Compilation failures when building danbing-tk with latest Eigen

[biozzq]

Dear all,

I encountered multiple compile errors while building danbing-tk after successfully cloning the repository with Eigen submodule. My build environment uses a conda GCC toolchain with C++14 standard enabled (The Makefile originally uses -std=c++11, but Eigen mandates C++14).

/public/home/zhengzhuqing/01.software/gcc/bin/x86_64-conda-linux-gnu-c++ -pthread -std=c++14 -I ./include -I ./include/eigen3 -O3 -o bin/danbing-tk src/aQueryFasta_thread.cpp
/public/home/zhengzhuqing/01.software/gcc/bin/x86_64-conda-linux-gnu-c++ -std=c++14 -I ./include -I ./include/eigen3 -O3 -o bin/fa2kmers src/fa2kmers.cpp
/public/home/zhengzhuqing/01.software/gcc/bin/x86_64-conda-linux-gnu-c++ -std=c++14 -I ./include -I ./include/eigen3 -O3 -o bin/genPanKmers src/genPanKmers.cpp
/public/home/zhengzhuqing/01.software/gcc/bin/x86_64-conda-linux-gnu-c++ -std=c++14 -I ./include -I ./include/eigen3 -O3 -o bin/ktools src/kmertools.cpp
/public/home/zhengzhuqing/01.software/gcc/bin/x86_64-conda-linux-gnu-c++ -std=c++14 -I ./include -I ./include/eigen3 -O3 -o bin/danbing-tk-pred src/pred.cpp
In file included from src/pred.cpp:1:
src/pred.h: In function 'uint64_t le2uint64(char*)':
src/pred.h:56:43: warning: left shift count >= width of type [-Wshift-count-overflow]
   56 |                (in[4]&0x00000000000000ff) << 32 |
      |                ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~
src/pred.h:57:43: warning: left shift count >= width of type [-Wshift-count-overflow]
   57 |                (in[5]&0x00000000000000ff) << 40 |
      |                ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~
src/pred.h:58:43: warning: left shift count >= width of type [-Wshift-count-overflow]
   58 |                (in[6]&0x00000000000000ff) << 48 |
      |                ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~
src/pred.h:59:43: warning: left shift count >= width of type [-Wshift-count-overflow]
   59 |                (in[7]&0x00000000000000ff) << 56;
      |                ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~
src/pred.h: In function 'void bias_correction(T&, ikmer_meta&, P&)':
src/pred.h:224:38: error: 'all' is not a member of 'Eigen'
  224 |                 auto igt = gt(Eigen::all, ikis);
      |                                      ^~~
src/pred.h:224:38: note: suggested alternatives:
In file included from ./include/eigen3/Eigen/Core:23,
                 from src/pred.h:4:
./include/eigen3/Eigen/src/Core/util/Macros.h:1404:34: note:   'Eigen::internal::all'
 1404 | EIGEN_DEVICE_FUNC constexpr bool all(T t, Ts... ts) {
      |                                  ^~~
In file included from ./include/eigen3/Eigen/Core:350:
./include/eigen3/Eigen/src/Core/util/IndexedViewHelper.h:87:41: note:   'Eigen::placeholders::all'
   87 | static constexpr Eigen::internal::all_t all;
      |                                         ^~~
./include/eigen3/Eigen/src/Core/util/IndexedViewHelper.h:87:41: note:   'Eigen::placeholders::all'
src/pred.h:230:29: error: 'all' is not a member of 'Eigen'
  230 |                 Bias(Eigen::all,tri) = bias;
      |                             ^~~
src/pred.h:230:29: note: suggested alternatives:
./include/eigen3/Eigen/src/Core/util/Macros.h:1404:34: note:   'Eigen::internal::all'
 1404 | EIGEN_DEVICE_FUNC constexpr bool all(T t, Ts... ts) {
      |                                  ^~~
./include/eigen3/Eigen/src/Core/util/IndexedViewHelper.h:87:41: note:   'Eigen::placeholders::all'
   87 | static constexpr Eigen::internal::all_t all;
      |                                         ^~~
./include/eigen3/Eigen/src/Core/util/IndexedViewHelper.h:87:41: note:   'Eigen::placeholders::all'
make: *** [Makefile:34: bin/danbing-tk-pred] Error 1

My compiler is conda GCC with C++14 support. Would you mind fixing these compile issues in the repository? Many thanks.

Best wishes,
Zheng zhuqing