Open kollienne opened 2 years ago
With gcc11 CXXFLAGS=-fPIE is required to install, otherwise ./configure (or installing via R) fails with the following output:
CXXFLAGS=-fPIE
./configure
This file contains any messages produced by compilers while running configure, to aid debugging if configure makes a mistake. It was created by seqminer configure 8.3, which was generated by GNU Autoconf 2.69. Invocation command line was $ ./configure ## --------- ## ## Platform. ## ## --------- ## hostname = xpc15a6.math.canterbury.ac.nz uname -m = x86_64 uname -r = 5.16.8-200.fc35.x86_64 uname -s = Linux uname -v = #1 SMP PREEMPT Tue Feb 8 20:58:59 UTC 2022 /usr/bin/uname -p = x86_64 /bin/uname -X = unknown /bin/arch = x86_64 /usr/bin/arch -k = unknown /usr/convex/getsysinfo = unknown /usr/bin/hostinfo = unknown /bin/machine = unknown /usr/bin/oslevel = unknown /bin/universe = unknown PATH: /home/kieran/.emacs.d/bin PATH: /usr/condabin PATH: /usr/lib64/ccache PATH: /usr/local/bin PATH: /usr/local/sbin PATH: /usr/bin PATH: /usr/sbin PATH: /var/lib/snapd/snap/bin PATH: /home/kieran/bin ## ----------- ## ## Core tests. ## ## ----------- ## configure:2057: CC = gcc -m64 configure:2059: CFLAGS = configure:2061: CXX = g++ -m64 -std=gnu++11 configure:2063: CXXFLAGS = -O2 -flto=auto -ffat-lto-objects -fexceptions -g -grecord-gcc-switches -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -fstack-protector-strong -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m64 -mtune=generic -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection configure:2184: checking for C++ compiler version configure:2193: g++ -m64 -std=gnu++11 --version >&5 g++ (GCC) 11.2.1 20220127 (Red Hat 11.2.1-9) Copyright (C) 2021 Free Software Foundation, Inc. This is free software; see the source for copying conditions. There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. configure:2204: $? = 0 configure:2193: g++ -m64 -std=gnu++11 -v >&5 Using built-in specs. COLLECT_GCC=/usr/bin/g++ COLLECT_LTO_WRAPPER=/usr/libexec/gcc/x86_64-redhat-linux/11/lto-wrapper OFFLOAD_TARGET_NAMES=nvptx-none OFFLOAD_TARGET_DEFAULT=1 Target: x86_64-redhat-linux Configured with: ../configure --enable-bootstrap --enable-languages=c,c++,fortran,objc,obj-c++,ada,go,d,lto --prefix=/usr --mandir=/usr/share/man --infodir=/usr/share/info --with-bugurl=http://bugzilla.redhat.com/bugzilla --enable-shared --enable-threads=posix --enable-checking=release --enable-multilib --with-system-zlib --enable-__cxa_atexit --disable-libunwind-exceptions --enable-gnu-unique-object --enable-linker-build-id --with-gcc-major-version-only --with-linker-hash-style=gnu --enable-plugin --enable-initfini-array --with-isl=/builddir/build/BUILD/gcc-11.2.1-20220127/obj-x86_64-redhat-linux/isl-install --enable-offload-targets=nvptx-none --without-cuda-driver --enable-gnu-indirect-function --enable-cet --with-tune=generic --with-arch_32=i686 --build=x86_64-redhat-linux --with-build-config=bootstrap-lto --enable-link-serialization=1 Thread model: posix Supported LTO compression algorithms: zlib zstd gcc version 11.2.1 20220127 (Red Hat 11.2.1-9) (GCC) ... rest of stderr output deleted ... configure:2204: $? = 0 configure:2193: g++ -m64 -std=gnu++11 -V >&5 g++: error: unrecognized command-line option '-V' g++: fatal error: no input files compilation terminated. configure:2204: $? = 1 configure:2193: g++ -m64 -std=gnu++11 -qversion >&5 g++: error: unrecognized command-line option '-qversion'; did you mean '--version'? g++: fatal error: no input files compilation terminated. configure:2204: $? = 1 configure:2224: checking whether the C++ compiler works configure:2246: g++ -m64 -std=gnu++11 -I/usr/local/include -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 conftest.cpp >&5 configure:2250: $? = 0 configure:2298: result: yes configure:2301: checking for C++ compiler default output file name configure:2303: result: a.out configure:2309: checking for suffix of executables configure:2316: g++ -m64 -std=gnu++11 -o conftest -I/usr/local/include -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 conftest.cpp >&5 configure:2320: $? = 0 configure:2342: result: configure:2364: checking whether we are cross compiling configure:2372: g++ -m64 -std=gnu++11 -o conftest -I/usr/local/include -Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 conftest.cpp >&5 /usr/bin/ld: /tmp/ccIrYH7b.o: relocation R_X86_64_32 against `.rodata' can not be used when making a PIE object; recompile with -fPIE collect2: error: ld returned 1 exit status configure:2376: $? = 1 configure:2383: ./conftest ./configure: line 2385: ./conftest: No such file or directory configure:2387: $? = 127 configure:2394: error: in `/home/kieran/src/seqminer': configure:2396: error: cannot run C++ compiled programs. If you meant to cross compile, use `--host'. See `config.log' for more details ## ---------------- ## ## Cache variables. ## ## ---------------- ## ac_cv_env_CCC_set= ac_cv_env_CCC_value= ac_cv_env_CPPFLAGS_set= ac_cv_env_CPPFLAGS_value= ac_cv_env_CXXCPP_set= ac_cv_env_CXXCPP_value= ac_cv_env_CXXFLAGS_set= ac_cv_env_CXXFLAGS_value= ac_cv_env_CXX_set= ac_cv_env_CXX_value= ac_cv_env_LDFLAGS_set= ac_cv_env_LDFLAGS_value= ac_cv_env_LIBS_set= ac_cv_env_LIBS_value= ac_cv_env_build_alias_set= ac_cv_env_build_alias_value= ac_cv_env_host_alias_set= ac_cv_env_host_alias_value= ac_cv_env_target_alias_set= ac_cv_env_target_alias_value= ## ----------------- ## ## Output variables. ## ## ----------------- ## CPPFLAGS='-I/usr/local/include' CXX='g++ -m64 -std=gnu++11' CXXCPP='' CXXFLAGS='' DEFS='' ECHO_C='' ECHO_N='-n' ECHO_T='' EGREP='' EXEEXT='' GREP='' HAVE_BZIP2='' HAVE_SQLITE='' HAVE_ZSTD='' LDFLAGS='-Wl,-z,relro -Wl,--as-needed -Wl,-z,now -specs=/usr/lib/rpm/redhat/redhat-hardened-ld -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1' LIBOBJS='' LIBS='' LTLIBOBJS='' OBJEXT='' PACKAGE_BUGREPORT='zhanxw@gmail.com' PACKAGE_NAME='seqminer' PACKAGE_STRING='seqminer 8.3' PACKAGE_TARNAME='seqminer' PACKAGE_URL='' PACKAGE_VERSION='8.3' PATH_SEPARATOR=':' PKG_CFLAGS='' PKG_CPPFLAGS='' PKG_LIBS='' SHELL='/bin/sh' ac_ct_CXX='' bindir='${exec_prefix}/bin' build_alias='' datadir='${datarootdir}' datarootdir='${prefix}/share' docdir='${datarootdir}/doc/${PACKAGE_TARNAME}' dvidir='${docdir}' exec_prefix='NONE' host_alias='' htmldir='${docdir}' includedir='${prefix}/include' infodir='${datarootdir}/info' libdir='${exec_prefix}/lib' libexecdir='${exec_prefix}/libexec' localedir='${datarootdir}/locale' localstatedir='${prefix}/var' mandir='${datarootdir}/man' oldincludedir='/usr/include' pdfdir='${docdir}' prefix='NONE' program_transform_name='s,x,x,' psdir='${docdir}' runstatedir='${localstatedir}/run' sbindir='${exec_prefix}/sbin' sharedstatedir='${prefix}/com' sysconfdir='${prefix}/etc' target_alias='' ## ----------- ## ## confdefs.h. ## ## ----------- ## /* confdefs.h */ #define PACKAGE_NAME "seqminer" #define PACKAGE_TARNAME "seqminer" #define PACKAGE_VERSION "8.3" #define PACKAGE_STRING "seqminer 8.3" #define PACKAGE_BUGREPORT "zhanxw@gmail.com" #define PACKAGE_URL "" configure: exit 1
Sorry that I cannot replicate this error on my end. Ubuntu: Ubuntu 20.04.3 LTS GCC: 11.2.0
Maybe you can try to manually modify CFLAGS or CXXFLAGS?
With gcc11
CXXFLAGS=-fPIE
is required to install, otherwise./configure
(or installing via R) fails with the following output: