Error During Compilation

Hello,

Trying to compile vt using gcc 4.4.7 on CentOS 6 and having issues with svm_train.cpp

[root@HPC05 ~]# uname -a Linux HPC05 2.6.32-573.12.1.el6.x86_64 #1 SMP Tue Dec 15 21:19:08 UTC 2015 x86_64 x86_64 x86_64 GNU/Linux [root@HPC05 ~]# cat /etc/issue CentOS release 6.7 (Final) Kernel \r on an \m

[root@HPC05 ~]# cd vt [root@HPC05 vt]# make cd lib/htslib; make libhts.a || exit 1; make[1]: Entering directory /root/vt/lib/htslib' echo '/* Empty config.h generated by Makefile */' > config.h gcc -g -Wall -O2 -I. -c -o kfunc.o kfunc.c gcc -g -Wall -O2 -I. -c -o knetfile.o knetfile.c gcc -g -Wall -O2 -I. -c -o kstring.o kstring.c gcc -g -Wall -O2 -I. -c -o bgzf.o bgzf.c gcc -g -Wall -O2 -I. -c -o errmod.o errmod.c gcc -g -Wall -O2 -I. -c -o faidx.o faidx.c gcc -g -Wall -O2 -I. -c -o hfile.o hfile.c gcc -g -Wall -O2 -I. -c -o hfile_net.o hfile_net.c echo '#define HTS_VERSION "1.3.2"' > version.h gcc -g -Wall -O2 -I. -c -o hts.o hts.c gcc -g -Wall -O2 -I. -c -o md5.o md5.c gcc -g -Wall -O2 -I. -c -o multipart.o multipart.c gcc -g -Wall -O2 -I. -c -o probaln.o probaln.c gcc -g -Wall -O2 -I. -c -o realn.o realn.c gcc -g -Wall -O2 -I. -c -o regidx.o regidx.c gcc -g -Wall -O2 -I. -c -o sam.o sam.c gcc -g -Wall -O2 -I. -c -o synced_bcf_reader.o synced_bcf_reader.c gcc -g -Wall -O2 -I. -c -o vcf_sweep.o vcf_sweep.c gcc -g -Wall -O2 -I. -c -o tbx.o tbx.c gcc -g -Wall -O2 -I. -c -o textutils.o textutils.c gcc -g -Wall -O2 -I. -c -o thread_pool.o thread_pool.c gcc -g -Wall -O2 -I. -c -o vcf.o vcf.c gcc -g -Wall -O2 -I. -c -o vcfutils.o vcfutils.c gcc -g -Wall -O2 -I. -c -o cram/cram_codecs.o cram/cram_codecs.c gcc -g -Wall -O2 -I. -c -o cram/cram_decode.o cram/cram_decode.c gcc -g -Wall -O2 -I. -c -o cram/cram_encode.o cram/cram_encode.c gcc -g -Wall -O2 -I. -c -o cram/cram_external.o cram/cram_external.c gcc -g -Wall -O2 -I. -c -o cram/cram_index.o cram/cram_index.c gcc -g -Wall -O2 -I. -c -o cram/cram_io.o cram/cram_io.c gcc -g -Wall -O2 -I. -c -o cram/cram_samtools.o cram/cram_samtools.c gcc -g -Wall -O2 -I. -c -o cram/cram_stats.o cram/cram_stats.c gcc -g -Wall -O2 -I. -c -o cram/files.o cram/files.c gcc -g -Wall -O2 -I. -c -o cram/mFILE.o cram/mFILE.c gcc -g -Wall -O2 -I. -c -o cram/open_trace_file.o cram/open_trace_file.c gcc -g -Wall -O2 -I. -c -o cram/pooled_alloc.o cram/pooled_alloc.c gcc -g -Wall -O2 -I. -c -o cram/rANS_static.o cram/rANS_static.c gcc -g -Wall -O2 -I. -c -o cram/sam_header.o cram/sam_header.c gcc -g -Wall -O2 -I. -c -o cram/string_alloc.o cram/string_alloc.c gcc -g -Wall -O2 -I. -c -o cram/vlen.o cram/vlen.c gcc -g -Wall -O2 -I. -c -o cram/zfio.o cram/zfio.c ar -rc libhts.a kfunc.o knetfile.o kstring.o bgzf.o errmod.o faidx.o hfile.o hfile_net.o hts.o md5.o multipart.o probaln.o realn.o regidx.o sam.o synced_bcf_reader.o vcf_sweep.o tbx.o textutils.o thread_pool.o vcf.o vcfutils.o cram/cram_codecs.o cram/cram_decode.o cram/cram_encode.o cram/cram_external.o cram/cram_index.o cram/cram_io.o cram/cram_samtools.o cram/cram_stats.o cram/files.o cram/mFILE.o cram/open_trace_file.o cram/pooled_alloc.o cram/rANS_static.o cram/sam_header.o cram/string_alloc.o cram/vlen.o cram/zfio.o ranlib libhts.a make[1]: Leaving directory/root/vt/lib/htslib' cd lib/Rmath; make libRmath.a || exit 1; make[1]: Entering directory /root/vt/lib/Rmath' gcc -Wall -O3 -fPIC -DMATHLIB_STANDALONE -std=gnu99 -IRmath -DNDEBUG -c bd0.c -o bd0.o gcc -Wall -O3 -fPIC -DMATHLIB_STANDALONE -std=gnu99 -IRmath -DNDEBUG -c dnbeta.c -o dnbeta.o gcc -Wall -O3 -fPIC -DMATHLIB_STANDALONE -std=gnu99 -IRmath -DNDEBUG -c i1mach.c -o i1mach.o gcc -Wall -O3 -fPIC -DMATHLIB_STANDALONE -std=gnu99 -IRmath -DNDEBUG -c pnbinom.c -o pnbinom.o gcc -Wall -O3 -fPIC -DMATHLIB_STANDALONE -std=gnu99 -IRmath -DNDEBUG -c qlnorm.c -o qlnorm.o gcc -Wall -O3 -fPIC -DMATHLIB_STANDALONE -std=gnu99 -IRmath -DNDEBUG -c rgeom.c -o rgeom.o gcc -Wall -O3 -fPIC -DMATHLIB_STANDALONE -std=gnu99 -IRmath -DNDEBUG -c bessel_i.c -o bessel_i.o gcc -Wall -O3 -fPIC -DMATHLIB_STANDALONE -std=gnu99 -IRmath -DNDEBUG -c dnbinom.c -o dnbinom.o gcc -Wall -O3 -fPIC -DMATHLIB_STANDALONE -std=gnu99 -IRmath -DNDEBUG -c imax2.c -o imax2.o gcc -Wall -O3 -fPIC -DMATHLIB_STANDALONE -std=gnu99 -IRmath -DNDEBUG -c pnchisq.c -o pnchisq.o gcc -Wall -O3 -fPIC -DMATHLIB_STANDALONE -std=gnu99 -IRmath -DNDEBUG -c qlogis.c -o qlogis.o gcc -Wall -O3 -fPIC -DMATHLIB_STANDALONE -std=gnu99 -IRmath -DNDEBUG -c rhyper.c -o rhyper.o gcc -Wall -O3 -fPIC -DMATHLIB_STANDALONE -std=gnu99 -IRmath -DNDEBUG -c bessel_j.c -o bessel_j.o gcc -Wall -O3 -fPIC -DMATHLIB_STANDALONE -std=gnu99 -IRmath -DNDEBUG -c dnchisq.c -o dnchisq.o gcc -Wall -O3 -fPIC -DMATHLIB_STANDALONE -std=gnu99 -IRmath -DNDEBUG -c imin2.c -o imin2.o gcc -Wall -O3 -fPIC -DMATHLIB_STANDALONE -std=gnu99 -IRmath -DNDEBUG -c pnf.c -o pnf.o gcc -Wall -O3 -fPIC -DMATHLIB_STANDALONE -std=gnu99 -IRmath -DNDEBUG -c qnbeta.c -o qnbeta.o gcc -Wall -O3 -fPIC -DMATHLIB_STANDALONE -std=gnu99 -IRmath -DNDEBUG -c rlnorm.c -o rlnorm.o gcc -Wall -O3 -fPIC -DMATHLIB_STANDALONE -std=gnu99 -IRmath -DNDEBUG -c bessel_k.c -o bessel_k.o gcc -Wall -O3 -fPIC -DMATHLIB_STANDALONE -std=gnu99 -IRmath -DNDEBUG -c dnf.c -o dnf.o gcc -Wall -O3 -fPIC -DMATHLIB_STANDALONE -std=gnu99 -IRmath -DNDEBUG -c lbeta.c -o lbeta.o gcc -Wall -O3 -fPIC -DMATHLIB_STANDALONE -std=gnu99 -IRmath -DNDEBUG -c pnorm.c -o pnorm.o gcc -Wall -O3 -fPIC -DMATHLIB_STANDALONE -std=gnu99 -IRmath -DNDEBUG -c qnbinom.c -o qnbinom.o gcc -Wall -O3 -fPIC -DMATHLIB_STANDALONE -std=gnu99 -IRmath -DNDEBUG -c rlogis.c -o rlogis.o gcc -Wall -O3 -fPIC -DMATHLIB_STANDALONE -std=gnu99 -IRmath -DNDEBUG -c bessel_y.c -o bessel_y.o gcc -Wall -O3 -fPIC -DMATHLIB_STANDALONE -std=gnu99 -IRmath -DNDEBUG -c dnorm.c -o dnorm.o gcc -Wall -O3 -fPIC -DMATHLIB_STANDALONE -std=gnu99 -IRmath -DNDEBUG -c lgamma.c -o lgamma.o gcc -Wall -O3 -fPIC -DMATHLIB_STANDALONE -std=gnu99 -IRmath -DNDEBUG -c pnt.c -o pnt.o gcc -Wall -O3 -fPIC -DMATHLIB_STANDALONE -std=gnu99 -IRmath -DNDEBUG -c qnchisq.c -o qnchisq.o gcc -Wall -O3 -fPIC -DMATHLIB_STANDALONE -std=gnu99 -IRmath -DNDEBUG -c rmultinom.c -o rmultinom.o gcc -Wall -O3 -fPIC -DMATHLIB_STANDALONE -std=gnu99 -IRmath -DNDEBUG -c beta.c -o beta.o gcc -Wall -O3 -fPIC -DMATHLIB_STANDALONE -std=gnu99 -IRmath -DNDEBUG -c dnt.c -o dnt.o gcc -Wall -O3 -fPIC -DMATHLIB_STANDALONE -std=gnu99 -IRmath -DNDEBUG -c lgammacor.c -o lgammacor.o gcc -Wall -O3 -fPIC -DMATHLIB_STANDALONE -std=gnu99 -IRmath -DNDEBUG -c polygamma.c -o polygamma.o gcc -Wall -O3 -fPIC -DMATHLIB_STANDALONE -std=gnu99 -IRmath -DNDEBUG -c qnf.c -o qnf.o gcc -Wall -O3 -fPIC -DMATHLIB_STANDALONE -std=gnu99 -IRmath -DNDEBUG -c rnbinom.c -o rnbinom.o gcc -Wall -O3 -fPIC -DMATHLIB_STANDALONE -std=gnu99 -IRmath -DNDEBUG -c chebyshev.c -o chebyshev.o gcc -Wall -O3 -fPIC -DMATHLIB_STANDALONE -std=gnu99 -IRmath -DNDEBUG -c dpois.c -o dpois.o gcc -Wall -O3 -fPIC -DMATHLIB_STANDALONE -std=gnu99 -IRmath -DNDEBUG -c log1p.c -o log1p.o gcc -Wall -O3 -fPIC -DMATHLIB_STANDALONE -std=gnu99 -IRmath -DNDEBUG -c ppois.c -o ppois.o gcc -Wall -O3 -fPIC -DMATHLIB_STANDALONE -std=gnu99 -IRmath -DNDEBUG -c qnorm.c -o qnorm.o gcc -Wall -O3 -fPIC -DMATHLIB_STANDALONE -std=gnu99 -IRmath -DNDEBUG -c rnchisq.c -o rnchisq.o gcc -Wall -O3 -fPIC -DMATHLIB_STANDALONE -std=gnu99 -IRmath -DNDEBUG -c choose.c -o choose.o gcc -Wall -O3 -fPIC -DMATHLIB_STANDALONE -std=gnu99 -IRmath -DNDEBUG -c dt.c -o dt.o dt.c: In function ‘dt’: dt.c:50: warning: ‘ax’ may be used uninitialized in this function gcc -Wall -O3 -fPIC -DMATHLIB_STANDALONE -std=gnu99 -IRmath -DNDEBUG -c mlutils.c -o mlutils.o gcc -Wall -O3 -fPIC -DMATHLIB_STANDALONE -std=gnu99 -IRmath -DNDEBUG -c pt.c -o pt.o gcc -Wall -O3 -fPIC -DMATHLIB_STANDALONE -std=gnu99 -IRmath -DNDEBUG -c qnt.c -o qnt.o gcc -Wall -O3 -fPIC -DMATHLIB_STANDALONE -std=gnu99 -IRmath -DNDEBUG -c rnorm.c -o rnorm.o gcc -Wall -O3 -fPIC -DMATHLIB_STANDALONE -std=gnu99 -IRmath -DNDEBUG -c d1mach.c -o d1mach.o gcc -Wall -O3 -fPIC -DMATHLIB_STANDALONE -std=gnu99 -IRmath -DNDEBUG -c dunif.c -o dunif.o gcc -Wall -O3 -fPIC -DMATHLIB_STANDALONE -std=gnu99 -IRmath -DNDEBUG -c pbeta.c -o pbeta.o gcc -Wall -O3 -fPIC -DMATHLIB_STANDALONE -std=gnu99 -IRmath -DNDEBUG -c ptukey.c -o ptukey.o gcc -Wall -O3 -fPIC -DMATHLIB_STANDALONE -std=gnu99 -IRmath -DNDEBUG -c qpois.c -o qpois.o gcc -Wall -O3 -fPIC -DMATHLIB_STANDALONE -std=gnu99 -IRmath -DNDEBUG -c rpois.c -o rpois.o gcc -Wall -O3 -fPIC -DMATHLIB_STANDALONE -std=gnu99 -IRmath -DNDEBUG -c dbeta.c -o dbeta.o gcc -Wall -O3 -fPIC -DMATHLIB_STANDALONE -std=gnu99 -IRmath -DNDEBUG -c dweibull.c -o dweibull.o gcc -Wall -O3 -fPIC -DMATHLIB_STANDALONE -std=gnu99 -IRmath -DNDEBUG -c pbinom.c -o pbinom.o gcc -Wall -O3 -fPIC -DMATHLIB_STANDALONE -std=gnu99 -IRmath -DNDEBUG -c punif.c -o punif.o gcc -Wall -O3 -fPIC -DMATHLIB_STANDALONE -std=gnu99 -IRmath -DNDEBUG -c qt.c -o qt.o gcc -Wall -O3 -fPIC -DMATHLIB_STANDALONE -std=gnu99 -IRmath -DNDEBUG -c rt.c -o rt.o gcc -Wall -O3 -fPIC -DMATHLIB_STANDALONE -std=gnu99 -IRmath -DNDEBUG -c dbinom.c -o dbinom.o gcc -Wall -O3 -fPIC -DMATHLIB_STANDALONE -std=gnu99 -IRmath -DNDEBUG -c expm1.c -o expm1.o gcc -Wall -O3 -fPIC -DMATHLIB_STANDALONE -std=gnu99 -IRmath -DNDEBUG -c pcauchy.c -o pcauchy.o gcc -Wall -O3 -fPIC -DMATHLIB_STANDALONE -std=gnu99 -IRmath -DNDEBUG -c pweibull.c -o pweibull.o gcc -Wall -O3 -fPIC -DMATHLIB_STANDALONE -std=gnu99 -IRmath -DNDEBUG -c qtukey.c -o qtukey.o gcc -Wall -O3 -fPIC -DMATHLIB_STANDALONE -std=gnu99 -IRmath -DNDEBUG -c runif.c -o runif.o gcc -Wall -O3 -fPIC -DMATHLIB_STANDALONE -std=gnu99 -IRmath -DNDEBUG -c dcauchy.c -o dcauchy.o gcc -Wall -O3 -fPIC -DMATHLIB_STANDALONE -std=gnu99 -IRmath -DNDEBUG -c fmax2.c -o fmax2.o gcc -Wall -O3 -fPIC -DMATHLIB_STANDALONE -std=gnu99 -IRmath -DNDEBUG -c pchisq.c -o pchisq.o gcc -Wall -O3 -fPIC -DMATHLIB_STANDALONE -std=gnu99 -IRmath -DNDEBUG -c qbeta.c -o qbeta.o gcc -Wall -O3 -fPIC -DMATHLIB_STANDALONE -std=gnu99 -IRmath -DNDEBUG -c qunif.c -o qunif.o gcc -Wall -O3 -fPIC -DMATHLIB_STANDALONE -std=gnu99 -IRmath -DNDEBUG -c rweibull.c -o rweibull.o gcc -Wall -O3 -fPIC -DMATHLIB_STANDALONE -std=gnu99 -IRmath -DNDEBUG -c dchisq.c -o dchisq.o gcc -Wall -O3 -fPIC -DMATHLIB_STANDALONE -std=gnu99 -IRmath -DNDEBUG -c fmin2.c -o fmin2.o gcc -Wall -O3 -fPIC -DMATHLIB_STANDALONE -std=gnu99 -IRmath -DNDEBUG -c pexp.c -o pexp.o gcc -Wall -O3 -fPIC -DMATHLIB_STANDALONE -std=gnu99 -IRmath -DNDEBUG -c qbinom.c -o qbinom.o gcc -Wall -O3 -fPIC -DMATHLIB_STANDALONE -std=gnu99 -IRmath -DNDEBUG -c qweibull.c -o qweibull.o gcc -Wall -O3 -fPIC -DMATHLIB_STANDALONE -std=gnu99 -IRmath -DNDEBUG -c dexp.c -o dexp.o gcc -Wall -O3 -fPIC -DMATHLIB_STANDALONE -std=gnu99 -IRmath -DNDEBUG -c fprec.c -o fprec.o gcc -Wall -O3 -fPIC -DMATHLIB_STANDALONE -std=gnu99 -IRmath -DNDEBUG -c pf.c -o pf.o gcc -Wall -O3 -fPIC -DMATHLIB_STANDALONE -std=gnu99 -IRmath -DNDEBUG -c qcauchy.c -o qcauchy.o gcc -Wall -O3 -fPIC -DMATHLIB_STANDALONE -std=gnu99 -IRmath -DNDEBUG -c rbeta.c -o rbeta.o gcc -Wall -O3 -fPIC -DMATHLIB_STANDALONE -std=gnu99 -IRmath -DNDEBUG -c sign.c -o sign.o gcc -Wall -O3 -fPIC -DMATHLIB_STANDALONE -std=gnu99 -IRmath -DNDEBUG -c df.c -o df.o gcc -Wall -O3 -fPIC -DMATHLIB_STANDALONE -std=gnu99 -IRmath -DNDEBUG -c fround.c -o fround.o gcc -Wall -O3 -fPIC -DMATHLIB_STANDALONE -std=gnu99 -IRmath -DNDEBUG -c pgamma.c -o pgamma.o gcc -Wall -O3 -fPIC -DMATHLIB_STANDALONE -std=gnu99 -IRmath -DNDEBUG -c qchisq.c -o qchisq.o gcc -Wall -O3 -fPIC -DMATHLIB_STANDALONE -std=gnu99 -IRmath -DNDEBUG -c rbinom.c -o rbinom.o gcc -Wall -O3 -fPIC -DMATHLIB_STANDALONE -std=gnu99 -IRmath -DNDEBUG -c signrank.c -o signrank.o gcc -Wall -O3 -fPIC -DMATHLIB_STANDALONE -std=gnu99 -IRmath -DNDEBUG -c dgamma.c -o dgamma.o gcc -Wall -O3 -fPIC -DMATHLIB_STANDALONE -std=gnu99 -IRmath -DNDEBUG -c fsign.c -o fsign.o gcc -Wall -O3 -fPIC -DMATHLIB_STANDALONE -std=gnu99 -IRmath -DNDEBUG -c pgeom.c -o pgeom.o gcc -Wall -O3 -fPIC -DMATHLIB_STANDALONE -std=gnu99 -IRmath -DNDEBUG -c qexp.c -o qexp.o gcc -Wall -O3 -fPIC -DMATHLIB_STANDALONE -std=gnu99 -IRmath -DNDEBUG -c rcauchy.c -o rcauchy.o gcc -Wall -O3 -fPIC -DMATHLIB_STANDALONE -std=gnu99 -IRmath -DNDEBUG -c dgeom.c -o dgeom.o gcc -Wall -O3 -fPIC -DMATHLIB_STANDALONE -std=gnu99 -IRmath -DNDEBUG -c ftrunc.c -o ftrunc.o gcc -Wall -O3 -fPIC -DMATHLIB_STANDALONE -std=gnu99 -IRmath -DNDEBUG -c phyper.c -o phyper.o gcc -Wall -O3 -fPIC -DMATHLIB_STANDALONE -std=gnu99 -IRmath -DNDEBUG -c qf.c -o qf.o gcc -Wall -O3 -fPIC -DMATHLIB_STANDALONE -std=gnu99 -IRmath -DNDEBUG -c rchisq.c -o rchisq.o gcc -Wall -O3 -fPIC -DMATHLIB_STANDALONE -std=gnu99 -IRmath -DNDEBUG -c stirlerr.c -o stirlerr.o gcc -Wall -O3 -fPIC -DMATHLIB_STANDALONE -std=gnu99 -IRmath -DNDEBUG -c dhyper.c -o dhyper.o gcc -Wall -O3 -fPIC -DMATHLIB_STANDALONE -std=gnu99 -IRmath -DNDEBUG -c gamma.c -o gamma.o gcc -Wall -O3 -fPIC -DMATHLIB_STANDALONE -std=gnu99 -IRmath -DNDEBUG -c plnorm.c -o plnorm.o gcc -Wall -O3 -fPIC -DMATHLIB_STANDALONE -std=gnu99 -IRmath -DNDEBUG -c qgamma.c -o qgamma.o gcc -Wall -O3 -fPIC -DMATHLIB_STANDALONE -std=gnu99 -IRmath -DNDEBUG -c rexp.c -o rexp.o gcc -Wall -O3 -fPIC -DMATHLIB_STANDALONE -std=gnu99 -IRmath -DNDEBUG -c toms708.c -o toms708.o gcc -Wall -O3 -fPIC -DMATHLIB_STANDALONE -std=gnu99 -IRmath -DNDEBUG -c dlnorm.c -o dlnorm.o gcc -Wall -O3 -fPIC -DMATHLIB_STANDALONE -std=gnu99 -IRmath -DNDEBUG -c gamma_cody.c -o gamma_cody.o gcc -Wall -O3 -fPIC -DMATHLIB_STANDALONE -std=gnu99 -IRmath -DNDEBUG -c plogis.c -o plogis.o gcc -Wall -O3 -fPIC -DMATHLIB_STANDALONE -std=gnu99 -IRmath -DNDEBUG -c qgeom.c -o qgeom.o gcc -Wall -O3 -fPIC -DMATHLIB_STANDALONE -std=gnu99 -IRmath -DNDEBUG -c rf.c -o rf.o gcc -Wall -O3 -fPIC -DMATHLIB_STANDALONE -std=gnu99 -IRmath -DNDEBUG -c wilcox.c -o wilcox.o gcc -Wall -O3 -fPIC -DMATHLIB_STANDALONE -std=gnu99 -IRmath -DNDEBUG -c dlogis.c -o dlogis.o gcc -Wall -O3 -fPIC -DMATHLIB_STANDALONE -std=gnu99 -IRmath -DNDEBUG -c gammalims.c -o gammalims.o gcc -Wall -O3 -fPIC -DMATHLIB_STANDALONE -std=gnu99 -IRmath -DNDEBUG -c pnbeta.c -o pnbeta.o gcc -Wall -O3 -fPIC -DMATHLIB_STANDALONE -std=gnu99 -IRmath -DNDEBUG -c qhyper.c -o qhyper.o gcc -Wall -O3 -fPIC -DMATHLIB_STANDALONE -std=gnu99 -IRmath -DNDEBUG -c rgamma.c -o rgamma.o gcc -Wall -O3 -fPIC -DMATHLIB_STANDALONE -std=gnu99 -IRmath -DNDEBUG -c sunif.c -o sunif.o gcc -Wall -O3 -fPIC -DMATHLIB_STANDALONE -std=gnu99 -IRmath -DNDEBUG -c sexp.c -o sexp.o gcc -Wall -O3 -fPIC -DMATHLIB_STANDALONE -std=gnu99 -IRmath -DNDEBUG -c snorm.c -o snorm.o rm -rf libRmath.a ar -rc libRmath.a bd0.o dnbeta.o i1mach.o pnbinom.o qlnorm.o rgeom.o bessel_i.o dnbinom.o imax2.o pnchisq.o qlogis.o rhyper.o bessel_j.o dnchisq.o imin2.o pnf.o qnbeta.o rlnorm.o bessel_k.o dnf.o lbeta.o pnorm.o qnbinom.o rlogis.o bessel_y.o dnorm.o lgamma.o pnt.o qnchisq.o rmultinom.o beta.o dnt.o lgammacor.o polygamma.o qnf.o rnbinom.o chebyshev.o dpois.o log1p.o ppois.o qnorm.o rnchisq.o choose.o dt.o mlutils.o pt.o qnt.o rnorm.o d1mach.o dunif.o pbeta.o ptukey.o qpois.o rpois.o dbeta.o dweibull.o pbinom.o punif.o qt.o rt.o dbinom.o expm1.o pcauchy.o pweibull.o qtukey.o runif.o dcauchy.o fmax2.o pchisq.o qbeta.o qunif.o rweibull.o