HDF5 download and compile error #371

conchoecia · 2018-04-20T04:26:33Z

When I try to compile nanopolish allowing it to download and compile all of its dependencies, it fails with the following error:

config.status: executing libtool commands
	    SUMMARY OF THE HDF5 CONFIGURATION
	    =================================

General Information:
-------------------
		   HDF5 Version: 1.8.14
		  Configured on: Thu Apr 19 21:23:56 PDT 2018
		  Configured by: root@erenna
		 Configure mode: production
		    Host system: x86_64-unknown-linux-gnu
	      Uname information: Linux erenna 4.4.0-59-generic #80-Ubuntu SMP Fri Jan 6 17:47:47 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux
		       Byte sex: little-endian
		      Libraries: static, shared
	     Installation point: /usr/local/bin/nanopolish/hdf5-1.8.14/..

Compiling Options:
------------------
               Compilation Mode: production
                     C Compiler: /usr/bin/gcc
                         CFLAGS:
                      H5_CFLAGS:   -ansi -pedantic -Wall -W -Wundef -Wshadow -Wpointer-arith -Wbad-function-cast -Wcast-qual -Wcast-align -Wwrite-strings -Wconversion -Waggregate-return -Wstrict-prototypes -Wmissing-prototypes -Wmissing-declarations -Wredundant-decls -Wnested-externs -Winline -O -fomit-frame-pointer -finline-functions
                      AM_CFLAGS:
                       CPPFLAGS:
                    H5_CPPFLAGS: -D_POSIX_C_SOURCE=199506L   -DNDEBUG -UH5_DEBUG_API
                    AM_CPPFLAGS: -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_BSD_SOURCE
               Shared C Library: yes
               Static C Library: yes
  Statically Linked Executables: no
                        LDFLAGS:
                     H5_LDFLAGS:
                     AM_LDFLAGS:  -L/usr/local/bin/nanopolish/hdf5-1.8.14/../lib
 	 	Extra libraries:  -lpthread -lz -ldl -lm
 		       Archiver: ar
 		 	 Ranlib: ranlib
 	      Debugged Packages:
		    API Tracing: no

Languages:
----------
                        Fortran: no

                            C++: no

Features:
---------
                  Parallel HDF5: no
             High Level library: yes
                   Threadsafety: yes
            Default API Mapping: v18
 With Deprecated Public Symbols: yes
         I/O filters (external): deflate(zlib)
         I/O filters (internal): shuffle,fletcher32,nbit,scaleoffset
                            MPE: no
                     Direct VFD: no
                        dmalloc: no
Clear file buffers before write: yes
           Using memory checker: no
         Function Stack Tracing: no
      Strict File Format Checks: no
   Optimization Instrumentation: no
       Large File Support (LFS): yes
make[1]: Entering directory '/usr/local/bin/nanopolish/hdf5-1.8.14'
Making all in src
make[2]: Entering directory '/usr/local/bin/nanopolish/hdf5-1.8.14/src'
make  all-am
make[3]: Entering directory '/usr/local/bin/nanopolish/hdf5-1.8.14/src'
  CC       H5.lo
In file included from /usr/local/include/assert.h:5:0,
                 from H5private.h:50,
                 from H5.c:24:
/usr/local/include/except.h:5:44: fatal error: config.h: No such file or directory
compilation terminated.
Makefile:1222: recipe for target 'H5.lo' failed
make[3]: *** [H5.lo] Error 1
make[3]: Leaving directory '/usr/local/bin/nanopolish/hdf5-1.8.14/src'
Makefile:850: recipe for target 'all' failed
make[2]: *** [all] Error 2
make[2]: Leaving directory '/usr/local/bin/nanopolish/hdf5-1.8.14/src'
Makefile:586: recipe for target 'all-recursive' failed
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory '/usr/local/bin/nanopolish/hdf5-1.8.14'
Makefile:88: recipe for target 'lib/libhdf5.a' failed
make: *** [lib/libhdf5.a] Error 2

The text was updated successfully, but these errors were encountered:

jts · 2018-04-20T13:45:08Z

What operating system are you using?

Can you send me the entire log from when you run make?

