Issue with building from source: ld throws errors
FMKerckhof opened this issue · 4 comments
FMKerckhof commented
Dear, I am trying to build epa-ng from source on Ubuntu server 18.04.5 LTS. I have checked the dependencies and all goes well until the end where ld is throwing errors:
[ 99%] Building CXX object src/CMakeFiles/epa_module.dir/util/stringify.cpp.o
[100%] Linking CXX executable ../../bin/epa-ng
/usr/bin/ld: /usr/local/lib/libz.a(inflate.o): relocation R_X86_64_32S against hidden symbol `zcfree' can not be used when making a PIE object
/usr/bin/ld: /usr/local/lib/libz.a(inftrees.o): relocation R_X86_64_32 against `.rodata' can not be used when making a PIE object; recompile with -fPIC
/usr/bin/ld: /usr/local/lib/libz.a(zutil.o): relocation R_X86_64_32 against `.rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC
/usr/bin/ld: /usr/local/lib/libz.a(crc32.o): relocation R_X86_64_32 against `.rodata' can not be used when making a PIE object; recompile with -fPIC
/usr/bin/ld: /usr/local/lib/libz.a(inffast.o): relocation R_X86_64_32S against `.rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC
/usr/bin/ld: final link failed: Nonrepresentable section on output
collect2: error: ld returned 1 exit status
src/CMakeFiles/epa_module.dir/build.make:598: recipe for target '../bin/epa-ng' failed
make[3]: *** [../bin/epa-ng] Error 1
make[3]: Leaving directory '/usr/local/programs/epa-ng/build'
CMakeFiles/Makefile2:901: recipe for target 'src/CMakeFiles/epa_module.dir/all' failed
make[2]: *** [src/CMakeFiles/epa_module.dir/all] Error 2
make[2]: Leaving directory '/usr/local/programs/epa-ng/build'
Makefile:94: recipe for target 'all' failed
make[1]: *** [all] Error 2
make[1]: Leaving directory '/usr/local/programs/epa-ng/build'
Makefile:11: recipe for target 'run_make' failed
make: *** [run_make] Error 2
how could I resolve this? Am I missing something?
pierrebarbera commented
Hi, could you please post the full build log?
EDIT: also please post which version of zlib your system has, and if you've installed zlib via apt install zlib1g-dev
FMKerckhof commented
Dear, thank you for your swift reply, I assume you mean with the build log the full output, or is there a log file that I would need to get from another location? If the former, please see below. My version of zlib1g-dev is: 1:1.2.11.dfsg-0ubuntu2 and has been installed using apt without custom ppa's.
Running cmake
-- The CXX compiler identification is GNU 7.5.0
-- The C compiler identification is GNU 7.5.0
-- Check for working CXX compiler: /usr/bin/c++
-- Check for working CXX compiler: /usr/bin/c++ -- works
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Check for working C compiler: /usr/bin/cc
-- Check for working C compiler: /usr/bin/cc -- works
-- Detecting C compiler ABI info
-- Detecting C compiler ABI info - done
-- Detecting C compile features
-- Detecting C compile features - done
-- Building EPA-ng version: 0.3.8
-- Build type: RELEASE
-- Looking for pthread.h
-- Looking for pthread.h - found
-- Looking for pthread_create
-- Looking for pthread_create - not found
-- Check if compiler accepts -pthread
-- Check if compiler accepts -pthread - yes
