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  • trouble installing PennCNV

    Hi
    I am trying to install PennCNV on mac os x 10.8.
    The text file is not running so I am trying to re-compile acording to instructions on homepage: http://www.openbioinformatics.org/pe...#_Toc214817843

    after typing make I get this error massage:
    khmm_wrap.c:288:20: error: string.h: No such file or directory

    However string.h is in this folder:
    /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.8.sdk/usr/include/string.h

    which is permanently part of my PATH: $echo $PATH /usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.8.sdk/usr/include/

    So what is going wrong?

  • #2
    Hi
    I am also trying to install PennCNV in mac (10.6.8)
    Was wondering if you were able to install it.
    I modified the Makefile as is given on PennCNV site.
    on running make I don't get any error but warning

    kc.c: In function ‘kcwarn’:
    kc.c:200: warning: format not a string literal and no format arguments

    However when I run ./detect_cnv.pl
    I get the error

    PennCNV compilation error: Can't locate loadable object for module khmm in @INC (@INC contains: ./ ./kext /Library/Perl/Updates/5.10.0/darwin-thread-multi-2level /Library/Perl/Updates/5.10.0 /System/Library/Perl/5.10.0/darwin-thread-multi-2level /System/Library/Perl/5.10.0 /Library/Perl/5.10.0/darwin-thread-multi-2level /Library/Perl/5.10.0 /Network/Library/Perl/5.10.0/darwin-thread-multi-2level /Network/Library/Perl/5.10.0 /Network/Library/Perl /System/Library/Perl/Extras/5.10.0/darwin-thread-multi-2level /System/Library/Perl/Extras/5.10.0 .) at kext/khmm.pm line 8
    Compilation failed in require at ./detect_cnv.pl line 10.

    PennCNV compilation error: Your system architecture is 'darwin-thread-multi-2level', which is not compatible with pre-compiled executables in PennCNV package.
    PennCNV compilation error: Please download source code from http://www.openbioinformatics.org/penncnv and compile executable program.

    Not sure what I should check for.

    Would be great if you could help me.

    Best
    shruti

    Comment


    • #3
      It appears that khmm.pm is not being loaded because the directory that has that file is not included in the @INC path.

      You can try one of the two methods mentioned at the beginning in this post.

      Comment


      • #4
        Same error

        Hi
        I encountered the same error as "shruti".

        $ ./detect_cnv.pl
        PennCNV compilation error: Can't locate loadable object for module khmm in @INC (@INC contains: ./ ./kext /./kext/ /usr/lib/perl5/site_perl/5.14/x86_64-cygwin-threads /usr/lib/perl5/site_perl/5.14 /usr/lib/perl5/vendor_perl/5.14/x86_64-cygwin-threads /usr/lib/perl5/vendor_perl/5.14 /usr/lib/perl5/5.14/x86_64-cygwin-threads /usr/lib/perl5/5.14 .) at khmm.pm line 8
        Compilation failed in require at ./detect_cnv.pl line 10.

        PennCNV compilation error: Your system architecture is 'cygwin-thread-multi', which is not compatible with pre-compiled executables in PennCNV package.
        PennCNV compilation error: Please download source code from http://www.openbioinformatics.org/penncnv and compile executable program.


        I tried to fix it by adding
        use lib "./kext";
        use khmm;
        in the detect_cnv.pl as suggested in perlmonk, but it didn't work.

        Is anyone who did overcome the error?
        Thank you.

        Comment


        • #5
          Can you try providing full directory path for "ktext" instead of just ./ for the "use lib" directive?

          Comment


          • #6
            Thank you for your reply, GenoMax

            This time I have inserted these two lines in detect_cnv.pl
            ...
            BEGIN {($_=$0)=~s{[^\\\/]+$}{};$_||="./"}
            use lib $_, $_."kext";
            use lib "/cygdrive/c/program files/affymetrix/gw6cnv/kext"; <---here
            use khmm; <--- and here

            eval {
            require "khmm.pm";
            };

            ...

            and the result is slightly different but much the same:
            $ ./detect_cnv.pl
            Can't locate loadable object for module khmm in @INC (@INC contains: /cygdrive/c/program files/affymetrix/gw6cnv/kext ./ ./kext /usr/lib/perl5/site_perl/5.14/x86_64-cygwin-threads /usr/lib/perl5/site_perl/5.14 /usr/lib/perl5/vendor_perl/5.14/x86_64-cygwin-threads /usr/lib/perl5/vendor_perl/5.14 /usr/lib/perl5/5.14/x86_64-cygwin-threads /usr/lib/perl5/5.14 .) at /cygdrive/c/program files/affymetrix/gw6cnv/kext/khmm.pm line 8
            Compilation failed in require at ./detect_cnv.pl line 10.
            BEGIN failed--compilation aborted at ./detect_cnv.pl line 10.


