gcc11 requires -fPIE

[kollienne]

With gcc11 CXXFLAGS=-fPIE is required to install, otherwise ./configure (or installing via R) fails with the following output:

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='[email protected]'
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 "[email protected]"
#define PACKAGE_URL ""

configure: exit 1

[zhanxw]

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?