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Jit's questions

  • Jit
    16 days ago
    Questions (0)

    > install.packages(c('ddalpha', 'recipes')) 

      There is a binary version available but the source version is later:

            binary  source needs_compilation

    ddalpha  1.3.1 1.3.1.1              TRUE

     

    Do you want to install from sources the package which needs compilation?

    y/n: y

    trying URL 'https://mirrors.nic.cz/R/bin/macosx/el-capitan/contrib/3.4/recipes_0.1.2.tgz'

    Content type 'application/octet-stream' length 998818 bytes (975 KB)

    ==================================================

    downloaded 975 KB

     

     

    The downloaded binary packages are in

    /tmp/RtmpUg5Cs2/downloaded_packages

    installing the source package ‘ddalpha’

     

    trying URL 'https://mirrors.nic.cz/R/src/contrib/ddalpha_1.3.1.1.tar.gz'

    Content type 'application/octet-stream' length 543279 bytes (530 KB)

    ==================================================

    downloaded 530 KB

     

    * installing *source* package ‘ddalpha’ ...

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

    ** libs

    clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c AlphaProcedure.cpp -o AlphaProcedure.o

    clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c Common.cpp -o Common.o

    clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c DKnn.cpp -o DKnn.o

    clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c HD.cpp -o HD.o

    HD.cpp:25:14: warning: unused variable 'eps_Cmb1' [-Wunused-const-variable]

    const double eps_Cmb1 = 1e-8;

                 ^

    1 warning generated.

    clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c Knn.cpp -o Knn.o

    Knn.cpp:146:15: warning: unused variable 'd' [-Wunused-variable]

            unsigned int d = points[0].size();unsigned int n = points.size();

                         ^

    Knn.cpp:209:15: warning: unused variable 'd' [-Wunused-variable]

            unsigned int d = points[0].size();

                         ^

    2 warnings generated.

    clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c Mahalanobis.cpp -o Mahalanobis.o

    Mahalanobis.cpp:32:6: warning: unused variable 'res' [-Wunused-variable]

            int res = lu_factorize(A, pm);

                ^

    1 warning generated.

    clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c OjaDepth.cpp -o OjaDepth.o

    OjaDepth.cpp:44:8: warning: unused variable 'sc' [-Wunused-variable]

                    bool sc = numSimplicesChecked == div0;

                         ^

    1 warning generated.

    clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c Polynomial.cpp -o Polynomial.o

    Polynomial.cpp:396:18: warning: unused variable 'tmp' [-Wunused-variable]

            for (int i = 0, tmp; i < numPoints; i++){ input2[i][0] = input[i][1]; input2[i][1] = input[i][0]; } // swap columns

                            ^

    1 warning generated.

    clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c PotentialDepth.cpp -o PotentialDepth.o

    clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c ProjectionDepth.cpp -o ProjectionDepth.o

    ProjectionDepth.cpp:16:12: warning: unused function 'CompareAsc' [-Wunused-function]

    static int CompareAsc(OrderRec x, OrderRec y)

               ^

    ProjectionDepth.cpp:21:12: warning: unused function 'CompareDec' [-Wunused-function]

    static int CompareDec(OrderRec x, OrderRec y)

               ^

    2 warnings generated.

    clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c SimplicialDepth.cpp -o SimplicialDepth.o

    SimplicialDepth.cpp:46:8: warning: unused variable 'sc' [-Wunused-variable]

                    bool sc = numSimplicesChecked == div0;

                         ^

    1 warning generated.

    clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c TukeyDepth.cpp -o TukeyDepth.o

    clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c ZonoidDepth.cpp -o ZonoidDepth.o

    ZonoidDepth.cpp:63:25: warning: using the result of an assignment as a condition without parentheses [-Wparentheses]

        if ( RowInverted[j] = z[j] < 0 ) {

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

    ZonoidDepth.cpp:63:25: note: place parentheses around the assignment to silence this warning

        if ( RowInverted[j] = z[j] < 0 ) {

                            ^

             (                        )

    ZonoidDepth.cpp:63:25: note: use '==' to turn this assignment into an equality comparison

        if ( RowInverted[j] = z[j] < 0 ) {

                            ^

                            ==

    1 warning generated.

    clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c asa047.cpp -o asa047.o

    clang++ -std=gnu++11 -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/BH/include" -I"/Library/Frameworks/R.framework/Versions/3.4/Resources/library/Rcpp/include" -I/usr/local/include   -fPIC  -Wall -g -O2 -c ddalpha.cpp -o ddalpha.o

    gfortran   -fPIC  -g -O2  -c depth.fd.f -o depth.fd.o

    make: gfortran: No such file or directory

    make: *** [depth.fd.o] Error 1

    ERROR: compilation failed for package ‘ddalpha’

    * removing ‘/Library/Frameworks/R.framework/Versions/3.4/Resources/library/ddalpha’

     

    The downloaded source packages are in

    ‘/private/tmp/RtmpUg5Cs2/downloaded_packages’

    Warning message:

    In install.packages(c("ddalpha", "recipes")) :

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

  • Jit
    684 days ago
    Questions (1)

    I run SatsumaSynteny on my server using following command:

    [jit@hm satsuma-code-0]$ ./SatsumaSynteny -q Genome/renamedG.fa -t Genome/genome_v4.fasta -o Genome/OutFile -m 128 -ni 10 -n 256 -chain_only

    But it kill the program with followng error: 

    ./SatsumaSynteny: /lib64/libc.so.6: version `GLIBC_2.14' not found (required by ./SatsumaSynteny)

    Can anyone please help to resolve this.

    My server detail:

    [jit@hm satsuma-code-0]$ lscpu
    Architecture: x86_64
    CPU op-mode(s): 32-bit, 64-bit
    Byte Order: Little Endian
    CPU(s): 12
    On-line CPU(s) list: 0-11
    Thread(s) per core: 1
    Core(s) per socket: 6
    Socket(s): 2
    NUMA node(s): 2
    Vendor ID: AuthenticAMD
    CPU family: 16
    Model: 8
    Stepping: 1
    CPU MHz: 2600.186
    BogoMIPS: 5200.03
    Virtualization: AMD-V
    L1d cache: 64K
    L1i cache: 64K
    L2 cache: 512K
    L3 cache: 5118K
    NUMA node0 CPU(s): 0,2-6
    NUMA node1 CPU(s): 1,7-11