[Octave-bug-tracker] [bug #61349] Make check fails after library update

[Arun Giridhar]

URL:
  <https://savannah.gnu.org/bugs/?61349>

                 Summary: Make check fails after library update
                 Project: GNU Octave
            Submitted by: arungiridhar
            Submitted on: Mon 18 Oct 2021 11:16:14 AM EDT
                Category: Configuration and Build System
                Severity: 3 - Normal
                Priority: 5 - Normal
              Item Group: Build Failure
                  Status: None
             Assigned to: None
         Originator Name: 
        Originator Email: 
             Open/Closed: Open
                 Release: dev
         Discussion Lock: Any
        Operating System: GNU/Linux

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Details:

After a recent system update that updated the system HDF5 libraries, Octave
failed "make check" with a library mismatch error. Text pasted below.

In this case, I reran configure and rebuilt Octave, and the problem went away.
On checking, it looks like the HDF5 libraries are all dynamically linked, not
static, so it ought to be possible to update the HDF5 libraries independently
of Octave without this error, since that is the primary reason for dynamic
linking. Is Octave triggering this error or are the HDF5 libraries being
overzealous? If within Octave, would it be possible to disable the version
check when Octave links to HDF5?

Could someone please check if this kind of library error happens with
precompiled Octave (MXE, Flatpak, AppImage etc)? If so, what is the solution
there?


  test/sparse.tst ................................................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 1.12.0, library is 1.12.1
            SUMMARY OF THE HDF5 CONFIGURATION
            =================================

General Information:
-------------------
                   HDF5 Version: 1.12.1
                  Configured on: Sun Jul 18 19:07:39 UTC 2021
                  Configured by: builduser@
                    Host system: x86_64-unknown-linux-gnu
              Uname information: Linux archange 5.12.15-arch1-1 #1 SMP PREEMPT
Wed, 07 Jul 2021 23:35:29 +0000 x86_64 GNU/Linux
                       Byte sex: little-endian
             Installation point: /usr

Compiling Options:
------------------
                     Build Mode: production
              Debugging Symbols: no
                        Asserts: no
                      Profiling: no
             Optimization Level: high

Linking Options:
----------------
                      Libraries: shared
  Statically Linked Executables: 
                        LDFLAGS:
-Wl,-O1,--sort-common,--as-needed,-z,relro,-z,now
                     H5_LDFLAGS: 
                     AM_LDFLAGS: 
                Extra libraries: -lsz -lz -ldl -lm 
                       Archiver: ar
                       AR_FLAGS: cr
                         Ranlib: ranlib

Languages:
----------
                              C: yes
                     C Compiler: /usr/bin/gcc ( gcc (GCC) 11.1.0)
                       CPPFLAGS: -D_FORTIFY_SOURCE=2
                    H5_CPPFLAGS: -D_GNU_SOURCE -D_POSIX_C_SOURCE=200809L  
-DNDEBUG -UH5_DEBUG_API
                    AM_CPPFLAGS: 
                        C Flags: -march=x86-64 -mtune=generic -O2 -pipe
-fno-plt
                     H5 C Flags:  -std=c99  -Wall -Wcast-qual -Wconversion
-Wextra -Wfloat-equal -Wformat=2 -Winit-self -Winvalid-pch
-Wmissing-include-dirs -Wno-c++-compat -Wno-format-nonliteral -Wshadow -Wundef
-Wwrite-strings -pedantic -Wlarger-than=2560 -Wlogical-op
-Wframe-larger-than=16384 -Wpacked-bitfield-compat -Wsync-nand
-Wstrict-overflow=5 -Wno-unsuffixed-float-constants -Wdouble-promotion
-Wtrampolines -Wstack-usage=8192 -Wmaybe-uninitialized -Wdate-time
-Warray-bounds=2 -Wc99-c11-compat -Wduplicated-cond -Whsa -Wnormalized
-Wnull-dereference -Wunused-const-variable -Walloca -Walloc-zero
-Wduplicated-branches -Wformat-overflow=2 -Wformat-truncation=1 -Wrestrict
-Wattribute-alias -Wcast-align=strict -Wshift-overflow=2 -Wattribute-alias=2
-Wmissing-profile -Wc11-c2x-compat -fstdarg-opt -fdiagnostics-urls=never
-fno-diagnostics-color -s -Wno-aggregate-return -Wno-inline
-Wno-missing-format-attribute -Wno-missing-noreturn -Wno-overlength-strings
-Wno-jump-misses-init -Wno-suggest-attribute=const
-Wno-suggest-attribute=noreturn -Wno-suggest-attribute=pure
-Wno-suggest-attribute=format -Wno-suggest-attribute=cold
-Wno-suggest-attribute=malloc  -Wbad-function-cast
-Wimplicit-function-declaration -Wmissing-declarations -Wmissing-prototypes
-Wnested-externs -Wold-style-definition -Wpacked -Wpointer-sign
-Wpointer-to-int-cast -Wredundant-decls -Wstrict-prototypes -Wswitch
-Wunused-function -Wunused-variable -Wunused-parameter -Wcast-align
-Wunused-but-set-variable -Wformat -Wincompatible-pointer-types -Wshadow
-Wcast-function-type -Wmaybe-uninitialized -O3
                     AM C Flags: 
               Shared C Library: yes
               Static C Library: no


