[R] trouble installing SparseM

[Uwe Ligges]

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.

Best,
Uwe



> Any suggestions would be most welcome.
>
> thanks in advance,
> Sincerely,
> Erin
>
>