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birgorg / birg

Bioconda Recipe Generator (BiRG) is an heuristic approach to automatically generating recipes for Bioconda
MIT License
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Kallisto fails sanity check #44

Closed Hogfeldt closed 5 years ago

Hogfeldt commented 5 years ago

When we run the sanity check, the test fails, because there is a mismatch between the hdf5 package used at compile time and the package used at run time.

Build environment:

## Package Plan ##

  environment location: /home/fuan/miniconda3/envs/bioconda_recipe_gen/conda-bld/kallisto2_1557212198257/_h_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placeho

The following NEW packages will be INSTALLED:

    hdf5:           1.10.4-nompi_h3c11f04_1106 conda-forge
    libgcc-ng:      8.2.0-hdf63c60_1                      
    libgfortran-ng: 7.3.0-hdf63c60_0                      
    libstdcxx-ng:   8.2.0-hdf63c60_1                      
    zlib:           1.2.11-h14c3975_1004       conda-forge

Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
Solving environment: ...working... done
Solving environment: ...working... done

## Package Plan ##

  environment location: /home/fuan/miniconda3/envs/bioconda_recipe_gen/conda-bld/kallisto2_1557212198257/_build_env

The following NEW packages will be INSTALLED:

    autoconf:               2.69-pl526h14c3975_9       conda-forge
    binutils_impl_linux-64: 2.31.1-h6176602_1                     
    binutils_linux-64:      2.31.1-h6176602_3                     
    bzip2:                  1.0.6-h14c3975_1002        conda-forge
    ca-certificates:        2019.3.9-hecc5488_0        conda-forge
    cmake:                  3.14.3-hf94ab9c_0          conda-forge
    curl:                   7.64.1-hf8cf82a_0          conda-forge
    expat:                  2.2.5-hf484d3e_1002        conda-forge
    gcc_impl_linux-64:      7.3.0-habb00fd_1           conda-forge
    gcc_linux-64:           7.3.0-h553295d_3           conda-forge
    gxx_impl_linux-64:      7.3.0-hdf63c60_1           conda-forge
    gxx_linux-64:           7.3.0-h553295d_3           conda-forge
    krb5:                   1.16.3-h05b26f9_1001       conda-forge
    libcurl:                7.64.1-hda55be3_0          conda-forge
    libedit:                3.1.20170329-hf8c457e_1001 conda-forge
    libgcc-ng:              8.2.0-hdf63c60_1                      
    libssh2:                1.8.2-h22169c7_2           conda-forge
    libstdcxx-ng:           8.2.0-hdf63c60_1                      
    libuv:                  1.28.0-h516909a_0          conda-forge
    m4:                     1.4.18-h14c3975_1001       conda-forge
    make:                   4.2.1-h14c3975_2004        conda-forge
    ncurses:                6.1-hf484d3e_1002          conda-forge
    openssl:                1.1.1b-h14c3975_1          conda-forge
    perl:                   5.26.2-h516909a_1006       conda-forge
    rhash:                  1.3.6-h14c3975_1001        conda-forge
    tk:                     8.6.9-h84994c4_1001        conda-forge
    xz:                     5.2.4-h14c3975_1001        conda-forge
    zlib:                   1.2.11-h14c3975_1004       conda-forge

Run time environment:

The following NEW packages will be INSTALLED:

    hdf5:           1.10.5-nompi_h3c11f04_1100 conda-forge
    kallisto2:      0.45.0-hd5b5912_0          local      
    libgcc-ng:      8.2.0-hdf63c60_1                      
    libgfortran-ng: 7.3.0-hdf63c60_0                      
    libstdcxx-ng:   8.2.0-hdf63c60_1                      
    zlib:           1.2.11-h14c3975_1004       conda-forge

Error message:

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 1.10.4, library is 1.10.5
        SUMMARY OF THE HDF5 CONFIGURATION
        =================================

General Information:
-------------------
                   HDF5 Version: 1.10.5
                  Configured on: Wed May  1 21:39:55 UTC 2019
                  Configured by: conda@ac5cc45aa948
                    Host system: x86_64-conda_cos6-linux-gnu
              Uname information: Linux ac5cc45aa948 4.15.0-1041-azure #45-Ubuntu SMP Fri Mar 15 14:41:00 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux
                       Byte sex: little-endian
             Installation point: /home/fuan/miniconda3/envs/bioconda_recipe_gen/conda-bld/kallisto2_1557212198257/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac

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

Linking Options:
----------------
                      Libraries: static, shared
  Statically Linked Executables: 
                        LDFLAGS: -Wl,-O2 -Wl,--sort-common -Wl,--as-needed -Wl,-z,relro -Wl,-z,now -Wl,--disable-new-dtags -Wl,-rpath,/home/fuan/miniconda3/envs/bioconda_recipe_gen/conda-bld/kallisto2_1557212198257/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac/lib -L/home/fuan/miniconda3/envs/bioconda_recipe_gen/conda-bld/kallisto2_1557212198257/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac/lib
                     H5_LDFLAGS: 
                     AM_LDFLAGS:  -L/home/fuan/miniconda3/envs/bioconda_recipe_gen/conda-bld/kallisto2_1557212198257/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac/lib
                Extra libraries: -lrt -lpthread -lz -ldl -lm 
                       Archiver: /home/conda/feedstock_root/build_artifacts/hdf5_1556746730134/_build_env/bin/x86_64-conda_cos6-linux-gnu-ar
                       AR_FLAGS: cr
                         Ranlib: /home/conda/feedstock_root/build_artifacts/hdf5_1556746730134/_build_env/bin/x86_64-conda_cos6-linux-gnu-ranlib