            ---
            Is there anything wrong ?
            ( I am not a programming expert at all, as you see.)
            Anyway I appreciate your comment very much.

            Karoon
            Bet Regards

            Comment


            • #7
              I am not a cygwin expert but I think you may need to escape the space in "program files" name.

              Try this:

              Code:
              use lib "/cygdrive/c/program\ files/affymetrix/gw6cnv/kext"

              Comment


              • #8
                Thank you, GenoMax.
                I tried as suggested, but got much the same result
                (inserted two lines in the same place in detect_cnv.pl):
                ---
                $ ./detect_cnv.pl
                Can't locate loadable object for module khmm in @INC (@INC contains: /cygdrive/c/program files/affymetrix/gw6cnv/kext ./ ./kext /usr/lib/perl5/site_perl/5.14/x86_64-cygwin-threads /usr/lib/perl5/site_perl/5.14 /usr/lib/perl5/vendor_perl/5.14/x86_64-cygwin-threads /usr/lib/perl5/vendor_perl/5.14 /usr/lib/perl5/5.14/x86_64-cygwin-threads /usr/lib/perl5/5.14 .) at /cygdrive/c/program files/affymetrix/gw6cnv/kext/khmm.pm line 8
                Compilation failed in require at ./detect_cnv.pl line 10.
                BEGIN failed--compilation aborted at ./detect_cnv.pl line 10.
                ----
                I am grateful if there are any more suggestions.
                Thank you

                Karoon
                Best Regards

                Comment


                • #9
                  Have you already taken into account the instructions for PennCNV install for windows here: http://www.openbioinformatics.org/pe...#_Toc214817843

                  Comment


                  • #10
                    Thank you GenoMax,
                    but I already saw the page and tried as instructed.
                    Maybe something is wrong with the Makefile, so I am going to check it again.


                    Karoon
                    Best Regards

                    Comment


                    • #11
                      Hi, I have the same problem as you and even following the instructions here http://penncnv.openbioinformatics.or...#_Toc214817843 I cant solve it.

                      The same error occurs.

                      Any lights?

                      Thank you

                      Comment


                      • #12
                        I managed to successfully install PennCNV

                        Hi cicconella,

                        I read the same webpage ( http://penncnv.openbioinformatics.or...#_Toc214817843 ) again and did exactly as instructed in "Compilation in Windows" section (a year ago).
                        That is, I installed MinGW and MSYS, and compiled from the sourcecodes. I don't know why it worked, but anyway I did exactly as the instruction in the webpage says.
                        I already installed PennCNV and finished analyses a year ago and do not remember well the details of installation. I am writing this answer looking back my programming note which was recorded at that time.

                        I appreciate GenoMax for kind answers.