                        Fortran: yes
               Fortran Compiler: /usr/bin/gfortran ( GNU Fortran (GCC)
11.1.0)
                  Fortran Flags: 
               H5 Fortran Flags:  -std=f2008  -Waliasing -Wall
-Wcharacter-truncation -Wextra -Wimplicit-interface -Wsurprising -Wunderflow
-pedantic -Warray-temporaries -Wintrinsics-std -Wimplicit-procedure
-Wreal-q-constant -Wfunction-elimination -Wrealloc-lhs -Wrealloc-lhs-all
-Wno-c-binding-type -Wuse-without-only -Winteger-division
-Wfrontend-loop-interchange  -fdiagnostics-urls=never -fno-diagnostics-color
-s -O3
               AM Fortran Flags: 
         Shared Fortran Library: yes
         Static Fortran Library: no

                            C++: yes
                   C++ Compiler: /usr/bin/g++ ( g++ (GCC) 11.1.0)
                      C++ Flags: -march=x86-64 -mtune=generic -O2 -pipe
-fno-plt
                   H5 C++ Flags:   -Wall -Wcast-qual -Wconversion
-Wctor-dtor-privacy -Weffc++ -Wextra -Wfloat-equal -Wformat=2 -Winit-self
-Winvalid-pch -Wmissing-include-dirs -Wno-format-nonliteral -Wnon-virtual-dtor
-Wold-style-cast -Woverloaded-virtual -Wreorder -Wshadow -Wsign-promo -Wundef
-Wwrite-strings -pedantic -Wlarger-than=2560 -Wlogical-op
-Wframe-larger-than=16384 -Wpacked-bitfield-compat -Wsync-nand
-Wstrict-overflow=5 -Wdouble-promotion -Wtrampolines -Wstack-usage=8192
-Wmaybe-uninitialized -Wdate-time -Wopenmp-simd -Warray-bounds=2
-Wduplicated-cond -Whsa -Wnormalized -Wnull-dereference
-Wunused-const-variable -Walloca -Walloc-zero -Wduplicated-branches
-Wformat-overflow=2 -Wformat-truncation=1 -Wrestrict -Wattribute-alias
-Wcast-align=strict -Wshift-overflow=2 -Wattribute-alias=2 -Wmissing-profile
-Wno-deprecated-copy -fstdarg-opt -fdiagnostics-urls=never
-fno-diagnostics-color -s  -Wcast-align -Wmissing-declarations -Wpacked
-Wredundant-decls -Wswitch -Wunused-but-set-variable -Wunused-function
-Wunused-variable -Wunused-parameter -Wshadow -O3
                   AM C++ Flags:  -DOLD_HEADER_FILENAME -DHDF_NO_NAMESPACE
-DNO_STATIC_CAST
             Shared C++ Library: yes
             Static C++ Library: no

                           Java: yes
                  Java Compiler: /usr/bin/java (openjdk 16.0.1 2021-04-20)


Features:
---------
                   Parallel HDF5: no
Parallel Filtered Dataset Writes: no
              Large Parallel I/O: no
              High-level library: yes
                Build HDF5 Tests: yes
                Build HDF5 Tools: yes
                    Threadsafety: no (recursive RW locks: no)
             Default API mapping: v112
  With deprecated public symbols: yes
          I/O filters (external): deflate(zlib),szip(encoder)
                             MPE: no
                   Map (H5M) API: no
                      Direct VFD: no
                      Mirror VFD: no
              (Read-Only) S3 VFD: no
            (Read-Only) HDFS VFD: no
                         dmalloc: no
  Packages w/ extra debug output: none
                     API tracing: no
            Using memory checker: no
 Memory allocation sanity checks: no
          Function stack tracing: no
                Use file locking: best-effort
       Strict file format checks: no
    Optimization instrumentation: no
Bye...
fatal: caught signal Aborted -- stopping myself...
make[3]: *** [Makefile:32211: check-local] Error 134






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