  -fPIC -fopenmp -O3   -c dawson.c -o dawson.o
/risapps/rhel6/gcc/7.1.0/bin/gcc -I"/risapps/rhel6/R/3.5.2-shlib/lib64/R/include" -DNDEBUG -I/risapps/rhel6/gsl/1.16/include -I.  -fPIC -fopenmp -O3 -I/risapps/rhel6/bzip2/1.0.6/include -I/risapps/rhel6/xz/5.2.2/include            -I/risapps/rhel6/zlib/1.2.8/include -I/risapps/rhel6/pcre/8.38/include -I/risapps/rhel6/curl/7.47.1/include   -fpic  -fPIC -fopenmp -O3   -c debye.c -o debye.o
/risapps/rhel6/gcc/7.1.0/bin/gcc -I"/risapps/rhel6/R/3.5.2-shlib/lib64/R/include" -DNDEBUG -I/risapps/rhel6/gsl/1.16/include -I.  -fPIC -fopenmp -O3 -I/risapps/rhel6/bzip2/1.0.6/include -I/risapps/rhel6/xz/5.2.2/include            -I/risapps/rhel6/zlib/1.2.8/include -I/risapps/rhel6/pcre/8.38/include -I/risapps/rhel6/curl/7.47.1/include   -fpic  -fPIC -fopenmp -O3   -c dilog.c -o dilog.o
/risapps/rhel6/gcc/7.1.0/bin/gcc -I"/risapps/rhel6/R/3.5.2-shlib/lib64/R/include" -DNDEBUG -I/risapps/rhel6/gsl/1.16/include -I.  -fPIC -fopenmp -O3 -I/risapps/rhel6/bzip2/1.0.6/include -I/risapps/rhel6/xz/5.2.2/include            -I/risapps/rhel6/zlib/1.2.8/include -I/risapps/rhel6/pcre/8.38/include -I/risapps/rhel6/curl/7.47.1/include   -fpic  -fPIC -fopenmp -O3   -c ellint.c -o ellint.o
ellint.c: In function ‘ellint_D_e’:
ellint.c:82:65: warning: passing argument 4 of ‘gsl_sf_ellint_D_e’ makes integer from pointer without a cast [-Wint-conversion]
     status[i] = gsl_sf_ellint_D_e(phi[i], k[i], sf_mode[*mode], &result) ;
                                                                 ^
In file included from ellint.c:1:0:
/risapps/rhel6/gsl/1.16/include/gsl/gsl_sf_ellint.h:84:5: note: expected ‘gsl_mode_t {aka unsigned int}’ but argument is of type ‘gsl_sf_result * {aka struct gsl_sf_result_struct *}’
 int gsl_sf_ellint_D_e(double phi, double k, double n, gsl_mode_t mode, gsl_sf_result * result);
     ^~~~~~~~~~~~~~~~~
ellint.c:82:17: 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:
/risapps/rhel6/gsl/1.16/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 ‘/rsrch2/iacs/iacs_dep/sseth/R/x86_64-pc-linux-gnu-library/3.5/gsl’
* restoring previous ‘/rsrch2/iacs/iacs_dep/sseth/R/x86_64-pc-linux-gnu-library/3.5/gsl’

The downloaded source packages are in
        ‘/tmp/Rtmpuid0ul/downloaded_packages’
Warning message:
In install.packages(update[instlib == l, "Package"], l, contriburl = contriburl,  :
  installation of package ‘gsl’ had non-zero exit status

Thanks!

RobinHankin commented 5 years ago

hi there, I have a patch but haven't uploaded it yet (I don't like having a short CRAN turnaround time)

best wishes

Robin hankin.robin@gmail.com hankin.robin@gmail.com

hankin.robin@gmail.com

hankin.robin@gmail.com

On Sun, Mar 24, 2019 at 11:11 AM sseth notifications@github.com wrote:

Is this a related issue?

** package ‘gsl’ successfully unpacked and MD5 sums checked

checking for gsl-config... /risapps/rhel6/gsl/1.16/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

/risapps/rhel6/gcc/7.1.0/bin/gcc -I"/risapps/rhel6/R/3.5.2-shlib/lib64/R/include" -DNDEBUG -I/risapps/rhel6/gsl/1.16/include -I. -fPIC -fopenmp -O3 -I/risapps/rhel6/bzip2/1.0.6/include -I/risapps/rhel6/xz/5.2.2/include -I/risapps/rhel6/zlib/1.2.8/include -I/risapps/rhel6/pcre/8.38/include -I/risapps/rhel6/curl/7.47.1/include -fpic -fPIC -fopenmp -O3 -c airy.c -o airy.o

/risapps/rhel6/gcc/7.1.0/bin/gcc -I"/risapps/rhel6/R/3.5.2-shlib/lib64/R/include" -DNDEBUG -I/risapps/rhel6/gsl/1.16/include -I. -fPIC -fopenmp -O3 -I/risapps/rhel6/bzip2/1.0.6/include -I/risapps/rhel6/xz/5.2.2/include -I/risapps/rhel6/zlib/1.2.8/include -I/risapps/rhel6/pcre/8.38/include -I/risapps/rhel6/curl/7.47.1/include -fpic -fPIC -fopenmp -O3 -c bessel.c -o bessel.o

/risapps/rhel6/gcc/7.1.0/bin/gcc -I"/risapps/rhel6/R/3.5.2-shlib/lib64/R/include" -DNDEBUG -I/risapps/rhel6/gsl/1.16/include -I. -fPIC -fopenmp -O3 -I/risapps/rhel6/bzip2/1.0.6/include -I/risapps/rhel6/xz/5.2.2/include -I/risapps/rhel6/zlib/1.2.8/include -I/risapps/rhel6/pcre/8.38/include -I/risapps/rhel6/curl/7.47.1/include -fpic -fPIC -fopenmp -O3 -c clausen.c -o clausen.o

/risapps/rhel6/gcc/7.1.0/bin/gcc -I"/risapps/rhel6/R/3.5.2-shlib/lib64/R/include" -DNDEBUG -I/risapps/rhel6/gsl/1.16/include -I. -fPIC -fopenmp -O3 -I/risapps/rhel6/bzip2/1.0.6/include -I/risapps/rhel6/xz/5.2.2/include -I/risapps/rhel6/zlib/1.2.8/include -I/risapps/rhel6/pcre/8.38/include -I/risapps/rhel6/curl/7.47.1/include -fpic -fPIC -fopenmp -O3 -c coulomb.c -o coulomb.o

/risapps/rhel6/gcc/7.1.0/bin/gcc -I"/risapps/rhel6/R/3.5.2-shlib/lib64/R/include" -DNDEBUG -I/risapps/rhel6/gsl/1.16/include -I. -fPIC -fopenmp -O3 -I/risapps/rhel6/bzip2/1.0.6/include -I/risapps/rhel6/xz/5.2.2/include -I/risapps/rhel6/zlib/1.2.8/include -I/risapps/rhel6/pcre/8.38/include -I/risapps/rhel6/curl/7.47.1/include -fpic -fPIC -fopenmp -O3 -c coupling.c -o coupling.o

/risapps/rhel6/gcc/7.1.0/bin/gcc -I"/risapps/rhel6/R/3.5.2-shlib/lib64/R/include" -DNDEBUG -I/risapps/rhel6/gsl/1.16/include -I. -fPIC -fopenmp -O3 -I/risapps/rhel6/bzip2/1.0.6/include -I/risapps/rhel6/xz/5.2.2/include -I/risapps/rhel6/zlib/1.2.8/include -I/risapps/rhel6/pcre/8.38/include -I/risapps/rhel6/curl/7.47.1/include -fpic -fPIC -fopenmp -O3 -c dawson.c -o dawson.o

/risapps/rhel6/gcc/7.1.0/bin/gcc -I"/risapps/rhel6/R/3.5.2-shlib/lib64/R/include" -DNDEBUG -I/risapps/rhel6/gsl/1.16/include -I. -fPIC -fopenmp -O3 -I/risapps/rhel6/bzip2/1.0.6/include -I/risapps/rhel6/xz/5.2.2/include -I/risapps/rhel6/zlib/1.2.8/include -I/risapps/rhel6/pcre/8.38/include -I/risapps/rhel6/curl/7.47.1/include -fpic -fPIC -fopenmp -O3 -c debye.c -o debye.o

/risapps/rhel6/gcc/7.1.0/bin/gcc -I"/risapps/rhel6/R/3.5.2-shlib/lib64/R/include" -DNDEBUG -I/risapps/rhel6/gsl/1.16/include -I. -fPIC -fopenmp -O3 -I/risapps/rhel6/bzip2/1.0.6/include -I/risapps/rhel6/xz/5.2.2/include -I/risapps/rhel6/zlib/1.2.8/include -I/risapps/rhel6/pcre/8.38/include -I/risapps/rhel6/curl/7.47.1/include -fpic -fPIC -fopenmp -O3 -c dilog.c -o dilog.o

/risapps/rhel6/gcc/7.1.0/bin/gcc -I"/risapps/rhel6/R/3.5.2-shlib/lib64/R/include" -DNDEBUG -I/risapps/rhel6/gsl/1.16/include -I. -fPIC -fopenmp -O3 -I/risapps/rhel6/bzip2/1.0.6/include -I/risapps/rhel6/xz/5.2.2/include -I/risapps/rhel6/zlib/1.2.8/include -I/risapps/rhel6/pcre/8.38/include -I/risapps/rhel6/curl/7.47.1/include -fpic -fPIC -fopenmp -O3 -c ellint.c -o ellint.o

ellint.c: In function ‘ellint_D_e’:

ellint.c:82:65: warning: passing argument 4 of ‘gsl_sf_ellint_D_e’ makes integer from pointer without a cast [-Wint-conversion]

 status[i] = gsl_sf_ellint_D_e(phi[i], k[i], sf_mode[*mode], &result) ;

                                                             ^

In file included from ellint.c:1:0:

/risapps/rhel6/gsl/1.16/include/gsl/gsl_sf_ellint.h:84:5: note: expected ‘gsl_mode_t {aka unsigned int}’ but argument is of type ‘gsl_sf_result {aka struct gsl_sf_result_struct }’

int gsl_sf_ellint_D_e(double phi, double k, double n, gsl_mode_t mode, gsl_sf_result * result);

 ^~~~~~~~~~~~~~~~~

ellint.c:82:17: 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:

/risapps/rhel6/gsl/1.16/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 ‘/rsrch2/iacs/iacs_dep/sseth/R/x86_64-pc-linux-gnu-library/3.5/gsl’

  • restoring previous ‘/rsrch2/iacs/iacs_dep/sseth/R/x86_64-pc-linux-gnu-library/3.5/gsl’

The downloaded source packages are in

    ‘/tmp/Rtmpuid0ul/downloaded_packages’

Warning message:

In install.packages(update[instlib == l, "Package"], l, contriburl = contriburl, :

installation of package ‘gsl’ had non-zero exit status

Thanks!

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RobinHankin commented 5 years ago

gsl_2.1-6 now on CRAN.