                        Good luck,
                        Karoon

                        Comment


                        • #13
                          Recently, I encountered the same questions in Linux. I solved the problem by following instructions from http://penncnv.openbioinformatics.or...on-from-source (Installation trouble shooting at the bottom of this page).
                          The related scripts how I solved it are as follows:
                          $ locate khmm.so
                          /home/biosoft/penncnv/kext/5.10.1/x86_64-linux-thread-multi/khmm.so
                          /home/biosoft/penncnv/kext/5.14.2/x86_64-linux-thread-multi/khmm.so
                          ## Here, we could see that the compatiable perl versions for Linux (*.so) are 5.10.1 and 5.14.2. Thus, I used perlbrew to install the corresponding perl version.
                          $ wget -O - https://raw.githubusercontent.com/gu...rlbrew-install | sh
                          $ source ~/perl5/perlbrew/etc/bashrc
                          $ perlbrew install perl-5.14.2 --thread --multi
                          $ perlbrew use perl-5.14.2
                          $ cd /home/biosoft/penncnv/example && perl ../detect_cnv.pl -test -hmm example.hmm -pfb example.pfb -conf -log ex1.log -out ex1.rawcnv father.txt mother.txt offspring.txt ## Success without error!
                          NOTICE: All program notification/warning messages that appear in STDERR will be also written to log file ex1.log
                          NOTICE: Reading marker coordinates and population frequency of B allele (PFB) from example.pfb ... Done with 93129 records
                          NOTICE: Reading LRR and BAF values for from father.txt ... Done with 93129 records in 4 chromosomes
                          NOTICE: Data from chromosome X will not be used in analysis
                          NOTICE: Median-adjusting LRR values for all autosome markers from father.txt by 0.0221
                          NOTICE: Median-adjusting BAF values for all autosome markers from father.txt by 0.0029
                          NOTICE: quality summary for father.txt: LRR_mean=0.0027 LRR_median=0.0000 LRR_SD=0.1335 BAF_mean=0.5063 BAF_median=0.5000 BAF_SD=0.0390 BAF_DRIFT=0.000037 WF=0.0184 GCWF=0.0136
                          NOTICE: Reading LRR and BAF values for from mother.txt ... Done with 93129 records in 4 chromosomes
                          NOTICE: Data from chromosome X will not be used in analysis
                          NOTICE: Median-adjusting LRR values for all autosome markers from mother.txt by -0.0199
                          NOTICE: Median-adjusting BAF values for all autosome markers from mother.txt by 0.0324
                          NOTICE: quality summary for mother.txt: LRR_mean=0.0039 LRR_median=0.0000 LRR_SD=0.1374 BAF_mean=0.5044 BAF_median=0.5000 BAF_SD=0.0418 BAF_DRIFT=0.000140 WF=0.0100 GCWF=0.0028
                          NOTICE: Reading LRR and BAF values for from offspring.txt ... Done with 93129 records in 4 chromosomes
                          NOTICE: Data from chromosome X will not be used in analysis
                          NOTICE: Median-adjusting LRR values for all autosome markers from offspring.txt by -0.0087
                          NOTICE: Median-adjusting BAF values for all autosome markers from offspring.txt by 0.0260
                          NOTICE: quality summary for offspring.txt: LRR_mean=0.0028 LRR_median=0.0000 LRR_SD=0.1263 BAF_mean=0.5045 BAF_median=0.5000 BAF_SD=0.0429 BAF_DRIFT=0.000293 WF=-0.0171 GCWF=-0.0100
                          08:34:14 root@localhost /home/biosoft/penncnv/example
                          I think the solution for other platform like windows will be similar to this. Hope it help you all!

                          Good luck,
                          Xinwu Guo

                          Comment


                          • #14
                            Originally posted by Karoon View Post
                            Thank you GenoMax,
                            but I already saw the page and tried as instructed.
                            Maybe something is wrong with the Makefile, so I am going to check it again.


                            Karoon
                            Best Regards
                            What change the Makefile?
                            I try to install PennCNV in linux server, but again to again error. T.T

                            This error ......

                            hyeonji/src/PennCNV-1.0.3$ perl detect_cnv.pl
                            PennCNV compilation error: Can't locate loadable object for module khmm in @INC (@INC contains: ./ ./kext /data/hyeonji/src/mirdeep2_0_0_7/lib/perl5 /etc/perl /usr/local/lib/perl/5.18.2 /usr/local/share/perl/5.18.2 /usr/lib/perl5 /usr/share/perl5 /usr/lib/perl/5.18 /usr/share/perl/5.18 /usr/local/lib/site_perl .) at kext/khmm.pm line 11.
                            Compilation failed in require at detect_cnv.pl line 10.

                            PennCNV compilation error: Your system architecture is 'x86_64-linux-gnu-thread-multi', which is not compatible with pre-compiled executables in PennCNV package.
                            PennCNV compilation error: Please download source code from http://www.openbioinformatics.org/penncnv and compile executable program.

                            I guess that probelm is no change Makefile. How solved you?

                            Thanks,
                            Hyeonji

                            Comment

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