Mock Version: 1.3.4
Mock Version: 1.3.4
ENTER ['do'](['bash', '--login', '-c', '/usr/bin/rpmbuild -bs --target i686 --nodeps /builddir/build/SPECS/mmseq.spec'], chrootPath='/var/lib/mock/f29-build-13123818-956413/root'env={'TERM': 'vt100', 'SHELL': '/bin/bash', 'HOME': '/builddir', 'HOSTNAME': 'mock', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'PROMPT_COMMAND': 'printf "\\033]0;<mock-chroot>\\007"', 'PS1': '<mock-chroot> \\s-\\v\\$ ', 'LANG': 'en_US.UTF-8'}shell=Falselogger=<mockbuild.trace_decorator.getLog object at 0x7f22bf8a7e80>timeout=172800uid=1000gid=425user='mockbuild'nspawn_args=[]printOutput=False)
Executing command: ['bash', '--login', '-c', '/usr/bin/rpmbuild -bs --target i686 --nodeps /builddir/build/SPECS/mmseq.spec'] with env {'TERM': 'vt100', 'SHELL': '/bin/bash', 'HOME': '/builddir', 'HOSTNAME': 'mock', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'PROMPT_COMMAND': 'printf "\\033]0;<mock-chroot>\\007"', 'PS1': '<mock-chroot> \\s-\\v\\$ ', 'LANG': 'en_US.UTF-8'} and shell False
Building target platforms: i686
Building for target i686
Wrote: /builddir/build/SRPMS/mmseq-1.0.8a-26.fc29.src.rpm
Child return code was: 0
ENTER ['do'](['bash', '--login', '-c', '/usr/bin/rpmbuild -bb --target i686 --nodeps /builddir/build/SPECS/mmseq.spec'], chrootPath='/var/lib/mock/f29-build-13123818-956413/root'env={'TERM': 'vt100', 'SHELL': '/bin/bash', 'HOME': '/builddir', 'HOSTNAME': 'mock', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'PROMPT_COMMAND': 'printf "\\033]0;<mock-chroot>\\007"', 'PS1': '<mock-chroot> \\s-\\v\\$ ', 'LANG': 'en_US.UTF-8'}shell=Falselogger=<mockbuild.trace_decorator.getLog object at 0x7f22bf8a7e80>timeout=172800uid=1000gid=425user='mockbuild'nspawn_args=[]printOutput=False)
Executing command: ['bash', '--login', '-c', '/usr/bin/rpmbuild -bb --target i686 --nodeps /builddir/build/SPECS/mmseq.spec'] with env {'TERM': 'vt100', 'SHELL': '/bin/bash', 'HOME': '/builddir', 'HOSTNAME': 'mock', 'PATH': '/usr/bin:/bin:/usr/sbin:/sbin', 'PROMPT_COMMAND': 'printf "\\033]0;<mock-chroot>\\007"', 'PS1': '<mock-chroot> \\s-\\v\\$ ', 'LANG': 'en_US.UTF-8'} and shell False
Building target platforms: i686
Building for target i686
Executing(%prep): /bin/sh -e /var/tmp/rpm-tmp.2o50JZ
+ umask 022
+ cd /builddir/build/BUILD
+ cd /builddir/build/BUILD
+ rm -rf mmseq-1.0.8a
+ /usr/bin/unzip -qq /builddir/build/SOURCES/1.0.8a.zip
+ STATUS=0
+ '[' 0 -ne 0 ']'
+ cd mmseq-1.0.8a
+ /usr/bin/chmod -Rf a+rX,u+w,g-w,o-w .
+ echo 'Patch #0 (mmseq-sam-header.patch):'
Patch #0 (mmseq-sam-header.patch):
+ /usr/bin/patch --no-backup-if-mismatch -p1 -b --suffix .mmseq-sam-header.patch --fuzz=0
patching file src/bam2hits.cpp
Patch #2 (mmseq-zlib.patch):
+ echo 'Patch #2 (mmseq-zlib.patch):'
+ /usr/bin/patch --no-backup-if-mismatch -p1 -b --suffix .mmseq-zlib.patch --fuzz=0
patching file src/Makefile
Patch #3 (mmseq-iostream-c++11.patch):
+ echo 'Patch #3 (mmseq-iostream-c++11.patch):'
+ /usr/bin/patch --no-backup-if-mismatch -p1 -b --suffix .mmseq-iostream-c++11.patch --fuzz=0
patching file src/hitsio.cpp
Patch #4 (mmseq-static-data-members-initialization-c++11.patch):
+ echo 'Patch #4 (mmseq-static-data-members-initialization-c++11.patch):'
+ /usr/bin/patch --no-backup-if-mismatch -p1 -b --suffix .mmseq-static-data-members-initialization-c++11.patch --fuzz=0
patching file src/bms.hpp
+ rm bin/bam2hits-linux bin/extract_transcripts-linux bin/hitstools-linux bin/mmcollapse-linux bin/mmdiff-linux bin/mmseq-linux bin/offsetGTF-linux bin/postdiff-linux bin/t2g_hits-linux
+ rm bin/bam2hits-mac bin/extract_transcripts-mac bin/hitstools-mac bin/mmcollapse-mac bin/mmdiff-mac bin/mmseq-mac bin/offsetGTF-mac bin/postdiff-mac bin/t2g_hits-mac
+ exit 0
Executing(%build): /bin/sh -e /var/tmp/rpm-tmp.D5xk9F
+ umask 022
+ cd /builddir/build/BUILD
+ cd mmseq-1.0.8a
+ cd src
+ make -j6 'CXXFLAGS=-O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection'
g++ -O3 -c sokal.cc
g++ -fopenmp -O3 -c uh.cpp 
g++ -DVERSION=1.0.8 -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fopenmp -O3 hitsio.cpp hitsio.hpp -c hitsio.cpp
gcc    -c -o fasta.o fasta.c
g++ -DVERSION=1.0.8 -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -O3 offsetGTF.cpp -o ../bin/offsetGTF
g++ -DVERSION=1.0.8 -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -O3 t2g_hits.cpp -o ../bin/t2g_hits
g++ -DVERSION=1.0.8 -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fopenmp -O2 bms.cpp bms.hpp -c bms.cpp
g++ -DVERSION=1.0.8 -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -O3 fasta.o extract_transcripts.cpp -o ../bin/extract_transcripts
offsetGTF.cpp: In function 'int main(int, char**)':
offsetGTF.cpp:115:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int>::size_type' {aka 'unsigned int'} [-Wsign-compare]
       while(gff_ind < gff_positions[chrom].size()) {
             ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
offsetGTF.cpp:117:57: warning: comparison of integer expressions of different signedness: 'std::__cxx11::basic_string<char>::size_type' {aka 'unsigned int'} and '__gnu_cxx::__alloc_traits<std::allocator<int>, int>::value_type' {aka 'int'} [-Wsign-compare]
               pos + tokens[3].size() - tokens[4].size() >= gff_positions[chrom][gff_ind]) {
offsetGTF.cpp:114:11: warning: unused variable 'curoff' [-Wunused-variable]
       int curoff=offset;
           ^~~~~~
offsetGTF.cpp:150:21: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int>::size_type' {aka 'unsigned int'} [-Wsign-compare]
       while(gff_ind < gff_positions[prevchrom].size()) {
             ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
offsetGTF.cpp:163:53: warning: comparison of integer expressions of different signedness: 'std::__cxx11::basic_string<char>::size_type' {aka 'unsigned int'} and '__gnu_cxx::__alloc_traits<std::allocator<int>, int>::value_type' {aka 'int'} [-Wsign-compare]
           pos + tokens[3].size() - tokens[4].size() >= gff_positions[chrom][gff_ind]) {
offsetGTF.cpp:177:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int>::size_type' {aka 'unsigned int'} [-Wsign-compare]
     while(gff_ind < gff_positions[chrom].size() && gff_positions[chrom][gff_ind] <= pos) {
           ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
offsetGTF.cpp:235:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'unsigned int'} [-Wsign-compare]
     for(int i=5; i < tokens.size(); i++) {
                  ~~^~~~~~~~~~~~~~~
offsetGTF.cpp:237:12: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'unsigned int'} [-Wsign-compare]
       if(i < tokens.size()-1) {
          ~~^~~~~~~~~~~~~~~~~
offsetGTF.cpp:108:7: warning: unused variable 'gff_pos' [-Wunused-variable]
   int gff_pos= -1;
       ^~~~~~~
t2g_hits.cpp: In function 'int main(int, char**)':
t2g_hits.cpp:90:24: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'unsigned int'} [-Wsign-compare]
         for(int i=2; i < tokens.size(); i++) {
                      ~~^~~~~~~~~~~~~~~
extract_transcripts.cpp: In function 'int main(int, char**)':
extract_transcripts.cpp:121:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'unsigned int'} [-Wsign-compare]
       for(int i=0; i < tokens2.size(); i++) {
                    ~~^~~~~~~~~~~~~~~~
extract_transcripts.cpp:168:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'unsigned int'} [-Wsign-compare]
     for(int i=0; i < tokens.size(); i++) {
                  ~~^~~~~~~~~~~~~~~
extract_transcripts.cpp:194:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int>::size_type' {aka 'unsigned int'} [-Wsign-compare]
       for(int i=0; i < it->starts()->size(); i++) {
                    ~~^~~~~~~~~~~~~~~~~~~~~~
extract_transcripts.cpp:202:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string<char>::size_type' {aka 'unsigned int'} [-Wsign-compare]
       while(faline < stitch.size()) {
             ~~~~~~~^~~~~~~~~~~~~~~
extract_transcripts.cpp:108:7: warning: unused variable 'line' [-Wunused-variable]
   int line=0;
       ^~~~
g++ -DVERSION=1.0.8 -DARMA_64BIT_WORD -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fopenmp -O3 uh.o sokal.o mmcollapse.cpp -o ../bin/mmcollapse -lgsl -lgslcblas -lboost_regex -lbam -lboost_iostreams -llapack -lblas -lgfortran -Wl,--as-needed -lz -larmadillo
bms.cpp: In member function 'arma::Col<int> BMS::m2v(arma::Mat<double>)':
bms.cpp:37:18: warning: comparison of integer expressions of different signedness: 'int' and 'const uword' {aka 'const unsigned int'} [-Wsign-compare]
   for(int i=0; i < P.n_cols; i++) {
                ~~^~~~~~~~~~
bms.cpp:38:20: warning: comparison of integer expressions of different signedness: 'int' and 'const uword' {aka 'const unsigned int'} [-Wsign-compare]
     for(int j=0; j < P.n_rows; j++) {
                  ~~^~~~~~~~~~
bms.cpp: In member function 'std::vector<double> BMS::meanvar(arma::Col<double>)':
bms.cpp:77:17: warning: comparison of integer expressions of different signedness: 'int' and 'const uword' {aka 'const unsigned int'} [-Wsign-compare]
   for(int i=0;i < v.n_elem; i++) {
               ~~^~~~~~~~~~
bms.cpp: In member function 'void BMS::print(bool)':
bms.cpp:94:30: warning: comparison of integer expressions of different signedness: 'int' and 'const uword' {aka 'const unsigned int'} [-Wsign-compare]
   for(int feature=0; feature < y->n_rows; feature++) {
                      ~~~~~~~~^~~~~~~~~~~
bms.cpp:98:22: warning: comparison of integer expressions of different signedness: 'int' and 'const uword' {aka 'const unsigned int'} [-Wsign-compare]
       for(int i=0; i < M.n_cols; i++) {
                    ~~^~~~~~~~~~
bms.cpp:103:22: warning: comparison of integer expressions of different signedness: 'int' and 'const uword' {aka 'const unsigned int'} [-Wsign-compare]
       for(int l=0; l < P[model].n_cols; l++) {
                    ~~^~~~~~~~~~~~~~~~~
bms.cpp: In member function 'void BMS::printtune(int)':
bms.cpp:133:30: warning: comparison of integer expressions of different signedness: 'int' and 'const uword' {aka 'const unsigned int'} [-Wsign-compare]
   for(int feature=0; feature < y->n_rows; feature++) {
                      ~~~~~~~~^~~~~~~~~~~
bms.cpp: In member function 'void BMS::set_pseudoprior_alpha()':
bms.cpp:186:20: warning: comparison of integer expressions of different signedness: 'int' and 'const uword' {aka 'const unsigned int'} [-Wsign-compare]
     for(int j=0; j < y->n_rows; j++) {
                  ~~^~~~~~~~~~~
bms.cpp: In member function 'void BMS::set_pseudoprior_beta()':
bms.cpp:254:18: warning: comparison of integer expressions of different signedness: 'int' and 'const uword' {aka 'const unsigned int'} [-Wsign-compare]
   for(int j=0; j < y->n_rows; j++) {
                ~~^~~~~~~~~~~
bms.cpp:256:22: warning: comparison of integer expressions of different signedness: 'int' and 'const uword' {aka 'const unsigned int'} [-Wsign-compare]
       for(int b=0; b < M.n_cols; b++) {
                    ~~^~~~~~~~~~
bms.cpp: In member function 'void BMS::set_pseudoprior_eta()':
bms.cpp:333:18: warning: comparison of integer expressions of different signedness: 'int' and 'const uword' {aka 'const unsigned int'} [-Wsign-compare]
   for(int j=0; j < y->n_rows; j++) {
                ~~^~~~~~~~~~~
bms.cpp:335:22: warning: comparison of integer expressions of different signedness: 'int' and 'const uword' {aka 'const unsigned int'} [-Wsign-compare]
       for(int c=0; c < P[model].n_cols; c++) {
                    ~~^~~~~~~~~~~~~~~~~
bms.cpp: In member function 'void BMS::set_pseudoprior_sigmasq()':
bms.cpp:416:18: warning: comparison of integer expressions of different signedness: 'int' and 'const uword' {aka 'const unsigned int'} [-Wsign-compare]
   for(int j=0; j < y->n_rows; j++) {
                ~~^~~~~~~~~~~
bms.cpp: In member function 'void BMS::set_pseudoprior_lambda()':
bms.cpp:505:18: warning: comparison of integer expressions of different signedness: 'int' and 'const uword' {aka 'const unsigned int'} [-Wsign-compare]
   for(int j=0; j < y->n_rows; j++) {
                ~~^~~~~~~~~~~
bms.cpp:507:22: warning: comparison of integer expressions of different signedness: 'int' and 'const uword' {aka 'const unsigned int'} [-Wsign-compare]
       for(int l=0; l < P[model].n_cols; l++) {
                    ~~^~~~~~~~~~~~~~~~~
bms.cpp: In member function 'void BMS::set_pseudoprior_rho()':
