Failure to compile on CentOS

[gwaldbieser]

I loaded the latest version 0.5.1__ released 04March2017

• CentOS Linux release 7.3.1611
  • gcc version 4.8.5 20150623

'Make modules' appeared to work. 'Make' reports several lines then fails:

g++ -static-libgcc -static-libstdc++ -Dcplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/argumentparser/src -Icodebase/gindex/src -Icodebase/seqlib/src -DRELEASE_VERSION -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread -o obj_linux/src/owler/owler.o src/owler/owler.cc mkdir -p obj_linux/src/owler/ g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/argumentparser/src -Icodebase/gindex/src -Icodebase/seqlib/src -DRELEASE_VERSION -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread -o obj_linux/src/owler/lcsk.o src/owler/lcsk.cc mkdir -p obj_linux/src/owler/ g++ -static-libgcc -static-libstdc++ -Dcplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/argumentparser/src -Icodebase/gindex/src -Icodebase/seqlib/src -DRELEASE_VERSION -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread -o obj_linux/src/owler/process_read.o src/owler/process_read.cc mkdir -p obj_linux/src/owler/ g++ -static-libgcc -static-libstdc++ -Dcplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/argumentparser/src -Icodebase/gindex/src -Icodebase/seqlib/src -DRELEASE_VERSION -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread -o obj_linux/src/owler/owler_experimental.o src/owler/owler_experimental.cc mkdir -p obj_linux/src/ g++ -static-libgcc -static-libstdc++ -D__cplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/argumentparser/src -Icodebase/gindex/src -Icodebase/seqlib/src -DRELEASE_VERSION -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread -o obj_linux/src/program_parameters.o src/program_parameters.cc mkdir -p obj_linux/src/ g++ -static-libgcc -static-libstdc++ -Dcplusplus=201103L -I"./src/" -I"/usr/include/" -I"codebase/seqlib/src/libs/seqan-library-2.0.1/include" -I"codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/" -Icodebase/argumentparser/src -Icodebase/gindex/src -Icodebase/seqlib/src -DRELEASE_VERSION -O3 -fdata-sections -ffunction-sections -c -fmessage-length=0 -ffreestanding -fopenmp -m64 -std=c++11 -Werror=return-type -pthread -o obj_linux/src/main.o src/main.cc mkdir -p ./bin/Linux-x64/ g++ -static-libgcc -static-libstdc++ -m64 -ffreestanding -L"/usr/local/lib" -o ./bin/Linux-x64/graphmap ./obj_linux/codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/utils.o ./obj_linux/codebase/gindex/src/main.o ./obj_linux/codebase/argumentparser/src/example.o ./obj_linux/codebase/argumentparser/src/argparser.o ./obj_linux/codebase/seqlib/src/test.o ./obj_linux/codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/sssort.o ./obj_linux/codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/trsort.o ./obj_linux/codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/divsufsort.o ./obj_linux/codebase/gindex/src/minimizer_index/experimental.o ./obj_linux/codebase/gindex/src/minimizer_index/compiled_shape.o ./obj_linux/codebase/gindex/src/minimizer_index/seed.o ./obj_linux/codebase/gindex/src/minimizer_index/minimizer_index.o ./obj_linux/codebase/gindex/src/minimizer_index/minimizer_generator.o ./obj_linux/codebase/gindex/src/minimizer_index/index_pos.o ./obj_linux/codebase/seqlib/src/utility/utility_general.o ./obj_linux/codebase/seqlib/src/utility/tictoc.o ./obj_linux/codebase/seqlib/src/utility/evalue_constants.o ./obj_linux/codebase/seqlib/src/utility/evalue.o ./obj_linux/codebase/seqlib/src/sequences/sequence_gfa_test.o ./obj_linux/codebase/seqlib/src/sequences/sequence_file.o ./obj_linux/codebase/seqlib/src/sequences/sequence_alignment.o ./obj_linux/codebase/seqlib/src/sequences/sequence_gfa.o ./obj_linux/codebase/seqlib/src/sequences/sequence_alignment_test.o ./obj_linux/codebase/seqlib/src/sequences/single_sequence.o ./obj_linux/codebase/seqlib/src/log_system/log_system.o ./obj_linux/codebase/seqlib/src/libs/edlib.o ./obj_linux/codebase/seqlib/src/libs/edlibcigar.o ./obj_linux/codebase/seqlib/src/libs/opal.o ./obj_linux/src/alignment/alignment.o ./obj_linux/src/alignment/semiglobal.o ./obj_linux/src/alignment/cigargen.o ./obj_linux/src/alignment/transcriptome_mod.o ./obj_linux/src/alignment/anchored.o ./obj_linux/src/alignment/alignment_wrappers.o ./obj_linux/src/index/index_util.o ./obj_linux/src/containers/path_graph_entry.o ./obj_linux/src/containers/mapping_data.o ./obj_linux/src/containers/vertices.o ./obj_linux/src/containers/region.o ./obj_linux/src/containers/score_registry.o ./obj_linux/src/graphmap/experimental.o ./obj_linux/src/graphmap/lcs_anchored.o ./obj_linux/src/graphmap/region_selection.o ./obj_linux/src/graphmap/process_read.o ./obj_linux/src/graphmap/transcriptome.o ./obj_linux/src/graphmap/lcs_semiglobal.o ./obj_linux/src/graphmap/filter_anchors.o ./obj_linux/src/graphmap/graphmap.o ./obj_linux/src/graphmap/core_graphmap.o ./obj_linux/src/owler/owler.o ./obj_linux/src/owler/lcsk.o ./obj_linux/src/owler/process_read.o ./obj_linux/src/owler/owler_experimental.o ./obj_linux/src/program_parameters.o ./obj_linux/src/main.o -lpthread -lgomp -lm -lz /usr/bin/ld: cannot find -lstdc++ collect2: error: ld returned 1 exit status make: *** [linux] Error 1