dchisq.o fmin2.o pexp.o qbinom.o qweibull.o dexp.o fprec.o pf.o qcauchy.o rbeta.o sign.o df.o fround.o pgamma.o qchisq.o rbinom.o signrank.o dgamma.o fsign.o pgeom.o qexp.o rcauchy.o dgeom.o ftrunc.o phyper.o qf.o rchisq.o stirlerr.o dhyper.o gamma.o plnorm.o qgamma.o rexp.o toms708.o dlnorm.o gamma_cody.o plogis.o qgeom.o rf.o wilcox.o dlogis.o gammalims.o pnbeta.o qhyper.o rgamma.o sunif.o sexp.o snorm.o make[1]: Leaving directory/root/vt/lib/Rmath' cd lib/pcre2; make libpcre2.a || exit 1; make[1]: Entering directory /root/vt/lib/pcre2' gcc -g -O3 -DHAVE_CONFIG_H -DPCRE2_CODE_UNIT_WIDTH=8 -I. -o pcre2_auto_possess.o -c pcre2_auto_possess.c gcc -g -O3 -DHAVE_CONFIG_H -DPCRE2_CODE_UNIT_WIDTH=8 -I. -o pcre2_chartables.o -c pcre2_chartables.c gcc -g -O3 -DHAVE_CONFIG_H -DPCRE2_CODE_UNIT_WIDTH=8 -I. -o pcre2_compile.o -c pcre2_compile.c gcc -g -O3 -DHAVE_CONFIG_H -DPCRE2_CODE_UNIT_WIDTH=8 -I. -o pcre2_config.o -c pcre2_config.c gcc -g -O3 -DHAVE_CONFIG_H -DPCRE2_CODE_UNIT_WIDTH=8 -I. -o pcre2_context.o -c pcre2_context.c gcc -g -O3 -DHAVE_CONFIG_H -DPCRE2_CODE_UNIT_WIDTH=8 -I. -o pcre2_dfa_match.o -c pcre2_dfa_match.c gcc -g -O3 -DHAVE_CONFIG_H -DPCRE2_CODE_UNIT_WIDTH=8 -I. -o pcre2_error.o -c pcre2_error.c gcc -g -O3 -DHAVE_CONFIG_H -DPCRE2_CODE_UNIT_WIDTH=8 -I. -o pcre2_jit_compile.o -c pcre2_jit_compile.c gcc -g -O3 -DHAVE_CONFIG_H -DPCRE2_CODE_UNIT_WIDTH=8 -I. -o pcre2_maketables.o -c pcre2_maketables.c gcc -g -O3 -DHAVE_CONFIG_H -DPCRE2_CODE_UNIT_WIDTH=8 -I. -o pcre2_match.o -c pcre2_match.c gcc -g -O3 -DHAVE_CONFIG_H -DPCRE2_CODE_UNIT_WIDTH=8 -I. -o pcre2_match_data.o -c pcre2_match_data.c gcc -g -O3 -DHAVE_CONFIG_H -DPCRE2_CODE_UNIT_WIDTH=8 -I. -o pcre2_newline.o -c pcre2_newline.c gcc -g -O3 -DHAVE_CONFIG_H -DPCRE2_CODE_UNIT_WIDTH=8 -I. -o pcre2_ord2utf.o -c pcre2_ord2utf.c gcc -g -O3 -DHAVE_CONFIG_H -DPCRE2_CODE_UNIT_WIDTH=8 -I. -o pcre2_pattern_info.o -c pcre2_pattern_info.c gcc -g -O3 -DHAVE_CONFIG_H -DPCRE2_CODE_UNIT_WIDTH=8 -I. -o pcre2_string_utils.o -c pcre2_string_utils.c gcc -g -O3 -DHAVE_CONFIG_H -DPCRE2_CODE_UNIT_WIDTH=8 -I. -o pcre2_study.o -c pcre2_study.c gcc -g -O3 -DHAVE_CONFIG_H -DPCRE2_CODE_UNIT_WIDTH=8 -I. -o pcre2_substitute.o -c pcre2_substitute.c gcc -g -O3 -DHAVE_CONFIG_H -DPCRE2_CODE_UNIT_WIDTH=8 -I. -o pcre2_substring.o -c pcre2_substring.c gcc -g -O3 -DHAVE_CONFIG_H -DPCRE2_CODE_UNIT_WIDTH=8 -I. -o pcre2_tables.o -c pcre2_tables.c gcc -g -O3 -DHAVE_CONFIG_H -DPCRE2_CODE_UNIT_WIDTH=8 -I. -o pcre2_ucd.o -c pcre2_ucd.c gcc -g -O3 -DHAVE_CONFIG_H -DPCRE2_CODE_UNIT_WIDTH=8 -I. -o pcre2_valid_utf.o -c pcre2_valid_utf.c gcc -g -O3 -DHAVE_CONFIG_H -DPCRE2_CODE_UNIT_WIDTH=8 -I. -o pcre2_xclass.o -c pcre2_xclass.c ar -rc libpcre2.a pcre2_auto_possess.o pcre2_chartables.o pcre2_compile.o pcre2_config.o pcre2_context.o pcre2_dfa_match.o pcre2_error.o pcre2_jit_compile.o pcre2_maketables.o pcre2_match.o pcre2_match_data.o pcre2_newline.o pcre2_ord2utf.o pcre2_pattern_info.o pcre2_string_utils.o pcre2_study.o pcre2_substitute.o pcre2_substring.o pcre2_tables.o pcre2_ucd.o pcre2_valid_utf.o pcre2_xclass.o ranlib libpcre2.a make[1]: Leaving directory/root/vt/lib/pcre2' cd lib/libsvm; make libsvm.a || exit 1; make[1]: Entering directory /root/vt/lib/libsvm' g++ -Wall -O3 -fPIC -c svm.cpp rm -rf libsvm.a ar -rc libsvm.a svm.o make[1]: Leaving directory/root/vt/lib/libsvm' g++ -pipe -std=c++0x -O3 -I./lib -I. -I./lib/htslib -I./lib/Rmath -I./lib/pcre2 -DSTDC_LIMIT_MACROS -o ahmm.o -c ahmm.cpp ahmm.cpp: In member function ‘void AHMM::collect_statistics(int32_t, int32_t, int32_t)’: ahmm.cpp:687: warning: overflow in implicit constant conversion ahmm.cpp:688: warning: overflow in implicit constant conversion ahmm.cpp:689: warning: overflow in implicit constant conversion ahmm.cpp:690: warning: overflow in implicit constant conversion ahmm.cpp: In member function ‘void AHMM::clear_statistics()’: ahmm.cpp:737: warning: overflow in implicit constant conversion ahmm.cpp:738: warning: overflow in implicit constant conversion ahmm.cpp:739: warning: overflow in implicit constant conversion ahmm.cpp:740: warning: overflow in implicit constant conversion ahmm.cpp:741: warning: overflow in implicit constant conversion ahmm.cpp:742: warning: overflow in implicit constant conversion ahmm.cpp:743: warning: overflow in implicit constant conversion ahmm.cpp:744: warning: overflow in implicit constant conversion ahmm.cpp:745: warning: overflow in implicit constant conversion ahmm.cpp:746: warning: overflow in implicit constant conversion ahmm.cpp:747: warning: overflow in implicit constant conversion ahmm.cpp:748: warning: overflow in implicit constant conversion ahmm.cpp:750: warning: overflow in implicit constant conversion ahmm.cpp:751: warning: overflow in implicit constant conversion ahmm.cpp:752: warning: overflow in implicit constant conversion ahmm.cpp:753: warning: overflow in implicit constant conversion g++ -pipe -std=c++0x -O3 -I./lib -I. -I./lib/htslib -I./lib/Rmath -I./lib/pcre2 -DSTDC_LIMIT_MACROS -o align.o -c align.cpp g++ -pipe -std=c++0x -O3 -I./lib -I. -I./lib/htslib -I./lib/Rmath -I./lib/pcre2 -DSTDC_LIMIT_MACROS -o allele.o -c allele.cpp g++ -pipe -std=c++0x -O3 -I./lib -I. -I./lib/htslib -I./lib/Rmath -I./lib/pcre2 -DSTDC_LIMIT_MACROS -o annotate_1000g.o -c annotate_1000g.cpp g++ -pipe -std=c++0x -O3 -I./lib -I. -I./lib/htslib -I./lib/Rmath -I./lib/pcre2 -DSTDC_LIMIT_MACROS -o annotate_dbsnp_rsid.o -c annotate_dbsnp_rsid.cpp g++ -pipe -std=c++0x -O3 -I./lib -I. -I./lib/htslib -I./lib/Rmath -I./lib/pcre2 -DSTDC_LIMIT_MACROS -o annotate_indels.o -c annotate_indels.cpp g++ -pipe -std=c++0x -O3 -I./lib -I. -I./lib/htslib -I./lib/Rmath -I./lib/pcre2 -DSTDC_LIMIT_MACROS -o annotate_mendelian.o -c annotate_mendelian.cpp g++ -pipe -std=c++0x -O3 -I./lib -I. -I./lib/htslib -I./lib/Rmath -I./lib/pcre2 -DSTDC_LIMIT_MACROS -o annotate_regions.o -c annotate_regions.cpp g++ -pipe -std=c++0x -O3 -I./lib -I. -I./lib/htslib -I./lib/Rmath -I./lib/pcre2 -DSTDC_LIMIT_MACROS -o annotate_variants.o -c annotate_variants.cpp g++ -pipe -std=c++0x -O3 -I./lib -I. -I./lib/htslib -I./lib/Rmath -I./lib/pcre2 -DSTDC_LIMIT_MACROS -o annotate_vntrs.o -c annotate_vntrs.cpp g++ -pipe -std=c++0x -O3 -I./lib -I. -I./lib/htslib -I./lib/Rmath -I./lib/pcre2 -DSTDC_LIMIT_MACROS -o augmented_bam_record.o -c augmented_bam_record.cpp g++ -pipe -std=c++0x -O3 -I./lib -I. -I./lib/htslib -I./lib/Rmath -I./lib/pcre2 -DSTDC_LIMIT_MACROS -o bcf_genotyping_buffered_reader.o -c bcf_genotyping_buffered_reader.cpp g++ -pipe -std=c++0x -O3 -I./lib -I. -I./lib/htslib -I./lib/Rmath -I./lib/pcre2 -DSTDC_LIMIT_MACROS -o bcf_single_genotyping_buffered_reader.o -c bcf_single_genotyping_buffered_reader.cpp g++ -pipe -std=c++0x -O3 -I./lib -I. -I./lib/htslib -I./lib/Rmath -I./lib/pcre2 -DSTDC_LIMIT_MACROS -o bam_ordered_reader.o -c bam_ordered_reader.cpp g++ -pipe -std=c++0x -O3 -I./lib -I. -I./lib/htslib -I./lib/Rmath -I./lib/pcre2 -DSTDC_LIMIT_MACROS -o bcf_ordered_reader.o -c bcf_ordered_reader.cpp g++ -pipe -std=c++0x -O3 -I./lib -I. -I./lib/htslib -I./lib/Rmath -I./lib/pcre2 -DSTDC_LIMIT_MACROS -o bcf_ordered_writer.o -c bcf_ordered_writer.cpp g++ -pipe -std=c++0x -O3 -I./lib -I. -I./lib/htslib -I./lib/Rmath -I./lib/pcre2 -DSTDC_LIMIT_MACROS -o bcf_synced_reader.o -c bcf_synced_reader.cpp g++ -pipe -std=c++0x -O3 -I./lib -I. -I./lib/htslib -I./lib/Rmath -I./lib/pcre2 -DSTDC_LIMIT_MACROS -o bed.o -c bed.cpp g++ -pipe -std=c++0x -O3 -I./lib -I. -I./lib/htslib -I./lib/Rmath -I./lib/pcre2 -DSTDC_LIMIT_MACROS -o candidate_motif_picker.o -c candidate_motif_picker.cpp g++ -pipe -std=c++0x -O3 -I./lib -I. -I./lib/htslib -I./lib/Rmath -I./lib/pcre2 -DSTDC_LIMIT_MACROS -o candidate_region_extractor.o -c candidate_region_extractor.cpp g++ -pipe -std=c++0x -O3 -I./lib -I. -I./lib/htslib -I./lib/Rmath -I./lib/pcre2 -DSTDC_LIMIT_MACROS -o cat.o -c cat.cpp g++ -pipe -std=c++0x -O3 -I./lib -I. -I./lib/htslib -I./lib/Rmath -I./lib/pcre2 -D__STDC_LIMIT_MACROS -o chmm.o -c chmm.cpp chmm.cpp: In member function ‘void CHMM::clear_statistics()’: chmm.cpp:1106: warning: overflow in implicit constant conversion chmm.cpp:1107: warning: overflow in implicit constant conversion chmm.cpp:1108: warning: overflow in implicit constant conversion chmm.cpp:1109: warning: overflow in implicit constant conversion chmm.cpp:1110: warning: overflow in implicit constant conversion chmm.cpp:1111: warning: overflow in implicit constant conversion chmm.cpp:1112: warning: overflow in implicit constant conversion chmm.cpp:1113: warning: overflow in implicit constant conversion chmm.cpp:1114: warning: overflow in implicit constant conversion chmm.cpp:1115: warning: overflow in implicit constant conversion chmm.cpp:1116: warning: overflow in implicit constant conversion chmm.cpp:1117: warning: overflow in implicit constant conversion chmm.cpp:1118: warning: overflow in implicit constant conversion chmm.cpp:1119: warning: overflow in implicit constant conversion chmm.cpp:1120: warning: overflow in implicit constant conversion chmm.cpp:1121: warning: overflow in implicit constant conversion g++ -pipe -std=c++0x -O3 -I./lib -I. -I./lib/htslib -I./lib/Rmath -I./lib/pcre2 -DSTDC_LIMIT_MACROS -o complex_genotyping_record.o -c complex_genotyping_record.cpp g++ -pipe -std=c++0x -O3 -I./lib -I. -I./lib/htslib -I./lib/Rmath -I./lib/pcre2 -DSTDC_LIMIT_MACROS -o compute_concordance.o -c compute_concordance.cpp g++ -pipe -std=c++0x -O3 -I./lib -I. -I./lib/htslib -I./lib/Rmath -I./lib/pcre2 -DSTDC_LIMIT_MACROS -o compute_features.o -c compute_features.cpp g++ -pipe -std=c++0x -O3 -I./lib -I. -I./lib/htslib -I./lib/Rmath -I./lib/pcre2 -DSTDC_LIMIT_MACROS -o compute_features2.o -c compute_features2.cpp g++ -pipe -std=c++0x -O3 -I./lib -I. -I./lib/htslib -I./lib/Rmath -I./lib/pcre2 -DSTDC_LIMIT_MACROS -o compute_rl_dist.o -c compute_rl_dist.cpp g++ -pipe -std=c++0x -O3 -I./lib -I. -I./lib/htslib -I./lib/Rmath -I./lib/pcre2 -DSTDC_LIMIT_MACROS -o config.o -c config.cpp g++ -pipe -std=c++0x -O3 -I./lib -I. -I./lib/htslib -I./lib/Rmath -I./lib/pcre2 -DSTDC_LIMIT_MACROS -o consolidate_multiallelics.o -c