bms.cpp:560:20: warning: comparison of integer expressions of different signedness: 'int' and 'const uword' {aka 'const unsigned int'} [-Wsign-compare]
     for(int j=0; j < y->n_rows; j++) {
                  ~~^~~~~~~~~~~
bms.cpp: In member function 'void BMS::copy_pseudo()':
bms.cpp:583:18: warning: comparison of integer expressions of different signedness: 'int' and 'const uword' {aka 'const unsigned int'} [-Wsign-compare]
   for(int j=0; j < y->n_rows; j++) {
                ~~^~~~~~~~~~~
bms.cpp:586:20: warning: comparison of integer expressions of different signedness: 'int' and 'const uword' {aka 'const unsigned int'} [-Wsign-compare]
     for(int c=0; c < P[0].n_cols; c++) {
                  ~~^~~~~~~~~~~~~
bms.cpp: In member function 'void BMS::update_alpha(int, int, bool)':
bms.cpp:604:20: warning: comparison of integer expressions of different signedness: 'int' and 'const uword' {aka 'const unsigned int'} [-Wsign-compare]
     for(int j=0; j < y->n_cols; j++) {
                  ~~^~~~~~~~~~~
bms.cpp:611:20: warning: comparison of integer expressions of different signedness: 'int' and 'const uword' {aka 'const unsigned int'} [-Wsign-compare]
     for(int i=0; i < y->n_cols; i++) {
                  ~~^~~~~~~~~~~
bms.cpp: In member function 'void BMS::update_beta(int, int, bool)':
bms.cpp:632:20: warning: comparison of integer expressions of different signedness: 'int' and 'const uword' {aka 'const unsigned int'} [-Wsign-compare]
     for(int j=0; j < y->n_cols; j++) {
                  ~~^~~~~~~~~~~
bms.cpp:639:20: warning: comparison of integer expressions of different signedness: 'int' and 'const uword' {aka 'const unsigned int'} [-Wsign-compare]
     for(int i=0; i < M.n_cols; i++) {
                  ~~^~~~~~~~~~
bms.cpp:647:20: warning: comparison of integer expressions of different signedness: 'int' and 'const uword' {aka 'const unsigned int'} [-Wsign-compare]
     for(int i=0; i < M.n_cols; i++) {
                  ~~^~~~~~~~~~
bms.cpp:652:20: warning: comparison of integer expressions of different signedness: 'int' and 'const uword' {aka 'const unsigned int'} [-Wsign-compare]
     for(int i=0; i < M.n_cols; i++) {
                  ~~^~~~~~~~~~
bms.cpp: In member function 'void BMS::update_eta(int, int, bool)':
bms.cpp:668:20: warning: comparison of integer expressions of different signedness: 'int' and 'const uword' {aka 'const unsigned int'} [-Wsign-compare]
     for(int l=0; l < P[model].n_cols; l++) {
                  ~~^~~~~~~~~~~~~~~~~
bms.cpp:670:22: warning: comparison of integer expressions of different signedness: 'int' and 'const uword' {aka 'const unsigned int'} [-Wsign-compare]
       for(int i=0; i < y->n_cols; i++) {
                    ~~^~~~~~~~~~~
bms.cpp:674:20: warning: comparison of integer expressions of different signedness: 'int' and 'const uword' {aka 'const unsigned int'} [-Wsign-compare]
     for(int l=0; l < P[model].n_cols; l++) {
                  ~~^~~~~~~~~~~~~~~~~
bms.cpp:680:20: warning: comparison of integer expressions of different signedness: 'int' and 'const uword' {aka 'const unsigned int'} [-Wsign-compare]
     for(int l=0; l < P[model].n_cols; l++) {
                  ~~^~~~~~~~~~~~~~~~~
bms.cpp:682:22: warning: comparison of integer expressions of different signedness: 'int' and 'const uword' {aka 'const unsigned int'} [-Wsign-compare]
       for(int i=0; i < y->n_cols; i++) {
                    ~~^~~~~~~~~~~
bms.cpp:688:20: warning: comparison of integer expressions of different signedness: 'int' and 'const uword' {aka 'const unsigned int'} [-Wsign-compare]
     for(int l=0; l < P[model].n_cols; l++) {
                  ~~^~~~~~~~~~~~~~~~~
bms.cpp:692:20: warning: comparison of integer expressions of different signedness: 'int' and 'const uword' {aka 'const unsigned int'} [-Wsign-compare]
     for(int l=0; l < P[model].n_cols; l++) {
                  ~~^~~~~~~~~~~~~~~~~
bms.cpp:697:20: warning: comparison of integer expressions of different signedness: 'int' and 'const uword' {aka 'const unsigned int'} [-Wsign-compare]
     for(int l=0; l < P[model].n_cols; l++) {
                  ~~^~~~~~~~~~~~~~~~~
bms.cpp: In member function 'void BMS::update_lambda(int, int, bool)':
bms.cpp:710:20: warning: comparison of integer expressions of different signedness: 'int' and 'const uword' {aka 'const unsigned int'} [-Wsign-compare]
     for(int l=0; l < P[model].n_cols; l++) {
                  ~~^~~~~~~~~~~~~~~~~
bms.cpp:715:20: warning: comparison of integer expressions of different signedness: 'int' and 'const uword' {aka 'const unsigned int'} [-Wsign-compare]
     for(int l=0; l < P[model].n_cols; l++) {
                  ~~^~~~~~~~~~~~~~~~~
bms.cpp:722:20: warning: comparison of integer expressions of different signedness: 'int' and 'const uword' {aka 'const unsigned int'} [-Wsign-compare]
     for(int l=0; l < P[model].n_cols; l++) {
                  ~~^~~~~~~~~~~~~~~~~
bms.cpp: In member function 'void BMS::update_sigmasq(int, int, bool, bool)':
bms.cpp:740:20: warning: comparison of integer expressions of different signedness: 'int' and 'const uword' {aka 'const unsigned int'} [-Wsign-compare]
     for(int i=0; i < y->n_cols; i++) {
                  ~~^~~~~~~~~~~
bms.cpp:751:20: warning: comparison of integer expressions of different signedness: 'int' and 'const uword' {aka 'const unsigned int'} [-Wsign-compare]
     for(int i=0; i < y->n_cols; i++) {
                  ~~^~~~~~~~~~~
bms.cpp:762:24: warning: comparison of integer expressions of different signedness: 'int' and 'const uword' {aka 'const unsigned int'} [-Wsign-compare]
         for(int i=0; i < y->n_cols; i++) {
                      ~~^~~~~~~~~~~
bms.cpp:774:24: warning: comparison of integer expressions of different signedness: 'int' and 'const uword' {aka 'const unsigned int'} [-Wsign-compare]
         for(int i=0; i < y->n_cols; i++) {
                      ~~^~~~~~~~~~~
bms.cpp: In member function 'void BMS::update_sigmasq_RW(int, int, bool, bool)':
bms.cpp:888:20: warning: comparison of integer expressions of different signedness: 'int' and 'const uword' {aka 'const unsigned int'} [-Wsign-compare]
     for(int i=0; i < y->n_cols; i++) {
                  ~~^~~~~~~~~~~
bms.cpp: In member function 'double BMS::log_target_posterior(int, int)':
bms.cpp:942:18: warning: comparison of integer expressions of different signedness: 'int' and 'const uword' {aka 'const unsigned int'} [-Wsign-compare]
   for(int i=0; i < y->n_cols; i++) {
                ~~^~~~~~~~~~~
bms.cpp:951:20: warning: comparison of integer expressions of different signedness: 'int' and 'const uword' {aka 'const unsigned int'} [-Wsign-compare]
     for(int j=0; j < M.n_cols; j++) {
                  ~~^~~~~~~~~~
bms.cpp:958:20: warning: comparison of integer expressions of different signedness: 'int' and 'const uword' {aka 'const unsigned int'} [-Wsign-compare]
     for(int l=0; l < P[model].n_cols; l++) {
                  ~~^~~~~~~~~~~~~~~~~
bms.cpp: In member function 'double BMS::log_target_pseudo(int, int)':
bms.cpp:979:20: warning: comparison of integer expressions of different signedness: 'int' and 'const uword' {aka 'const unsigned int'} [-Wsign-compare]
     for(int l=0; l < M.n_cols; l++) {
                  ~~^~~~~~~~~~
bms.cpp:985:20: warning: comparison of integer expressions of different signedness: 'int' and 'const uword' {aka 'const unsigned int'} [-Wsign-compare]
     for(int l=0; l < P[model].n_cols; l++) {
                  ~~^~~~~~~~~~~~~~~~~
bms.cpp: In member function 'void BMS::print_pseudo()':
bms.cpp:1094:20: warning: comparison of integer expressions of different signedness: 'int' and 'const uword' {aka 'const unsigned int'} [-Wsign-compare]
     for(int l=0; l < M.n_cols; l++) {
                  ~~^~~~~~~~~~
bms.cpp:1097:20: warning: comparison of integer expressions of different signedness: 'int' and 'const uword' {aka 'const unsigned int'} [-Wsign-compare]
     for(int l=0; l < P[model].n_cols; l++) {
                  ~~^~~~~~~~~~~~~~~~~
bms.cpp:1108:18: warning: comparison of integer expressions of different signedness: 'int' and 'const uword' {aka 'const unsigned int'} [-Wsign-compare]
   for(int i=0; i < y->n_rows; i++) {
                ~~^~~~~~~~~~~
bms.cpp:1111:22: warning: comparison of integer expressions of different signedness: 'int' and 'const uword' {aka 'const unsigned int'} [-Wsign-compare]
       for(int l=0; l < M.n_cols; l++) {
                    ~~^~~~~~~~~~
bms.cpp:1114:22: warning: comparison of integer expressions of different signedness: 'int' and 'const uword' {aka 'const unsigned int'} [-Wsign-compare]
       for(int l=0; l < P[model].n_cols; l++) {
                    ~~^~~~~~~~~~~~~~~~~
bms.cpp: In constructor 'BMS::BMS(const arma::Mat<double>*, const arma::Mat<double>&, arma::Mat<double>, arma::Mat<double>, arma::Mat<double>, arma::Mat<int>, double, double, double, std::__cxx11::string, gsl_rng**, int, bool)':
bms.cpp:1196:20: warning: comparison of integer expressions of different signedness: 'int' and 'const uword' {aka 'const unsigned int'} [-Wsign-compare]
     for(int i=0; i < y->n_cols; i++) {
                  ~~^~~~~~~~~~~
bms.cpp:1200:25: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int, std::allocator<int> >::size_type' {aka 'unsigned int'} [-Wsign-compare]
         if(C(i,model)+1 > _n.size()) {
            ~~~~~~~~~~~~~^~~~~~~~~~~
bms.cpp: In member function 'void BMS::initialise_streams(std::__cxx11::string)':
bms.cpp:1356:18: warning: comparison of integer expressions of different signedness: 'int' and 'const uword' {aka 'const unsigned int'} [-Wsign-compare]
   for(int i=0; i < M.n_cols; i++) {
                ~~^~~~~~~~~~
bms.cpp:1362:18: warning: comparison of integer expressions of different signedness: 'int' and 'const uword' {aka 'const unsigned int'} [-Wsign-compare]
   for(int i=0; i < M.n_cols; i++) {
                ~~^~~~~~~~~~
bms.cpp:1368:18: warning: comparison of integer expressions of different signedness: 'int' and 'const uword' {aka 'const unsigned int'} [-Wsign-compare]
   for(int i=0; i < P[0].n_cols; i++) {
                ~~^~~~~~~~~~~~~
bms.cpp:1374:18: warning: comparison of integer expressions of different signedness: 'int' and 'const uword' {aka 'const unsigned int'} [-Wsign-compare]
   for(int i=0; i < P[1].n_cols; i++) {
                ~~^~~~~~~~~~~~~
bms.cpp:1380:18: warning: comparison of integer expressions of different signedness: 'int' and 'const uword' {aka 'const unsigned int'} [-Wsign-compare]
   for(int i=0; i < P[0].n_cols; i++) {
                ~~^~~~~~~~~~~~~
hitsio.cpp: In member function 'void HitsfileWriter::writeHeaderSchema0()':
hitsio.cpp:163:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'unsigned int'} [-Wsign-compare]
  for(int i = 0; i < transcriptName.size(); i++) {
                 ~~^~~~~~~~~~~~~~~~~~~~~~~
bms.cpp:1386:18: warning: comparison of integer expressions of different signedness: 'int' and 'const uword' {aka 'const unsigned int'} [-Wsign-compare]
   for(int i=0; i < P[1].n_cols; i++) {
                ~~^~~~~~~~~~~~~
hitsio.cpp: In member function 'void HitsfileWriter::writeReadMapRecordSchema0()':
hitsio.cpp:184:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'unsigned int'} [-Wsign-compare]
  for(int i = 0; i < currentReadTranscripts.size(); i++) {
                 ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
hitsio.cpp: In member function 'void HitsfileWriter::writeHeaderSchema1()':
hitsio.cpp:24:10: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare]
  if (VAL > numeric_limits<uint32_t>::max()) { \
          ^
hitsio.cpp:191:2: note: in expansion of macro 'WRITE_UINT'
  WRITE_UINT(ofs, hitsfileSchema);
  ^~~~~~~~~~
hitsio.cpp:193:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'unsigned int'} [-Wsign-compare]
  for(int i = 0; i < transcriptName.size(); i++) {
                 ~~^~~~~~~~~~~~~~~~~~~~~~~
hitsio.cpp:24:10: warning: comparison of integer expressions of different signedness: 'std::map<std::__cxx11::basic_string<char>, int>::mapped_type' {aka 'int'} and 'unsigned int' [-Wsign-compare]
  if (VAL > numeric_limits<uint32_t>::max()) { \
hitsio.cpp:196:3: note: in expansion of macro 'WRITE_UINT'
   WRITE_UINT(ofs, transcriptTrueLength[transcriptName[i] ])
   ^~~~~~~~~~
