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Error in installing while using fftw #223

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mohseniaref opened this issue Jul 13, 2016 · 1 comment
Closed

Error in installing while using fftw #223

mohseniaref opened this issue Jul 13, 2016 · 1 comment

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@mohseniaref
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Hi,

Would you please guide me how to solve this problem?

best regards,
Mohammad Mohseni Aref

install.packages("Rssa")
--2016-07-13 18:57:53-- https://cran.mtu.edu/src/contrib/Rssa_0.13-1.tar.gz
Resolving cran.mtu.edu (cran.mtu.edu)... 141.219.191.249
Connecting to cran.mtu.edu (cran.mtu.edu)|141.219.191.249|:443... connected.
HTTP request sent, awaiting response... 200 OK
Length: 1033571 (1009K) [application/x-gzip]
Saving to: ‘/tmp/Rtmp1ptmKz/downloaded_packages/Rssa_0.13-1.tar.gz’

 0K .......... .......... .......... .......... ..........  4%  146K 7s
50K .......... .......... .......... .......... ..........  9%  292K 5s

100K .......... .......... .......... .......... .......... 14% 10.8M 3s
150K .......... .......... .......... .......... .......... 19% 299K 3s
200K .......... .......... .......... .......... .......... 24% 8.95M 2s
250K .......... .......... .......... .......... .......... 29% 11.1M 2s
300K .......... .......... .......... .......... .......... 34% 11.8M 1s
350K .......... .......... .......... .......... .......... 39% 318K 1s
400K .......... .......... .......... .......... .......... 44% 10.4M 1s
450K .......... .......... .......... .......... .......... 49% 10.6M 1s
500K .......... .......... .......... .......... .......... 54% 10.2M 1s
550K .......... .......... .......... .......... .......... 59% 11.6M 1s
600K .......... .......... .......... .......... .......... 64% 9.86M 0s
650K .......... .......... .......... .......... .......... 69% 11.6M 0s
700K .......... .......... .......... .......... .......... 74% 354K 0s
750K .......... .......... .......... .......... .......... 79% 11.1M 0s
800K .......... .......... .......... .......... .......... 84% 9.93M 0s
850K .......... .......... .......... .......... .......... 89% 10.5M 0s
900K .......... .......... .......... .......... .......... 94% 11.7M 0s
950K .......... .......... .......... .......... .......... 99% 11.1M 0s
1000K ......... 100% 12.4M=1.0s

2016-07-13 18:57:55 (962 KB/s) - ‘/tmp/Rtmp1ptmKz/downloaded_packages/Rssa_0.13-1.tar.gz’ saved [1033571/1033571]

  • installing source package ‘Rssa’ ...
    ** package ‘Rssa’ successfully unpacked and MD5 sums checked
    checking for gcc... gcc -std=gnu99
    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 -std=gnu99 accepts -g... yes
    checking for gcc -std=gnu99 option to accept ISO C89... none needed
    checking how to run the C preprocessor... gcc -std=gnu99 -E
    checking for grep that handles long lines and -e... /bin/grep
    checking for egrep... /bin/grep -E
    checking for ANSI C header files... yes
    checking for sys/types.h... yes
    checking for sys/stat.h... yes
    checking for stdlib.h... yes
    checking for string.h... yes
    checking for memory.h... yes
    checking for strings.h... yes
    checking for inttypes.h... yes
    checking for stdint.h... yes
    checking for unistd.h... yes
    checking fftw3.h usability... yes
    checking fftw3.h presence... yes
    checking for fftw3.h... yes
    checking for fftw_execute in -lfftw3... yes
    configure: creating ./config.status
    config.status: creating src/Makevars
    config.status: creating R/init.R
    config.status: creating src/config.h
    ** libs
    gcc -std=gnu99 -I/home/geodesy/software/rbase/R-3.1.3/include -DNDEBUG -I/usr/local/include -I. -I. -fpic -g -O2 -c extmat.c -o extmat.o
    gcc -std=gnu99 -I/home/geodesy/software/rbase/R-3.1.3/include -DNDEBUG -I/usr/local/include -I. -I. -fpic -g -O2 -c hankel.c -o hankel.o
    gcc -std=gnu99 -I/home/geodesy/software/rbase/R-3.1.3/include -DNDEBUG -I/usr/local/include -I. -I. -fpic -g -O2 -c hbhankel.c -o hbhankel.o
    gcc -std=gnu99 -I/home/geodesy/software/rbase/R-3.1.3/include -DNDEBUG -I/usr/local/include -I. -I. -fpic -g -O2 -c masks.c -o masks.o
    gcc -std=gnu99 -I/home/geodesy/software/rbase/R-3.1.3/include -DNDEBUG -I/usr/local/include -I. -I. -fpic -g -O2 -c toeplitz.c -o toeplitz.o
    gcc -std=gnu99 -shared -L/home/geodesy/software/rbase/R-3.1.3/lib -L/usr/local/lib -o Rssa.so extmat.o hankel.o hbhankel.o masks.o toeplitz.o -lfftw3 -L/home/geodesy/software/rbase/R-3.1.3/lib -lR
    /usr/bin/ld: /usr/local/lib/libfftw3.a(mapflags.o): relocation R_X86_64_32 against `.rodata' can not be used when making a shared object; recompile with -fPIC
    /usr/local/lib/libfftw3.a: error adding symbols: Bad value
    collect2: error: ld returned 1 exit status
    make: *** [Rssa.so] Error 1
    ERROR: compilation failed for package ‘Rssa’
  • removing ‘/home/geodesy/software/rbase/R-3.1.3/library/Rssa’
    Warning in install.packages :
    installation of package ‘Rssa’ had non-zero exit status

The downloaded source packages are in
‘/tmp/Rtmp1ptmKz/downloaded_packages’
Updating HTML index of packages in '.Library'
Making 'packages.html' ... done

@asl
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asl commented Jul 13, 2016

Looks like you have fftw installed improperly (e.g. "by hands"). I would suggest you to install it via package manager on your distribution.

@asl asl closed this as completed Aug 15, 2017
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