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Hierarchical Alignment Format
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halPhyloP compilation issues #178

Open marta-fb opened 3 years ago

marta-fb commented 3 years ago

Hi,

I'm trying to install the support for phyloP. I followed the instructions but I get this error during compilation:

cd phyloP && make progs
make[1]: Entering directory '/shared/home/mf485/software/hal/phyloP'
h5c++  -MM -MT ../objs/phyloP/impl/halPhyloPMain.o -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -DENABLE_PHYLOP -I../../phast/include -I../../phast/src/lib/pcre -I/home/mf485/software/clapack/INCLUDE -I/home/mf485/software/clapack/F2CLIBS -I../api/inc -Iimpl -Iinc -I../liftover/inc -I../liftover/inc -c impl/halPhyloPMain.cpp >impl/halPhyloPMain.depend
In file included from impl/halPhyloPMain.cpp:9:0:
inc/halPhyloP.h:18:10: fatal error: fit_column.h: No such file or directory
 #include "fit_column.h"
          ^~~~~~~~~~~~~~
compilation terminated.
make[1]: *** [../rules.mk:18: ../objs/phyloP/impl/halPhyloPMain.o] Error 1
make[1]: Leaving directory '/shared/home/mf485/software/hal/phyloP'
make: *** [Makefile:17: phyloP.progs] Error 2

I re-downloaded hal and the rest of the tools compiled without any problems. Am I doing something wrong?

Thanks, Marta

diekhans commented 3 years ago

Hi Marta,

PHAST renamed the header files. Try grabbing an older version of phast.

Mark

Marta Farré notifications@github.com writes:

Hi,

I'm trying to install the support for phyloP. I followed the instructions but I get this error during compilation:

cd phyloP && make progs
make[1]: Entering directory '/shared/home/mf485/software/hal/phyloP'
h5c++  -MM -MT ../objs/phyloP/impl/halPhyloPMain.o -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -DENABLE_PHYLOP -I../../phast/include -I../../phast/src/lib/pcre -I/home/mf485/software/clapack/INCLUDE -I/home/mf485/software/clapack/F2CLIBS -I../api/inc -Iimpl -Iinc -I../liftover/inc -I../liftover/inc -c impl/halPhyloPMain.cpp >impl/halPhyloPMain.depend
In file included from impl/halPhyloPMain.cpp:9:0:
inc/halPhyloP.h:18:10: fatal error: fit_column.h: No such file or directory
 #include "fit_column.h"
          ^~~~~~~~~~~~~~
compilation terminated.
make[1]: *** [../rules.mk:18: ../objs/phyloP/impl/halPhyloPMain.o] Error 1
make[1]: Leaving directory '/shared/home/mf485/software/hal/phyloP'
make: *** [Makefile:17: phyloP.progs] Error 2

I re-downloaded hal and the rest of the tools compiled without any problems. Am I doing something wrong?

Thanks, Marta

-- You are receiving this because you are subscribed to this thread. Reply to this email directly or view it on GitHub: https://github.com/ComparativeGenomicsToolkit/hal/issues/178 Hi,

I'm trying to install the support for phyloP. I followed the instructions but I get this error during compilation:

cd phyloP && make progs make[1]: Entering directory '/shared/home/mf485/software/hal/phyloP' h5c++ -MM -MT ../objs/phyloP/impl/halPhyloPMain.o -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -DENABLE_PHYLOP -I../../phast/include -I../../phast/src/lib/pcre -I/home/mf485/software/clapack/INCLUDE -I/home/mf485/software/clapack/F2CLIBS -I../api/inc -Iimpl -Iinc -I../liftover/inc -I../liftover/inc -c impl/halPhyloPMain.cpp >impl/halPhyloPMain.depend In file included from impl/halPhyloPMain.cpp:9:0: inc/halPhyloP.h:18:10: fatal error: fit_column.h: No such file or directory

include "fit_column.h"

      ^~~~~~~~~~~~~~

compilation terminated. make[1]: [../rules.mk:18: ../objs/phyloP/impl/halPhyloPMain.o] Error 1 make[1]: Leaving directory '/shared/home/mf485/software/hal/phyloP' make: [Makefile:17: phyloP.progs] Error 2

I re-downloaded hal and the rest of the tools compiled without any problems. Am I doing something wrong?