hitsio.cpp: In member function 'void HitsfileWriter::writeReadMapRecordSchema1()':
hitsio.cpp:236:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'unsigned int'} [-Wsign-compare]
  for(int i = 0; i < currentReadTranscripts.size(); i++) {
                 ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
hitsio.cpp: In member function 'void HitsfileReader::readHeaderSchema1(std::vector<std::__cxx11::basic_string<char> >*, std::map<std::__cxx11::basic_string<char>, double>*, std::map<std::__cxx11::basic_string<char>, int>*, std::map<std::__cxx11::basic_string<char>, std::vector<std::__cxx11::basic_string<char> > >*, std::vector<std::vector<std::__cxx11::basic_string<char> > >*)':
hitsio.cpp:356:9: warning: unused variable 'nextStrLen' [-Wunused-variable]
  size_t nextStrLen;
         ^~~~~~~~~~
hitsio.cpp: In member function 'bool HitsfileReader::readReadMapRecordTranscriptID(std::__cxx11::string&)':
hitsio.cpp:447:1: warning: control reaches end of non-void function [-Wreturn-type]
 }
 ^
mmcollapse.cpp: In function 'void get_unidentifiable_transcripts(std::__cxx11::string, std::vector<std::__cxx11::basic_string<char> >&, std::vector<std::__cxx11::basic_string<char> >&, std::vector<std::__cxx11::basic_string<char> >&, std::map<std::__cxx11::basic_string<char>, std::map<std::__cxx11::basic_string<char>, double> >&, std::map<std::__cxx11::basic_string<char>, std::map<std::__cxx11::basic_string<char>, double> >&, std::map<std::__cxx11::basic_string<char>, std::map<std::__cxx11::basic_string<char>, double> >&, std::map<std::__cxx11::basic_string<char>, int>&, std::vector<std::__cxx11::basic_string<char> >&, std::map<std::__cxx11::basic_string<char>, bool>&)':
mmcollapse.cpp:156:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'unsigned int'} [-Wsign-compare]
   for(int i=0; i < tokens.size(); i++) {
                ~~^~~~~~~~~~~~~~~
mmcollapse.cpp:211:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'unsigned int'} [-Wsign-compare]
     for(int i=0; i < tokens2.size(); i++) isIdent[tokens2[i]]=1;
                  ~~^~~~~~~~~~~~~~~~
mmcollapse.cpp:214:26: warning: 'static eT arma::Math<eT>::inf() [with eT = double]' is deprecated [-Wdeprecated-declarations]
       sd.push_back(math::inf());
                          ^~~
In file included from /usr/include/armadillo:119,
                 from mmcollapse.cpp:28:
/usr/include/armadillo_bits/constants_old.hpp:62:29: note: declared here
   arma_deprecated static eT inf()       { return priv::Datum_helper::inf<eT>(); }  // use datum::inf instead
                             ^~~
mmcollapse.cpp:214:30: warning: 'static eT arma::Math<eT>::inf() [with eT = double]' is deprecated [-Wdeprecated-declarations]
       sd.push_back(math::inf());
                              ^
In file included from /usr/include/armadillo:119,
                 from mmcollapse.cpp:28:
/usr/include/armadillo_bits/constants_old.hpp:62:29: note: declared here
   arma_deprecated static eT inf()       { return priv::Datum_helper::inf<eT>(); }  // use datum::inf instead
                             ^~~
mmcollapse.cpp:214:30: warning: 'static eT arma::Math<eT>::inf() [with eT = double]' is deprecated [-Wdeprecated-declarations]
       sd.push_back(math::inf());
                              ^
In file included from /usr/include/armadillo:119,
                 from mmcollapse.cpp:28:
/usr/include/armadillo_bits/constants_old.hpp:62:29: note: declared here
   arma_deprecated static eT inf()       { return priv::Datum_helper::inf<eT>(); }  // use datum::inf instead
                             ^~~
mmcollapse.cpp:215:28: warning: 'static eT arma::Math<eT>::inf() [with eT = double]' is deprecated [-Wdeprecated-declarations]
       iact.push_back(math::inf());
                            ^~~
In file included from /usr/include/armadillo:119,
                 from mmcollapse.cpp:28:
/usr/include/armadillo_bits/constants_old.hpp:62:29: note: declared here
   arma_deprecated static eT inf()       { return priv::Datum_helper::inf<eT>(); }  // use datum::inf instead
                             ^~~
mmcollapse.cpp:215:32: warning: 'static eT arma::Math<eT>::inf() [with eT = double]' is deprecated [-Wdeprecated-declarations]
       iact.push_back(math::inf());
                                ^
In file included from /usr/include/armadillo:119,
                 from mmcollapse.cpp:28:
/usr/include/armadillo_bits/constants_old.hpp:62:29: note: declared here
   arma_deprecated static eT inf()       { return priv::Datum_helper::inf<eT>(); }  // use datum::inf instead
                             ^~~
mmcollapse.cpp:215:32: warning: 'static eT arma::Math<eT>::inf() [with eT = double]' is deprecated [-Wdeprecated-declarations]
       iact.push_back(math::inf());
                                ^
In file included from /usr/include/armadillo:119,
                 from mmcollapse.cpp:28:
/usr/include/armadillo_bits/constants_old.hpp:62:29: note: declared here
   arma_deprecated static eT inf()       { return priv::Datum_helper::inf<eT>(); }  // use datum::inf instead
                             ^~~
mmcollapse.cpp:257:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'unsigned int'} [-Wsign-compare]
   for(int i=0; i < tokens.size(); i++) {
                ~~^~~~~~~~~~~~~~~
mmcollapse.cpp:317:28: warning: 'static eT arma::Math<eT>::inf() [with eT = double]' is deprecated [-Wdeprecated-declarations]
         sd.push_back(math::inf());
                            ^~~
In file included from /usr/include/armadillo:119,
                 from mmcollapse.cpp:28:
/usr/include/armadillo_bits/constants_old.hpp:62:29: note: declared here
   arma_deprecated static eT inf()       { return priv::Datum_helper::inf<eT>(); }  // use datum::inf instead
                             ^~~
mmcollapse.cpp:317:32: warning: 'static eT arma::Math<eT>::inf() [with eT = double]' is deprecated [-Wdeprecated-declarations]
         sd.push_back(math::inf());
                                ^
In file included from /usr/include/armadillo:119,
                 from mmcollapse.cpp:28:
/usr/include/armadillo_bits/constants_old.hpp:62:29: note: declared here
   arma_deprecated static eT inf()       { return priv::Datum_helper::inf<eT>(); }  // use datum::inf instead
                             ^~~
mmcollapse.cpp:317:32: warning: 'static eT arma::Math<eT>::inf() [with eT = double]' is deprecated [-Wdeprecated-declarations]
         sd.push_back(math::inf());
                                ^
In file included from /usr/include/armadillo:119,
                 from mmcollapse.cpp:28:
/usr/include/armadillo_bits/constants_old.hpp:62:29: note: declared here
   arma_deprecated static eT inf()       { return priv::Datum_helper::inf<eT>(); }  // use datum::inf instead
                             ^~~
mmcollapse.cpp:318:30: warning: 'static eT arma::Math<eT>::inf() [with eT = double]' is deprecated [-Wdeprecated-declarations]
         iact.push_back(math::inf());
                              ^~~
In file included from /usr/include/armadillo:119,
                 from mmcollapse.cpp:28:
/usr/include/armadillo_bits/constants_old.hpp:62:29: note: declared here
   arma_deprecated static eT inf()       { return priv::Datum_helper::inf<eT>(); }  // use datum::inf instead
                             ^~~
mmcollapse.cpp:318:34: warning: 'static eT arma::Math<eT>::inf() [with eT = double]' is deprecated [-Wdeprecated-declarations]
         iact.push_back(math::inf());
                                  ^
In file included from /usr/include/armadillo:119,
                 from mmcollapse.cpp:28:
/usr/include/armadillo_bits/constants_old.hpp:62:29: note: declared here
   arma_deprecated static eT inf()       { return priv::Datum_helper::inf<eT>(); }  // use datum::inf instead
                             ^~~
mmcollapse.cpp:318:34: warning: 'static eT arma::Math<eT>::inf() [with eT = double]' is deprecated [-Wdeprecated-declarations]
         iact.push_back(math::inf());
                                  ^
In file included from /usr/include/armadillo:119,
                 from mmcollapse.cpp:28:
/usr/include/armadillo_bits/constants_old.hpp:62:29: note: declared here
   arma_deprecated static eT inf()       { return priv::Datum_helper::inf<eT>(); }  // use datum::inf instead
                             ^~~
mmcollapse.cpp: In function 'void collapse(arma::cube&, std::vector<std::__cxx11::basic_string<char> >&, std::map<std::__cxx11::basic_string<char>, int>&, std::vector<int, std::allocator<int> >)':
mmcollapse.cpp:398:18: warning: comparison of integer expressions of different signedness: 'int' and 'const uword' {aka 'const unsigned int'} [-Wsign-compare]
   for(int s=0; s < R.n_slices; s++) {
                ~~^~~~~~~~~~~~
mmcollapse.cpp:399:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'unsigned int'} [-Wsign-compare]
     for(int t=0; t < candidates.size(); t++) {
                  ~~^~~~~~~~~~~~~~~~~~~
mmcollapse.cpp:400:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int, std::allocator<int> >::size_type' {aka 'unsigned int'} [-Wsign-compare]
       for(int j=1; j < indexes.size(); j++) {
                    ~~^~~~~~~~~~~~~~~~
mmcollapse.cpp:412:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int, std::allocator<int> >::size_type' {aka 'unsigned int'} [-Wsign-compare]
     for(int j=1; j < indexes.size(); j++) {
                  ~~^~~~~~~~~~~~~~~~
mmcollapse.cpp:415:22: warning: comparison of integer expressions of different signedness: 'int' and 'const uword' {aka 'const unsigned int'} [-Wsign-compare]
       for(int i=0; i < R.n_cols; i++) {
                    ~~^~~~~~~~~~
mmcollapse.cpp:416:33: warning: 'static eT arma::Math<eT>::nan() [with eT = double]' is deprecated [-Wdeprecated-declarations]
         R(indexes[j],i,s)=math::nan();
                                 ^~~
In file included from /usr/include/armadillo:119,
                 from mmcollapse.cpp:28:
/usr/include/armadillo_bits/constants_old.hpp:59:29: note: declared here
   arma_deprecated static eT nan()       { return priv::Datum_helper::nan<eT>(); }  // use datum::nan instead
                             ^~~
mmcollapse.cpp:416:37: warning: 'static eT arma::Math<eT>::nan() [with eT = double]' is deprecated [-Wdeprecated-declarations]
         R(indexes[j],i,s)=math::nan();
                                     ^
In file included from /usr/include/armadillo:119,
                 from mmcollapse.cpp:28:
/usr/include/armadillo_bits/constants_old.hpp:59:29: note: declared here
   arma_deprecated static eT nan()       { return priv::Datum_helper::nan<eT>(); }  // use datum::nan instead
                             ^~~
mmcollapse.cpp:416:37: warning: 'static eT arma::Math<eT>::nan() [with eT = double]' is deprecated [-Wdeprecated-declarations]
         R(indexes[j],i,s)=math::nan();
                                     ^
In file included from /usr/include/armadillo:119,
                 from mmcollapse.cpp:28:
/usr/include/armadillo_bits/constants_old.hpp:59:29: note: declared here
   arma_deprecated static eT nan()       { return priv::Datum_helper::nan<eT>(); }  // use datum::nan instead
                             ^~~
mmcollapse.cpp:417:33: warning: 'static eT arma::Math<eT>::nan() [with eT = double]' is deprecated [-Wdeprecated-declarations]
         R(i,indexes[j],s)=math::nan();
                                 ^~~
In file included from /usr/include/armadillo:119,
                 from mmcollapse.cpp:28:
/usr/include/armadillo_bits/constants_old.hpp:59:29: note: declared here
   arma_deprecated static eT nan()       { return priv::Datum_helper::nan<eT>(); }  // use datum::nan instead
                             ^~~
mmcollapse.cpp:417:37: warning: 'static eT arma::Math<eT>::nan() [with eT = double]' is deprecated [-Wdeprecated-declarations]
         R(i,indexes[j],s)=math::nan();
                                     ^
In file included from /usr/include/armadillo:119,
                 from mmcollapse.cpp:28:
/usr/include/armadillo_bits/constants_old.hpp:59:29: note: declared here
   arma_deprecated static eT nan()       { return priv::Datum_helper::nan<eT>(); }  // use datum::nan instead
                             ^~~
mmcollapse.cpp:417:37: warning: 'static eT arma::Math<eT>::nan() [with eT = double]' is deprecated [-Wdeprecated-declarations]