-- Found Threads: TRUE
-- Enabling Prefetching
-- Checking for OpenMP
-- Found OpenMP_C: -fopenmp (found version "4.5")
-- Found OpenMP_CXX: -fopenmp (found version "4.5")
-- Found OpenMP: TRUE (found version "4.5")
-- Checking for OpenMP -- found
-- pll-modules static build enabled
-- Found BISON: /usr/bin/bison (found version "3.0.4")
-- Found FLEX: /usr/bin/flex (found version "2.6.4")
-- SSE enabled. To disable it, run cmake with -DENABLE_SSE=false
-- AVX enabled. To disable it, run cmake with -DENABLE_AVX=false
-- AVX2 enabled. To disable it, run cmake with -DENABLE_AVX2=false
-- Libpll static build enabled
-- pll_static
-- Will compile pll-module optimize
-- Will compile pll-module algorithm
-- Will compile pll-module binary
-- Will compile pll-module msa
-- Will compile pll-module tree
-- Will compile pll-module util
-- Configuring Genesis
-- CMake version 3.10.2
-- Genesis version: v0.20.0
-- Building Genesis as a dependency
-- Build type: RELEASE
-- Unity build: FULL
-- C++ compiler: GNU 7.5.0 at /usr/bin/c++
-- C compiler : GNU 7.5.0 at /usr/bin/cc
-- Check if the system is big endian
-- Searching 16 bit integer
-- Looking for sys/types.h
-- Looking for sys/types.h - found
-- Looking for stdint.h
-- Looking for stdint.h - found
-- Looking for stddef.h
-- Looking for stddef.h - found
-- Check size of unsigned short
-- Check size of unsigned short - done
-- Using unsigned short
-- Check if the system is big endian - little endian
-- Looking for zlib
-- Found ZLIB: /usr/local/lib/libz.a (found version "1.2.11")
-- Found zlib: /usr/include 1.2.11
-- Using zlib
-- Looking for Threads
-- Found Threads: -pthread
-- Using Threads
-- Building static lib
-- Finished configuring Genesis
-- Using flags: -std=c++14 -Wall -Wextra -Wno-unknown-pragmas -pedantic -DEPA_VERSION='"0.3.8"' -D__PREFETCH -fopenmp -D__OMP
-- PLLMODULES_LIBRARIES: pllmodutil_static;pllmodtree_static;pllmodmsa_static;pllmodbinary_static;pllmodalgorithm_static;pllmodoptimize_static
-- GENESIS_LINK_LIBRARIES: /usr/local/lib/libz.a;-pthread;genesis_lib_static
-- Could NOT find GTest (missing: GTEST_INCLUDE_DIR)
-- GTest not found
CMake Warning at test/src/CMakeLists.txt:6 (message):
Skipping building tests. To enable tests:
cmake libs/CLI11/extern/googletest/googletest/CMakeLists.txt
make -C libs/CLI11/extern/googletest/googletestmake update
-- Configuring done
-- Generating done
-- Build files have been written to: /usr/local/programs/epa-ng/build
Running make
make -C build
make[1]: Entering directory '/usr/local/programs/epa-ng/build'
make[2]: Entering directory '/usr/local/programs/epa-ng/build'
make[3]: Entering directory '/usr/local/programs/epa-ng/build'
[ 1%] [FLEX][lex_rtree_t] Building scanner with flex 2.6.4
[ 2%] [BISON][parse_utree_t] Building parser with bison 3.0.4
[ 2%] [FLEX][lex_utree_t] Building scanner with flex 2.6.4
[ 3%] [BISON][parse_rtree_t] Building parser with bison 3.0.4
Scanning dependencies of target pll_obj
make[3]: Leaving directory '/usr/local/programs/epa-ng/build'
make[3]: Entering directory '/usr/local/programs/epa-ng/build'
[ 4%] Building C object libs/pll-modules/libs/libpll/src/CMakeFiles/pll_obj.dir/compress.c.o
[ 5%] Building C object libs/pll-modules/libs/libpll/src/CMakeFiles/pll_obj.dir/parse_utree.c.o
[ 6%] Building C object libs/pll-modules/libs/libpll/src/CMakeFiles/pll_obj.dir/lex_utree.c.o
[ 7%] Building C object libs/pll-modules/libs/libpll/src/CMakeFiles/pll_obj.dir/parse_rtree.c.o
[ 8%] Building C object libs/pll-modules/libs/libpll/src/CMakeFiles/pll_obj.dir/lex_rtree.c.o
[ 8%] Building C object libs/pll-modules/libs/libpll/src/CMakeFiles/pll_obj.dir/core_derivatives.c.o
[ 9%] Building C object libs/pll-modules/libs/libpll/src/CMakeFiles/pll_obj.dir/core_likelihood.c.o
[ 10%] Building C object libs/pll-modules/libs/libpll/src/CMakeFiles/pll_obj.dir/core_partials.c.o
[ 11%] Building C object libs/pll-modules/libs/libpll/src/CMakeFiles/pll_obj.dir/core_pmatrix.c.o
[ 12%] Building C object libs/pll-modules/libs/libpll/src/CMakeFiles/pll_obj.dir/derivatives.c.o
[ 13%] Building C object libs/pll-modules/libs/libpll/src/CMakeFiles/pll_obj.dir/fasta.c.o
[ 14%] Building C object libs/pll-modules/libs/libpll/src/CMakeFiles/pll_obj.dir/fast_parsimony.c.o
[ 15%] Building C object libs/pll-modules/libs/libpll/src/CMakeFiles/pll_obj.dir/gamma.c.o
[ 15%] Building C object libs/pll-modules/libs/libpll/src/CMakeFiles/pll_obj.dir/hardware.c.o
[ 16%] Building C object libs/pll-modules/libs/libpll/src/CMakeFiles/pll_obj.dir/likelihood.c.o
[ 17%] Building C object libs/pll-modules/libs/libpll/src/CMakeFiles/pll_obj.dir/list.c.o
[ 18%] Building C object libs/pll-modules/libs/libpll/src/CMakeFiles/pll_obj.dir/maps.c.o
[ 19%] Building C object libs/pll-modules/libs/libpll/src/CMakeFiles/pll_obj.dir/models.c.o
[ 20%] Building C object libs/pll-modules/libs/libpll/src/CMakeFiles/pll_obj.dir/output.c.o
[ 21%] Building C object libs/pll-modules/libs/libpll/src/CMakeFiles/pll_obj.dir/parsimony.c.o
[ 22%] Building C object libs/pll-modules/libs/libpll/src/CMakeFiles/pll_obj.dir/partials.c.o
[ 22%] Building C object libs/pll-modules/libs/libpll/src/CMakeFiles/pll_obj.dir/phylip.c.o
[ 23%] Building C object libs/pll-modules/libs/libpll/src/CMakeFiles/pll_obj.dir/pll.c.o
[ 24%] Building C object libs/pll-modules/libs/libpll/src/CMakeFiles/pll_obj.dir/random.c.o
[ 25%] Building C object libs/pll-modules/libs/libpll/src/CMakeFiles/pll_obj.dir/repeats.c.o
[ 26%] Building C object libs/pll-modules/libs/libpll/src/CMakeFiles/pll_obj.dir/rtree.c.o
[ 27%] Building C object libs/pll-modules/libs/libpll/src/CMakeFiles/pll_obj.dir/stepwise.c.o
[ 28%] Building C object libs/pll-modules/libs/libpll/src/CMakeFiles/pll_obj.dir/utree.c.o
[ 29%] Building C object libs/pll-modules/libs/libpll/src/CMakeFiles/pll_obj.dir/utree_moves.c.o
[ 30%] Building C object libs/pll-modules/libs/libpll/src/CMakeFiles/pll_obj.dir/utree_svg.c.o
[ 30%] Building C object libs/pll-modules/libs/libpll/src/CMakeFiles/pll_obj.dir/core_derivatives_sse.c.o
[ 31%] Building C object libs/pll-modules/libs/libpll/src/CMakeFiles/pll_obj.dir/core_likelihood_sse.c.o
[ 32%] Building C object libs/pll-modules/libs/libpll/src/CMakeFiles/pll_obj.dir/core_partials_sse.c.o
[ 33%] Building C object libs/pll-modules/libs/libpll/src/CMakeFiles/pll_obj.dir/core_pmatrix_sse.c.o
[ 34%] Building C object libs/pll-modules/libs/libpll/src/CMakeFiles/pll_obj.dir/fast_parsimony_sse.c.o
[ 35%] Building C object libs/pll-modules/libs/libpll/src/CMakeFiles/pll_obj.dir/core_derivatives_avx.c.o
[ 36%] Building C object libs/pll-modules/libs/libpll/src/CMakeFiles/pll_obj.dir/core_likelihood_avx.c.o
[ 37%] Building C object libs/pll-modules/libs/libpll/src/CMakeFiles/pll_obj.dir/core_partials_avx.c.o
[ 37%] Building C object libs/pll-modules/libs/libpll/src/CMakeFiles/pll_obj.dir/core_pmatrix_avx.c.o
[ 38%] Building C object libs/pll-modules/libs/libpll/src/CMakeFiles/pll_obj.dir/fast_parsimony_avx.c.o
[ 39%] Building C object libs/pll-modules/libs/libpll/src/CMakeFiles/pll_obj.dir/core_derivatives_avx2.c.o
[ 40%] Building C object libs/pll-modules/libs/libpll/src/CMakeFiles/pll_obj.dir/core_likelihood_avx2.c.o
[ 41%] Building C object libs/pll-modules/libs/libpll/src/CMakeFiles/pll_obj.dir/core_partials_avx2.c.o
[ 42%] Building C object libs/pll-modules/libs/libpll/src/CMakeFiles/pll_obj.dir/core_pmatrix_avx2.c.o
[ 43%] Building C object libs/pll-modules/libs/libpll/src/CMakeFiles/pll_obj.dir/fast_parsimony_avx2.c.o
make[3]: Leaving directory '/usr/local/programs/epa-ng/build'
[ 43%] Built target pll_obj
make[3]: Entering directory '/usr/local/programs/epa-ng/build'
Scanning dependencies of target pll_static
make[3]: Leaving directory '/usr/local/programs/epa-ng/build'
make[3]: Entering directory '/usr/local/programs/epa-ng/build'
[ 44%] Linking C static library libpll.a
make[3]: Leaving directory '/usr/local/programs/epa-ng/build'
[ 44%] Built target pll_static
make[3]: Entering directory '/usr/local/programs/epa-ng/build'
Scanning dependencies of target pllmodoptimize_obj
make[3]: Leaving directory '/usr/local/programs/epa-ng/build'
make[3]: Entering directory '/usr/local/programs/epa-ng/build'
[ 45%] Building C object libs/pll-modules/src/optimize/CMakeFiles/pllmodoptimize_obj.dir/opt_algorithms.c.o
[ 46%] Building C object libs/pll-modules/src/optimize/CMakeFiles/pllmodoptimize_obj.dir/pll_optimize.c.o
[ 47%] Building C object libs/pll-modules/src/optimize/CMakeFiles/pllmodoptimize_obj.dir/lbfgsb/lbfgsb.c.o
[ 48%] Building C object libs/pll-modules/src/optimize/CMakeFiles/pllmodoptimize_obj.dir/lbfgsb/linesearch.c.o
[ 48%] Building C object libs/pll-modules/src/optimize/CMakeFiles/pllmodoptimize_obj.dir/lbfgsb/linpack.c.o
[ 49%] Building C object libs/pll-modules/src/optimize/CMakeFiles/pllmodoptimize_obj.dir/lbfgsb/miniCBLAS.c.o
[ 50%] Building C object libs/pll-modules/src/optimize/CMakeFiles/pllmodoptimize_obj.dir/lbfgsb/subalgorithms.c.o
[ 51%] Building C object libs/pll-modules/src/optimize/CMakeFiles/pllmodoptimize_obj.dir/__/pllmod_common.c.o
make[3]: Leaving directory '/usr/local/programs/epa-ng/build'
[ 51%] Built target pllmodoptimize_obj
make[3]: Entering directory '/usr/local/programs/epa-ng/build'
Scanning dependencies of target pllmodoptimize_static
make[3]: Leaving directory '/usr/local/programs/epa-ng/build'
make[3]: Entering directory '/usr/local/programs/epa-ng/build'
[ 52%] Linking C static library libpllmodoptimize.a
make[3]: Leaving directory '/usr/local/programs/epa-ng/build'
[ 52%] Built target pllmodoptimize_static
