error in install.sh

[little-raccoon]

CentOS Linux 7 perl v5.26.2 gcc version 8.3.0

error: ++ pwd -P

• ROOT=/lustre1/leili_pkuhpc/software/MaSuRCA-3.4.2
• '[' -z '' ']'
• DEST=/lustre1/leili_pkuhpc/software/MaSuRCA-3.4.2
• mkdir -p dist-bin
• PATH=/home/leili_pkuhpc/.aspera/connect/bin:/home/leili_pkuhpc/lustre1/software/fasttree:/home/leili_pkuhpc/lustre1/software/bedtools_v2.29.2/bedtools2/bin:/home/leili_pkuhpc/lustre1/software/OrthoFinder/bin:/home/leili_pkuhpc/lustre1/software/OrthoFinder:/home/leili_pkuhpc/lustre1/software/samtools-1.3.1/bin:/appsnew/usr/gcc/gcc-8.3.0/bin:/appsnew/bioapps/blast-2.9.0+/bin:/home/leili_pkuhpc/anaconda2/bin:/home/leili_pkuhpc/lustre1/software/psRobot_v1.2/bin:/home/leili_pkuhpc/lustre1/software/psRobot_v1.2/bin:/home/leili_pkuhpc/lustre1/limo/software/cufflinks-2.2.1.Linux_x86_64:/apps/bioapps/jdk-sun/bin:/apps/bioapps/bin:/apps/bioinfo/virtualenv-python2.7/install//bin:/rm/rm_prog/slurm/18.08.7/bin:/usr/lib64/qt-3.3/bin:/rm/rm_prog/pmix/3.1.2/bin:/home/leili_pkuhpc/perl5/bin:/usr/local/cuda/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/usr/lpp/mmfs/bin:/opt/ibutils/bin:/data01/oldbin/newbin:/bootstrap/cn/managements:/apps/mdapps/bin:/bin:/apps/mdapps/amber14/bin:/apps/mdapps/NAMD_2.10_Linux-x86_64-ibverbs:/apps/mdapps/mmtsb/bin:/apps/mdapps/mmtsb/perl:/usr/local/MATLAB/R2013a/bin/matlab:/home/leili_pkuhpc/lustre1/kuangzheng/meme/bin:/home/leili_pkuhpc/lustre1/kuangzheng/bowtie-1.1.2:/home/leili_pkuhpc/lustre1/kuangzheng/FASTX:/home/leili_pkuhpc/lustre1/kuangzheng/viennaRNA-2.2.10/bin:/home/leili_pkuhpc/lustre1/kuangzheng/fastqc_v0.11.5:/home/leili_pkuhpc/lustre1/kuangzheng/MEGA7:/home/leili_pkuhpc/lustre1/kuangzheng/softwares/sratoolkit.2.8.1-centos_linux64/bin:/apps/bioinfo/R-3.3.2/bin:/home/leili_pkuhpc/lustre1/software/Python-3.6.4/exec_path/bin:/home/leili_pkuhpc/lustre1/software/Python-3.6.4/python3_path/bin:/home/leili_pkuhpc/lustre1/kuangzheng/softwares/MAFFT/bin:/home/leili_pkuhpc/lustre1/kuangzheng/softwares/Gblocks_0.91b:/home/leili_pkuhpc/lustre1/guozhl/MCScanX/MCScanX/:/home/leili_pkuhpc/lustre1/guozhl/MCScanX/MCScanX/downstream_analyses:/home/leili_pkuhpc/lustre1/guozhl/MCScanX/MCScanX/downstream_analyses:/home/leili_pkuhpc/.local/bin:/home/leili_pkuhpc/lustre1/software/muscle:/home/leili_pkuhpc/lustre1/software/blast_old/blast-2.2.26/bin:/home/leili_pkuhpc/lustre1/software/mDust/mdust-master:/home/leili_pkuhpc/lustre1/software/RepeatMasker:/home/leili_pkuhpc/lustre1/software/edirect/edirect:/home/leili_pkuhpc/lustre1/software/TrimGalore-0.5.0:/home/leili_pkuhpc/lustre1/software/Bismark_v0.19.1:/apps/bioinfo/vcftools/bin:/home/leili_pkuhpc/lustre1/software/standard-RAxML-master:/home/leili_pkuhpc/lustre1/kuangzheng/data_folder/OUTREACH/Cu_pr/interpro/interproscan-5.30-69.0:/home/leili_pkuhpc/lustre1/software/TrimGalore-0.5.0:/home/leili_pkuhpc/lustre1/software/CleaveLand4-4.5:/home/leili_pkuhpc/lustre1/software/CleaveLand4-4.5/GSTAr_v1-0:/home/leili_pkuhpc/lustre1/software/twoBit2Fa:/home/leili_pkuhpc/lustre1/software/last-963/src:/home/leili_pkuhpc/lustre1/software/fasta36-36.3.8/bin:/home/leili_pkuhpc/lustre1/software/bedops/bin:/home/leili_pkuhpc/lustre1/software/blat:/home/leili_pkuhpc/lustre1/kuangzheng/softwares/RNAhybrid-2.1.2/bin:/home/leili_pkuhpc/lustre1/guozhl/MITEs/MITE_softwares/MITE_Hunter/:/home/leili_pkuhpc/lustre1/guozhl/MITEs/MITE_softwares/MITE_Hunter2/:/home/leili_pkuhpc/lustre1/software/miteFinder-master:/home/leili_pkuhpc/lustre1/software/MITE-Tracker:/home/leili_pkuhpc/lustre1/kuangzheng/softwares/deeptools/bin:/home/leili_pkuhpc/lustre1/kuangzheng/softwares/fasttree:/home/leili_pkuhpc/lustre1/software/iqtree-1.6.12-Linux/bin:/home/leili_pkuhpc/bin:/home/leili_pkuhpc/lustre1/limo/software/hisat2-2.0.1-beta:/home/leili_pkuhpc/lustre1/limo/software/cufflinks-2.2.1.Linux_x86_64:/home/leili_pkuhpc/lustre1/haoc/bin:/home/leili_pkuhpc/lustre1/haoc/tools/stringtie-1.3.3.Linux_x86_64:/home/leili_pkuhpc/lustre1/haoc/tools/gffcompare:/apps/bioinfo/R-3.3.2/bin/R:/home/leili_pkuhpc/lustre1/software/zlib-1.2.11:/lustre1/leili_pkuhpc/software/MaSuRCA-3.4.2/dist-bin ++ which make
• ln -sf /usr/bin/make /lustre1/leili_pkuhpc/software/MaSuRCA-3.4.2/dist-bin/gmake
• ln -sf /lustre1/leili_pkuhpc/software/MaSuRCA-3.4.2/PkgConfig.pm /lustre1/leili_pkuhpc/software/MaSuRCA-3.4.2/dist-bin/pkg-config ++ grep -c '^processor' /proc/cpuinfo
• export NUM_THREADS=24
• NUM_THREADS=24
• BINDIR=/lustre1/leili_pkuhpc/software/MaSuRCA-3.4.2/bin
• LIBDIR=/lustre1/leili_pkuhpc/software/MaSuRCA-3.4.2/lib
• export PKG_CONFIG_PATH=/lustre1/leili_pkuhpc/software/MaSuRCA-3.4.2/lib/pkgconfig:
• PKG_CONFIG_PATH=/lustre1/leili_pkuhpc/software/MaSuRCA-3.4.2/lib/pkgconfig:
• cd global-1
• ./configure --prefix=/lustre1/leili_pkuhpc/software/MaSuRCA-3.4.2 --bindir=/lustre1/leili_pkuhpc/software/MaSuRCA-3.4.2/bin --libdir=/lustre1/leili_pkuhpc/software/MaSuRCA-3.4.2/lib
• make -j 24 install-special libtool: install: warning: relinking swig/perl5/jellyfish.la' libtool: relink: warning:/appsnew/usr/gcc/gcc-8.3.0/lib/gcc/x86_64-pc-linux-gnu/8.3.0/../../../../lib64/libstdc++.la' seems to be moved src2/runByDirectory.cc: In function 'int main(int, char*)': src2/runByDirectory.cc:227:16: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<_IO_FILE>::size_type' {aka 'long unsigned int'} [-Wsign-compare] if(num_eof == readSeqFilesByDir.size()) atEnd = true;

