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Ecogenomics / BamM

Metagenomics-focused BAM file manipulation
http://ecogenomics.github.io/BamM/
GNU Lesser General Public License v3.0
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libcfu/lib not included in code #39

Open osvatic opened 8 years ago

osvatic commented 8 years ago

I am running the standard install and it is not finding the libcfu/lib folder in the bundle.

error from setup.py: checking for libcfu headers in /home/labuser/BamM/c/libcfu-0.03/include... found checking for libcfu libraries in /home/labuser/BamM/c/libcfu-0.03/lib... not found configure: error: Cannot find libcfu Traceback (most recent call last): File "setup.py", line 31, in check_call([join(getcwd(), "configure")] + configure_args) File "/home/labuser/anaconda3/envs/py2.7.11/lib/python2.7/subprocess.py", line 541, in check_call raise CalledProcessError(retcode, cmd) subprocess.CalledProcessError: Command '['/home/labuser/BamM/c/configure']' returned non-zero exit status 1

Any place to get that?

timbalam commented 8 years ago

Hi osvatic,

Thanks for the report. Can you tell me which version of BamM you are installing? Can you also send me the full output of the setup.py command?

The lib folder is supposed to be built during the setup process, so something isn't working properly.

Regards, Tim

On 10/08/2016 3:06 AM, osvatic wrote:

I am running the standard install and it is not finding the libcfu/lib folder in the bundle.

error from setup.py: checking for libcfu headers in /home/labuser/BamM/c/libcfu-0.03/include... found checking for libcfu libraries in /home/labuser/BamM/c/libcfu-0.03/lib... not found configure: error: Cannot find libcfu Traceback (most recent call last): File "setup.py", line 31, in check_call([join(getcwd(), "configure")] + configure_args) File "/home/labuser/anaconda3/envs/py2.7.11/lib/python2.7/subprocess.py", line 541, in check_call raise CalledProcessError(retcode, cmd) subprocess.CalledProcessError: Command '['/home/labuser/BamM/c/configure']' returned non-zero exit status 1

Any place to get that?

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osvatic commented 8 years ago

I am installing the latest verison, just downloaded on Monday. Als, I am using a different version of autmake (1.14.1) than what it says generated the files originally.

Here is the entire install output:

(py2.7.11)labuser@Swingleylab-desktop:~/BamM$ sudo python setup.py install checking for gcc... gcc 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 accepts -g... yes checking for gcc option to accept ISO C89... none needed checking for g++... g++ checking whether we are using the GNU C++ compiler... yes checking whether g++ accepts -g... yes checking for lgamma,log,exp in -lm... yes libcfu location not specified - building from local version ./configure: line 2139: AM_INIT_AUTOMAKE: command not found ./configure: line 2141: AC_PROG_LIBTOOL: command not found checking for gcc... gcc 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 accepts -g... yes checking for gcc option to accept ISO C89... none needed checking for g++... g++ checking whether we are using the GNU C++ compiler... yes checking whether g++ accepts -g... yes checking for pthread_mutex_init... ./configure: line 1518: ac_fn_cxx_try_link: command not found no ./configure: line 5140: syntax error: unexpected end of file /bin/bash ./config.status --recheck running CONFIG_SHELL=/bin/bash /bin/bash ./configure --no-create --no-recursion ./configure: line 2139: AM_INIT_AUTOMAKE: command not found ./configure: line 2141: AC_PROG_LIBTOOL: command not found checking for gcc... gcc 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 accepts -g... yes checking for gcc option to accept ISO C89... none needed checking for g++... g++ checking whether we are using the GNU C++ compiler... yes checking whether g++ accepts -g... yes checking for pthread_mutex_init... ./configure: line 1518: ac_fn_cxx_try_link: command not found no ./configure: line 5140: syntax error: unexpected end of file make: *\ [config.status] Error 2 checking for libcfu headers in /home/labuser/BamM/c/libcfu-0.03/include... found checking for libcfu libraries in /home/labuser/BamM/c/libcfu-0.03/lib... not found configure: error: Cannot find libcfu Traceback (most recent call last): File "setup.py", line 31, in check_call([join(getcwd(), "configure")] + configure_args) File "/usr/lib/python2.7/subprocess.py", line 540, in check_call raise CalledProcessError(retcode, cmd) subprocess.CalledProcessError: Command '['/home/labuser/BamM/c/configure']' returned non-zero exit status 1

timbalam commented 8 years ago

Thanks,

There is an autogen.sh script in the 'c' directory of the BamM source. If it is some automake compatibility issue causing it to not work, running ./autogen.sh from the c directory first, and then trying python setup.py install again might fix it. Can you try that?

