That problem is at least two-fold:
1. A failing heuristic in glmnet/configure.in
2. glmnet/src/glmnet/src/newGLMnet_f.f90 does not compile.
Several problems:
- gfortran does not recognise lines starting with [c|C]
comments
- starting at line 517, a line number column was inserted
after column 72
- long lines had been wrapped by inserting [*], often inside
parameter names
-> looks very wrong, much like a listing file
Quick fix procedure:
ad 1. unpack the archive
apply the patch shown below or edit configure.in (replace ${FC}
by ${F77} in line 38)
delete glmnet/configure
repack the archive
try to install the newly packed archive via R CMD INSTALL (will
fail)
ad 2. I could also attach a patch also for glmnet/src/newGLMnet_f.f90
- but it is rather big (you may contact me)
- while the package will compile and load without error,
running example(glmnet) results in:
glmnet> fit1=glmnet(x,y)
Error in validObject(.Object) :
invalid class "dgCMatrix" object: length(Dimnames[[2]])'
must match Dim[2]
In addition: Warning message:
from glmnet Fortran code - Convergence for 1th lambda value
not reached after
maxit=100000 iterations; solutions for larger
lambdas returned
So there seem to be many problems worth of a bug report to the author(s) of
glmnet.
Kind regards
Hugo
--- cut here ---
diff -ur a/glmnet/configure.in b/glmnet/configure.in
--- a/glmnet/configure.in 2011-06-15 20:05:30.000000000 +0200
+++ b/glmnet/configure.in 2011-06-24 10:08:21.000000000 +0200
@@ -35,7 +35,7 @@
FC=`basename "${FC}"`
fi
-case "${FC}" in
+case "${F77}" in
gfortran*)
echo " R configured for gfortran; Good!"
AC_SUBST(OUR_FCFLAGS, "-fdefault-real-8 -ffixed-form")
--- cut here ---
On Thursday 23 June 2011 22:39:33 Juergen Rose wrote:
> Hi,
>
> is there any chance to install glmnet with gcc-4.5.2? For me it fails on
> all systems with:
>
> trying URL
> 'http://mirrors.softliste.de/cran/src/contrib/glmnet_1.7.tar.gz'
> Content type 'application/x-gzip' length 522888 bytes (510 Kb)
> opened URL
> ==================================================
> downloaded 510 Kb
>
> * installing *source* package ‘glmnet’ ...
> This package has only been tested with gfortran.
> So some checks are needed.
> R_HOME is /usr/lib64/R
> Attempting to determine R_ARCH...
> R_ARCH is
> Attempting to detect how R was configured for Fortran 90....
> Unsupported Fortran 90 compiler or Fortran 90
> compilers unavailable! Stop!
> ERROR: configuration failed for package ‘glmnet’
>
> How can I get more information, what a problem has happened?
>
> Otherwise I have no problem to compile a small Fortran 90 program:
> root@orca:/home/rose/Txt/src/Test/Fortran(57)# cat hello.f90
> program Hello
> print *,'Hello world'
> end program Hello
> root@orca:/home/rose/Txt/src/Test/Fortran(58)# gfortran -cpp -dM
> hello.f90
> root@orca:/home/rose/Txt/src/Test/Fortran(59)# ./a.out
> Hello world
>
> ______________________________________________
> R-help@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>
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