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galaxy001 / pirs

profile basd Illumina pair-end Reads Simulator
https://code.google.com/p/pirs/
GNU General Public License v2.0
26 stars 7 forks source link

/usr/bin/ld: cannot find -lz #7

Closed Morteza-M-Saber closed 4 years ago

Morteza-M-Saber commented 6 years ago

I installed zlib 1.2.11 in a local directory because I do not have root privilege and trying to install pirs using 'MAKE' it returns the following error. Does this error mean that the program is looking for zlib in '/usr/bin/ld'? How to tell PIRS's 'MAKE' to look for zlib in specific directory?

I would really appreciate your help.

cd ./src/pirs && make -f gccMakefile
make[1]: Entering directory '/home/masih/Baterial_simulator/pirs-master/src/pirs'
g++ -Wfloat-equal -Wall -pipe -mtune=generic -msse2 -fopenmp -DSFMT_MEXP=19937 -DHAVE_CONFIG_H -DPKGDATADIR='"/usr/local/share/pirs"' -I. -I.. -ISFMT-src-1.4 -static -O2 -o pirs IndelProfile.cpp BaseCallingProfile.cpp pirs_simulate.cpp InputStream.cpp mt19937-64.cpp OutputStream.cpp GCBiasProfile.cpp Profile.cpp MaskQvalsByEamss.cpp pirs_diploid.cpp main.cpp util.cpp SFMT-src-1.4/SFMT.c -Wl,-O1 -Wl,--sort-common -Wl,--enable-new-dtags -Wl,--hash-style=both -lz -lpthread
pirs_simulate.cpp:175:1: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix]
 "                 "DEFAULT_BASE_CALLING_PROFILE"\n"
 ^
pirs_simulate.cpp:181:1: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix]
 "                 "DEFAULT_INDEL_PROFILE"\n"
 ^
pirs_simulate.cpp:187:1: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix]
 "                 "DEFAULT_GC_BIAS_PROFILE_100",\n"
 ^
pirs_simulate.cpp:188:1: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix]
 "                 "DEFAULT_GC_BIAS_PROFILE_150",\n"
 ^
pirs_simulate.cpp:189:1: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix]
 "                 "DEFAULT_GC_BIAS_PROFILE_200",\n"
 ^
pirs_simulate.cpp:733:19: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix]
   out_file.printf("%c%s_read_%d_%"PRIu64"/%d\n",
                   ^
pirs_simulate.cpp:739:19: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix]
   out_file.printf("%c%s_read_%"PRIu64"/%d\n",
                   ^
pirs_simulate.cpp:767:23: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix]
  info_log_file.printf("read_%d_%"PRIu64"/%d\t%s\t%s\t%zu\t%c\t%d\t%d\t",
                       ^
pirs_simulate.cpp:1302:10: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix]
     info("Simulated %"PRIu64" of %"PRIu64" read pairs\n",
          ^
pirs_simulate.cpp:1302:29: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix]
     info("Simulated %"PRIu64" of %"PRIu64" read pairs\n",
                             ^
pirs_simulate.cpp:1609:21: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix]
   insert_log.printf("%d\t%"PRIu64"\n", it->first, it->second);
                     ^
pirs_simulate.cpp:1626:3: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix]
   "# The total number of read pairs that were simulated was %"PRIu64".\n"
   ^
pirs_simulate.cpp:1643:20: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix]
   error_log.printf("%d\t%"PRIu64"\t%g\n",
                    ^
pirs_simulate.cpp:1648:19: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix]
  error_log.printf("total\t%"PRIu64"\t%g\n",
                   ^
pirs_simulate.cpp:1756:26: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix]
  log_parameter(info_log, "Random seed:                      %"PRIu64"\n",
                          ^
pirs_simulate.cpp:1784:7: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix]
  info("Program:        "PROGRAM "\n");
       ^
pirs_simulate.cpp:1785:7: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix]
  info("Version:        "VERSION "\n");
       ^
pirs_simulate.cpp:1786:7: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix]
  info("Author:         "AUTHOR "\n");
       ^
pirs_simulate.cpp:1787:7: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix]
  info("Contact:        "CONTACT "\n");
       ^
pirs_simulate.cpp:1788:7: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix]
  info("Compile Date:   "__DATE__ " time: " __TIME__ "\n");
       ^
pirs_simulate.cpp:1835:7: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix]
  info("Bases in reference sequences:    %"PRIu64"\n",
       ^
pirs_simulate.cpp:1837:7: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix]
  info("Read pairs simulated:            %"PRIu64"\n",
       ^
pirs_simulate.cpp:1839:7: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix]
  info("Bases in reads:                  %"PRIu64"\n",
       ^
pirs_simulate.cpp:1844:7: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix]
  info("Substitution error count:        %"PRIu64"\n",
       ^
pirs_simulate.cpp:1848:7: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix]
  info("Insertion count:                 %"PRIu64"\n",
       ^
pirs_simulate.cpp:1850:7: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix]
  info("Deletion count:                  %"PRIu64"\n",
       ^
pirs_simulate.cpp:1866:7: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix]
  info("Bases masked by EAMSS algorithm: %"PRIu64"\n", counters.masked_bases);
       ^
pirs_simulate.cpp:1927:8: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix]
   info("Note: A random seed (%"PRIu64") was specified on the command line.\n",
        ^
pirs_diploid.cpp:639:7: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix]
  info("   [%#"PRIx64", %#"PRIx64", %#"PRIx64"\n",
       ^
pirs_diploid.cpp:639:21: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix]
  info("   [%#"PRIx64", %#"PRIx64", %#"PRIx64"\n",
                     ^
pirs_diploid.cpp:639:33: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix]
  info("   [%#"PRIx64", %#"PRIx64", %#"PRIx64"\n",
                                 ^
pirs_diploid.cpp:641:7: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix]
  info("    %#"PRIx64", %#"PRIx64", %#"PRIx64"\n",
       ^
pirs_diploid.cpp:641:21: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix]
  info("    %#"PRIx64", %#"PRIx64", %#"PRIx64"\n",
                     ^
pirs_diploid.cpp:641:33: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix]
  info("    %#"PRIx64", %#"PRIx64", %#"PRIx64"\n",
                                 ^
pirs_diploid.cpp:643:7: warning: invalid suffix on literal; C++11 requires a space between literal and string macro [-Wliteral-suffix]
  info("    %#"PRIx64"]\n", het_type_tab[6]);
       ^
/usr/bin/ld: cannot find -lz
collect2: error: ld returned 1 exit status
make[1]: *** [gccMakefile:43: pirs] Error 1
make[1]: Leaving directory '/home/masih/Baterial_simulator/pirs-master/src/pirs'
make: *** [Makefile:11: simulator] Error 2
galaxy001 commented 6 years ago

Using Homebrew on Mac or Linuxbrew on Linux, will make things easier.