Languages:
----------
                              C: yes
                     C Compiler: /home/conda/feedstock_root/build_artifacts/hdf5_1556746730134/_build_env/bin/x86_64-conda_cos6-linux-gnu-cc
                       CPPFLAGS: -DNDEBUG -D_FORTIFY_SOURCE=2 -O2
                    H5_CPPFLAGS: -D_GNU_SOURCE -D_POSIX_C_SOURCE=200809L   -DNDEBUG -UH5_DEBUG_API
                    AM_CPPFLAGS:  -I/home/fuan/miniconda3/envs/bioconda_recipe_gen/conda-bld/kallisto2_1557212198257/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac/include
                        C Flags: -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -pipe -I/home/fuan/miniconda3/envs/bioconda_recipe_gen/conda-bld/kallisto2_1557212198257/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac/include -fdebug-prefix-map=${SRC_DIR}=/usr/local/src/conda/${PKG_NAME}-${PKG_VERSION} -fdebug-prefix-map=${PREFIX}=/usr/local/src/conda-prefix
                     H5 C Flags:  -std=c99  -pedantic -Wall -Wextra -Wbad-function-cast -Wc++-compat -Wcast-align -Wcast-qual -Wconversion -Wdeclaration-after-statement -Wdisabled-optimization -Wfloat-equal -Wformat=2 -Winit-self -Winvalid-pch -Wmissing-declarations -Wmissing-include-dirs -Wmissing-prototypes -Wnested-externs -Wold-style-definition -Wpacked -Wpointer-arith -Wredundant-decls -Wshadow -Wstrict-prototypes -Wswitch-default -Wswitch-enum -Wundef -Wunused-macros -Wunsafe-loop-optimizations -Wwrite-strings -finline-functions -s -Wno-inline -Wno-aggregate-return -Wno-missing-format-attribute -Wno-missing-noreturn -O
                     AM C Flags: 
               Shared C Library: yes
               Static C Library: yes

                        Fortran: yes
               Fortran Compiler: /home/conda/feedstock_root/build_artifacts/hdf5_1556746730134/_build_env/bin/x86_64-conda_cos6-linux-gnu-gfortran
                  Fortran Flags: 
               H5 Fortran Flags:  -pedantic -Wall -Wextra -Wunderflow -Wimplicit-interface -Wsurprising -Wno-c-binding-type  -s -O2
               AM Fortran Flags: 
         Shared Fortran Library: yes
         Static Fortran Library: yes

                            C++: yes
                   C++ Compiler: /home/conda/feedstock_root/build_artifacts/hdf5_1556746730134/_build_env/bin/x86_64-conda_cos6-linux-gnu-c++
                      C++ Flags: -fvisibility-inlines-hidden -std=c++17 -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -pipe -I/home/fuan/miniconda3/envs/bioconda_recipe_gen/conda-bld/kallisto2_1557212198257/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_plac/include -fdebug-prefix-map=${SRC_DIR}=/usr/local/src/conda/${PKG_NAME}-${PKG_VERSION} -fdebug-prefix-map=${PREFIX}=/usr/local/src/conda-prefix
                   H5 C++ Flags:   -pedantic -Wall -W -Wundef -Wshadow -Wpointer-arith -Wcast-qual -Wcast-align -Wwrite-strings -Wconversion -Wredundant-decls -Winline -Wsign-promo -Woverloaded-virtual -Wold-style-cast -Weffc++ -Wreorder -Wnon-virtual-dtor -Wctor-dtor-privacy -Wabi -finline-functions -s -O
                   AM C++ Flags: 
             Shared C++ Library: yes
             Static C++ Library: yes

                           Java: no

Features:
---------
                   Parallel HDF5: no
Parallel Filtered Dataset Writes: no
              Large Parallel I/O: no
              High-level library: yes
                    Threadsafety: yes
             Default API mapping: v110
  With deprecated public symbols: yes
          I/O filters (external): deflate(zlib)
                             MPE: no
                      Direct VFD: no
                         dmalloc: no
  Packages w/ extra debug output: none
                     API tracing: no
            Using memory checker: yes
 Memory allocation sanity checks: no
          Function stack tracing: no
       Strict file format checks: no
    Optimization instrumentation: no
Bye...
/home/fuan/miniconda3/envs/bioconda_recipe_gen/conda-bld/kallisto2_1557212198257/test_tmp/run_test.sh: line 7: 18665 Aborted                 (core dumped) kallisto quant t.fq -i t.idx --single -l 300 -s 2 -o tmp
Tests failed for kallisto2-0.45.0-hd5b5912_0.tar.bz2 - moving package to /home/fuan/miniconda3/envs/bioconda_recipe_gen/conda-bld/broken
Hogfeldt commented 5 years ago

Opened an issue at https://github.com/bioconda/bioconda-utils/issues/529

Hogfeldt commented 5 years ago

The sanity check now passes, we had to update bioconda-utils from 0.1.10 to 0.1.12.