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  • sbberes
    Member
    • Jan 2009
    • 22
    #1

    Maq make error on Ubuntu 9.04 64 bit

    Update: Searching the web found an Unbutu Maq patch that may address the issue.
    SBB

    Hello bioinformatics gurus,
    I am trying to run Maq under vmware fusion using an Unbuntu 64 bit virtual machine on my MacPro. I have the Maq linux 64 bit distribution. When I try to ./configure, make, make install, I get an error 2 message in make. Initially it suggested that maybe I needed to get the latest versions of Autoconf and GNU m4 - which I did. This did not solve the problem. Currently the problem seems to be associated with an inability to find zlib.h. I used the package manager to add the latest version of the zlib dev package, and specifically added zlib.h to my path. However ./configure still does not seem to be able to identify zlib.h, and make fails with the same error message. The ./configure and make output are below. Thanks in advance for any assistance.
    S. Beres
    Molecular biologist by training--Bioinformaticist by necessity

    sbberes@ubuntu:~/Desktop/Bioinformatics/MAQ/maq-0.7.1$ ./configure
    checking for a BSD-compatible install... /usr/bin/install -c
    checking whether build environment is sane... yes
    checking for a thread-safe mkdir -p... /bin/mkdir -p
    checking for gawk... no
    checking for mawk... mawk
    checking whether make sets $(MAKE)... yes
    checking build system type... x86_64-unknown-linux-gnu
    checking host system type... x86_64-unknown-linux-gnu
    checking for gcc... gcc
    checking for C compiler default output file name... a.out
    checking whether the C compiler works... yes
    checking whether we are cross compiling... no
    checking for suffix of executables...
    checking for suffix of object files... o
    checking whether we are using the GNU C compiler... yes
    checking whether gcc accepts -g... yes
    checking for gcc option to accept ISO C89... none needed
    checking for g++... no
    checking for c++... no
    checking for gpp... no
    checking for aCC... no
    checking for CC... no
    checking for cxx... no
    checking for cc++... no
    checking for cl.exe... no
    checking for FCC... no
    checking for KCC... no
    checking for RCC... no
    checking for xlC_r... no
    checking for xlC... no
    checking whether we are using the GNU C++ compiler... no
    checking whether g++ accepts -g... no
    checking if gcc accepts -m64... yes
    checking how to run the C preprocessor... gcc -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 zlib.h usability... no
    checking zlib.h presence... no
    checking for zlib.h... no
    configure: creating ./config.status
    config.status: creating Makefile
    config.status: creating config.h
    config.status: config.h is unchanged

    sbberes@ubuntu:~/Desktop/Bioinformatics/MAQ/maq-0.7.1$ make
    make all-am
    make[1]: Entering directory `/home/sbberes/Desktop/Bioinformatics/MAQ/maq-0.7.1'
    gcc -DHAVE_CONFIG_H -I. -Wall -m64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -c main.c
    gcc -DHAVE_CONFIG_H -I. -Wall -m64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -c const.c
    gcc -DHAVE_CONFIG_H -I. -Wall -m64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -c seq.c
    gcc -DHAVE_CONFIG_H -I. -Wall -m64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -c bfa.c
    bfa.c:1:18: error: zlib.h: No such file or directory
    bfa.c: In function ‘nst_load_bfa1’:
    bfa.c:31: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result
    bfa.c:32: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result
    bfa.c:33: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result
    bfa.c:35: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result
    bfa.c:37: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result
    bfa.c: In function ‘nst_bfa_len’:
    bfa.c:46: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result
    bfa.c:48: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result
    make[1]: *** [bfa.o] Error 1
    make[1]: Leaving directory `/home/sbberes/Desktop/Bioinformatics/MAQ/maq-0.7.1'
    make: *** [all] Error 2
    Last edited by sbberes; 10-13-2009, 05:55 PM. Reason: update information
    Tags: None
    • nilshomer
      Nils Homer
      • Nov 2008
      • 1283
      #2
      Originally posted by sbberes View Post
      Hello bioinformatics gurus,
      I am trying to run Maq under vmware fusion using an Unbuntu 64 bit virtual machine on my MacPro. I have the Maq linux 64 bit distribution. When I try to ./configure, make, make install, I get an error 2 message in make. Initially it suggested that maybe I needed to get the latest versions of Autoconf and GNU m4 - which I did. This did not solve the problem. Currently the problem seems to be associated with an inability to find zlib.h. I used the package manager to add the latest version of the zlib dev package, and specifically added zlib.h to my path. However ./configure still does not seem to be able to identify zlib.h, and make fails with the same error message. The ./configure and make output are below. Thanks in advance for any assistance.
      S. Beres
      Molecular biologist by training--Bioinformaticist by necessity