make[3]: Entering directory '/usr/local/programs/epa-ng/build'
Scanning dependencies of target pllmodalgorithm_obj
make[3]: Leaving directory '/usr/local/programs/epa-ng/build'
make[3]: Entering directory '/usr/local/programs/epa-ng/build'
[ 52%] Building C object libs/pll-modules/src/algorithm/CMakeFiles/pllmodalgorithm_obj.dir/algo_callback.c.o
[ 53%] Building C object libs/pll-modules/src/algorithm/CMakeFiles/pllmodalgorithm_obj.dir/algo_search.c.o
[ 54%] Building C object libs/pll-modules/src/algorithm/CMakeFiles/pllmodalgorithm_obj.dir/pllmod_algorithm.c.o
[ 55%] Building C object libs/pll-modules/src/algorithm/CMakeFiles/pllmodalgorithm_obj.dir/__/pllmod_common.c.o
make[3]: Leaving directory '/usr/local/programs/epa-ng/build'
[ 55%] Built target pllmodalgorithm_obj
make[3]: Entering directory '/usr/local/programs/epa-ng/build'
Scanning dependencies of target pllmodalgorithm_static
make[3]: Leaving directory '/usr/local/programs/epa-ng/build'
make[3]: Entering directory '/usr/local/programs/epa-ng/build'
[ 56%] Linking C static library libpllmodalgorithm.a
make[3]: Leaving directory '/usr/local/programs/epa-ng/build'
[ 56%] Built target pllmodalgorithm_static
make[3]: Entering directory '/usr/local/programs/epa-ng/build'
Scanning dependencies of target pllmodbinary_obj
make[3]: Leaving directory '/usr/local/programs/epa-ng/build'
make[3]: Entering directory '/usr/local/programs/epa-ng/build'
[ 57%] Building C object libs/pll-modules/src/binary/CMakeFiles/pllmodbinary_obj.dir/binary_io_operations.c.o
[ 58%] Building C object libs/pll-modules/src/binary/CMakeFiles/pllmodbinary_obj.dir/pll_binary.c.o
[ 59%] Building C object libs/pll-modules/src/binary/CMakeFiles/pllmodbinary_obj.dir/__/pllmod_common.c.o
make[3]: Leaving directory '/usr/local/programs/epa-ng/build'
[ 59%] Built target pllmodbinary_obj
make[3]: Entering directory '/usr/local/programs/epa-ng/build'
Scanning dependencies of target pllmodbinary_static
make[3]: Leaving directory '/usr/local/programs/epa-ng/build'
make[3]: Entering directory '/usr/local/programs/epa-ng/build'
[ 59%] Linking C static library libpllmodbinary.a
make[3]: Leaving directory '/usr/local/programs/epa-ng/build'
[ 59%] Built target pllmodbinary_static
make[3]: Entering directory '/usr/local/programs/epa-ng/build'
Scanning dependencies of target pllmodmsa_obj
make[3]: Leaving directory '/usr/local/programs/epa-ng/build'
make[3]: Entering directory '/usr/local/programs/epa-ng/build'
[ 60%] Building C object libs/pll-modules/src/msa/CMakeFiles/pllmodmsa_obj.dir/pll_msa.c.o
[ 61%] Building C object libs/pll-modules/src/msa/CMakeFiles/pllmodmsa_obj.dir/__/pllmod_common.c.o
make[3]: Leaving directory '/usr/local/programs/epa-ng/build'
[ 61%] Built target pllmodmsa_obj
make[3]: Entering directory '/usr/local/programs/epa-ng/build'
Scanning dependencies of target pllmodmsa_static
make[3]: Leaving directory '/usr/local/programs/epa-ng/build'
make[3]: Entering directory '/usr/local/programs/epa-ng/build'
[ 62%] Linking C static library libpllmodmsa.a
make[3]: Leaving directory '/usr/local/programs/epa-ng/build'
[ 62%] Built target pllmodmsa_static
make[3]: Entering directory '/usr/local/programs/epa-ng/build'
[ 63%] [FLEX][lex_split_t] Building scanner with flex 2.6.4
[ 64%] [BISON][split_utree_t] Building parser with bison 3.0.4
Scanning dependencies of target pllmodtree_obj
make[3]: Leaving directory '/usr/local/programs/epa-ng/build'
make[3]: Entering directory '/usr/local/programs/epa-ng/build'
[ 65%] Building C object libs/pll-modules/src/tree/CMakeFiles/pllmodtree_obj.dir/consensus.c.o
[ 65%] Building C object libs/pll-modules/src/tree/CMakeFiles/pllmodtree_obj.dir/pll_tree.c.o
[ 66%] Building C object libs/pll-modules/src/tree/CMakeFiles/pllmodtree_obj.dir/rtree_operations.c.o
[ 67%] Building C object libs/pll-modules/src/tree/CMakeFiles/pllmodtree_obj.dir/tree_hashtable.c.o
[ 68%] Building C object libs/pll-modules/src/tree/CMakeFiles/pllmodtree_obj.dir/treeinfo.c.o
[ 69%] Building C object libs/pll-modules/src/tree/CMakeFiles/pllmodtree_obj.dir/utree_distances.c.o
[ 70%] Building C object libs/pll-modules/src/tree/CMakeFiles/pllmodtree_obj.dir/tbe_functions.c.o
[ 71%] Building C object libs/pll-modules/src/tree/CMakeFiles/pllmodtree_obj.dir/utree_operations.c.o
[ 72%] Building C object libs/pll-modules/src/tree/CMakeFiles/pllmodtree_obj.dir/split_utree.c.o
[ 72%] Building C object libs/pll-modules/src/tree/CMakeFiles/pllmodtree_obj.dir/lex_split.c.o
make[3]: Leaving directory '/usr/local/programs/epa-ng/build'
[ 72%] Built target pllmodtree_obj
make[3]: Entering directory '/usr/local/programs/epa-ng/build'
Scanning dependencies of target pllmodtree_static
make[3]: Leaving directory '/usr/local/programs/epa-ng/build'
make[3]: Entering directory '/usr/local/programs/epa-ng/build'
[ 73%] Linking C static library libpllmodtree.a
make[3]: Leaving directory '/usr/local/programs/epa-ng/build'
[ 73%] Built target pllmodtree_static
make[3]: Entering directory '/usr/local/programs/epa-ng/build'
Scanning dependencies of target pllmodutil_obj
make[3]: Leaving directory '/usr/local/programs/epa-ng/build'
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[ 74%] Building C object libs/pll-modules/src/util/CMakeFiles/pllmodutil_obj.dir/models.c.o
[ 75%] Building C object libs/pll-modules/src/util/CMakeFiles/pllmodutil_obj.dir/models_aa.c.o
[ 76%] Building C object libs/pll-modules/src/util/CMakeFiles/pllmodutil_obj.dir/models_dna.c.o
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[ 79%] Building C object libs/pll-modules/src/util/CMakeFiles/pllmodutil_obj.dir/__/pllmod_common.c.o
make[3]: Leaving directory '/usr/local/programs/epa-ng/build'
[ 79%] Built target pllmodutil_obj
make[3]: Entering directory '/usr/local/programs/epa-ng/build'
Scanning dependencies of target pllmodutil_static
make[3]: Leaving directory '/usr/local/programs/epa-ng/build'
make[3]: Entering directory '/usr/local/programs/epa-ng/build'
[ 80%] Linking C static library libpllmodutil.a
make[3]: Leaving directory '/usr/local/programs/epa-ng/build'
[ 80%] Built target pllmodutil_static
make[3]: Entering directory '/usr/local/programs/epa-ng/build'
Scanning dependencies of target genesis_lib_static
make[3]: Leaving directory '/usr/local/programs/epa-ng/build'
make[3]: Entering directory '/usr/local/programs/epa-ng/build'