         R(i,indexes[j],s)=math::nan();
                                     ^
In file included from /usr/include/armadillo:119,
                 from mmcollapse.cpp:28:
/usr/include/armadillo_bits/constants_old.hpp:59:29: note: declared here
   arma_deprecated static eT nan()       { return priv::Datum_helper::nan<eT>(); }  // use datum::nan instead
                             ^~~
mmcollapse.cpp:424:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int, std::allocator<int> >::size_type' {aka 'unsigned int'} [-Wsign-compare]
   for(int i=0; i < indexes.size(); i++) {
                ~~^~~~~~~~~~~~~~~~
mmcollapse.cpp:429:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'unsigned int'} [-Wsign-compare]
   for(int i=1; i < tset.size(); i++) {
                ~~^~~~~~~~~~~~~
mmcollapse.cpp:435:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int, std::allocator<int> >::size_type' {aka 'unsigned int'} [-Wsign-compare]
   for(int i=1; i < indexes.size(); i++) {
                ~~^~~~~~~~~~~~~~~~
mmcollapse.cpp: In function 'std::map<int, int> join_traces(arma::mat&, std::vector<std::__cxx11::basic_string<char> >&, std::vector<std::__cxx11::basic_string<char> >)':
mmcollapse.cpp:443:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'unsigned int'} [-Wsign-compare]
   for(int t=0; t < allnames.size(); t++) tmap[allnames[t]]=t;
                ~~^~~~~~~~~~~~~~~~~
mmcollapse.cpp:450:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'unsigned int'} [-Wsign-compare]
   for(int c=0; c < candidates.size(); c++) {
                ~~^~~~~~~~~~~~~~~~~~~
mmcollapse.cpp:454:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'unsigned int'} [-Wsign-compare]
     for(int t=0; t < tokens.size(); t++) {
                  ~~^~~~~~~~~~~~~~~
mmcollapse.cpp:462:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int, std::allocator<int> >::size_type' {aka 'unsigned int'} [-Wsign-compare]
     for(int t=1; t < indexes.size(); t++) {
                  ~~^~~~~~~~~~~~~~~~
mmcollapse.cpp:467:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int, std::allocator<int> >::size_type' {aka 'unsigned int'} [-Wsign-compare]
     for(int t=1; t < indexes.size(); t++) {
                  ~~^~~~~~~~~~~~~~~~
mmcollapse.cpp:474:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int, std::allocator<int> >::size_type' {aka 'unsigned int'} [-Wsign-compare]
   for(int i=0; i < toshed.size(); i++) {
                ~~^~~~~~~~~~~~~~~
mmcollapse.cpp: In function 'void mean_corrs(const cube&, const umat&, arma::mat&, arma::mat&, std::vector<int, std::allocator<int> >, std::vector<int, std::allocator<int> >, double)':
mmcollapse.cpp:484:21: warning: comparison of integer expressions of different signedness: 'int' and 'const uword' {aka 'const unsigned int'} [-Wsign-compare]
     for(int v= 0; v < R.n_rows; v++) {
                   ~~^~~~~~~~~~
mmcollapse.cpp:490:22: warning: comparison of integer expressions of different signedness: 'int' and 'arma::uword' {aka 'unsigned int'} [-Wsign-compare]
       for(int i=0; i < u.size(); i++) {
                    ~~^~~~~~~~~~
mmcollapse.cpp: In function 'void get_corrs(arma::cube&, arma::mat&, const std::vector<std::__cxx11::basic_string<char> >&, std::map<std::__cxx11::basic_string<char>, int>&)':
mmcollapse.cpp:517:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'unsigned int'} [-Wsign-compare]
   for(int s=0; s < basenames.size(); s++) {
                ~~^~~~~~~~~~~~~~~~~~
mmcollapse.cpp:541:24: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'unsigned int'} [-Wsign-compare]
         for(int t=0; t < tokens.size(); t++) {
                      ~~^~~~~~~~~~~~~~~
mmcollapse.cpp:544:60: warning: 'static eT arma::Math<eT>::nan() [with eT = double]' is deprecated [-Wdeprecated-declarations]
             if(str=="NA") myM(i,cand2ind[tokens[t]])=math::nan();
                                                            ^~~
In file included from /usr/include/armadillo:119,
                 from mmcollapse.cpp:28:
/usr/include/armadillo_bits/constants_old.hpp:59:29: note: declared here
   arma_deprecated static eT nan()       { return priv::Datum_helper::nan<eT>(); }  // use datum::nan instead
                             ^~~
mmcollapse.cpp:544:64: warning: 'static eT arma::Math<eT>::nan() [with eT = double]' is deprecated [-Wdeprecated-declarations]
             if(str=="NA") myM(i,cand2ind[tokens[t]])=math::nan();
                                                                ^
In file included from /usr/include/armadillo:119,
                 from mmcollapse.cpp:28:
/usr/include/armadillo_bits/constants_old.hpp:59:29: note: declared here
   arma_deprecated static eT nan()       { return priv::Datum_helper::nan<eT>(); }  // use datum::nan instead
                             ^~~
mmcollapse.cpp:544:64: warning: 'static eT arma::Math<eT>::nan() [with eT = double]' is deprecated [-Wdeprecated-declarations]
             if(str=="NA") myM(i,cand2ind[tokens[t]])=math::nan();
                                                                ^
In file included from /usr/include/armadillo:119,
                 from mmcollapse.cpp:28:
/usr/include/armadillo_bits/constants_old.hpp:59:29: note: declared here
   arma_deprecated static eT nan()       { return priv::Datum_helper::nan<eT>(); }  // use datum::nan instead
                             ^~~
mmcollapse.cpp: In function 'int main(int, char**)':
mmcollapse.cpp:628:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'unsigned int'} [-Wsign-compare]
   for(int i=1; i < basenames.size(); i++) {
                ~~^~~~~~~~~~~~~~~~~~
mmcollapse.cpp:687:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'unsigned int'} [-Wsign-compare]
   for(int s=0; s < basenames.size(); s++) {
                ~~^~~~~~~~~~~~~~~~~~
mmcollapse.cpp:703:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'unsigned int'} [-Wsign-compare]
   for(int i=0; i < candidates.size(); i++) ts.push_back(i);
                ~~^~~~~~~~~~~~~~~~~~~
mmcollapse.cpp:728:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<double>::size_type' {aka 'unsigned int'} [-Wsign-compare]
     for(int i=0 ;i < maxcorrs.size(); i++) {
                  ~~^~~~~~~~~~~~~~~~~
mmcollapse.cpp:734:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<double>::size_type' {aka 'unsigned int'} [-Wsign-compare]
     for(int i=0 ;i < mincorrs.size(); i++) {
                  ~~^~~~~~~~~~~~~~~~~
mmcollapse.cpp:798:24: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<double>::size_type' {aka 'unsigned int'} [-Wsign-compare]
         for(int i=0 ;i < maxcorrs.size(); i++) {
                      ~~^~~~~~~~~~~~~~~~~
mmcollapse.cpp:804:24: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<double>::size_type' {aka 'unsigned int'} [-Wsign-compare]
         for(int i=0 ;i < mincorrs.size(); i++) {
                      ~~^~~~~~~~~~~~~~~~~
mmcollapse.cpp:823:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'unsigned int'} [-Wsign-compare]
   for(int s=0; s < basenames.size(); s++) {
                ~~^~~~~~~~~~~~~~~~~~
mmcollapse.cpp:848:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'unsigned int'} [-Wsign-compare]
       for(int t=0; t < tokens.size(); t++) {
                    ~~^~~~~~~~~~~~~~~
mmcollapse.cpp:878:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'unsigned int'} [-Wsign-compare]
       for(int t=0; t < tokens2.size(); t++) {
                    ~~^~~~~~~~~~~~~~~~
mmcollapse.cpp:930:20: warning: comparison of integer expressions of different signedness: 'int' and 'const uword' {aka 'const unsigned int'} [-Wsign-compare]
     for(int t=0; t < M.n_cols; t++) {
                  ~~^~~~~~~~~~
mmcollapse.cpp:959:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'unsigned int'} [-Wsign-compare]
     for(int i=1; i < tokens2.size(); i++) {
                  ~~^~~~~~~~~~~~~~~~
mmcollapse.cpp:972:21: warning: comparison of integer expressions of different signedness: 'boost::numeric::ublas::compressed_matrix<bool>::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare]
       if(MM.size1() < i+1 ) factor1=2;
          ~~~~~~~~~~~^~~~~
mmcollapse.cpp:973:21: warning: comparison of integer expressions of different signedness: 'boost::numeric::ublas::compressed_matrix<bool>::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare]
       if(MM.size2() < j+1 ) factor2=2;
          ~~~~~~~~~~~^~~~~
mmcollapse.cpp:1006:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'unsigned int'} [-Wsign-compare]
     for(int t=0; t < ids.size(); t++) {
                  ~~^~~~~~~~~~~~
mmcollapse.cpp:1079:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'unsigned int'} [-Wsign-compare]
     for(int i=0; i < ids.size(); i++) {
                  ~~^~~~~~~~~~~~
mmcollapse.cpp:1088:22: warning: comparison of integer expressions of different signedness: 'int' and 'const uword' {aka 'const unsigned int'} [-Wsign-compare]
     for(int v = 0; v < M.n_cols; v++) {
                    ~~^~~~~~~~~~
mmcollapse.cpp:836:9: warning: unused variable 'isident' [-Wunused-variable]
     int isident=0;
         ^~~~~~~
hitsio.cpp: In member function 'void HitsfileWriter::writeHeaderSchema0()':
hitsio.cpp:163:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'unsigned int'} [-Wsign-compare]
  for(int i = 0; i < transcriptName.size(); i++) {
                 ~~^~~~~~~~~~~~~~~~~~~~~~~
hitsio.cpp: In member function 'void HitsfileWriter::writeReadMapRecordSchema0()':
hitsio.cpp:184:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'unsigned int'} [-Wsign-compare]
  for(int i = 0; i < currentReadTranscripts.size(); i++) {
                 ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
hitsio.cpp: In member function 'void HitsfileWriter::writeHeaderSchema1()':
hitsio.cpp:24:10: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare]
  if (VAL > numeric_limits<uint32_t>::max()) { \
          ^
hitsio.cpp:191:2: note: in expansion of macro 'WRITE_UINT'
  WRITE_UINT(ofs, hitsfileSchema);
  ^~~~~~~~~~
hitsio.cpp:193:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'unsigned int'} [-Wsign-compare]
  for(int i = 0; i < transcriptName.size(); i++) {
                 ~~^~~~~~~~~~~~~~~~~~~~~~~
hitsio.cpp:24:10: warning: comparison of integer expressions of different signedness: 'std::map<std::__cxx11::basic_string<char>, int>::mapped_type' {aka 'int'} and 'unsigned int' [-Wsign-compare]
  if (VAL > numeric_limits<uint32_t>::max()) { \
hitsio.cpp:196:3: note: in expansion of macro 'WRITE_UINT'
   WRITE_UINT(ofs, transcriptTrueLength[transcriptName[i] ])
   ^~~~~~~~~~
hitsio.cpp: In member function 'void HitsfileWriter::writeReadMapRecordSchema1()':
hitsio.cpp:236:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'unsigned int'} [-Wsign-compare]
  for(int i = 0; i < currentReadTranscripts.size(); i++) {
                 ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
hitsio.cpp: In member function 'void HitsfileReader::readHeaderSchema1(std::vector<std::__cxx11::basic_string<char> >*, std::map<std::__cxx11::basic_string<char>, double>*, std::map<std::__cxx11::basic_string<char>, int>*, std::map<std::__cxx11::basic_string<char>, std::vector<std::__cxx11::basic_string<char> > >*, std::vector<std::vector<std::__cxx11::basic_string<char> > >*)':
hitsio.cpp:356:9: warning: unused variable 'nextStrLen' [-Wunused-variable]
  size_t nextStrLen;
         ^~~~~~~~~~
hitsio.cpp: In member function 'bool HitsfileReader::readReadMapRecordTranscriptID(std::__cxx11::string&)':
hitsio.cpp:447:1: warning: control reaches end of non-void function [-Wreturn-type]
 }
 ^
g++ -DVERSION=1.0.8 -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fopenmp -O3 sokal.o uh.o hitsio.o mmseq.cpp -o ../bin/mmseq -lgsl -lgslcblas -lboost_regex -lbam -lboost_iostreams -llapack -lblas -lgfortran -Wl,--as-needed -lz -larmadillo
g++ -DVERSION=1.0.8 -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fopenmp -O3 fasta.o hitsio.o bam2hits.cpp -o ../bin/bam2hits -lgsl -lgslcblas -lboost_regex -lbam -lboost_iostreams -llapack -lblas -lgfortran -Wl,--as-needed -lz -larmadillo
g++ -DVERSION=1.0.8 -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fopenmp -O3 hitsio.o hitstools.cpp -o ../bin/hitstools -lgsl -lgslcblas -lboost_regex -lbam -lboost_iostreams -llapack -lblas -lgfortran -Wl,--as-needed -lz -larmadillo