[vatese]

I added -lstdc++ to the LD_FLAGS on the Makefile and it works. Hope it helps.

[gwaldbieser]

It didn't work for me. I deleted the directory and restarted from scratch as root: $git clone https://github.com/isovic/graphmap.git graphmap $cd graphmap

Edited this line in Makefile

LD_FLAGS = -lstdc++ -static-libgcc -static-libstdc++ -m64 -ffreestanding (I also tried putting it at the end of the line) $make modules [root@rambo graphmap]# make modules git submodule update --init --recursive Submodule 'codebase/argumentparser' (https://github.com/isovic/argumentparser.git) registered for path 'codebase/argumentparser' Submodule 'codebase/gindex' (https://github.com/isovic/gindex) registered for path 'codebase/gindex' Submodule 'codebase/seqlib' (https://github.com/isovic/seqlib.git) registered for path 'codebase/seqlib' Cloning into 'codebase/argumentparser'... remote: Counting objects: 90, done. remote: Compressing objects: 100% (41/41), done. remote: Total 90 (delta 47), reused 90 (delta 47), pack-reused 0 Unpacking objects: 100% (90/90), done. Submodule path 'codebase/argumentparser': checked out '72af9764acefbcc92ff76e3aba8a83d9a3e33671' Cloning into 'codebase/gindex'... remote: Counting objects: 274, done. remote: Total 274 (delta 0), reused 0 (delta 0), pack-reused 274 Receiving objects: 100% (274/274), 1.82 MiB | 305.00 KiB/s, done. Resolving deltas: 100% (126/126), done. Submodule path 'codebase/gindex': checked out 'b1fb5ad35763632db66377348bb16fec29f381e4' Submodule 'codebase/seqlib' (https://github.com/isovic/seqlib) registered for path 'codebase/seqlib' Cloning into 'codebase/seqlib'... remote: Counting objects: 2473, done. remote: Total 2473 (delta 0), reused 0 (delta 0), pack-reused 2473 Receiving objects: 100% (2473/2473), 7.48 MiB | 288.00 KiB/s, done. Resolving deltas: 100% (1381/1381), done. Submodule path 'codebase/gindex/codebase/seqlib': checked out 'bcfbcb1c77461c300d2ec0de03c0e1657a95cde2' Cloning into 'codebase/seqlib'... remote: Counting objects: 2473, done. remote: Total 2473 (delta 0), reused 0 (delta 0), pack-reused 2473 Receiving objects: 100% (2473/2473), 7.48 MiB | 410.00 KiB/s, done. Resolving deltas: 100% (1381/1381), done. Submodule path 'codebase/seqlib': checked out '61ce79526e7e35b68057565caaf20d6ddc5906a0'