  
  src2/runByDirectory.cc: In function 'int analyzeGap(arguments, FILE*, FILE*)':
  src2/runByDirectory.cc:287:30: warning: catching polymorphic type 'class std::runtime_error' by value [-Wcatch-value=]
  } catch(std::runtime_error e) {
                            ^
  In file included from /lustre1/leili_pkuhpc/software/MaSuRCA-3.4.2/include/jellyfish-1/jellyfish/jellyfish.hpp:22,
               from src/create_k_unitigs_large_k2.cc:24:
  /lustre1/leili_pkuhpc/software/MaSuRCA-3.4.2/include/jellyfish-1/jellyfish/hash_counter.hpp: In instantiation of 'bool jellyfish::cooperative::hash_counter<Key, word, atomic_t, mem_block_t>::double_size(bool) [with Key = jellyfish::mer_dna_ns::mer_base_static<long unsigned int, 0>; word = long unsigned int; atomic_t = atomic::gcc; mem_block_t = allocators::mmap]':
  /lustre1/leili_pkuhpc/software/MaSuRCA-3.4.2/include/jellyfish-1/jellyfish/hash_counter.hpp:189:28:   required from 'bool jellyfish::cooperative::hash_counter<Key, word, atomic_t, mem_block_t>::handle_full_ary() [with Key = jellyfish::mer_dna_ns::mer_base_static<long unsigned int, 0>; word = long unsigned int; atomic_t = atomic::gcc; mem_block_t = allocators::mmap]'
  /lustre1/leili_pkuhpc/software/MaSuRCA-3.4.2/include/jellyfish-1/jellyfish/hash_counter.hpp:175:12:   required from 'void jellyfish::cooperative::hash_counter<Key, word, atomic_t, mem_block_t>::done() [with Key = jellyfish::mer_dna_ns::mer_base_static<long unsigned int, 0>; word = long unsigned int; atomic_t = atomic::gcc; mem_block_t = allocators::mmap]'
  src/create_k_unitigs_large_k2.cc:66:16:   required from here
  /lustre1/leili_pkuhpc/software/MaSuRCA-3.4.2/include/jellyfish-1/jellyfish/hash_counter.hpp:209:10: warning: catching polymorphic type 'class jellyfish::large_hash::array_base<jellyfish::mer_dna_ns::mer_base_static<long unsigned int, 0>, long unsigned int, atomic::gcc, jellyfish::large_hash::array<jellyfish::mer_dna_ns::mer_base_static<long unsigned int, 0>, long unsigned int, atomic::gcc, allocators::mmap> >::ErrorAllocation' by value [-Wcatch-value=]
      } catch(typename array::ErrorAllocation e) {
        ^~~~~
  sparsePregraph/io_func.cpp: In function 'void* open_file_robust(const char*, const char*, const char*)':
  sparsePregraph/io_func.cpp:943:1: warning: control reaches end of non-void function [-Wreturn-type]
  }
  ^
  sparsePregraph/io_func.cpp: In function 'void* open_file_robust(const char*, const char*, const char*)':
  sparsePregraph/io_func.cpp:943:1: warning: control reaches end of non-void function [-Wreturn-type]
  }
  ^
  In file included from src_jf_aligner/zstr.hpp:16,
               from src_jf_aligner/merge_coords.cc:9:
  src_jf_aligner/strict_fstream.hpp: In static member function 'static void strict_fstream::detail::static_method_holder::check_peek(std::istream*, const string&, std::ios_base::openmode)':
  src_jf_aligner/strict_fstream.hpp:128:39: warning: catching polymorphic type 'class std::ios_base::failure' by value [-Wcatch-value=]
       catch (std::ios_base::failure e) {}
                                     ^
  libtool: install: warning: relinking `swig/perl5/mummer.la'
  libtool: relink: warning: `/appsnew/usr/gcc/gcc-8.3.0/lib/gcc/x86_64-pc-linux-gnu/8.3.0/../../../../lib64/libstdc++.la' seems to be moved

• echo 'creating sr_config_example.txt with correct PATHS'
• /lustre1/leili_pkuhpc/software/MaSuRCA-3.4.2/bin/masurca -g sr_config_example.txt Error: Refusing to overwrite existing configuration file 'sr_config_example.txt' err.txt std.txt

[alekseyzimin]

This is not a problem, you can delete sr_config_example.txt file before re-running install.sh. I fixed this in the latest release 3.4.2.