On 25/04/2012 08:05, Uwe Ligges wrote:
On 25.04.2012 08:21, Erin Hodgess wrote:
Dear R People:
I am attempting to install SparseM on R 2.15.0 on a Linux 11.10 system.
Here is the output
install.packages("SparseM",depen=TRUE)
Installing package(s) into
‘/home/erin/R/x86_64-pc-linux-gnu-library/2.15’
(as ‘lib’ is unspecified)
--- Please select a CRAN mirror for use in this session ---
Loading Tcl/Tk interface ... done
trying URL 'http://cran.at.r-project.org/src/contrib/SparseM_0.96.tar.gz'
Content type 'application/x-gzip' length 749740 bytes (732 Kb)
opened URL
==================================================
downloaded 732 Kb
* installing *source* package ‘SparseM’ ...
** package ‘SparseM’ successfully unpacked and MD5 sums checked
** libs
gfortran -fpic -O3 -pipe -g -c bckslv.f -o bckslv.o
gfortran -fpic -O3 -pipe -g -c chol.f -o chol.o
gfortran -fpic -O3 -pipe -g -c chol2csr.f -o chol2csr.o
gfortran -fpic -O3 -pipe -g -c cholesky.f -o cholesky.o
gfortran -fpic -O3 -pipe -g -c csr.f -o csr.o
gfortran -fpic -O3 -pipe -g -c extract.f -o extract.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -O3 -pipe
-g -c iohb.c -o iohb.o
iohb.c: In function ‘readHB_info’:
iohb.c:267: warning: cast from pointer to integer of different size
iohb.c: In function ‘readHB_header’:
iohb.c:309: warning: cast from pointer to integer of different size
iohb.c:310: warning: cast from pointer to integer of different size
iohb.c:328: warning: cast from pointer to integer of different size
iohb.c:346: warning: cast from pointer to integer of different size
iohb.c:347: warning: cast from pointer to integer of different size
iohb.c:348: warning: cast from pointer to integer of different size
iohb.c:349: warning: cast from pointer to integer of different size
iohb.c:362: warning: cast from pointer to integer of different size
iohb.c:305: warning: ignoring return value of ‘fgets’, declared with
attribute warn_unused_result
iohb.c:313: warning: ignoring return value of ‘fgets’, declared with
attribute warn_unused_result
iohb.c:323: warning: ignoring return value of ‘fgets’, declared with
attribute warn_unused_result
iohb.c:336: warning: ignoring return value of ‘fgets’, declared with
attribute warn_unused_result
iohb.c:354: warning: ignoring return value of ‘fgets’, declared with
attribute warn_unused_result
iohb.c: In function ‘readHB_mat_double’:
iohb.c:423: warning: cast from pointer to integer of different size
iohb.c:446: warning: cast from pointer to integer of different size
iohb.c:474: warning: cast from pointer to integer of different size
iohb.c:427: warning: ignoring return value of ‘fgets’, declared with
attribute warn_unused_result
iohb.c:450: warning: ignoring return value of ‘fgets’, declared with
attribute warn_unused_result
iohb.c:478: warning: ignoring return value of ‘fgets’, declared with
attribute warn_unused_result
iohb.c: In function ‘readHB_aux_double’:
iohb.c:660: warning: cast from pointer to integer of different size
iohb.c:627: warning: ignoring return value of ‘fgets’, declared with
attribute warn_unused_result
iohb.c:638: warning: ignoring return value of ‘fgets’, declared with
attribute warn_unused_result
iohb.c:645: warning: ignoring return value of ‘fgets’, declared with
attribute warn_unused_result
iohb.c:665: warning: ignoring return value of ‘fgets’, declared with
attribute warn_unused_result
iohb.c:693: warning: ignoring return value of ‘fgets’, declared with
attribute warn_unused_result
iohb.c: In function ‘readHB_mat_char’:
iohb.c:975: warning: cast from pointer to integer of different size
iohb.c:998: warning: cast from pointer to integer of different size
iohb.c:1026: warning: cast from pointer to integer of different size
iohb.c:979: warning: ignoring return value of ‘fgets’, declared with
attribute warn_unused_result
iohb.c:1002: warning: ignoring return value of ‘fgets’, declared with
attribute warn_unused_result
iohb.c:1030: warning: ignoring return value of ‘fgets’, declared with
attribute warn_unused_result
iohb.c: In function ‘readHB_aux_char’:
iohb.c:1192: warning: ignoring return value of ‘fgets’, declared with
attribute warn_unused_result
iohb.c:1203: warning: ignoring return value of ‘fgets’, declared with
attribute warn_unused_result
iohb.c:1213: warning: ignoring return value of ‘fgets’, declared with
attribute warn_unused_result
iohb.c:1231: warning: ignoring return value of ‘fgets’, declared with
attribute warn_unused_result
iohb.c:1262: warning: ignoring return value of ‘fgets’, declared with
attribute warn_unused_result
iohb.c: In function ‘ParseRfmt’:
iohb.c:1537: warning: cast from pointer to integer of different size
iohb.c:1547: warning: cast from pointer to integer of different size
iohb.c:1551: warning: cast from pointer to integer of different size
iohb.c: In function ‘substr’:
iohb.c:1585: warning: cast from pointer to integer of different size
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -O3 -pipe
-g -c readwrite.c -o readwrite.o
readwrite.c: In function ‘read_HB1’:
readwrite.c:33: warning: cast from pointer to integer of different size
gfortran -fpic -O3 -pipe -g -c sparskit.f -o sparskit.o
gfortran -fpic -O3 -pipe -g -c subscr.f -o subscr.o
gcc -std=gnu99 -shared -o SparseM.so bckslv.o chol.o chol2csr.o
cholesky.o csr.o extract.o iohb.o readwrite.o sparskit.o subscr.o
-lgfortran -lm -lquadmath -L/usr/lib/R/lib -lR
/usr/bin/ld: cannot find -lgfortran
/usr/bin/ld: cannot find -lquadmath
collect2: ld returned 1 exit status
make: *** [SparseM.so] Error 1
ERROR: compilation failed for package ‘SparseM’
* removing ‘/home/erin/R/x86_64-pc-linux-gnu-library/2.15/SparseM’
The downloaded source packages are in
‘/tmp/RtmprWTQJN/downloaded_packages’
Warning message:
In install.packages("SparseM", depen = TRUE) :
installation of package ‘SparseM’ had non-zero exit status
It can't seem to find -lgfortran. However, the gfortran exists.
I doubt the libraries are in one of the standard location that are
looked up.
This is one of those Linux packaging dogmas that keep on catching out
people.
For run-time use, there is /usr/lib64/libgfortran.so.3 (and perhaps
other versions): for linking you need libgfortran.so .
I am presuming this is an *Ubuntu* 11.10 system (that is not a Linux
number). On that system, the runtime libs are in libgfortran3, and
libgfortran.so is in gfortran-4.6-multilib.
I suggest you follow the advice of the R manuals and install r-base-dev,
which will pull in all the pieces you need to build R or most packages.
Best,
Uwe
Any suggestions would be most welcome.
thanks in advance,
Sincerely,
Erin
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--
Brian D. Ripley, rip...@stats.ox.ac.uk
Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/
University of Oxford, Tel: +44 1865 272861 (self)
1 South Parks Road, +44 1865 272866 (PA)
Oxford OX1 3TG, UK Fax: +44 1865 272595
______________________________________________
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.