git submodule foreach git pull origin master

$make 1>makelog 2>&1 & $tail -5 makelog mkdir -p ./bin/Linux-x64/ g++ -lstdc++ -static-libgcc -static-libstdc++ -m64 -ffreestanding -L"/usr/local/lib" -o ./bin/Linux-x64/graphmap ./obj_linux/codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/utils.o ./obj_linux/codebase/gindex/src/main.o ./obj_linux/codebase/argumentparser/src/example.o ./obj_linux/codebase/argumentparser/src/argparser.o ./obj_linux/codebase/seqlib/src/test.o ./obj_linux/codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/sssort.o ./obj_linux/codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/trsort.o ./obj_linux/codebase/seqlib/src/libs/libdivsufsort-2.0.1-64bit/divsufsort.o ./obj_linux/codebase/gindex/src/minimizer_index/experimental.o ./obj_linux/codebase/gindex/src/minimizer_index/compiled_shape.o ./obj_linux/codebase/gindex/src/minimizer_index/seed.o ./obj_linux/codebase/gindex/src/minimizer_index/minimizer_index.o ./obj_linux/codebase/gindex/src/minimizer_index/minimizer_generator.o ./obj_linux/codebase/gindex/src/minimizer_index/index_pos.o ./obj_linux/codebase/seqlib/src/utility/utility_general.o ./obj_linux/codebase/seqlib/src/utility/tictoc.o ./obj_linux/codebase/seqlib/src/utility/evalue_constants.o ./obj_linux/codebase/seqlib/src/utility/evalue.o ./obj_linux/codebase/seqlib/src/sequences/sequence_gfa_test.o ./obj_linux/codebase/seqlib/src/sequences/sequence_file.o ./obj_linux/codebase/seqlib/src/sequences/sequence_alignment.o ./obj_linux/codebase/seqlib/src/sequences/sequence_gfa.o ./obj_linux/codebase/seqlib/src/sequences/sequence_alignment_test.o ./obj_linux/codebase/seqlib/src/sequences/single_sequence.o ./obj_linux/codebase/seqlib/src/log_system/log_system.o ./obj_linux/codebase/seqlib/src/libs/edlib.o ./obj_linux/codebase/seqlib/src/libs/edlibcigar.o ./obj_linux/codebase/seqlib/src/libs/opal.o ./obj_linux/src/alignment/alignment.o ./obj_linux/src/alignment/semiglobal.o ./obj_linux/src/alignment/cigargen.o ./obj_linux/src/alignment/transcriptome_mod.o ./obj_linux/src/alignment/anchored.o ./obj_linux/src/alignment/alignment_wrappers.o ./obj_linux/src/index/index_util.o ./obj_linux/src/containers/path_graph_entry.o ./obj_linux/src/containers/mapping_data.o ./obj_linux/src/containers/vertices.o ./obj_linux/src/containers/region.o ./obj_linux/src/containers/score_registry.o ./obj_linux/src/graphmap/experimental.o ./obj_linux/src/graphmap/lcs_anchored.o ./obj_linux/src/graphmap/region_selection.o ./obj_linux/src/graphmap/process_read.o ./obj_linux/src/graphmap/transcriptome.o ./obj_linux/src/graphmap/lcs_semiglobal.o ./obj_linux/src/graphmap/filter_anchors.o ./obj_linux/src/graphmap/graphmap.o ./obj_linux/src/graphmap/core_graphmap.o ./obj_linux/src/owler/owler.o ./obj_linux/src/owler/lcsk.o ./obj_linux/src/owler/process_read.o ./obj_linux/src/owler/owler_experimental.o ./obj_linux/src/program_parameters.o ./obj_linux/src/main.o -lpthread -lgomp -lm -lz /usr/bin/ld: cannot find -lstdc++ collect2: error: ld returned 1 exit status make: *** [linux] Error 1

[vatese]

Do you have libstdc++-devel or libstdc++-static installed?

rpm -qa | grep libstdc++-devel

[gwaldbieser]

Wed Apr 12 12:32:36$ rpm -qa | grep libstdc++ libstdc++-devel-4.8.5-11.el7.x86_64 libstdc++-4.8.5-11.el7.x86_64 compat-libstdc++-33-3.2.3-72.el7.x86_64 libstdc++-4.8.5-11.el7.i686

From: Miguel Esteva [mailto:notifications@github.com] Sent: Tuesday, April 11, 2017 6:11 PM To: isovic/graphmap graphmap@noreply.github.com Cc: Waldbieser, Geoff Geoff.Waldbieser@ARS.USDA.GOV; Author author@noreply.github.com Subject: Re: [isovic/graphmap] Failure to compile on CentOS (#63)

Do you have libstdc++-devel or libstdc++-static installed?

rpm -qa | grep libstdc++-devel

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/isovic/graphmap/issues/63#issuecomment-293426302, or mute the threadhttps://github.com/notifications/unsubscribe-auth/ASb-WntpNuEgHejrSxaJew3og6j4rY3lks5rvAhmgaJpZM4M3c1R.

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[vatese]

Try:

yum install libstdc++-static

[gwaldbieser]

That did it. Thanks for your help! Geoff

From: Miguel Esteva [mailto:notifications@github.com] Sent: Wednesday, April 12, 2017 4:20 PM To: isovic/graphmap graphmap@noreply.github.com Cc: Waldbieser, Geoff Geoff.Waldbieser@ARS.USDA.GOV; Author author@noreply.github.com Subject: Re: [isovic/graphmap] Failure to compile on CentOS (#63)

Try:

yum install libstdc++-static

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/isovic/graphmap/issues/63#issuecomment-293711173, or mute the threadhttps://github.com/notifications/unsubscribe-auth/ASb-WimryMBppG21c5WM99yMTndjHan0ks5rvUAYgaJpZM4M3c1R.

This electronic message contains information generated by the USDA solely for the intended recipients. Any unauthorized interception of this message or the use or disclosure of the information it contains may violate the law and subject the violator to civil or criminal penalties. If you believe you have received this message in error, please notify the sender and delete the email immediately.

[paulmenzel]

Can this be closed then? Or should a configure script be added to ensure all dependencies are installed? Meson is the new kid on the block, but Autotools and CMake should also to the trick.

[gwaldbieser]

You can close it.

From: Paul Menzel [mailto:notifications@github.com] Sent: Friday, September 22, 2017 10:10 AM To: isovic/graphmap graphmap@noreply.github.com Cc: Waldbieser, Geoff Geoff.Waldbieser@ARS.USDA.GOV; Author author@noreply.github.com Subject: Re: [isovic/graphmap] Failure to compile on CentOS (#63)

Can this be closed then? Or should a configure script be added to ensure all dependencies are installed? Mesonhttps://mesonbuild.com is the new kid on the block, but Autotools and CMake should also to the trick.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/isovic/graphmap/issues/63#issuecomment-331474340, or mute the threadhttps://github.com/notifications/unsubscribe-auth/ASb-Wsb7LYX5Jb7I5_SxS-JEqo8PmUxZks5sk82xgaJpZM4M3c1R.

This electronic message contains information generated by the USDA solely for the intended recipients. Any unauthorized interception of this message or the use or disclosure of the information it contains may violate the law and subject the violator to civil or criminal penalties. If you believe you have received this message in error, please notify the sender and delete the email immediately.