consolidate_multiallelics.cpp g++ -pipe -std=c++0x -O3 -I./lib -I. -I./lib/htslib -I./lib/Rmath -I./lib/pcre2 -DSTDC_LIMIT_MACROS -o consolidate_vntrs.o -c consolidate_vntrs.cpp g++ -pipe -std=c++0x -O3 -I./lib -I. -I./lib/htslib -I./lib/Rmath -I./lib/pcre2 -DSTDC_LIMIT_MACROS -o consolidate.o -c consolidate.cpp g++ -pipe -std=c++0x -O3 -I./lib -I. -I./lib/htslib -I./lib/Rmath -I./lib/pcre2 -DSTDC_LIMIT_MACROS -o construct_probes.o -c construct_probes.cpp g++ -pipe -std=c++0x -O3 -I./lib -I. -I./lib/htslib -I./lib/Rmath -I./lib/pcre2 -DSTDC_LIMIT_MACROS -o decompose.o -c decompose.cpp g++ -pipe -std=c++0x -O3 -I./lib -I. -I./lib/htslib -I./lib/Rmath -I./lib/pcre2 -DSTDC_LIMIT_MACROS -o decompose2.o -c decompose2.cpp g++ -pipe -std=c++0x -O3 -I./lib -I. -I./lib/htslib -I./lib/Rmath -I./lib/pcre2 -DSTDC_LIMIT_MACROS -o decompose_blocksub.o -c decompose_blocksub.cpp g++ -pipe -std=c++0x -O3 -I./lib -I. -I./lib/htslib -I./lib/Rmath -I./lib/pcre2 -DSTDC_LIMIT_MACROS -o discover.o -c discover.cpp g++ -pipe -std=c++0x -O3 -I./lib -I. -I./lib/htslib -I./lib/Rmath -I./lib/pcre2 -DSTDC_LIMIT_MACROS -o estimate.o -c estimate.cpp g++ -pipe -std=c++0x -O3 -I./lib -I. -I./lib/htslib -I./lib/Rmath -I./lib/pcre2 -DSTDC_LIMIT_MACROS -o estimator.o -c estimator.cpp g++ -pipe -std=c++0x -O3 -I./lib -I. -I./lib/htslib -I./lib/Rmath -I./lib/pcre2 -DSTDC_LIMIT_MACROS -o extract_vntrs.o -c extract_vntrs.cpp g++ -pipe -std=c++0x -O3 -I./lib -I. -I./lib/htslib -I./lib/Rmath -I./lib/pcre2 -DSTDC_LIMIT_MACROS -o filter.o -c filter.cpp g++ -pipe -std=c++0x -O3 -I./lib -I. -I./lib/htslib -I./lib/Rmath -I./lib/pcre2 -DSTDC_LIMIT_MACROS -o filter_overlap.o -c filter_overlap.cpp g++ -pipe -std=c++0x -O3 -I./lib -I. -I./lib/htslib -I./lib/Rmath -I./lib/pcre2 -DSTDC_LIMIT_MACROS -o flank_detector.o -c flank_detector.cpp g++ -pipe -std=c++0x -O3 -I./lib -I. -I./lib/htslib -I./lib/Rmath -I./lib/pcre2 -DSTDC_LIMIT_MACROS -o fuzzy_aligner.o -c fuzzy_aligner.cpp g++ -pipe -std=c++0x -O3 -I./lib -I. -I./lib/htslib -I./lib/Rmath -I./lib/pcre2 -DSTDC_LIMIT_MACROS -o fuzzy_partition.o -c fuzzy_partition.cpp g++ -pipe -std=c++0x -O3 -I./lib -I. -I./lib/htslib -I./lib/Rmath -I./lib/pcre2 -DSTDC_LIMIT_MACROS -o gencode.o -c gencode.cpp g++ -pipe -std=c++0x -O3 -I./lib -I. -I./lib/htslib -I./lib/Rmath -I./lib/pcre2 -DSTDC_LIMIT_MACROS -o genome_interval.o -c genome_interval.cpp g++ -pipe -std=c++0x -O3 -I./lib -I. -I./lib/htslib -I./lib/Rmath -I./lib/pcre2 -DSTDC_LIMIT_MACROS -o genotype.o -c genotype.cpp g++ -pipe -std=c++0x -O3 -I./lib -I. -I./lib/htslib -I./lib/Rmath -I./lib/pcre2 -DSTDC_LIMIT_MACROS -o genotyping_record.o -c genotyping_record.cpp g++ -pipe -std=c++0x -O3 -I./lib -I. -I./lib/htslib -I./lib/Rmath -I./lib/pcre2 -DSTDC_LIMIT_MACROS -o ghmm.o -c ghmm.cpp g++ -pipe -std=c++0x -O3 -I./lib -I. -I./lib/htslib -I./lib/Rmath -I./lib/pcre2 -DSTDC_LIMIT_MACROS -o hts_utils.o -c hts_utils.cpp g++ -pipe -std=c++0x -O3 -I./lib -I. -I./lib/htslib -I./lib/Rmath -I./lib/pcre2 -DSTDC_LIMIT_MACROS -o hfilter.o -c hfilter.cpp g++ -pipe -std=c++0x -O3 -I./lib -I. -I./lib/htslib -I./lib/Rmath -I./lib/pcre2 -DSTDC_LIMIT_MACROS -o indel_genotyping_record.o -c indel_genotyping_record.cpp g++ -pipe -std=c++0x -O3 -I./lib -I. -I./lib/htslib -I./lib/Rmath -I./lib/pcre2 -DSTDC_LIMIT_MACROS -o index.o -c index.cpp g++ -pipe -std=c++0x -O3 -I./lib -I. -I./lib/htslib -I./lib/Rmath -I./lib/pcre2 -DSTDC_LIMIT_MACROS -o info2tab.o -c info2tab.cpp g++ -pipe -std=c++0x -O3 -I./lib -I. -I./lib/htslib -I./lib/Rmath -I./lib/pcre2 -DSTDC_LIMIT_MACROS -o interval_tree.o -c interval_tree.cpp g++ -pipe -std=c++0x -O3 -I./lib -I. -I./lib/htslib -I./lib/Rmath -I./lib/pcre2 -DSTDC_LIMIT_MACROS -o interval.o -c interval.cpp g++ -pipe -std=c++0x -O3 -I./lib -I. -I./lib/htslib -I./lib/Rmath -I./lib/pcre2 -DSTDC_LIMIT_MACROS -o lfhmm.o -c lfhmm.cpp lfhmm.cpp: In member function ‘void LFHMM::collect_statistics(int32_t, int32_t, int32_t)’: lfhmm.cpp:761: warning: overflow in implicit constant conversion lfhmm.cpp: In member function ‘void LFHMM::clear_statistics()’: lfhmm.cpp:868: warning: overflow in implicit constant conversion lfhmm.cpp:869: warning: overflow in implicit constant conversion lfhmm.cpp:870: warning: overflow in implicit constant conversion lfhmm.cpp:871: warning: overflow in implicit constant conversion lfhmm.cpp:872: warning: overflow in implicit constant conversion lfhmm.cpp:873: warning: overflow in implicit constant conversion lfhmm.cpp:874: warning: overflow in implicit constant conversion lfhmm.cpp:875: warning: overflow in implicit constant conversion lfhmm.cpp:876: warning: overflow in implicit constant conversion lfhmm.cpp:877: warning: overflow in implicit constant conversion lfhmm.cpp:878: warning: overflow in implicit constant conversion lfhmm.cpp:879: warning: overflow in implicit constant conversion lfhmm.cpp:881: warning: overflow in implicit constant conversion lfhmm.cpp:882: warning: overflow in implicit constant conversion lfhmm.cpp:883: warning: overflow in implicit constant conversion lfhmm.cpp:884: warning: overflow in implicit constant conversion g++ -pipe -std=c++0x -O3 -I./lib -I. -I./lib/htslib -I./lib/Rmath -I./lib/pcre2 -DSTDC_LIMIT_MACROS -o lhmm.o -c lhmm.cpp g++ -pipe -std=c++0x -O3 -I./lib -I. -I./lib/htslib -I./lib/Rmath -I./lib/pcre2 -DSTDC_LIMIT_MACROS -o lhmm1.o -c lhmm1.cpp g++ -pipe -std=c++0x -O3 -I./lib -I. -I./lib/htslib -I./lib/Rmath -I./lib/pcre2 -DSTDC_LIMIT_MACROS -o log_tool.o -c log_tool.cpp g++ -pipe -std=c++0x -O3 -I./lib -I. -I./lib/htslib -I./lib/Rmath -I./lib/pcre2 -DSTDC_LIMIT_MACROS -o merge.o -c merge.cpp g++ -pipe -std=c++0x -O3 -I./lib -I. -I./lib/htslib -I./lib/Rmath -I./lib/pcre2 -DSTDC_LIMIT_MACROS -o merge_candidate_variants.o -c merge_candidate_variants.cpp g++ -pipe -std=c++0x -O3 -I./lib -I. -I./lib/htslib -I./lib/Rmath -I./lib/pcre2 -DSTDC_LIMIT_MACROS -o merge_genotypes.o -c merge_genotypes.cpp g++ -pipe -std=c++0x -O3 -I./lib -I. -I./lib/htslib -I./lib/Rmath -I./lib/pcre2 -DSTDC_LIMIT_MACROS -o milk_filter.o -c milk_filter.cpp g++ -pipe -std=c++0x -O3 -I./lib -I. -I./lib/htslib -I./lib/Rmath -I./lib/pcre2 -DSTDC_LIMIT_MACROS -o motif_tree.o -c motif_tree.cpp g++ -pipe -std=c++0x -O3 -I./lib -I. -I./lib/htslib -I./lib/Rmath -I./lib/pcre2 -DSTDC_LIMIT_MACROS -o motif_map.o -c motif_map.cpp g++ -pipe -std=c++0x -O3 -I./lib -I. -I./lib/htslib -I./lib/Rmath -I./lib/pcre2 -DSTDC_LIMIT_MACROS -o multi_partition.o -c multi_partition.cpp g++ -pipe -std=c++0x -O3 -I./lib -I. -I./lib/htslib -I./lib/Rmath -I./lib/pcre2 -DSTDC_LIMIT_MACROS -o multiallelics_consolidator.o -c multiallelics_consolidator.cpp g++ -pipe -std=c++0x -O3 -I./lib -I. -I./lib/htslib -I./lib/Rmath -I./lib/pcre2 -DSTDC_LIMIT_MACROS -o needle.o -c needle.cpp g++ -pipe -std=c++0x -O3 -I./lib -I. -I./lib/htslib -I./lib/Rmath -I./lib/pcre2 -DSTDC_LIMIT_MACROS -o normalize.o -c normalize.cpp g++ -pipe -std=c++0x -O3 -I./lib -I. -I./lib/htslib -I./lib/Rmath -I./lib/pcre2 -DSTDC_LIMIT_MACROS -o nuclear_pedigree.o -c nuclear_pedigree.cpp g++ -pipe -std=c++0x -O3 -I./lib -I. -I./lib/htslib -I./lib/Rmath -I./lib/pcre2 -DSTDC_LIMIT_MACROS -o ordered_bcf_overlap_matcher.o -c ordered_bcf_overlap_matcher.cpp g++ -pipe -std=c++0x -O3 -I./lib -I. -I./lib/htslib -I./lib/Rmath -I./lib/pcre2 -DSTDC_LIMIT_MACROS -o ordered_region_overlap_matcher.o -c ordered_region_overlap_matcher.cpp g++ -pipe -std=c++0x -O3 -I./lib -I. -I./lib/htslib -I./lib/Rmath -I./lib/pcre2 -DSTDC_LIMIT_MACROS -o partition.o -c partition.cpp g++ -pipe -std=c++0x -O3 -I./lib -I. -I./lib/htslib -I./lib/Rmath -I./lib/pcre2 -DSTDC_LIMIT_MACROS -o paste.o -c paste.cpp g++ -pipe -std=c++0x -O3 -I./lib -I. -I./lib/htslib -I./lib/Rmath -I./lib/pcre2 -DSTDC_LIMIT_MACROS -o paste_and_compute_features_sequential.o -c paste_and_compute_features_sequential.cpp g++ -pipe -std=c++0x -O3 -I./lib -I. -I./lib/htslib -I./lib/Rmath -I./lib/pcre2 -DSTDC_LIMIT_MACROS -o paste_genotypes.o -c paste_genotypes.cpp g++ -pipe -std=c++0x -O3 -I./lib -I. -I./lib/htslib -I./lib/Rmath -I./lib/pcre2 -DSTDC_LIMIT_MACROS -o pedigree.o -c pedigree.cpp g++ -pipe -std=c++0x -O3 -I./lib -I. -I./lib/htslib -I./lib/Rmath -I./lib/pcre2 -DSTDC_LIMIT_MACROS -o peek.o -c peek.cpp g++ -pipe -std=c++0x -O3 -I./lib -I. -I./lib/htslib -I./lib/Rmath -I./lib/pcre2 -DSTDC_LIMIT_MACROS -o pileup.o -c pileup.cpp g++ -pipe -std=c++0x -O3 -I./lib -I. -I./lib/htslib -I./lib/Rmath -I./lib/pcre2 -DSTDC_LIMIT_MACROS -o pregex.o -c pregex.cpp g++ -pipe -std=c++0x -O3 -I./lib -I. -I./lib/htslib -I./lib/Rmath -I./lib/pcre2 -DSTDC_LIMIT_MACROS -o profile_afs.o -c profile_afs.cpp g++ -pipe -std=c++0x -O3 -I./lib -I. -I./lib/htslib -I./lib/Rmath -I./lib/pcre2 -DSTDC_LIMIT_MACROS -o profile_chm1.o -c profile_chm1.cpp profile_chm1.cpp: In member function ‘void::Igor::print_stats()’: profile_chm1.cpp:626: warning: name lookup of ‘i’ changed profile_chm1.cpp:607: warning: matches this ‘i’ under ISO standard rules profile_chm1.cpp:612: warning: matches this ‘i’ under old rules g++ -pipe -std=c++0x -O3 -I./lib -I. -I./lib/htslib -I./lib/Rmath -I./lib/pcre2 -DSTDC_LIMIT_MACROS -o profile_chrom.o -c profile_chrom.cpp g++ -pipe -std=c++0x -O3 -I./lib -I. -I./lib/htslib -I./lib/Rmath -I./lib/pcre2 -DSTDC_LIMIT_MACROS -o profile_fic_hwe.o -c profile_fic_hwe.cpp g++ -pipe -std=c++0x -O3 -I./lib -I. -I./lib/htslib -I./lib/Rmath -I./lib/pcre2 -DSTDC_LIMIT_MACROS -o profile_hwe.o -c profile_hwe.cpp g++ -pipe -std=c++0x -O3 -I./lib -I. -I./lib/htslib -I./lib/Rmath -I./lib/pcre2 -DSTDC_LIMIT_MACROS -o profile_indels.o -c profile_indels.cpp g++ -pipe -std=c++0x -O3 -I./lib -I. -I./lib/htslib -I./lib/Rmath -I./lib/pcre2 -DSTDC_LIMIT_MACROS -o profile_len.o -c profile_len.cpp g++ -pipe -std=c++0x -O3 -I./lib -I. -I./lib/htslib -I./lib/Rmath -I./lib/pcre2 -DSTDC_LIMIT_MACROS -o profile_mendelian.o -c profile_mendelian.cpp g++ -pipe -std=c++0x -O3 -I./lib -I. -I./lib/htslib -I./lib/Rmath -I./lib/pcre2 -DSTDC_LIMIT_MACROS -o profile_na12878.o -c profile_na12878.cpp profile_na12878.cpp: In member function ‘void::Igor::print_stats()’: profile_na12878.cpp:925: warning: name lookup of ‘i’ changed profile_na12878.cpp:904: warning: matches this ‘i’ under ISO standard rules profile_na12878.cpp:911: warning: matches this ‘i’ under old rules g++ -pipe -std=c++0x -O3 -I./lib -I. -I./lib/htslib -I./lib/Rmath -I./lib/pcre2 -DSTDC_LIMIT_MACROS -o profile_snps.o -c profile_snps.cpp g++ -pipe -std=c++0x -O3 -I./lib -I. -I./lib/htslib -I./lib/Rmath -I./lib/pcre2 -DSTDC_LIMIT_MACROS -o profile_vntrs.o -c profile_vntrs.cpp g++ -pipe -std=c++0x -O3 -I./lib -I. -I./lib/htslib -I./lib/Rmath -I./lib/pcre2 -DSTDC_LIMIT_MACROS -o program.o -c program.cpp g++ -pipe -std=c++0x -O3 -I./lib -I. -I./lib/htslib -I./lib/Rmath -I./lib/pcre2 -DSTDC_LIMIT_MACROS -o read_filter.o -c read_filter.cpp g++ -pipe -std=c++0x -O3 -I./lib -I. -I./lib/htslib -I./lib/Rmath -I./lib/pcre2 -DSTDC_LIMIT_MACROS -o reference_sequence.o -c reference_sequence.cpp g++ -pipe -std=c++0x -O3 -I./lib -I. -I./lib/htslib -I./lib/Rmath -I./lib/pcre2 -DSTDC_LIMIT_MACROS -o rfhmm.o -c rfhmm.cpp rfhmm.cpp: In member function ‘void RFHMM::clear_statistics()’: rfhmm.cpp:833: warning: overflow in implicit constant conversion rfhmm.cpp:834: warning: overflow in implicit constant conversion rfhmm.cpp:835: warning: overflow in implicit constant conversion rfhmm.cpp:836: warning: overflow in implicit constant conversion rfhmm.cpp:837: warning: overflow in implicit constant conversion rfhmm.cpp:838: warning: overflow in implicit constant conversion rfhmm.cpp:839: warning: overflow in implicit constant conversion rfhmm.cpp:840: warning: overflow in implicit constant conversion rfhmm.cpp:841: warning: overflow in implicit constant conversion rfhmm.cpp:842: warning: overflow in implicit constant conversion rfhmm.cpp:843: warning: overflow in implicit constant conversion rfhmm.cpp:844: warning: overflow in implicit constant conversion rfhmm.cpp:845: warning: overflow in implicit constant conversion rfhmm.cpp:846: warning: overflow in implicit constant conversion rfhmm.cpp:847: warning: overflow in implicit constant conversion rfhmm.cpp:848: warning: overflow in implicit constant conversion g++ -pipe -std=c++0x -O3 -I./lib -I. -I./lib/htslib -I./lib/Rmath -I./lib/pcre2 -DSTDC_LIMIT_MACROS -o rfhmm_x.o -c rfhmm_x.cpp rfhmm_x.cpp: In member function ‘void RFHMM_X::clear_statistics()’: rfhmm_x.cpp:928: warning: overflow in implicit constant conversion rfhmm_x.cpp:929: warning: overflow in implicit constant conversion rfhmm_x.cpp:930: warning: overflow in implicit constant conversion rfhmm_x.cpp:931: warning: overflow in implicit constant conversion rfhmm_x.cpp:932: warning: overflow in implicit constant conversion rfhmm_x.cpp:933: warning: overflow in implicit constant conversion rfhmm_x.cpp:934: warning: overflow in implicit constant conversion rfhmm_x.cpp:935: warning: overflow in implicit constant conversion rfhmm_x.cpp:936: warning: overflow in implicit constant conversion rfhmm_x.cpp:937: warning: overflow in implicit constant conversion rfhmm_x.cpp:938: warning: overflow in implicit constant conversion rfhmm_x.cpp:939: warning: overflow in implicit constant conversion rfhmm_x.cpp:940: warning: overflow in implicit constant conversion rfhmm_x.cpp:941: warning: overflow in implicit constant conversion rfhmm_x.cpp:942: warning: overflow in implicit constant conversion rfhmm_x.cpp:943: warning: overflow in implicit constant conversion g++ -pipe -std=c++0x -O3 -I./lib -I. -I./lib/htslib -I./lib/Rmath -I./lib/pcre2 -DSTDC_LIMIT_MACROS -o rminfo.o -c rminfo.cpp g++ -pipe -std=c++0x -O3 -I./lib -I. -I./lib/htslib -I./lib/Rmath -I./lib/pcre2 -DSTDC_LIMIT_MACROS -o seq.o -c seq.cpp g++ -pipe -std=c++0x -O3 -I./lib -I. -I./lib/htslib -I./lib/Rmath -I./lib/pcre2 -DSTDC_LIMIT_MACROS -o set_ref.o -c set_ref.cpp g++ -pipe -std=c++0x -O3 -I./lib -I. -I./lib/htslib -I./lib/Rmath -I./lib/pcre2 -DSTDC_LIMIT_MACROS -o snp_genotyping_record.o -c snp_genotyping_record.cpp g++ -pipe -std=c++0x -O3 -I./lib -I. -I./lib/htslib -I./lib/Rmath -I./lib/pcre2 -DSTDC_LIMIT_MACROS -o sort.o -c sort.cpp g++ -pipe -std=c++0x -O3 -I./lib -I. -I./lib/htslib -I./lib/Rmath -I./lib/pcre2 -DSTDC_LIMIT_MACROS -o subset.o -c subset.cpp g++ -pipe -std=c++0x -O3 -I./lib -I. -I./lib/htslib -I./lib/Rmath -I./lib/pcre2 -DSTDC_LIMIT_MACROS -o sv_tree.o -c sv_tree.cpp g++ -pipe -std=c++0x -O3 -I./lib -I. -I./lib/htslib -I./lib/Rmath -I./lib/pcre2 -DSTDC_LIMIT_MACROS -o svm_train.o -c svm_train.cpp svm_train.cpp: In member function ‘void::Igor::inverse_normalize(std::vector<float, std::allocator >&, std::vector<float, std::allocator >&)’: svm_train.cpp:165: error: no matching function for call to ‘sort(gnu_cxx::__normal_iterator<float*, std::vector<float, std::allocator<float*> > >, gnu_cxx::__normal_iterator<float*, std::vector<float, std::allocator<float*> > >, ::Igor::inverse_normalize(std::vector<float, std::allocator >&, std::vector<float, std::allocator >&)::&)’ make: *** [svm_train.o] Error 1

Please let me know if there are any dependencies not included with your git repo that we may require prior to compilation.

atks / vt

Error During Compilation #65