Skip to content

Instantly share code, notes, and snippets.

@gawbul
Created June 15, 2015 09:20
Show Gist options
  • Save gawbul/8b3fdaa4c6ea2a084d7c to your computer and use it in GitHub Desktop.
Save gawbul/8b3fdaa4c6ea2a084d7c to your computer and use it in GitHub Desktop.
poretools error
[smoss@bioservd ~]$ poretools
Warning! ***HDF5 library version mismatched error***
The HDF5 header files used to compile this application do not match
the version used by the HDF5 library to which this application is linked.
Data corruption or segmentation faults may occur if the application continues.
This can happen when an application was compiled by one version of HDF5 but
linked with a different version of static or shared HDF5 library.
You should recompile the application or check your shared library related
settings such as 'LD_LIBRARY_PATH'.
You can, at your own risk, disable this warning by setting the environment
variable 'HDF5_DISABLE_VERSION_CHECK' to a value of '1'.
Setting it to 2 or higher will suppress the warning messages totally.
Headers are 1.8.8, library is 1.8.14
SUMMARY OF THE HDF5 CONFIGURATION
=================================
General Information:
-------------------
HDF5 Version: 1.8.14
Configured on: Mon Jun 15 09:56:15 BST 2015
Configured by: smoss@bioservd
Configure mode: production
Host system: x86_64-unknown-linux-gnu
Uname information: Linux bioservd 3.2.0-4-amd64 #1 SMP Debian 3.2.54-2 x86_64 GNU/Linux
Byte sex: little-endian
Libraries: static, shared
Installation point: /home/smoss/.linuxbrew/Cellar/hdf5/1.8.14
Compiling Options:
------------------
Compilation Mode: production
C Compiler: /home/smoss/.linuxbrew/bin/gcc-5
CFLAGS: -Os -w -pipe -march=core2
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: -isystem/home/smoss/.linuxbrew/include
H5_CPPFLAGS: -D_POSIX_C_SOURCE=199506L -DNDEBUG -UH5_DEBUG_API
AM_CPPFLAGS: -I/home/smoss/.linuxbrew/opt/szip/include -D_LARGEFILE_SOURCE -D_LARGEFILE64_SOURCE -D_BSD_SOURCE
Shared C Library: yes
Static C Library: yes
Statically Linked Executables: no
LDFLAGS: -L/home/smoss/.linuxbrew/lib -Wl,-rpath,/home/smoss/.linuxbrew/lib
H5_LDFLAGS:
AM_LDFLAGS: -L/home/smoss/.linuxbrew/Cellar/hdf5/1.8.14/lib -L/home/smoss/.linuxbrew/opt/szip/lib
Extra libraries: -lsz -lz -lrt -ldl -lm
Archiver: ar
Ranlib: ranlib
Debugged Packages:
API Tracing: no
Languages:
----------
Fortran: no
C++: yes
C++ Compiler: /home/smoss/.linuxbrew/bin/g++-5
C++ Flags: -Os -w -pipe -march=core2
H5 C++ Flags:
AM C++ Flags:
Shared C++ Library: yes
Static C++ Library: yes
Features:
---------
Parallel HDF5: no
High Level library: yes
Threadsafety: no
Default API Mapping: v18
With Deprecated Public Symbols: yes
I/O filters (external): deflate(zlib),szip(encoder)
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
Bye...
Aborted
@briantjacobs
Copy link

@gawbul, I'm running into a similar problem to this error. Did you figure out how to fix this?

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment