Linking problem while trying to compile

[AV-2]

While trying to install the module under perl 5.38.0 using cpanm, having the development headers of Nauty installed, the process runs into a problem when trying to link the libraries:

cpanm (App::cpanminus) 1.7047 on perl 5.038000 built for x86_64-linux
Work directory is /home/asterionv/.cpanm/work/1690995067.675694
You have make /usr/bin/make
You have /usr/bin/wget
You have /usr/bin/tar: tar (GNU tar) 1.34
Copyright (C) 2021 Free Software Foundation, Inc.
License GPLv3+: GNU GPL version 3 or later <https://gnu.org/licenses/gpl.html>.
This is free software: you are free to change and redistribute it.
There is NO WARRANTY, to the extent permitted by law.

Written by John Gilmore and Jay Fenlason.
You have /usr/bin/unzip
Searching install () on cpanmetadb ...
--> Working on install
Fetching http://www.cpan.org/authors/id/D/DA/DAGOLDEN/install-0.01.tar.gz
-> OK
Unpacking install-0.01.tar.gz
Entering install-0.01
Checking configure dependencies from META.yml
Checking if you have ExtUtils::MakeMaker 6.58 ... Yes (7.70)
Configuring install-0.01
Running Makefile.PL
Checking if your kit is complete...
Looks good
Generating a Unix-style Makefile
Writing Makefile for install
Writing MYMETA.yml and MYMETA.json
-> OK
Checking dependencies from MYMETA.json ...
Checking if you have ExtUtils::MakeMaker 0 ... Yes (7.70)
Building and testing install-0.01
cp lib/install.pm blib/lib/install.pm
Manifying 1 pod document
PERL_DL_NONLAZY=1 "/home/asterionv/perl5/perlbrew/perls/perl-5.38.0/bin/perl" "-MExtUtils::Command::MM" "-MTest::Harness" "-e" "undef *Test::Harness::Switches; test_harness(0, 'blib/lib', 'blib/arch')" t/*.t
t/install.t .. ok
All tests successful.
Files=1, Tests=1,  0 wallclock secs ( 0.01 usr  0.00 sys +  0.04 cusr  0.00 csys =  0.05 CPU)
Result: PASS
Manifying 1 pod document
Installing /home/asterionv/perl5/perlbrew/perls/perl-5.38.0/lib/site_perl/5.38.0/install.pm
Installing /home/asterionv/perl5/perlbrew/perls/perl-5.38.0/man/man3/install.3
Appending installation info to /home/asterionv/perl5/perlbrew/perls/perl-5.38.0/lib/5.38.0/x86_64-linux/perllocal.pod
-> OK
Successfully installed install-0.01
Installing /home/asterionv/perl5/perlbrew/perls/perl-5.38.0/lib/site_perl/5.38.0/x86_64-linux/.meta/install-0.01/MYMETA.json
Installing /home/asterionv/perl5/perlbrew/perls/perl-5.38.0/lib/site_perl/5.38.0/x86_64-linux/.meta/install-0.01/install.json
Searching Graph::Nauty () on cpanmetadb ...
--> Working on Graph::Nauty
Fetching http://www.cpan.org/authors/id/M/ME/MERKYS/Graph-Nauty-0.5.1.tar.gz
-> OK
Unpacking Graph-Nauty-0.5.1.tar.gz
Entering Graph-Nauty-0.5.1
Checking configure dependencies from META.json
Checking if you have ExtUtils::MakeMaker 6.58 ... Yes (7.70)
Configuring Graph-Nauty-0.5.1
Running Makefile.PL
Checking if your kit is complete...
Looks good
Generating a Unix-style Makefile
Writing Makefile for Graph::Nauty
Writing MYMETA.yml and MYMETA.json
-> OK
Checking dependencies from MYMETA.json ...
Checking if you have ExtUtils::MakeMaker 0 ... Yes (7.70)
Checking if you have Test::More 0 ... Yes (1.302194)
Checking if you have Data::Dumper 0 ... Yes (2.188)
Checking if you have Graph::Undirected 0 ... Yes (undef)
Checking if you have Scalar::Util 0 ... Yes (1.63)
Building and testing Graph-Nauty-0.5.1
cp lib/Graph/Nauty.pm blib/lib/Graph/Nauty.pm
cp lib/Graph/Nauty/EdgeVertex.pm blib/lib/Graph/Nauty/EdgeVertex.pm
Running Mkbootstrap for Nauty ()
chmod 644 "Nauty.bs"
"/home/asterionv/perl5/perlbrew/perls/perl-5.38.0/bin/perl" -MExtUtils::Command::MM -e 'cp_nonempty' -- Nauty.bs blib/arch/auto/Graph/Nauty/Nauty.bs 644
"/home/asterionv/perl5/perlbrew/perls/perl-5.38.0/bin/perl" "/home/asterionv/perl5/perlbrew/perls/perl-5.38.0/lib/5.38.0/ExtUtils/xsubpp"  -typemap '/home/asterionv/perl5/perlbrew/perls/perl-5.38.0/lib/5.38.0/ExtUtils/typemap' -typemap '/home/asterionv/.cpanm/work/1690995067.675694/Graph-Nauty-0.5.1/typemap'  Nauty.xs > Nauty.xsc
Please specify prototyping behavior for Nauty.xs (see perlxs manual)
mv Nauty.xsc Nauty.c
cc -c   -fwrapv -fno-strict-aliasing -pipe -fstack-protector-strong -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -O2   -DVERSION=\"0.5.1\" -DXS_VERSION=\"0.5.1\" -fPIC "-I/home/asterionv/perl5/perlbrew/perls/perl-5.38.0/lib/5.38.0/x86_64-linux/CORE"   Nauty.c
rm -f blib/arch/auto/Graph/Nauty/Nauty.so
cc  -shared -O2 -L/usr/local/lib -fstack-protector-strong  Nauty.o  -o blib/arch/auto/Graph/Nauty/Nauty.so  \
   -lnauty   \
  
/usr/bin/ld: /usr/local/lib/libnauty.a(nauty.o): warning: relocation against `stdout@@GLIBC_2.2.5' in read-only section `.text'
/usr/bin/ld: /usr/local/lib/libnauty.a(nauty.o): relocation R_X86_64_PC32 against symbol `labelorg' can not be used when making a shared object; recompile with -fPIC
/usr/bin/ld: final link failed: bad value
collect2: error: ld returned 1 exit status
make: *** [Makefile:481: blib/arch/auto/Graph/Nauty/Nauty.so] Error 1
-> FAIL Installing Graph::Nauty failed. See /home/asterionv/.cpanm/work/1690995067.675694/build.log for details. Retry with --force to force install it.
1 distribution installed

The suggestion of "recompiling with -fPIC" is a mistifying since the flag is already part of the command.
The following post in stackoverflow suggests to use the -no-pie flag:
https://stackoverflow.com/questions/71482016/relocation-r-x86-64-32s-against-symbol-stdoutglibc-2-2-5-can-not-be-used-whe

So I run the following commands:

cc -c   -fwrapv -fno-strict-aliasing -pipe -fstack-protector-strong -I/usr/local/include -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -O2   -DVERSION=\"0.5.1\" -DXS_VERSION=\"0.5.1\" -fPIC "-I/home/asterionv/perl5/perlbrew/perls/perl-5.38.0/lib/5.38.0/x86_64-linux/CORE" -no-pie   Nauty.c
rm -f blib/arch/auto/Graph/Nauty/Nauty.so
cc  -shared -O2 -L/usr/local/lib -fstack-protector-strong  Nauty.o -no-pie -o blib/arch/auto/Graph/Nauty/Nauty.so  -lnauty  

and for the last one I get as output

/usr/bin/ld: /usr/lib/gcc/x86_64-linux-gnu/12/../../../x86_64-linux-gnu/crt1.o: in function `_start':
(.text+0x1b): undefined reference to `main'
/usr/bin/ld: Nauty.o: in function `XS_Graph__Nauty_aresame_sg':
Nauty.c:(.text+0x18): undefined reference to `PL_markstack_ptr'
/usr/bin/ld: Nauty.c:(.text+0x1f): undefined reference to `PL_stack_base'
/usr/bin/ld: Nauty.c:(.text+0x37): undefined reference to `PL_stack_sp'
/usr/bin/ld: Nauty.c:(.text+0xc7): undefined reference to `PL_sv_immortals'
/usr/bin/ld: Nauty.c:(.text+0x158): undefined reference to `PL_stack_sp'
/usr/bin/ld: Nauty.c:(.text+0x193): undefined reference to `PL_sv_immortals'
/usr/bin/ld: Nauty.c:(.text+0x1bc): undefined reference to `Perl_hv_common_key_len'
/usr/bin/ld: Nauty.c:(.text+0x1dc): undefined reference to `Perl_sv_2iv_flags'
/usr/bin/ld: Nauty.c:(.text+0x207): undefined reference to `Perl_hv_common_key_len'
/usr/bin/ld: Nauty.c:(.text+0x227): undefined reference to `Perl_sv_2iv_flags'
/usr/bin/ld: Nauty.c:(.text+0x2b2): undefined reference to `Perl_hv_common_key_len'
/usr/bin/ld: Nauty.c:(.text+0x2dd): undefined reference to `Perl_hv_common_key_len'
/usr/bin/ld: Nauty.c:(.text+0x308): undefined reference to `Perl_hv_common_key_len'
/usr/bin/ld: Nauty.c:(.text+0x326): undefined reference to `Perl_sv_2iv_flags'
/usr/bin/ld: Nauty.c:(.text+0x34b): undefined reference to `Perl_av_fetch'
/usr/bin/ld: Nauty.c:(.text+0x386): undefined reference to `Perl_sv_2iv_flags'
/usr/bin/ld: Nauty.c:(.text+0x3ab): undefined reference to `Perl_av_fetch'
/usr/bin/ld: Nauty.c:(.text+0x3ee): undefined reference to `Perl_sv_2iv_flags'
/usr/bin/ld: Nauty.c:(.text+0x41a): undefined reference to `Perl_av_fetch'
/usr/bin/ld: Nauty.c:(.text+0x45c): undefined reference to `Perl_hv_common_key_len'
/usr/bin/ld: Nauty.c:(.text+0x47c): undefined reference to `Perl_sv_2iv_flags'
/usr/bin/ld: Nauty.c:(.text+0x4a7): undefined reference to `Perl_hv_common_key_len'
/usr/bin/ld: Nauty.c:(.text+0x4c7): undefined reference to `Perl_sv_2iv_flags'
/usr/bin/ld: Nauty.c:(.text+0x545): undefined reference to `Perl_hv_common_key_len'
/usr/bin/ld: Nauty.c:(.text+0x570): undefined reference to `Perl_hv_common_key_len'
/usr/bin/ld: Nauty.c:(.text+0x59b): undefined reference to `Perl_hv_common_key_len'
/usr/bin/ld: Nauty.c:(.text+0x5b6): undefined reference to `Perl_sv_2iv_flags'
/usr/bin/ld: Nauty.c:(.text+0x5d8): undefined reference to `Perl_av_fetch'
/usr/bin/ld: Nauty.c:(.text+0x616): undefined reference to `Perl_sv_2iv_flags'
/usr/bin/ld: Nauty.c:(.text+0x638): undefined reference to `Perl_av_fetch'
/usr/bin/ld: Nauty.c:(.text+0x676): undefined reference to `Perl_sv_2iv_flags'
/usr/bin/ld: Nauty.c:(.text+0x698): undefined reference to `Perl_av_fetch'
/usr/bin/ld: Nauty.c:(.text+0x8c0): undefined reference to `Perl_croak_xs_usage'
/usr/bin/ld: Nauty.o: in function `XS_Graph__Nauty_sparsenauty':
Nauty.c:(.text+0x90b): undefined reference to `PL_markstack_ptr'
/usr/bin/ld: Nauty.c:(.text+0x912): undefined reference to `PL_stack_base'
/usr/bin/ld: Nauty.c:(.text+0x926): undefined reference to `PL_stack_sp'
/usr/bin/ld: Nauty.c:(.text+0x97f): undefined reference to `Perl_av_len'
/usr/bin/ld: Nauty.c:(.text+0x9ae): undefined reference to `Perl_sv_2iv_flags'
/usr/bin/ld: Nauty.c:(.text+0x9c7): undefined reference to `Perl_av_len'
/usr/bin/ld: Nauty.c:(.text+0x9e5): undefined reference to `Perl_av_fetch'
/usr/bin/ld: Nauty.c:(.text+0xa2b): undefined reference to `Perl_av_len'
/usr/bin/ld: Nauty.c:(.text+0xa56): undefined reference to `Perl_sv_2iv_flags'
/usr/bin/ld: Nauty.c:(.text+0xa6f): undefined reference to `Perl_av_len'
/usr/bin/ld: Nauty.c:(.text+0xa8d): undefined reference to `Perl_av_fetch'
/usr/bin/ld: Nauty.c:(.text+0xadf): undefined reference to `Perl_sv_2uv_flags'
/usr/bin/ld: Nauty.c:(.text+0xc5e): undefined reference to `PL_sv_root'
/usr/bin/ld: Nauty.c:(.text+0xc7b): undefined reference to `PL_sv_count'
/usr/bin/ld: Nauty.c:(.text+0xc98): undefined reference to `PL_body_roots'
/usr/bin/ld: Nauty.c:(.text+0xcaf): undefined reference to `PL_body_roots'
/usr/bin/ld: Nauty.c:(.text+0xd1e): undefined reference to `Perl_newSViv'
/usr/bin/ld: Nauty.c:(.text+0xd3d): undefined reference to `Perl_hv_common_key_len'
/usr/bin/ld: Nauty.c:(.text+0xd4b): undefined reference to `Perl_newSViv'
/usr/bin/ld: Nauty.c:(.text+0xd6a): undefined reference to `Perl_hv_common_key_len'
/usr/bin/ld: Nauty.c:(.text+0xd76): undefined reference to `Perl_newSViv'
/usr/bin/ld: Nauty.c:(.text+0xd95): undefined reference to `Perl_hv_common_key_len'
/usr/bin/ld: Nauty.c:(.text+0xda1): undefined reference to `Perl_newSViv'
/usr/bin/ld: Nauty.c:(.text+0xdc0): undefined reference to `Perl_hv_common_key_len'
/usr/bin/ld: Nauty.c:(.text+0xdcc): undefined reference to `Perl_newSViv'
/usr/bin/ld: Nauty.c:(.text+0xdeb): undefined reference to `Perl_hv_common_key_len'
/usr/bin/ld: Nauty.c:(.text+0xe05): undefined reference to `PL_sv_count'
/usr/bin/ld: Nauty.c:(.text+0xe24): undefined reference to `PL_body_roots'
/usr/bin/ld: Nauty.c:(.text+0xe3b): undefined reference to `PL_body_roots'
/usr/bin/ld: Nauty.c:(.text+0xeca): undefined reference to `Perl_newSViv'
/usr/bin/ld: Nauty.c:(.text+0xed8): undefined reference to `Perl_av_store'
/usr/bin/ld: Nauty.c:(.text+0xf00): undefined reference to `PL_sv_count'
/usr/bin/ld: Nauty.c:(.text+0xf4f): undefined reference to `Perl_hv_common_key_len'
/usr/bin/ld: Nauty.c:(.text+0x1036): undefined reference to `PL_sv_count'
/usr/bin/ld: Nauty.c:(.text+0x106b): undefined reference to `Perl_sv_2mortal'
/usr/bin/ld: Nauty.c:(.text+0x1080): undefined reference to `PL_stack_sp'
/usr/bin/ld: Nauty.c:(.text+0x1104): undefined reference to `Perl_hv_common_key_len'
/usr/bin/ld: Nauty.c:(.text+0x1124): undefined reference to `Perl_sv_2iv_flags'
/usr/bin/ld: Nauty.c:(.text+0x1155): undefined reference to `Perl_hv_common_key_len'
/usr/bin/ld: Nauty.c:(.text+0x1175): undefined reference to `Perl_sv_2iv_flags'
/usr/bin/ld: Nauty.c:(.text+0x120a): undefined reference to `Perl_hv_common_key_len'