Regards, Tim

On 12/08/2016 1:23 AM, osvatic wrote:

I am installing the latest verison, just downloaded on Monday. Als, I am using a different version of autmake (1.14.1) than what it says generated the files originally.

Here is the entire install output:

(py2.7.11)labuser@Swingleylab-desktop:~/BamM$ sudo python setup.py install checking for gcc... gcc 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 accepts -g... yes checking for gcc option to accept ISO C89... none needed checking for g++... g++ checking whether we are using the GNU C++ compiler... yes checking whether g++ accepts -g... yes checking for lgamma,log,exp in -lm... yes libcfu location not specified - building from local version ./configure: line 2139: AM_INIT_AUTOMAKE: command not found ./configure: line 2141: AC_PROG_LIBTOOL: command not found checking for gcc... gcc 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 accepts -g... yes checking for gcc option to accept ISO C89... none needed checking for g++... g++ checking whether we are using the GNU C++ compiler... yes checking whether g++ accepts -g... yes checking for pthread_mutex_init... ./configure: line 1518: ac_fn_cxx_try_link: command not found no ./configure: line 5140: syntax error: unexpected end of file /bin/bash ./config.status --recheck running CONFIG_SHELL=/bin/bash /bin/bash ./configure --no-create --no-recursion ./configure: line 2139: AM_INIT_AUTOMAKE: command not found ./configure: line 2141: AC_PROG_LIBTOOL: command not found checking for gcc... gcc 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 accepts -g... yes checking for gcc option to accept ISO C89... none needed checking for g++... g++ checking whether we are using the GNU C++ compiler... yes checking whether g++ accepts -g... yes checking for pthread_mutex_init... ./configure: line 1518: ac_fn_cxx_try_link: command not found no ./configure: line 5140: syntax error: unexpected end of file make: *\ [config.status] Error 2 checking for libcfu headers in /home/labuser/BamM/c/libcfu-0.03/include... found checking for libcfu libraries in /home/labuser/BamM/c/libcfu-0.03/lib... not found configure: error: Cannot find libcfu Traceback (most recent call last): File "setup.py", line 31, in check_call([join(getcwd(), "configure")] + configure_args) File "/usr/lib/python2.7/subprocess.py", line 540, in check_call raise CalledProcessError(retcode, cmd) subprocess.CalledProcessError: Command '['/home/labuser/BamM/c/configure']' returned non-zero exit status 1

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geboro commented 7 years ago

This seems to be a problem with the automake version. In ubuntu 14.04, the latest release of automake is 1.14, but the compiler complains about requiring version 1.11. A downgrade fixed this: sudo apt-get install automake1.11

jvollme commented 7 years ago

I had the same issue and i can confirm that downgrading to automake1.11 fixed this. Maybe the dependencies info in the BamM manual should be changed to include the automake-version?

jvollme commented 7 years ago

BTW, I think this issue #44 is the same problem?

minillinim commented 7 years ago

To fix this I installed autoconf-archive to get the missing macros and then I went into the c/libcfu-0.03 folder and ran aclocal The python setup.py install route worked perfectly after that.

Not 100% sure if the autoconf-archive stuff was needed. but @timbalam, you may need to run the aclocal part and push the updated autogen.sh into the repo.

Hope this helps

EDIT: installing autoconf-archive is not needed

manifestoso commented 7 years ago

@minillinim completely agree. @timbalam should we update the documentation for v1.7.3. This version is likely to be only able to build by specific autoconf (v2.68) and automake (v1.11.3). Issue #48 filed.