bms.cpp: In member function 'arma::Col<int> BMS::m2v(arma::Mat<double>)':
bms.cpp:37:18: warning: comparison of integer expressions of different signedness: 'int' and 'const uword' {aka 'const unsigned int'} [-Wsign-compare]
   for(int i=0; i < P.n_cols; i++) {
                ~~^~~~~~~~~~
bms.cpp:38:20: warning: comparison of integer expressions of different signedness: 'int' and 'const uword' {aka 'const unsigned int'} [-Wsign-compare]
     for(int j=0; j < P.n_rows; j++) {
                  ~~^~~~~~~~~~
bms.cpp: In member function 'std::vector<double> BMS::meanvar(arma::Col<double>)':
bms.cpp:77:17: warning: comparison of integer expressions of different signedness: 'int' and 'const uword' {aka 'const unsigned int'} [-Wsign-compare]
   for(int i=0;i < v.n_elem; i++) {
               ~~^~~~~~~~~~
bms.cpp: In member function 'void BMS::print(bool)':
bms.cpp:94:30: warning: comparison of integer expressions of different signedness: 'int' and 'const uword' {aka 'const unsigned int'} [-Wsign-compare]
   for(int feature=0; feature < y->n_rows; feature++) {
                      ~~~~~~~~^~~~~~~~~~~
bms.cpp:98:22: warning: comparison of integer expressions of different signedness: 'int' and 'const uword' {aka 'const unsigned int'} [-Wsign-compare]
       for(int i=0; i < M.n_cols; i++) {
                    ~~^~~~~~~~~~
bms.cpp:103:22: warning: comparison of integer expressions of different signedness: 'int' and 'const uword' {aka 'const unsigned int'} [-Wsign-compare]
       for(int l=0; l < P[model].n_cols; l++) {
                    ~~^~~~~~~~~~~~~~~~~
bms.cpp: In member function 'void BMS::printtune(int)':
bms.cpp:133:30: warning: comparison of integer expressions of different signedness: 'int' and 'const uword' {aka 'const unsigned int'} [-Wsign-compare]
   for(int feature=0; feature < y->n_rows; feature++) {
                      ~~~~~~~~^~~~~~~~~~~
bms.cpp: In member function 'void BMS::set_pseudoprior_alpha()':
bms.cpp:186:20: warning: comparison of integer expressions of different signedness: 'int' and 'const uword' {aka 'const unsigned int'} [-Wsign-compare]
     for(int j=0; j < y->n_rows; j++) {
                  ~~^~~~~~~~~~~
bms.cpp: In member function 'void BMS::set_pseudoprior_beta()':
bms.cpp:254:18: warning: comparison of integer expressions of different signedness: 'int' and 'const uword' {aka 'const unsigned int'} [-Wsign-compare]
   for(int j=0; j < y->n_rows; j++) {
                ~~^~~~~~~~~~~
bms.cpp:256:22: warning: comparison of integer expressions of different signedness: 'int' and 'const uword' {aka 'const unsigned int'} [-Wsign-compare]
       for(int b=0; b < M.n_cols; b++) {
                    ~~^~~~~~~~~~
bms.cpp: In member function 'void BMS::set_pseudoprior_eta()':
bms.cpp:333:18: warning: comparison of integer expressions of different signedness: 'int' and 'const uword' {aka 'const unsigned int'} [-Wsign-compare]
   for(int j=0; j < y->n_rows; j++) {
                ~~^~~~~~~~~~~
bms.cpp:335:22: warning: comparison of integer expressions of different signedness: 'int' and 'const uword' {aka 'const unsigned int'} [-Wsign-compare]
       for(int c=0; c < P[model].n_cols; c++) {
                    ~~^~~~~~~~~~~~~~~~~
bms.cpp: In member function 'void BMS::set_pseudoprior_sigmasq()':
bms.cpp:416:18: warning: comparison of integer expressions of different signedness: 'int' and 'const uword' {aka 'const unsigned int'} [-Wsign-compare]
   for(int j=0; j < y->n_rows; j++) {
                ~~^~~~~~~~~~~
bms.cpp: In member function 'void BMS::set_pseudoprior_lambda()':
bms.cpp:505:18: warning: comparison of integer expressions of different signedness: 'int' and 'const uword' {aka 'const unsigned int'} [-Wsign-compare]
   for(int j=0; j < y->n_rows; j++) {
                ~~^~~~~~~~~~~
bms.cpp:507:22: warning: comparison of integer expressions of different signedness: 'int' and 'const uword' {aka 'const unsigned int'} [-Wsign-compare]
       for(int l=0; l < P[model].n_cols; l++) {
                    ~~^~~~~~~~~~~~~~~~~
bms.cpp: In member function 'void BMS::set_pseudoprior_rho()':
bms.cpp:560:20: warning: comparison of integer expressions of different signedness: 'int' and 'const uword' {aka 'const unsigned int'} [-Wsign-compare]
     for(int j=0; j < y->n_rows; j++) {
                  ~~^~~~~~~~~~~
bms.cpp: In member function 'void BMS::copy_pseudo()':
bms.cpp:583:18: warning: comparison of integer expressions of different signedness: 'int' and 'const uword' {aka 'const unsigned int'} [-Wsign-compare]
   for(int j=0; j < y->n_rows; j++) {
                ~~^~~~~~~~~~~
bms.cpp:586:20: warning: comparison of integer expressions of different signedness: 'int' and 'const uword' {aka 'const unsigned int'} [-Wsign-compare]
     for(int c=0; c < P[0].n_cols; c++) {
                  ~~^~~~~~~~~~~~~
bms.cpp: In member function 'void BMS::update_alpha(int, int, bool)':
bms.cpp:604:20: warning: comparison of integer expressions of different signedness: 'int' and 'const uword' {aka 'const unsigned int'} [-Wsign-compare]
     for(int j=0; j < y->n_cols; j++) {
                  ~~^~~~~~~~~~~
bms.cpp:611:20: warning: comparison of integer expressions of different signedness: 'int' and 'const uword' {aka 'const unsigned int'} [-Wsign-compare]
     for(int i=0; i < y->n_cols; i++) {
                  ~~^~~~~~~~~~~
bms.cpp: In member function 'void BMS::update_beta(int, int, bool)':
bms.cpp:632:20: warning: comparison of integer expressions of different signedness: 'int' and 'const uword' {aka 'const unsigned int'} [-Wsign-compare]
     for(int j=0; j < y->n_cols; j++) {
                  ~~^~~~~~~~~~~
bms.cpp:639:20: warning: comparison of integer expressions of different signedness: 'int' and 'const uword' {aka 'const unsigned int'} [-Wsign-compare]
     for(int i=0; i < M.n_cols; i++) {
                  ~~^~~~~~~~~~
bms.cpp:647:20: warning: comparison of integer expressions of different signedness: 'int' and 'const uword' {aka 'const unsigned int'} [-Wsign-compare]
     for(int i=0; i < M.n_cols; i++) {
                  ~~^~~~~~~~~~
bms.cpp:652:20: warning: comparison of integer expressions of different signedness: 'int' and 'const uword' {aka 'const unsigned int'} [-Wsign-compare]
     for(int i=0; i < M.n_cols; i++) {
                  ~~^~~~~~~~~~
bms.cpp: In member function 'void BMS::update_eta(int, int, bool)':
bms.cpp:668:20: warning: comparison of integer expressions of different signedness: 'int' and 'const uword' {aka 'const unsigned int'} [-Wsign-compare]
     for(int l=0; l < P[model].n_cols; l++) {
                  ~~^~~~~~~~~~~~~~~~~
bms.cpp:670:22: warning: comparison of integer expressions of different signedness: 'int' and 'const uword' {aka 'const unsigned int'} [-Wsign-compare]
       for(int i=0; i < y->n_cols; i++) {
                    ~~^~~~~~~~~~~
bms.cpp:674:20: warning: comparison of integer expressions of different signedness: 'int' and 'const uword' {aka 'const unsigned int'} [-Wsign-compare]
     for(int l=0; l < P[model].n_cols; l++) {
                  ~~^~~~~~~~~~~~~~~~~
bms.cpp:680:20: warning: comparison of integer expressions of different signedness: 'int' and 'const uword' {aka 'const unsigned int'} [-Wsign-compare]
     for(int l=0; l < P[model].n_cols; l++) {
                  ~~^~~~~~~~~~~~~~~~~
bms.cpp:682:22: warning: comparison of integer expressions of different signedness: 'int' and 'const uword' {aka 'const unsigned int'} [-Wsign-compare]
       for(int i=0; i < y->n_cols; i++) {
                    ~~^~~~~~~~~~~
bms.cpp:688:20: warning: comparison of integer expressions of different signedness: 'int' and 'const uword' {aka 'const unsigned int'} [-Wsign-compare]
     for(int l=0; l < P[model].n_cols; l++) {
                  ~~^~~~~~~~~~~~~~~~~
bms.cpp:692:20: warning: comparison of integer expressions of different signedness: 'int' and 'const uword' {aka 'const unsigned int'} [-Wsign-compare]
     for(int l=0; l < P[model].n_cols; l++) {
                  ~~^~~~~~~~~~~~~~~~~
bms.cpp:697:20: warning: comparison of integer expressions of different signedness: 'int' and 'const uword' {aka 'const unsigned int'} [-Wsign-compare]
     for(int l=0; l < P[model].n_cols; l++) {
                  ~~^~~~~~~~~~~~~~~~~
bms.cpp: In member function 'void BMS::update_lambda(int, int, bool)':
bms.cpp:710:20: warning: comparison of integer expressions of different signedness: 'int' and 'const uword' {aka 'const unsigned int'} [-Wsign-compare]
     for(int l=0; l < P[model].n_cols; l++) {
                  ~~^~~~~~~~~~~~~~~~~
bms.cpp:715:20: warning: comparison of integer expressions of different signedness: 'int' and 'const uword' {aka 'const unsigned int'} [-Wsign-compare]
     for(int l=0; l < P[model].n_cols; l++) {
                  ~~^~~~~~~~~~~~~~~~~
bms.cpp:722:20: warning: comparison of integer expressions of different signedness: 'int' and 'const uword' {aka 'const unsigned int'} [-Wsign-compare]
     for(int l=0; l < P[model].n_cols; l++) {
                  ~~^~~~~~~~~~~~~~~~~
bms.cpp: In member function 'void BMS::update_sigmasq(int, int, bool, bool)':
bms.cpp:740:20: warning: comparison of integer expressions of different signedness: 'int' and 'const uword' {aka 'const unsigned int'} [-Wsign-compare]
     for(int i=0; i < y->n_cols; i++) {
                  ~~^~~~~~~~~~~
bms.cpp:751:20: warning: comparison of integer expressions of different signedness: 'int' and 'const uword' {aka 'const unsigned int'} [-Wsign-compare]
     for(int i=0; i < y->n_cols; i++) {
                  ~~^~~~~~~~~~~
bms.cpp:762:24: warning: comparison of integer expressions of different signedness: 'int' and 'const uword' {aka 'const unsigned int'} [-Wsign-compare]
         for(int i=0; i < y->n_cols; i++) {
                      ~~^~~~~~~~~~~
bms.cpp:774:24: warning: comparison of integer expressions of different signedness: 'int' and 'const uword' {aka 'const unsigned int'} [-Wsign-compare]
         for(int i=0; i < y->n_cols; i++) {
                      ~~^~~~~~~~~~~
bms.cpp: In member function 'void BMS::update_sigmasq_RW(int, int, bool, bool)':
bms.cpp:888:20: warning: comparison of integer expressions of different signedness: 'int' and 'const uword' {aka 'const unsigned int'} [-Wsign-compare]
     for(int i=0; i < y->n_cols; i++) {
                  ~~^~~~~~~~~~~
bms.cpp: In member function 'double BMS::log_target_posterior(int, int)':
bms.cpp:942:18: warning: comparison of integer expressions of different signedness: 'int' and 'const uword' {aka 'const unsigned int'} [-Wsign-compare]
   for(int i=0; i < y->n_cols; i++) {
                ~~^~~~~~~~~~~
bms.cpp:951:20: warning: comparison of integer expressions of different signedness: 'int' and 'const uword' {aka 'const unsigned int'} [-Wsign-compare]
     for(int j=0; j < M.n_cols; j++) {
                  ~~^~~~~~~~~~
bms.cpp:958:20: warning: comparison of integer expressions of different signedness: 'int' and 'const uword' {aka 'const unsigned int'} [-Wsign-compare]
     for(int l=0; l < P[model].n_cols; l++) {
                  ~~^~~~~~~~~~~~~~~~~
bms.cpp: In member function 'double BMS::log_target_pseudo(int, int)':
bms.cpp:979:20: warning: comparison of integer expressions of different signedness: 'int' and 'const uword' {aka 'const unsigned int'} [-Wsign-compare]
     for(int l=0; l < M.n_cols; l++) {
                  ~~^~~~~~~~~~
bms.cpp:985:20: warning: comparison of integer expressions of different signedness: 'int' and 'const uword' {aka 'const unsigned int'} [-Wsign-compare]
     for(int l=0; l < P[model].n_cols; l++) {
                  ~~^~~~~~~~~~~~~~~~~
bms.cpp: In member function 'void BMS::print_pseudo()':
bms.cpp:1094:20: warning: comparison of integer expressions of different signedness: 'int' and 'const uword' {aka 'const unsigned int'} [-Wsign-compare]
     for(int l=0; l < M.n_cols; l++) {
                  ~~^~~~~~~~~~
bms.cpp:1097:20: warning: comparison of integer expressions of different signedness: 'int' and 'const uword' {aka 'const unsigned int'} [-Wsign-compare]
     for(int l=0; l < P[model].n_cols; l++) {
                  ~~^~~~~~~~~~~~~~~~~
bms.cpp:1108:18: warning: comparison of integer expressions of different signedness: 'int' and 'const uword' {aka 'const unsigned int'} [-Wsign-compare]
   for(int i=0; i < y->n_rows; i++) {