/usr/bin/ld: Nauty.c:(.text+0x123b): undefined reference to `Perl_hv_common_key_len'
/usr/bin/ld: Nauty.c:(.text+0x1265): undefined reference to `Perl_hv_common_key_len'
/usr/bin/ld: Nauty.c:(.text+0x1296): undefined reference to `Perl_sv_2iv_flags'
/usr/bin/ld: Nauty.c:(.text+0x12bd): undefined reference to `Perl_av_fetch'
/usr/bin/ld: Nauty.c:(.text+0x12fe): undefined reference to `Perl_sv_2iv_flags'
/usr/bin/ld: Nauty.c:(.text+0x1324): undefined reference to `Perl_av_fetch'
/usr/bin/ld: Nauty.c:(.text+0x1366): undefined reference to `Perl_sv_2iv_flags'
/usr/bin/ld: Nauty.c:(.text+0x138c): undefined reference to `Perl_av_fetch'
/usr/bin/ld: Nauty.c:(.text+0x13d6): undefined reference to `PL_sv_count'
/usr/bin/ld: Nauty.c:(.text+0x13f4): undefined reference to `PL_body_roots'
/usr/bin/ld: Nauty.c:(.text+0x140b): undefined reference to `PL_body_roots'
/usr/bin/ld: Nauty.c:(.text+0x1482): undefined reference to `Perl_newSViv'
/usr/bin/ld: Nauty.c:(.text+0x14a1): undefined reference to `Perl_hv_common_key_len'
/usr/bin/ld: Nauty.c:(.text+0x14ad): undefined reference to `Perl_newSViv'
/usr/bin/ld: Nauty.c:(.text+0x14cc): undefined reference to `Perl_hv_common_key_len'
/usr/bin/ld: Nauty.c:(.text+0x14e5): undefined reference to `PL_sv_count'
/usr/bin/ld: Nauty.c:(.text+0x1502): undefined reference to `PL_body_roots'
/usr/bin/ld: Nauty.c:(.text+0x1519): undefined reference to `PL_body_roots'
/usr/bin/ld: Nauty.c:(.text+0x1584): undefined reference to `PL_sv_count'
/usr/bin/ld: Nauty.c:(.text+0x15a1): undefined reference to `PL_body_roots'
/usr/bin/ld: Nauty.c:(.text+0x15b8): undefined reference to `PL_body_roots'
/usr/bin/ld: Nauty.c:(.text+0x1626): undefined reference to `PL_sv_count'
/usr/bin/ld: Nauty.c:(.text+0x1645): undefined reference to `PL_body_roots'
/usr/bin/ld: Nauty.c:(.text+0x165c): undefined reference to `PL_body_roots'
/usr/bin/ld: Nauty.c:(.text+0x1708): undefined reference to `Perl_newSViv'
/usr/bin/ld: Nauty.c:(.text+0x1719): undefined reference to `Perl_av_store'
/usr/bin/ld: Nauty.c:(.text+0x1790): undefined reference to `Perl_newSViv'
/usr/bin/ld: Nauty.c:(.text+0x17a1): undefined reference to `Perl_av_store'
/usr/bin/ld: Nauty.c:(.text+0x1817): undefined reference to `Perl_newSViv'
/usr/bin/ld: Nauty.c:(.text+0x1828): undefined reference to `Perl_av_store'
/usr/bin/ld: Nauty.c:(.text+0x1975): undefined reference to `PL_sv_count'
/usr/bin/ld: Nauty.c:(.text+0x19c9): undefined reference to `Perl_hv_common_key_len'
/usr/bin/ld: Nauty.c:(.text+0x19e9): undefined reference to `PL_sv_count'
/usr/bin/ld: Nauty.c:(.text+0x1a37): undefined reference to `Perl_hv_common_key_len'
/usr/bin/ld: Nauty.c:(.text+0x1a50): undefined reference to `PL_sv_count'
/usr/bin/ld: Nauty.c:(.text+0x1a9f): undefined reference to `Perl_hv_common_key_len'
/usr/bin/ld: Nauty.c:(.text+0x1ab8): undefined reference to `PL_sv_count'
/usr/bin/ld: Nauty.c:(.text+0x1b06): undefined reference to `Perl_hv_common_key_len'
/usr/bin/ld: Nauty.c:(.text+0x1b20): undefined reference to `PL_sv_count'
/usr/bin/ld: Nauty.c:(.text+0x1b3e): undefined reference to `PL_body_roots'
