I am relatively new to Ubuntu. I have set up a Ubuntu 18.04 subsystem on my Windows 10 PC for bioinformatics applications.
During multiple application installations, I have received the following error after running ./configure & make:
bgzf.h:33:10: fatal error: zlib.h: No such file or directory #include <zlib.h> The configure command returns:
checking for ZLIB... yes Whereis returns:
zlib: /usr/local/bin/zlib.h /usr/include/zlib.h /usr/share/man/man3/zlib.3.gz echo | gcc -E -v - returns:
Reading specs from /home/USER/anaconda3/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/specs COLLECT_GCC=gcc Target: x86_64-conda_cos6-linux-gnu Configured with: /home/rdonnelly/mc/conda-bld/compilers_linux-64_1534865402226/work/.build/x86_64-conda_cos6-linux-gnu/src/gcc/configure --build=x86_64-build_pc-linux-gnu --host=x86_64-build_pc-linux-gnu --target=x86_64-conda_cos6-linux-gnu --prefix=/home/rdonnelly/mc/conda-bld/compilers_linux-64_1534865402226/work/gcc_built --with-sysroot=/home/rdonnelly/mc/conda-bld/compilers_linux-64_1534865402226/work/gcc_built/x86_64-conda_cos6-linux-gnu/sysroot --enable-languages=c,c++,fortran,objc,obj-c++ --with-pkgversion='crosstool-NG 1.23.0.449-a04d0' --enable-__cxa_atexit --disable-libmudflap --enable-libgomp --disable-libssp --enable-libquadmath --enable-libquadmath-support --enable-libsanitizer --enable-libmpx --with-gmp=/home/rdonnelly/mc/conda-bld/compilers_linux-64_1534865402226/work/.build/x86_64-conda_cos6-linux-gnu/buildtools --with-mpfr=/home/rdonnelly/mc/conda-bld/compilers_linux-64_1534865402226/work/.build/x86_64-conda_cos6-linux-gnu/buildtools --with-mpc=/home/rdonnelly/mc/conda-bld/compilers_linux-64_1534865402226/work/.build/x86_64-conda_cos6-linux-gnu/buildtools --with-isl=/home/rdonnelly/mc/conda-bld/compilers_linux-64_1534865402226/work/.build/x86_64-conda_cos6-linux-gnu/buildtools --enable-lto --enable-threads=posix --enable-target-optspace --enable-plugin --enable-gold --disable-nls --disable-multilib --with-local-prefix=/home/rdonnelly/mc/conda-bld/compilers_linux-64_1534865402226/work/gcc_built/x86_64-conda_cos6-linux-gnu/sysroot --enable-long-long --enable-default-pie Thread model: posix gcc version 7.3.0 (crosstool-NG 1.23.0.449-a04d0) COLLECT_GCC_OPTIONS='-E' '-v' '-mtune=generic' '-march=x86-64' /home/USER/anaconda3/bin/../libexec/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/cc1 -E -quiet -v -iprefix /home/USER/anaconda3/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/ -isysroot /home/USER/anaconda3/bin/../x86_64-conda_cos6-linux-gnu/sysroot - -mtune=generic -march=x86-64 ignoring duplicate directory "/home/USER/anaconda3/bin/../lib/gcc/../../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/include" ignoring nonexistent directory "/home/USER/anaconda3/bin/../x86_64-conda_cos6-linux-gnu/sysroot/home/rdonnelly/mc/conda-bld/compilers_linux-64_1534865402226/work/gcc_built/x86_64-conda_cos6-linux-gnu/sysroot/include" ignoring duplicate directory "/home/USER/anaconda3/bin/../lib/gcc/../../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/include-fixed" ignoring duplicate directory "/home/USER/anaconda3/bin/../lib/gcc/../../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/include" #include "..." search starts here: #include <...> search starts here: /home/USER/anaconda3/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/include /home/USER/anaconda3/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/include-fixed /home/USER/anaconda3/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/include /home/USER/anaconda3/bin/../x86_64-conda_cos6-linux-gnu/sysroot/usr/include End of search list. # 1 "<stdin>" # 1 "<built-in>" # 1 "<command-line>" # 1 "<stdin>" COMPILER_PATH=/home/USER/anaconda3/bin/../libexec/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/:/home/USER/anaconda3/bin/../libexec/gcc/:/home/USER/anaconda3/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ LIBRARY_PATH=/home/USER/anaconda3/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/:/home/USER/anaconda3/bin/../lib/gcc/:/home/USER/anaconda3/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/lib/../lib/:/home/USER/anaconda3/bin/../x86_64-conda_cos6-linux-gnu/sysroot/lib/../lib/:/home/USER/anaconda3/bin/../x86_64-conda_cos6-linux-gnu/sysroot/usr/lib/../lib/:/home/USER/anaconda3/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/lib/:/home/USER/anaconda3/bin/../x86_64-conda_cos6-linux-gnu/sysroot/lib/:/home/USER/anaconda3/bin/../x86_64-conda_cos6-linux-gnu/sysroot/usr/lib/ COLLECT_GCC_OPTIONS='-E' '-v' '-mtune=generic' '-march=x86-64' Other posts have suggested a zlib-dev installation, already have the latest zlib1g-dev,version (1:1.2.11.dfsg-0ubuntu2).