                ~~^~~~~~~~~~~
bms.cpp:1111:22: warning: comparison of integer expressions of different signedness: 'int' and 'const uword' {aka 'const unsigned int'} [-Wsign-compare]
       for(int l=0; l < M.n_cols; l++) {
                    ~~^~~~~~~~~~
bms.cpp:1114:22: warning: comparison of integer expressions of different signedness: 'int' and 'const uword' {aka 'const unsigned int'} [-Wsign-compare]
       for(int l=0; l < P[model].n_cols; l++) {
                    ~~^~~~~~~~~~~~~~~~~
bms.cpp: In constructor 'BMS::BMS(const arma::Mat<double>*, const arma::Mat<double>&, arma::Mat<double>, arma::Mat<double>, arma::Mat<double>, arma::Mat<int>, double, double, double, std::__cxx11::string, gsl_rng**, int, bool)':
bms.cpp:1196:20: warning: comparison of integer expressions of different signedness: 'int' and 'const uword' {aka 'const unsigned int'} [-Wsign-compare]
     for(int i=0; i < y->n_cols; i++) {
                  ~~^~~~~~~~~~~
bms.cpp:1200:25: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int, std::allocator<int> >::size_type' {aka 'unsigned int'} [-Wsign-compare]
         if(C(i,model)+1 > _n.size()) {
            ~~~~~~~~~~~~~^~~~~~~~~~~
bms.cpp: In member function 'void BMS::initialise_streams(std::__cxx11::string)':
bms.cpp:1356:18: warning: comparison of integer expressions of different signedness: 'int' and 'const uword' {aka 'const unsigned int'} [-Wsign-compare]
   for(int i=0; i < M.n_cols; i++) {
                ~~^~~~~~~~~~
bms.cpp:1362:18: warning: comparison of integer expressions of different signedness: 'int' and 'const uword' {aka 'const unsigned int'} [-Wsign-compare]
   for(int i=0; i < M.n_cols; i++) {
                ~~^~~~~~~~~~
bms.cpp:1368:18: warning: comparison of integer expressions of different signedness: 'int' and 'const uword' {aka 'const unsigned int'} [-Wsign-compare]
   for(int i=0; i < P[0].n_cols; i++) {
                ~~^~~~~~~~~~~~~
bms.cpp:1374:18: warning: comparison of integer expressions of different signedness: 'int' and 'const uword' {aka 'const unsigned int'} [-Wsign-compare]
   for(int i=0; i < P[1].n_cols; i++) {
                ~~^~~~~~~~~~~~~
bms.cpp:1380:18: warning: comparison of integer expressions of different signedness: 'int' and 'const uword' {aka 'const unsigned int'} [-Wsign-compare]
   for(int i=0; i < P[0].n_cols; i++) {
                ~~^~~~~~~~~~~~~
bms.cpp:1386:18: warning: comparison of integer expressions of different signedness: 'int' and 'const uword' {aka 'const unsigned int'} [-Wsign-compare]
   for(int i=0; i < P[1].n_cols; i++) {
                ~~^~~~~~~~~~~~~
hitstools.cpp: In function 'void convert(char*, std::__cxx11::string)':
hitstools.cpp:50:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'unsigned int'} [-Wsign-compare]
  for(int i = 0; i < transcriptName.size(); i++) {
                 ~~^~~~~~~~~~~~~~~~~~~~~~~
hitstools.cpp: In function 'int main(int, char**)':
hitstools.cpp:95:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'unsigned int'} [-Wsign-compare]
   for(int i = 0; i < transcriptName.size(); i++) {
                  ~~^~~~~~~~~~~~~~~~~~~~~~~
hitstools.cpp:135:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'unsigned int'} [-Wsign-compare]
     for(int i = 0; i < transcriptName.size(); i++) {
                    ~~^~~~~~~~~~~~~~~~~~~~~~~
mmseq.cpp: In function 'std::vector<double> meanvar(std::vector<double>, double, double)':
mmseq.cpp:129:17: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<double>::size_type' {aka 'unsigned int'} [-Wsign-compare]
   for(int i=0;i < v.size(); i++) {
               ~~^~~~~~~~~~
mmseq.cpp: In function 'int main(int, char**)':
mmseq.cpp:243:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'unsigned int'} [-Wsign-compare]
       for(int i=0; i < tokens.size(); i++) {
                    ~~^~~~~~~~~~~~~~~
mmseq.cpp:422:20: warning: comparison of integer expressions of different signedness: 'boost::numeric::ublas::compressed_matrix<bool>::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare]
       if(M.size1() < m ) factor1=2;
          ~~~~~~~~~~^~~
mmseq.cpp:423:20: warning: comparison of integer expressions of different signedness: 'boost::numeric::ublas::compressed_matrix<bool>::size_type' {aka 'unsigned int'} and 'int' [-Wsign-compare]
       if(M.size2() < n ) factor2=2;
          ~~~~~~~~~~^~~
mmseq.cpp:593:23: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare]
   for(unsigned t=0; t < n; t++)  {
                     ~~^~~
mmseq.cpp:735:25: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare]
     for(unsigned t=0; t < n; t++)
                       ~~^~~
mmseq.cpp:764:27: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare]
       for(unsigned t=0; t < n; t++)
                         ~~^~~
mmseq.cpp:773:11: warning: unused variable 'threadid' [-Wunused-variable]
       int threadid=OMP_GET_THREAD_NUM;
           ^~~~~~~~
mmseq.cpp:828:23: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare]
   for(unsigned t=0; t < n; t++)
                     ~~^~~
mmseq.cpp:911:27: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare]
       for(unsigned t=0; t < n; t++) {
                         ~~^~~
mmseq.cpp:939:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::vector<std::__cxx11::basic_string<char> > >::size_type' {aka 'unsigned int'} [-Wsign-compare]
   for(int i=0; i < identical_transcripts.size() * trace_length; i++) mu_trace_identical[i]=0;
                ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
mmseq.cpp:960:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::map<std::__cxx11::basic_string<char>, std::vector<std::__cxx11::basic_string<char> > >::size_type' {aka 'unsigned int'} [-Wsign-compare]
   for(int i=0; i < gene2transcripts.size() * trace_length; i++) mu_trace_gene[i]=0;
                ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
mmseq.cpp:1097:23: warning: comparison of integer expressions of different signedness: 'unsigned int' and 'int' [-Wsign-compare]
   for(unsigned t=0; t < n; t++) gofs << indexSid[t] << " ";
                     ~~^~~
mmseq.cpp:1111:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<double>::size_type' {aka 'unsigned int'} [-Wsign-compare]
   for(int i=0; i < percentiles.size(); i++) {
                ~~^~~~~~~~~~~~~~~~~~~~
mmseq.cpp:1135:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<double>::size_type' {aka 'unsigned int'} [-Wsign-compare]
     for(int j=0; j < percentiles.size(); j++) {
                  ~~^~~~~~~~~~~~~~~~~~~~
mmseq.cpp:1143:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<double>::size_type' {aka 'unsigned int'} [-Wsign-compare]
     for(int j=0; j < percentiles.size(); j++) {
                  ~~^~~~~~~~~~~~~~~~~~~~
mmseq.cpp:1148:17: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::vector<std::__cxx11::basic_string<char> > >::size_type' {aka 'unsigned int'} [-Wsign-compare]
   for(int i=0;i < identical_transcripts.size(); i++) {
               ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
mmseq.cpp:1155:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<double>::size_type' {aka 'unsigned int'} [-Wsign-compare]
     for(int j=0; j < percentiles.size(); j++) {
                  ~~^~~~~~~~~~~~~~~~~~~~
mmseq.cpp:1160:17: warning: comparison of integer expressions of different signedness: 'int' and 'std::map<std::__cxx11::basic_string<char>, std::vector<std::__cxx11::basic_string<char> > >::size_type' {aka 'unsigned int'} [-Wsign-compare]
   for(int i=0;i < gene2transcripts.size(); i++) {
               ~~^~~~~~~~~~~~~~~~~~~~~~~~~
mmseq.cpp:1167:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<double>::size_type' {aka 'unsigned int'} [-Wsign-compare]
     for(int j=0; j < percentiles.size(); j++) {
                  ~~^~~~~~~~~~~~~~~~~~~~
mmseq.cpp:1178:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<double>::size_type' {aka 'unsigned int'} [-Wsign-compare]
     for(int j=0; j < percentiles.size(); j++) {
                  ~~^~~~~~~~~~~~~~~~~~~~
mmseq.cpp:1188:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<double>::size_type' {aka 'unsigned int'} [-Wsign-compare]
     for(int j=0; j < percentiles.size(); j++) {
                  ~~^~~~~~~~~~~~~~~~~~~~
mmseq.cpp:1207:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::vector<std::__cxx11::basic_string<char> > >::size_type' {aka 'unsigned int'} [-Wsign-compare]
     for(int t=0; t < identical_transcripts.size() ; t++) {
                  ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
mmseq.cpp:1211:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::map<std::__cxx11::basic_string<char>, std::vector<std::__cxx11::basic_string<char> > >::size_type' {aka 'unsigned int'} [-Wsign-compare]
     for(int t=0; t < gene2transcripts.size(); t++){
                  ~~^~~~~~~~~~~~~~~~~~~~~~~~~
mmseq.cpp:1225:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::vector<std::__cxx11::basic_string<char> > >::size_type' {aka 'unsigned int'} [-Wsign-compare]
   for(int i=0; i < identical_transcripts.size() ; i++) meanmu_identical[i] /= trace_length;
                ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
mmseq.cpp:1226:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::map<std::__cxx11::basic_string<char>, std::vector<std::__cxx11::basic_string<char> > >::size_type' {aka 'unsigned int'} [-Wsign-compare]
   for(int i=0; i < gene2transcripts.size(); i++) meanmu_gene[i]/= trace_length;
                ~~^~~~~~~~~~~~~~~~~~~~~~~~~
mmseq.cpp:1329:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::vector<std::__cxx11::basic_string<char> > >::size_type' {aka 'unsigned int'} [-Wsign-compare]
   for(int t=0; t < identical_transcripts.size(); t++) {
                ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
mmseq.cpp:1348:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::map<std::__cxx11::basic_string<char>, std::vector<std::__cxx11::basic_string<char> > >::size_type' {aka 'unsigned int'} [-Wsign-compare]
   for(int g=0; g < gene2transcripts.size(); g++) {
                ~~^~~~~~~~~~~~~~~~~~~~~~~~~
mmseq.cpp:1472:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<double>::size_type' {aka 'unsigned int'} [-Wsign-compare]
   for(int i=0; i < percentiles.size(); i++) {
                ~~^~~~~~~~~~~~~~~~~~~~
mmseq.cpp:1474:9: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<double>::size_type' {aka 'unsigned int'} [-Wsign-compare]
     if(i==percentiles.size()-1) {
        ~^~~~~~~~~~~~~~~~~~~~~~
mmseq.cpp:1481:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<double>::size_type' {aka 'unsigned int'} [-Wsign-compare]
   for(int i=0; i < percentiles.size(); i++) {
                ~~^~~~~~~~~~~~~~~~~~~~
mmseq.cpp:1483:9: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<double>::size_type' {aka 'unsigned int'} [-Wsign-compare]
     if(i==percentiles.size()-1) {
        ~^~~~~~~~~~~~~~~~~~~~~~
mmseq.cpp:1505:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<double>::size_type' {aka 'unsigned int'} [-Wsign-compare]
       for(int i=0; i < percentiles.size(); i++) {
                    ~~^~~~~~~~~~~~~~~~~~~~
mmseq.cpp:1507:13: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<double>::size_type' {aka 'unsigned int'} [-Wsign-compare]
         if(i==percentiles.size()-1) {
            ~^~~~~~~~~~~~~~~~~~~~~~
mmseq.cpp:1513:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<double>::size_type' {aka 'unsigned int'} [-Wsign-compare]
       for(int i=0; i < percentiles.size(); i++) {
                    ~~^~~~~~~~~~~~~~~~~~~~
mmseq.cpp:1515:13: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<double>::size_type' {aka 'unsigned int'} [-Wsign-compare]
         if(i==percentiles.size()-1) {
            ~^~~~~~~~~~~~~~~~~~~~~~
mmseq.cpp:1535:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<double>::size_type' {aka 'unsigned int'} [-Wsign-compare]
       for(int i=0; i < percentiles.size(); i++) {
                    ~~^~~~~~~~~~~~~~~~~~~~
mmseq.cpp:1537:13: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<double>::size_type' {aka 'unsigned int'} [-Wsign-compare]
         if(i==percentiles.size()-1) {
            ~^~~~~~~~~~~~~~~~~~~~~~
mmseq.cpp:1543:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<double>::size_type' {aka 'unsigned int'} [-Wsign-compare]