/usr/bin/ld: Nauty.c:(.text+0x1b55): undefined reference to `PL_body_roots'
/usr/bin/ld: Nauty.c:(.text+0x1be2): undefined reference to `Perl_newSViv'
/usr/bin/ld: Nauty.c:(.text+0x1bf0): undefined reference to `Perl_av_store'
/usr/bin/ld: Nauty.c:(.text+0x1c18): undefined reference to `PL_sv_count'
/usr/bin/ld: Nauty.c:(.text+0x1c66): undefined reference to `Perl_hv_common_key_len'
/usr/bin/ld: Nauty.c:(.text+0x1c74): undefined reference to `Perl_sv_backoff'
/usr/bin/ld: Nauty.c:(.text+0x1c9c): undefined reference to `Perl_hv_common_key_len'
/usr/bin/ld: Nauty.c:(.text+0x1e09): undefined reference to `Perl_more_sv'
/usr/bin/ld: Nauty.c:(.text+0x1e16): undefined reference to `Perl_more_sv'
/usr/bin/ld: Nauty.c:(.text+0x1e29): undefined reference to `Perl_more_sv'
/usr/bin/ld: Nauty.c:(.text+0x1e48): undefined reference to `Perl_more_bodies'
/usr/bin/ld: Nauty.c:(.text+0x1e59): undefined reference to `Perl_more_sv'
/usr/bin/ld: Nauty.c:(.text+0x1e78): undefined reference to `Perl_more_bodies'
/usr/bin/ld: Nauty.c:(.text+0x1f34): undefined reference to `Perl_sv_backoff'
/usr/bin/ld: Nauty.c:(.text+0x1f86): undefined reference to `Perl_more_sv'
/usr/bin/ld: Nauty.c:(.text+0x1f9a): undefined reference to `Perl_more_sv'
/usr/bin/ld: Nauty.c:(.text+0x1fc4): undefined reference to `Perl_more_bodies'
/usr/bin/ld: Nauty.c:(.text+0x1fe3): undefined reference to `Perl_more_sv'
/usr/bin/ld: Nauty.c:(.text+0x201b): undefined reference to `Perl_more_bodies'
/usr/bin/ld: Nauty.c:(.text+0x2042): undefined reference to `Perl_more_bodies'
/usr/bin/ld: Nauty.c:(.text+0x204c): undefined reference to `Perl_more_sv'
/usr/bin/ld: Nauty.c:(.text+0x2076): undefined reference to `Perl_more_bodies'
/usr/bin/ld: Nauty.c:(.text+0x208e): undefined reference to `Perl_more_sv'
/usr/bin/ld: Nauty.c:(.text+0x20aa): undefined reference to `Perl_more_bodies'
/usr/bin/ld: Nauty.c:(.text+0x20b4): undefined reference to `Perl_more_sv'
/usr/bin/ld: Nauty.c:(.text+0x20c1): undefined reference to `Perl_more_sv'
/usr/bin/ld: Nauty.c:(.text+0x20ce): undefined reference to `Perl_more_sv'
/usr/bin/ld: Nauty.c:(.text+0x20e2): undefined reference to `Perl_more_sv'
/usr/bin/ld: Nauty.c:(.text+0x2104): undefined reference to `Perl_more_sv'
/usr/bin/ld: Nauty.c:(.text+0x215c): undefined reference to `Perl_croak_xs_usage'
/usr/bin/ld: Nauty.o: in function `boot_Graph__Nauty':
Nauty.c:(.text+0x21b5): undefined reference to `Perl_xs_handshake'
/usr/bin/ld: Nauty.c:(.text+0x21ca): undefined reference to `Perl_newXS_deffile'
/usr/bin/ld: Nauty.c:(.text+0x21dd): undefined reference to `Perl_newXS_deffile'
/usr/bin/ld: Nauty.c:(.text+0x21e5): undefined reference to `Perl_xs_boot_epilog'

It seems to me that the last command is not seeing what was compiled by the first command, but that is just my guess. The end result is that no module is installed.

[merkys]

From my experience, the message telling to "recompile with -fPIC" might be instructing to do so for Nauty library itself, not the Perl module. How did you compile/install Nauty?