Could you please advise on the best route to overcome this error? Thank you so much.
Output from echo | gcc -E -v -
Reading specs from /home/USER/anaconda3/bin/../lib/gcc/x86_64-conda_cos6- linux-gnu/7.3.0/specs COLLECT_GCC=gcc Target: x86_64-conda_cos6-linux-gnu Configured with: /home/rdonnelly/mc/conda-bld/compilers_linux-64_1534865402226/work/.build/x86_64-conda_cos6-linux-gnu/src/gcc/configure --build=x86_64-build_pc-linux-gnu --host=x86_64-build_pc-linux-gnu --target=x86_64-conda_cos6-linux-gnu --prefix=/home/rdonnelly/mc/conda-bld/compilers_linux-64_1534865402226/work/gcc_built --with-sysroot=/home/rdonnelly/mc/conda-bld/compilers_linux-64_1534865402226/work/gcc_built/x86_64-conda_cos6-linux-gnu/sysroot --enable-languages=c,c++,fortran,objc,obj-c++ --with-pkgversion='crosstool-NG 1.23.0.449-a04d0' --enable-__cxa_atexit --disable-libmudflap --enable-libgomp --disable-libssp --enable-libquadmath --enable-libquadmath-support --enable-libsanitizer --enable-libmpx --with-gmp=/home/rdonnelly/mc/conda-bld/compilers_linux-64_1534865402226/work/.build/x86_64-conda_cos6-linux-gnu/buildtools --with-mpfr=/home/rdonnelly/mc/conda-bld/compilers_linux-64_1534865402226/work/.build/x86_64-conda_cos6-linux-gnu/buildtools --with-mpc=/home/rdonnelly/mc/conda-bld/compilers_linux-64_1534865402226/work/.build/x86_64-conda_cos6-linux-gnu/buildtools --with-isl=/home/rdonnelly/mc/conda-bld/compilers_linux-64_1534865402226/work/.build/x86_64-conda_cos6-linux-gnu/buildtools --enable-lto --enable-threads=posix --enable-target-optspace --enable-plugin --enable-gold --disable-nls --disable-multilib --with-local-prefix=/home/rdonnelly/mc/conda-bld/compilers_linux-64_1534865402226/work/gcc_built/x86_64-conda_cos6-linux-gnu/sysroot --enable-long-long --enable-default-pie Thread model: posix gcc version 7.3.0 (crosstool-NG 1.23.0.449-a04d0) COLLECT_GCC_OPTIONS='-E' '-v' '-mtune=generic' '-march=x86-64' /home/USER/anaconda3/bin/../libexec/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/cc1 -E -quiet -v -iprefix /home/USER/anaconda3/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/ -isysroot /home/USER/anaconda3/bin/../x86_64-conda_cos6-linux-gnu/sysroot - -mtune=generic -march=x86-64 ignoring duplicate directory "/home/USER/anaconda3/bin/../lib/gcc/../../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/include" ignoring nonexistent directory "/home/USER/anaconda3/bin/../x86_64-conda_cos6-linux-gnu/sysroot/home/rdonnelly/mc/conda-bld/compilers_linux-64_1534865402226/work/gcc_built/x86_64-conda_cos6-linux-gnu/sysroot/include" ignoring duplicate directory "/home/USER/anaconda3/bin/../lib/gcc/../../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/include-fixed" ignoring duplicate directory "/home/USER/anaconda3/bin/../lib/gcc/../../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/include" #include "..." search starts here: #include <...> search starts here: /home/USER/anaconda3/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/include /home/USER/anaconda3/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/include-fixed /home/USER/anaconda3/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/include /home/USER/anaconda3/bin/../x86_64-conda_cos6-linux-gnu/sysroot/usr/include End of search list. # 1 "<stdin>" # 1 "<built-in>" # 1 "<command-line>" # 1 "<stdin>" COMPILER_PATH=/home/USER/anaconda3/bin/../libexec/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/:/home/USER/anaconda3/bin/../libexec/gcc/:/home/USER/anaconda3/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ LIBRARY_PATH=/home/USER/anaconda3/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/:/home/USER/anaconda3/bin/../lib/gcc/:/home/USER/anaconda3/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/lib/../lib/:/home/USER/anaconda3/bin/../x86_64-conda_cos6-linux-gnu/sysroot/lib/../lib/:/home/USER/anaconda3/bin/../x86_64-conda_cos6-linux-gnu/sysroot/usr/lib/../lib/:/home/USER/anaconda3/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/lib/:/home/USER/anaconda3/bin/../x86_64-conda_cos6-linux-gnu/sysroot/lib/:/home/USER/anaconda3/bin/../x86_64-conda_cos6-linux-gnu/sysroot/usr/lib/ COLLECT_GCC_OPTIONS='-E' '-v' '-mtune=generic' '-march=x86-64' 