       for(int i=0; i < percentiles.size(); i++) {
                    ~~^~~~~~~~~~~~~~~~~~~~
mmseq.cpp:1545:13: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<double>::size_type' {aka 'unsigned int'} [-Wsign-compare]
         if(i==percentiles.size()-1) {
            ~^~~~~~~~~~~~~~~~~~~~~~
mmseq.cpp:1559:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<double>::size_type' {aka 'unsigned int'} [-Wsign-compare]
   for(int i=0; i < percentiles.size(); i++) {
                ~~^~~~~~~~~~~~~~~~~~~~
mmseq.cpp:1561:9: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<double>::size_type' {aka 'unsigned int'} [-Wsign-compare]
     if(i==percentiles.size()-1) {
        ~^~~~~~~~~~~~~~~~~~~~~~
mmseq.cpp:1581:24: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<double>::size_type' {aka 'unsigned int'} [-Wsign-compare]
         for(int i=0; i < percentiles.size(); i++) {
                      ~~^~~~~~~~~~~~~~~~~~~~
mmseq.cpp:1583:15: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<double>::size_type' {aka 'unsigned int'} [-Wsign-compare]
           if(i==percentiles.size()-1) {
              ~^~~~~~~~~~~~~~~~~~~~~~
mmseq.cpp:1598:24: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<double>::size_type' {aka 'unsigned int'} [-Wsign-compare]
         for(int i=0; i < percentiles.size(); i++) {
                      ~~^~~~~~~~~~~~~~~~~~~~
mmseq.cpp:1600:15: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<double>::size_type' {aka 'unsigned int'} [-Wsign-compare]
           if(i==percentiles.size()-1) {
              ~^~~~~~~~~~~~~~~~~~~~~~
mmseq.cpp:1618:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<double>::size_type' {aka 'unsigned int'} [-Wsign-compare]
   for(int i=0; i < percentiles.size(); i++) {
                ~~^~~~~~~~~~~~~~~~~~~~
mmseq.cpp:1620:9: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<double>::size_type' {aka 'unsigned int'} [-Wsign-compare]
     if(i==percentiles.size()-1) {
        ~^~~~~~~~~~~~~~~~~~~~~~
mmseq.cpp:1643:24: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<double>::size_type' {aka 'unsigned int'} [-Wsign-compare]
         for(int i=0; i < percentiles.size(); i++) {
                      ~~^~~~~~~~~~~~~~~~~~~~
mmseq.cpp:1645:15: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<double>::size_type' {aka 'unsigned int'} [-Wsign-compare]
           if(i==percentiles.size()-1) {
              ~^~~~~~~~~~~~~~~~~~~~~~
mmseq.cpp:1655:24: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<double>::size_type' {aka 'unsigned int'} [-Wsign-compare]
         for(int i=0; i < percentiles.size(); i++) {
                      ~~^~~~~~~~~~~~~~~~~~~~
mmseq.cpp:1657:15: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<double>::size_type' {aka 'unsigned int'} [-Wsign-compare]
           if(i==percentiles.size()-1) {
              ~^~~~~~~~~~~~~~~~~~~~~~
mmseq.cpp:307:8: warning: unused variable 'buf16384' [-Wunused-variable]
   char buf16384[16384];
        ^~~~~~~~
mmseq.cpp:390:8: warning: variable 'doublehit' set but not used [-Wunused-but-set-variable]
   bool doublehit;
        ^~~~~~~~~
bam2hits.cpp: In function 'void outputMergeHeaders(std::vector<FastaRecord>&, char, const char*, bool, HitsfileWriter&)':
bam2hits.cpp:109:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<FastaRecord>::size_type' {aka 'unsigned int'} [-Wsign-compare]
   for(int i=0; i < sortedfastas.size()-1; i++) {
                ~~^~~~~~~~~~~~~~~~~~~~~~~
bam2hits.cpp:119:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<FastaRecord>::size_type' {aka 'unsigned int'} [-Wsign-compare]
       for(int j=0; j < curSet.size()-1; j++) {
                    ~~^~~~~~~~~~~~~~~~~
bam2hits.cpp:137:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<FastaRecord>::size_type' {aka 'unsigned int'} [-Wsign-compare]
   for(int j=0; j < curSet.size()-1; j++) {
                ~~^~~~~~~~~~~~~~~~~
bam2hits.cpp: In function 'std::vector<Alignment> repetitiveTranscriptFilter(std::vector<Alignment>&, int)':
bam2hits.cpp:218:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<Alignment>::size_type' {aka 'unsigned int'} [-Wsign-compare]
   for(int j=0; j < alns.size(); j++) {
                ~~^~~~~~~~~~~~~
bam2hits.cpp:219:10: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int>::size_type' {aka 'unsigned int'} [-Wsign-compare]
     if(i < torem.size() && j==torem[i]) {
        ~~^~~~~~~~~~~~~~
bam2hits.cpp: In function 'int main(int, char**)':
bam2hits.cpp:518:15: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string<char>::size_type' {aka 'unsigned int'} [-Wsign-compare]
         if(_B != tg[0].size()-2) {
            ~~~^~~~~~~~~~~~~~~~~
bam2hits.cpp:520:17: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string<char>::size_type' {aka 'unsigned int'} [-Wsign-compare]
           if(_A == tg[0].size()-2) {
              ~~~^~~~~~~~~~~~~~~~~
bam2hits.cpp:522:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string<char>::size_type' {aka 'unsigned int'} [-Wsign-compare]
             if(_A != tg[1].size()-2) {
                ~~~^~~~~~~~~~~~~~~~~
bam2hits.cpp:558:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'unsigned int'} [-Wsign-compare]
       for(int i=1; i < tokens2.size(); i++) {
                    ~~^~~~~~~~~~~~~~~~
bam2hits.cpp:608:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<FastaRecord>::size_type' {aka 'unsigned int'} [-Wsign-compare]
     for(int i=0; i < fastas.size(); i++) {
                  ~~^~~~~~~~~~~~~~~
bam2hits.cpp:643:19: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<FastaRecord>::size_type' {aka 'unsigned int'} [-Wsign-compare]
     for(int i=0;i < fastas.size(); i++) transcriptCounts[i] /= (double)fastas[i].seq().size();
                 ~~^~~~~~~~~~~~~~~
bam2hits.cpp:657:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<FastaRecord>::size_type' {aka 'unsigned int'} [-Wsign-compare]
     for(int i=0; i < fastas.size(); i++) {
                  ~~^~~~~~~~~~~~~~~
bam2hits.cpp:660:25: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string<char>::size_type' {aka 'unsigned int'} [-Wsign-compare]
         for(int j =0; j < fastas[i].seq().size(); j++) {
                       ~~^~~~~~~~~~~~~~~~~~~~~~~~
bam2hits.cpp:661:44: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string<char>::size_type' {aka 'unsigned int'} [-Wsign-compare]
           int tag = (j <= MSEQ_BEFORE || j >= fastas[i].seq().size()-MSEQ_AFTER) ? -2 : 0;
                                          ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
bam2hits.cpp:790:36: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string<char>::size_type' {aka 'unsigned int'} [-Wsign-compare]
       for(int j=MSEQ_BEFORE + 1; j <= fastas[i].seq().length()-MSEQ_AFTER; j++) {
                                  ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
bam2hits.cpp:669:11: warning: unused variable 'binpath' [-Wunused-variable]
     char *binpath = strdup(argv[0]);
           ^~~~~~~
bam2hits.cpp:918:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int>::size_type' {aka 'unsigned int'} [-Wsign-compare]
     for(int j=1; j < frequencies.size()-WINDOWFORISIZEMODE + 1; j++) {
                  ~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
bam2hits.cpp:946:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int>::size_type' {aka 'unsigned int'} [-Wsign-compare]
     for(int i=0; i < testIsizes.size(); i++) {
                  ~~^~~~~~~~~~~~~~~~~~~
bam2hits.cpp:957:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int>::size_type' {aka 'unsigned int'} [-Wsign-compare]
     for(int i=0; i < heights.size(); i++) {
                  ~~^~~~~~~~~~~~~~~~
bam2hits.cpp:995:24: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string<char>::size_type' {aka 'unsigned int'} [-Wsign-compare]
       for(int fl=1; fl <= (it->seq()).size(); fl++) {
                     ~~~^~~~~~~~~~~~~~~~~~~~~
g++ -DVERSION=1.0.8 -O2 -g -pipe -Wall -Werror=format-security -Wp,-D_FORTIFY_SOURCE=2 -Wp,-D_GLIBCXX_ASSERTIONS -fexceptions -fstack-protector-strong -grecord-gcc-switches -specs=/usr/lib/rpm/redhat/redhat-hardened-cc1 -specs=/usr/lib/rpm/redhat/redhat-annobin-cc1 -m32 -march=i686 -mtune=generic -msse2 -mfpmath=sse -mstackrealign -fasynchronous-unwind-tables -fstack-clash-protection -fcf-protection -fopenmp -O2 bms.o mmdiff.cpp -o ../bin/mmdiff -lgsl -lgslcblas -lboost_regex -lbam -lboost_iostreams -llapack -lblas -lgfortran -Wl,--as-needed -lz -larmadillo
mmdiff.cpp: In function 'void parse_mmseq(std::vector<std::__cxx11::basic_string<char> >, std::vector<std::__cxx11::basic_string<char> >&, arma::Mat<double>&, arma::Mat<double>&, arma::Mat<double>&, int, int, double, bool)':
mmdiff.cpp:99:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'unsigned int'} [-Wsign-compare]
   for(int i=0; i < filenames.size(); i++) {
                ~~^~~~~~~~~~~~~~~~~~
mmdiff.cpp:110:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'unsigned int'} [-Wsign-compare]
     for(int j=0; j < tokens.size(); j++) {
                  ~~^~~~~~~~~~~~~~~
mmdiff.cpp:137:16: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'unsigned int'} [-Wsign-compare]
       if(k + 1 > features.size()) {
          ~~~~~~^~~~~~~~~~~~~~~~~
mmdiff.cpp:146:14: warning: comparison of integer expressions of different signedness: 'int' and 'const uword' {aka 'const unsigned int'} [-Wsign-compare]
       if(k+1 > y.n_rows) {
          ~~~~^~~~~~~~~~
mmdiff.cpp:151:20: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
       if(!useprops && tokens[lmg_ind]=="NA" || useprops && tokens[mp_ind]=="NA") {
          ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~
mmdiff.cpp:172:62: warning: comparison of integer expressions of different signedness: 'int' and 'const uword' {aka 'const unsigned int'} [-Wsign-compare]
   if(range_start >=0 && range_end > range_start && range_end < y.n_rows) {
                                                    ~~~~~~~~~~^~~~~~~~~~
mmdiff.cpp:93:46: warning: variable 'mcse_ind' set but not used [-Wunused-but-set-variable]
   int feature_ind=-1, lmg_ind=-1, sd_ind=-1, mcse_ind=-1, iact_ind=-1, mp_ind=-1, sp_ind=-1, uh_ind=-1;
                                              ^~~~~~~~
mmdiff.cpp:93:59: warning: variable 'iact_ind' set but not used [-Wunused-but-set-variable]
   int feature_ind=-1, lmg_ind=-1, sd_ind=-1, mcse_ind=-1, iact_ind=-1, mp_ind=-1, sp_ind=-1, uh_ind=-1;
                                                           ^~~~~~~~
mmdiff.cpp: In function 'void apply_normalisation(std::vector<std::__cxx11::basic_string<char> >, arma::Mat<double>&, arma::Mat<double>&, double)':
mmdiff.cpp:211:18: warning: comparison of integer expressions of different signedness: 'int' and 'const uword' {aka 'const unsigned int'} [-Wsign-compare]
   for(int i=0; i < uh.n_rows; i++) {
                ~~^~~~~~~~~~~
mmdiff.cpp:213:20: warning: comparison of integer expressions of different signedness: 'int' and 'const uword' {aka 'const unsigned int'} [-Wsign-compare]
     for(int j=0; j < uh.n_cols; j++) {
                  ~~^~~~~~~~~~~
mmdiff.cpp:229:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int, std::allocator<int> >::size_type' {aka 'unsigned int'} [-Wsign-compare]
   for(int i=0; i < use.size(); i++) {
                ~~^~~~~~~~~~~~
mmdiff.cpp:231:20: warning: comparison of integer expressions of different signedness: 'int' and 'const uword' {aka 'const unsigned int'} [-Wsign-compare]
     for(int j=0; j < y.n_cols; j++) {
                  ~~^~~~~~~~~~
mmdiff.cpp:238:28: warning: comparison of integer expressions of different signedness: 'int' and 'const uword' {aka 'const unsigned int'} [-Wsign-compare]
   for(int sample=0; sample < y.n_cols; sample++) {
                     ~~~~~~~^~~~~~~~~~
mmdiff.cpp:240:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int, std::allocator<int> >::size_type' {aka 'unsigned int'} [-Wsign-compare]
     for(int i=0; i < use.size(); i++) {
                  ~~^~~~~~~~~~~~
mmdiff.cpp:245:20: warning: comparison of integer expressions of different signedness: 'int' and 'const uword' {aka 'const unsigned int'} [-Wsign-compare]
     for(int i=0; i < y.n_rows; i++) {
                  ~~^~~~~~~~~~
mmdiff.cpp: In function 'void apply_permutation(arma::Mat<double>&, arma::Mat<double>&)':