[ 81%] Building CXX object libs/genesis/lib/genesis/CMakeFiles/genesis_lib_static.dir/__/__/__/__/genesis_unity_sources/lib/all.cpp.o
[ 82%] Linking CXX static library ../../../../../libs/genesis/bin/libgenesis.a
make[3]: Leaving directory '/usr/local/programs/epa-ng/build'
[ 82%] Built target genesis_lib_static
make[3]: Entering directory '/usr/local/programs/epa-ng/build'
Scanning dependencies of target epa_module
make[3]: Leaving directory '/usr/local/programs/epa-ng/build'
make[3]: Entering directory '/usr/local/programs/epa-ng/build'
[ 82%] Building CXX object src/CMakeFiles/epa_module.dir/core/place.cpp.o
[ 83%] Building CXX object src/CMakeFiles/epa_module.dir/core/pll/epa_pll_util.cpp.o
[ 84%] Building CXX object src/CMakeFiles/epa_module.dir/core/pll/optimize.cpp.o
[ 85%] Building CXX object src/CMakeFiles/epa_module.dir/core/pll/pll_util.cpp.o
[ 86%] Building CXX object src/CMakeFiles/epa_module.dir/core/raxml/Model.cpp.o
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[ 97%] Building CXX object src/CMakeFiles/epa_module.dir/tree/Tree.cpp.o
[ 98%] Building CXX object src/CMakeFiles/epa_module.dir/tree/tiny_util.cpp.o
[ 99%] Building CXX object src/CMakeFiles/epa_module.dir/util/stringify.cpp.o
[100%] Linking CXX executable ../../bin/epa-ng
/usr/bin/ld: /usr/local/lib/libz.a(inflate.o): relocation R_X86_64_32S against hidden symbol `zcfree' can not be used when making a PIE object
/usr/bin/ld: /usr/local/lib/libz.a(inftrees.o): relocation R_X86_64_32 against `.rodata' can not be used when making a PIE object; recompile with -fPIC
/usr/bin/ld: /usr/local/lib/libz.a(zutil.o): relocation R_X86_64_32 against `.rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC
/usr/bin/ld: /usr/local/lib/libz.a(crc32.o): relocation R_X86_64_32 against `.rodata' can not be used when making a PIE object; recompile with -fPIC
/usr/bin/ld: /usr/local/lib/libz.a(inffast.o): relocation R_X86_64_32S against `.rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC
/usr/bin/ld: final link failed: Nonrepresentable section on output
collect2: error: ld returned 1 exit status
src/CMakeFiles/epa_module.dir/build.make:598: recipe for target '../bin/epa-ng' failed
make[3]: *** [../bin/epa-ng] Error 1
make[3]: Leaving directory '/usr/local/programs/epa-ng/build'
CMakeFiles/Makefile2:901: recipe for target 'src/CMakeFiles/epa_module.dir/all' failed
make[2]: *** [src/CMakeFiles/epa_module.dir/all] Error 2
make[2]: Leaving directory '/usr/local/programs/epa-ng/build'
Makefile:94: recipe for target 'all' failed
make[1]: *** [all] Error 2
make[1]: Leaving directory '/usr/local/programs/epa-ng/build'
Makefile:11: recipe for target 'run_make' failed
make: *** [run_make] Error 2
pierrebarbera commented
it looks like cmake is selecting the wrong installation of zlib here, as it seems you have an installation at /usr/local/lib/libz.a. The one from the zlib1g-dev package should be located at /usr/lib/x86_64-linux-gnu/libz.so. So bare minimum, it selects the statically linked over the dynamically linked. Can you try this?
make clean
mkdir build && cd build
cmake .. -DZLIB_ROOT=/usr/lib/x86_64-linux-gnu/
make
FMKerckhof commented
Thanks @Pbdas, that seems to have resolved the issue.