      sbberes@ubuntu:~/Desktop/Bioinformatics/MAQ/maq-0.7.1$ ./configure
      checking for a BSD-compatible install... /usr/bin/install -c
      checking whether build environment is sane... yes
      checking for a thread-safe mkdir -p... /bin/mkdir -p
      checking for gawk... no
      checking for mawk... mawk
      checking whether make sets $(MAKE)... yes
      checking build system type... x86_64-unknown-linux-gnu
      checking host system type... x86_64-unknown-linux-gnu
      checking for gcc... gcc
      checking for C compiler default output file name... a.out
      checking whether the C compiler works... yes
      checking whether we are cross compiling... no
      checking for suffix of executables...
      checking for suffix of object files... o
      checking whether we are using the GNU C compiler... yes
      checking whether gcc accepts -g... yes
      checking for gcc option to accept ISO C89... none needed
      checking for g++... no
      checking for c++... no
      checking for gpp... no
      checking for aCC... no
      checking for CC... no
      checking for cxx... no
      checking for cc++... no
      checking for cl.exe... no
      checking for FCC... no
      checking for KCC... no
      checking for RCC... no
      checking for xlC_r... no
      checking for xlC... no
      checking whether we are using the GNU C++ compiler... no
      checking whether g++ accepts -g... no
      checking if gcc accepts -m64... yes
      checking how to run the C preprocessor... gcc -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 zlib.h usability... no
      checking zlib.h presence... no
      checking for zlib.h... no
      configure: creating ./config.status
      config.status: creating Makefile
      config.status: creating config.h
      config.status: config.h is unchanged

      sbberes@ubuntu:~/Desktop/Bioinformatics/MAQ/maq-0.7.1$ make
      make all-am
      make[1]: Entering directory `/home/sbberes/Desktop/Bioinformatics/MAQ/maq-0.7.1'
      gcc -DHAVE_CONFIG_H -I. -Wall -m64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -c main.c
      gcc -DHAVE_CONFIG_H -I. -Wall -m64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -c const.c
      gcc -DHAVE_CONFIG_H -I. -Wall -m64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -c seq.c
      gcc -DHAVE_CONFIG_H -I. -Wall -m64 -D_FASTMAP -DMAQ_LONGREADS -g -O2 -c bfa.c
      bfa.c:1:18: error: zlib.h: No such file or directory
      bfa.c: In function ‘nst_load_bfa1’:
      bfa.c:31: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result
      bfa.c:32: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result
      bfa.c:33: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result
      bfa.c:35: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result
      bfa.c:37: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result
      bfa.c: In function ‘nst_bfa_len’:
      bfa.c:46: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result
      bfa.c:48: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result
      make[1]: *** [bfa.o] Error 1
      make[1]: Leaving directory `/home/sbberes/Desktop/Bioinformatics/MAQ/maq-0.7.1'
      make: *** [all] Error 2

      Make sure you have zlib installed.

        Comment

        • simonandrews
          Simon Andrews
          • May 2009
          • 870
          #3
          Originally posted by sbberes View Post

          checking zlib.h presence... no
          checking for zlib.h... no


          bfa.c:1:18: error: zlib.h: No such file or directory
          make[1]: *** [bfa.o] Error 1
          As Nilshomer said the problem is the missing zlib.h, however there is a bug in maq as the configure should have failed if this was a requirement.

          A quick fix in ubuntu would be:

          sudo apt-get install zliblg-dev

            Comment

            • sbberes
              Member
              • Jan 2009
              • 22
              #4
              Thanks for the advice

              Thanks for the prompt feedback. The first thing I did when I got the error messages was check for zlibg and then run an install. However that did not seem to solve the problem. Reran the install this morning and now ./configure finds zlib. Maq make still failed now complaining that the version of autoconf was to new. Was able to solve the problem by installing the latest version of g++ and dependancies.

              Again thanks for the assistance.
              Steve Beres

                Comment

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