Jared

conchoecia · 2018-04-20T19:25:28Z

I have attached the log. I am using Ubuntu 16. Thank you for taking a look!

nanopolish_make_ubuntu16.txt

jts · 2018-04-20T20:22:50Z

Have you built nanopolish on this machine before?

conchoecia · 2018-04-20T22:27:27Z

Yes, I believe that each time I just built the package with the default command, make, and did not install the dependencies on the system otherwise.

jts · 2018-04-23T13:24:53Z

Which version of GCC are you using?

conchoecia · 2018-04-23T13:57:47Z

I am using:

gcc (Ubuntu 5.4.1-2ubuntu1~16.04) 5.4.1 20160904

Maybe that is the reason it isn't working, after all? I may just end up using the Docker image.

jts · 2018-04-23T14:00:09Z

I haven't tested it with that version of GCC. If you can install gcc-4.8 through your package manager, it would be very useful in figuring out where the problem is.

Jared

conchoecia · 2018-04-23T14:05:53Z

I switched to gcc 4.8 and it appears that another problem with pthreads has cropped up.

Cheers
Darrin

compile_with_4.8.txt

jts · 2018-05-14T20:28:55Z

Sorry for leaving this issue. Is it still a problem or did you find a way around it?

Jared

conchoecia · 2018-05-14T21:37:57Z

I didn't end up finding a solution, and have only lightly searched to try to solve the problem. I'm kind of a make newbie so haven't tried to edit the Makefile much, either.

jts · 2018-05-15T19:38:33Z

Can you try installing it as a normal user (without root privileges) in a location outside of /usr/?

conchoecia · 2018-05-16T17:37:30Z

It failed in the same way, I think:

normal_fail.txt

jts · 2018-05-16T19:20:57Z

can you run ls -ltr /usr/local/include and send me the contents?

jts · 2018-05-16T19:29:53Z

Also can you run echo | gcc -E -Wp,-v - and send the result as well

jts · 2018-05-16T20:41:24Z

Ok we (I've had help from @larsgt and @usajusaj) think we know what happened. In a different repository someone reported a similar problem:

ContinuumIO/anaconda-issues#7047

The problem in this case was traced to the gmap program. I looked in the gmap source and it includes assert.h and except.h. I suspect you've installed gmap and it wrote its headers into /usr/local/include. gcc has mistakenly picked up gmap's assert.h instead of the C standard library version (this is a very unfortunate name to use). This causes the HDF5/nanopolish compilation to fail.

Unfortunately there is nothing I can do to fix this. You are likely to run into compilation issues with other software packages as well. You'll have to find a way to clean up the bad headers.

Jared

conchoecia · 2018-05-17T21:31:08Z

Yeah... @brianjohnhaas said that this was causing some issues in the Trinity install as well. Let me get back to you on this one in a few days....

Thanks for the sleuthing!

Darrin

conchoecia · 2018-05-24T07:31:29Z

You were right! I renamed those headers and nanopolish compiled fine. Now we just need to track down those GMAP devs and talk to them about dumping headers into /usr/local/include...

brianjohnhaas · 2018-05-24T11:57:12Z

I think the newest versions of gmap behave themselves wrt the header issue. The gmap author knows about the conflicts introduced in the earlier release and had remedied it. Still worth writing him just to confirm.

…

On Thu, May 24, 2018 at 3:31 AM, darrin t schultz ***@***.***> wrote: You were right! I renamed those headers and nanopolish compiled fine. Now we just need to track down those GMAP devs and talk to them about dumping headers into /usr/local/include... — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#371 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AHMVX-DT5Xdl7D2HjggiUSOJ2guPE38qks5t1mHTgaJpZM4Tc2hJ> .

-- -- Brian J. Haas The Broad Institute http://broadinstitute.org/~bhaas <http://broad.mit.edu/~bhaas>

jts · 2018-05-24T12:33:16Z

Thanks @brianjohnhaas, it is good to hear this is being fixed by gmap for everyone.

jts added the awaiting followup label May 14, 2018

jts closed this as completed May 28, 2018

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HDF5 download and compile error #371

HDF5 download and compile error #371

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HDF5 download and compile error #371

HDF5 download and compile error #371

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