[Bioc-devel] Problem with non-portable compiler flags on package test

[Martin Morgan]

Your configure outsmarts the check system, so your options are to omit the flags or to live with the warning. Either solution is fine with Bioconductor.

Martin

On 4/12/19, 4:17 AM, "Bioc-devel on behalf of Jochen Knaus" <bioc-devel-bounces using r-project.org on behalf of jo using imbi.uni-freiburg.de> wrote:

    Hi everybody,
    
    for our new R package "Netboost" we have a problem about non portable 
    compiler flags. Basically we support AVX in our own C++ code (using 
    compiler intrinsics to use the AVX units). Of course we have a non-AVX 
    code path.
    
    For building we use autotools and configure to determine at installation 
    time if the AVX unit is available and supported by the given compilers. 
    If available then compilation is done with AVX, if not, then ordinary 
    code path is used.
    
    The problem is the R package test, which does see the set AVX flag in 
    "Makevars" (as Makevars.in is configured to use AVX if the test is 
    executed on a machine supporting AVX).
    
    Note: due to bundled software, this is a Linux only package, so no 
    support for Microsoft compilers is required (with other flag names).
    
    Is there any way around this warning, which is a real false-positive, as 
    the flag is not set in environments not suitable.
    
    Thanks a lot for any help!
    
    Jo
    
    
    Details:
    
    for testing we use GNU Autotools and the AX_EXT M4-macroset to determine 
    the hardware and compiler support for additional features: 
    https://www.gnu.org/software/autoconf-archive/ax_ext.html
    
    configure.ac:
    
    m4_include([m4/ax_gcc_x86_avx_xgetbv.m4])
    m4_include([m4/ax_gcc_x86_cpuid.m4])
    m4_include([m4/ax_check_compile_flag.m4])
    m4_include([m4/ax_ext.m4])
    
    # Probe CPU and compilers
    AX_EXT
    
    src/Makevars.in:
    
    PKG_CXXFLAGS=`${R_HOME}/bin/Rscript -e "Rcpp:::CxxFlags()"` @SIMD_FLAGS@
    
    Running R CMD CHECK with --as-cran, we get the warning:
    
    http://bioconductor.org/spb_reports/netboost_buildreport_20190412033232.html
    
    * checking compilation flags used ... WARNING Compilation used the 
    following non-portable flag(s): -Wno-deprecated -maes -mavx -mavx2 -mfma 
    -mmmx -msse -msse3 -msse4.1 -msse4.2 -mssse3
    
    (Basically we only need -mavx and optionally FMA, but AX_EXT sets all).
    
    -- 
    Jochen Knaus
    Institute of Biometry and Statistics
    Faculty of Medicine and Medical Center - University of Freiburg
    Office: IMBI library
    Postal address: Stefan-Meier-Str. 26, D-79104 Freiburg
    Phone: +49/761/203-5528
    Mail: jo using imbi.uni-freiburg.de
    Homepage: http://www.imbi.uni-freiburg.de
    
    
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