mmdiff.cpp:256:17: warning: comparison of integer expressions of different signedness: 'int' and 'const uword' {aka 'const unsigned int'} [-Wsign-compare]
   for(int j=0; j< y.n_cols; j++) randinds.push_back(j);
                ~^~~~~~~~~~
mmdiff.cpp:257:18: warning: comparison of integer expressions of different signedness: 'int' and 'const uword' {aka 'const unsigned int'} [-Wsign-compare]
   for(int i=0; i < y.n_rows; i++) {
                ~~^~~~~~~~~~
mmdiff.cpp:259:20: warning: comparison of integer expressions of different signedness: 'int' and 'const uword' {aka 'const unsigned int'} [-Wsign-compare]
     for(int j=0; j < y.n_cols; j++) {
                  ~~^~~~~~~~~~
mmdiff.cpp: In function 'void parse_matrices(std::__cxx11::string, arma::Mat<double>&, arma::Mat<double>&, arma::Mat<double>&, arma::Mat<int>&, int)':
mmdiff.cpp:309:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'unsigned int'} [-Wsign-compare]
     for(int t=0; t < tokens.size(); t++) {
                  ~~^~~~~~~~~~~~~~~
mmdiff.cpp: In function 'int main(int, char**)':
mmdiff.cpp:419:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'unsigned int'} [-Wsign-compare]
       for(int i=0; i < arguments.size(); i++) {
                    ~~^~~~~~~~~~~~~~~~~~
mmdiff.cpp:430:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'unsigned int'} [-Wsign-compare]
       for(int i=0; i < arguments.size(); i++) {
                    ~~^~~~~~~~~~~~~~~~~~
mmdiff.cpp:438:16: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'unsigned int'} [-Wsign-compare]
       while(ss < arguments.size()) {
             ~~~^~~~~~~~~~~~~~~~~~
mmdiff.cpp:450:13: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'unsigned int'} [-Wsign-compare]
       if(ss != arguments.size()) {
          ~~~^~~~~~~~~~~~~~~~~~~
mmdiff.cpp:577:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'unsigned int'} [-Wsign-compare]
   for(int i=0; i < arguments.size(); i++) {
                ~~^~~~~~~~~~~~~~~~~~
mmdiff.cpp:639:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int, std::allocator<int> >::size_type' {aka 'unsigned int'} [-Wsign-compare]
     for(int i=0; i < simple_de.size(); i++) {
                  ~~^~~~~~~~~~~~~~~~~~
mmdiff.cpp:758:17: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
     if(inburnin && iter == OUTLEN/10 || !inburnin && iter==tuneiters) {
        ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~
mmdiff.cpp:763:32: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'unsigned int'} [-Wsign-compare]
     for(int feature=0; feature < features.size(); feature++) {
                        ~~~~~~~~^~~~~~~~~~~~~~~~~
mmdiff.cpp:836:17: warning: suggest parentheses around '&&' within '||' [-Wparentheses]
     if(inburnin && iter % subsample_burnin ==0 || !inburnin && iter >= tuneiters && (iter - tuneiters) % subsample_iter == 0) {
        ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
mmdiff.cpp:885:22: warning: comparison of integer expressions of different signedness: 'int' and 'const uword' {aka 'const unsigned int'} [-Wsign-compare]
       for(int l=0; l < M.n_cols; l++) {
                    ~~^~~~~~~~~~
mmdiff.cpp:897:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'unsigned int'} [-Wsign-compare]
   for(int f=0; f < samplenames.size(); f++) {
                ~~^~~~~~~~~~~~~~~~~~~~
mmdiff.cpp:901:22: warning: comparison of integer expressions of different signedness: 'int' and 'std::__cxx11::basic_string<char>::size_type' {aka 'unsigned int'} [-Wsign-compare]
       found2 = found2==string::npos ? -1 : found2;
                ~~~~~~^~~~~~~~
mmdiff.cpp:906:18: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'unsigned int'} [-Wsign-compare]
   for(int f=0; f < samplenames.size(); f++) {
                ~~^~~~~~~~~~~~~~~~~~~~
mmdiff.cpp:908:10: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'unsigned int'} [-Wsign-compare]
     if(f < samplenames.size()-1) cout << "\t";
        ~~^~~~~~~~~~~~~~~~~~~~~~
mmdiff.cpp:913:30: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'unsigned int'} [-Wsign-compare]
   for(int feature=0; feature < features.size(); feature++) {
                      ~~~~~~~~^~~~~~~~~~~~~~~~~
mmdiff.cpp:924:24: warning: comparison of integer expressions of different signedness: 'int' and 'const uword' {aka 'const unsigned int'} [-Wsign-compare]
         for(int l=0; l < M.n_cols; l++) {
                      ~~^~~~~~~~~~
mmdiff.cpp:934:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'unsigned int'} [-Wsign-compare]
     for(int f=0; f < samplenames.size(); f++) {
                  ~~^~~~~~~~~~~~~~~~~~~~
mmdiff.cpp:937:20: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'unsigned int'} [-Wsign-compare]
     for(int f=0; f < samplenames.size(); f++) {
                  ~~^~~~~~~~~~~~~~~~~~~~
mmdiff.cpp:939:12: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'unsigned int'} [-Wsign-compare]
       if(f < samplenames.size()-1) cout << "\t";
          ~~^~~~~~~~~~~~~~~~~~~~~~
mmdiff.cpp:949:34: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<std::__cxx11::basic_string<char> >::size_type' {aka 'unsigned int'} [-Wsign-compare]
       for(int feature=0; feature < features.size(); feature++) {
                          ~~~~~~~~^~~~~~~~~~~~~~~~~
/usr/bin/ld: /tmp/cc6hQWK1.o: in function `main':
/builddir/build/BUILD/mmseq-1.0.8a/src/bam2hits.cpp:651: warning: the use of `tmpnam' is dangerous, better use `mkstemp'
+ exit 0
Executing(%install): /bin/sh -e /var/tmp/rpm-tmp.Ma6tPs
+ umask 022
+ cd /builddir/build/BUILD
+ '[' /builddir/build/BUILDROOT/mmseq-1.0.8a-26.fc29.i386 '!=' / ']'
+ rm -rf /builddir/build/BUILDROOT/mmseq-1.0.8a-26.fc29.i386
++ dirname /builddir/build/BUILDROOT/mmseq-1.0.8a-26.fc29.i386
+ mkdir -p /builddir/build/BUILDROOT
+ mkdir /builddir/build/BUILDROOT/mmseq-1.0.8a-26.fc29.i386
+ cd mmseq-1.0.8a
+ rm -rf /builddir/build/BUILDROOT/mmseq-1.0.8a-26.fc29.i386
+ mkdir -p /builddir/build/BUILDROOT/mmseq-1.0.8a-26.fc29.i386/usr/bin
+ install -p -m 0755 bin/bam2hits /builddir/build/BUILDROOT/mmseq-1.0.8a-26.fc29.i386/usr/bin
+ install -p -m 0755 bin/extract_transcripts /builddir/build/BUILDROOT/mmseq-1.0.8a-26.fc29.i386/usr/bin
+ install -p -m 0755 bin/hitstools /builddir/build/BUILDROOT/mmseq-1.0.8a-26.fc29.i386/usr/bin
+ install -p -m 0755 bin/mmcollapse /builddir/build/BUILDROOT/mmseq-1.0.8a-26.fc29.i386/usr/bin
+ install -p -m 0755 bin/mmdiff /builddir/build/BUILDROOT/mmseq-1.0.8a-26.fc29.i386/usr/bin
+ install -p -m 0755 bin/mmseq /builddir/build/BUILDROOT/mmseq-1.0.8a-26.fc29.i386/usr/bin
+ install -p -m 0755 bin/offsetGTF /builddir/build/BUILDROOT/mmseq-1.0.8a-26.fc29.i386/usr/bin
+ install -p -m 0755 bin/t2g_hits /builddir/build/BUILDROOT/mmseq-1.0.8a-26.fc29.i386/usr/bin
+ install -p -m 0755 bin/fastagrep.sh bin/mouse_strain_transcriptome.sh bin/usage.sh /builddir/build/BUILDROOT/mmseq-1.0.8a-26.fc29.i386/usr/bin
+ install -p -m 0755 bin/filterGTF.rb bin/haploref.rb bin/testregexp.rb /builddir/build/BUILDROOT/mmseq-1.0.8a-26.fc29.i386/usr/bin
+ install -p -m 0755 bin/ensembl_gtf_to_gff.pl /builddir/build/BUILDROOT/mmseq-1.0.8a-26.fc29.i386/usr/bin
+ /usr/lib/rpm/find-debuginfo.sh -j6 --strict-build-id -m -i --build-id-seed 1.0.8a-26.fc29 --unique-debug-suffix -1.0.8a-26.fc29.i386 --unique-debug-src-base mmseq-1.0.8a-26.fc29.i386 --run-dwz --dwz-low-mem-die-limit 10000000 --dwz-max-die-limit 50000000 -S debugsourcefiles.list /builddir/build/BUILD/mmseq-1.0.8a
extracting debug info from /builddir/build/BUILDROOT/mmseq-1.0.8a-26.fc29.i386/usr/bin/mmdiff
extracting debug info from /builddir/build/BUILDROOT/mmseq-1.0.8a-26.fc29.i386/usr/bin/mmcollapse
extracting debug info from /builddir/build/BUILDROOT/mmseq-1.0.8a-26.fc29.i386/usr/bin/t2g_hits
extracting debug info from /builddir/build/BUILDROOT/mmseq-1.0.8a-26.fc29.i386/usr/bin/extract_transcripts
extracting debug info from /builddir/build/BUILDROOT/mmseq-1.0.8a-26.fc29.i386/usr/bin/offsetGTF
extracting debug info from /builddir/build/BUILDROOT/mmseq-1.0.8a-26.fc29.i386/usr/bin/hitstools
extracting debug info from /builddir/build/BUILDROOT/mmseq-1.0.8a-26.fc29.i386/usr/bin/bam2hits
extracting debug info from /builddir/build/BUILDROOT/mmseq-1.0.8a-26.fc29.i386/usr/bin/mmseq
/usr/lib/rpm/sepdebugcrcfix: Updated 8 CRC32s, 0 CRC32s did match.
525 blocks
+ /usr/lib/rpm/check-buildroot
+ /usr/lib/rpm/redhat/brp-ldconfig
/sbin/ldconfig: Warning: ignoring configuration file that cannot be opened: /etc/ld.so.conf: No such file or directory
+ /usr/lib/rpm/brp-compress
+ /usr/lib/rpm/brp-strip-static-archive /usr/bin/strip
+ /usr/lib/rpm/brp-python-bytecompile /usr/bin/python 1 1
+ /usr/lib/rpm/brp-python-hardlink
+ /usr/lib/rpm/redhat/brp-mangle-shebangs
mangling shebang in /usr/bin/testregexp.rb from /usr/bin/env ruby to #!/usr/bin/ruby
mangling shebang in /usr/bin/ensembl_gtf_to_gff.pl from /usr/bin/env perl to #!/usr/bin/perl
mangling shebang in /usr/bin/filterGTF.rb from /usr/bin/env ruby to #!/usr/bin/ruby
mangling shebang in /usr/bin/haploref.rb from /usr/bin/env ruby to #!/usr/bin/ruby
*** WARNING: ./usr/bin/usage.sh is executable but has empty or no shebang, removing executable bit
Processing files: mmseq-1.0.8a-26.fc29.i686
Executing(%doc): /bin/sh -e /var/tmp/rpm-tmp.bQjibp
+ umask 022
+ cd /builddir/build/BUILD
+ cd mmseq-1.0.8a
+ DOCDIR=/builddir/build/BUILDROOT/mmseq-1.0.8a-26.fc29.i386/usr/share/doc/mmseq
+ export LC_ALL=C
+ LC_ALL=C
+ export DOCDIR
+ /usr/bin/mkdir -p /builddir/build/BUILDROOT/mmseq-1.0.8a-26.fc29.i386/usr/share/doc/mmseq
+ cp -pr README.md /builddir/build/BUILDROOT/mmseq-1.0.8a-26.fc29.i386/usr/share/doc/mmseq
+ cp -pr COPYING /builddir/build/BUILDROOT/mmseq-1.0.8a-26.fc29.i386/usr/share/doc/mmseq
+ cp -pr doc/ /builddir/build/BUILDROOT/mmseq-1.0.8a-26.fc29.i386/usr/share/doc/mmseq
+ exit 0
Provides: mmseq = 1.0.8a-26.fc29 mmseq(x86-32) = 1.0.8a-26.fc29
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Requires: /bin/bash /bin/sh /usr/bin/perl /usr/bin/ruby libarmadillo.so.8 libbam.so.1 libblas.so.3 libboost_iostreams.so.1.66.0 libboost_regex.so.1.66.0 libc.so.6 libc.so.6(GLIBC_2.0) libc.so.6(GLIBC_2.1) libc.so.6(GLIBC_2.1.3) libc.so.6(GLIBC_2.2) libc.so.6(GLIBC_2.3) libc.so.6(GLIBC_2.3.4) libc.so.6(GLIBC_2.4) libgcc_s.so.1 libgcc_s.so.1(GCC_3.0) libgfortran.so.5 libgomp.so.1 libgomp.so.1(GOMP_1.0) libgomp.so.1(GOMP_4.0) libgomp.so.1(OMP_1.0) libgsl.so.23 libgslcblas.so.0 liblapack.so.3 libm.so.6 libm.so.6(GLIBC_2.0) libm.so.6(GLIBC_2.1) libstdc++.so.6 libstdc++.so.6(CXXABI_1.3) libstdc++.so.6(CXXABI_1.3.8) libstdc++.so.6(CXXABI_1.3.9) libstdc++.so.6(GLIBCXX_3.4) libstdc++.so.6(GLIBCXX_3.4.11) libstdc++.so.6(GLIBCXX_3.4.15) libstdc++.so.6(GLIBCXX_3.4.20) libstdc++.so.6(GLIBCXX_3.4.21) libstdc++.so.6(GLIBCXX_3.4.9) perl(strict) rtld(GNU_HASH)
Processing files: mmseq-debugsource-1.0.8a-26.fc29.i686
Provides: mmseq-debugsource = 1.0.8a-26.fc29 mmseq-debugsource(x86-32) = 1.0.8a-26.fc29
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Processing files: mmseq-debuginfo-1.0.8a-26.fc29.i686
Provides: debuginfo(build-id) = 058dc29839b425c300130c7ad1e80b33de488eac debuginfo(build-id) = 0809a3e982b5732d9093213729d65773ba27712a debuginfo(build-id) = 16876debb38939edce221ba1e3263c70864d2ad1 debuginfo(build-id) = 17016a0eb4bade6fb49a816f5edd7fb103d738a3 debuginfo(build-id) = 592d107a03752a0541f631b2e3322f4c6ef3e373 debuginfo(build-id) = c82a809fcb51365949ad651bddabc9110e246e29 debuginfo(build-id) = eb6259418fa0fada68166f56652659341827d3ec debuginfo(build-id) = fa3a620762bcafdea1ba3ac77e1decb29d760f80 mmseq-debuginfo = 1.0.8a-26.fc29 mmseq-debuginfo(x86-32) = 1.0.8a-26.fc29
Requires(rpmlib): rpmlib(CompressedFileNames) <= 3.0.4-1 rpmlib(FileDigests) <= 4.6.0-1 rpmlib(PayloadFilesHavePrefix) <= 4.0-1
Recommends: mmseq-debugsource(x86-32) = 1.0.8a-26.fc29
Checking for unpackaged file(s): /usr/lib/rpm/check-files /builddir/build/BUILDROOT/mmseq-1.0.8a-26.fc29.i386
Wrote: /builddir/build/RPMS/mmseq-1.0.8a-26.fc29.i686.rpm
Wrote: /builddir/build/RPMS/mmseq-debugsource-1.0.8a-26.fc29.i686.rpm
Wrote: /builddir/build/RPMS/mmseq-debuginfo-1.0.8a-26.fc29.i686.rpm
Executing(%clean): /bin/sh -e /var/tmp/rpm-tmp.nD211u
+ umask 022
+ cd /builddir/build/BUILD
+ cd mmseq-1.0.8a
+ /usr/bin/rm -rf /builddir/build/BUILDROOT/mmseq-1.0.8a-26.fc29.i386
+ exit 0
Child return code was: 0