Thanks, Marta

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub, or unsubscribe.*

marta-fb commented 3 years ago

Hi Mark,

Thanks. I just tried with phast-1.4 but now I get this error. Any ideas of what might be wrong?

cd phyloP && make progs make[1]: Entering directory '/shared/home/mf485/software/hal/phyloP' h5c++ -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -DENABLE_PHYLOP -I../../phast/include -I../../phast/src/lib/pcre -I../../clapack/INCLUDE -I../../clapack/F2CLIBS -I../api/inc -Iimpl -Iinc -I../liftover/inc -I../liftover/inc -I tests -o ../bin/halPhyloP ../objs/phyloP/impl/halPhyloPMain.o ../objs/phyloP/impl/halPhyloPBed.o ../objs/phyloP/impl/halPhyloP.o ../lib/libHalLiftover.a ../lib/libHal.a ../../sonLib/lib/sonLib.a ../../sonLib/lib/cuTest.a -L../../phast/lib -lphast -L../../clapack -L../../clapack/F2CLIBS -llapack -ltmg -lblaswr -lf2c /shared/home/mf485/anaconda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: ../../phast/lib/libphast.a(lists.o): relocation R_X86_64_32 against.rodata.str1.8' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: ../../phast/lib/libphast.a(numerical_opt.o): relocation R_X86_64_32 against .rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: ../../phast/lib/libphast.a(vector.o): relocation R_X86_64_32 against.rodata.str1.8' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: ../../phast/lib/libphast.a(stringsplus.o): relocation R_X86_64_32 against .rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: ../../phast/lib/libphast.a(hashtable.o): relocation R_X86_64_32 against symbolequal' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: ../../phast/lib/libphast.a(matrix.o): relocation R_X86_64_32 against .rodata.str1.8' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: ../../phast/lib/libphast.a(misc.o): relocation R_X86_64_32 against.rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: ../../phast/lib/libphast.a(sufficient_stats.o): relocation R_X86_64_32 against .rodata.str1.8' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: ../../phast/lib/libphast.a(maf.o): relocation R_X86_64_32 against.rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: ../../phast/lib/libphast.a(msa.o): relocation R_X86_64_32S against .rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: ../../phast/lib/libphast.a(category_map.o): relocation R_X86_64_32 against.rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: ../../phast/lib/libphast.a(gff.o): relocation R_X86_64_32 against .rodata.str1.8' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: ../../phast/lib/libphast.a(fit_column.o): relocation R_X86_64_32 against.rodata.str1.8' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: ../../phast/lib/libphast.a(trees.o): relocation R_X86_64_32 against .rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: ../../phast/lib/libphast.a(tree_model.o): relocation R_X86_64_32 against.rodata.str1.8' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: ../../phast/lib/libphast.a(pcre_exec.o): relocation R_X86_64_32S against .rodata' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: ../../phast/lib/libphast.a(pcre_compile.o): relocation R_X86_64_32S against.rodata' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: ../../phast/lib/libphast.a(complex_matrix.o): relocation R_X86_64_32 against .rodata.str1.8' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: ../../phast/lib/libphast.a(memory_handler.o): relocation R_X86_64_32 against.rodata.str1.8' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: ../../phast/lib/libphast.a(prob_vector.o): relocation R_X86_64_32 against .rodata.str1.8' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: ../../phast/lib/libphast.a(complex_vector.o): relocation R_X86_64_32 against.rodata.str1.8' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: ../../phast/lib/libphast.a(markov_matrix.o): relocation R_X86_64_32 against .rodata.str1.8' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: ../../phast/lib/libphast.a(local_alignment.o): relocation R_X86_64_32 against.rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: ../../phast/lib/libphast.a(bed.o): relocation R_X86_64_32 against .rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: ../../phast/lib/libphast.a(wig.o): relocation R_X86_64_32 against.rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: ../../phast/lib/libphast.a(genepred.o): relocation R_X86_64_32 against .rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: ../../phast/lib/libphast.a(dgamma.o): relocation R_X86_64_32 against.rodata.str1.8' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: ../../phast/lib/libphast.a(tree_likelihoods.o): relocation R_X86_64_32 against .rodata.str1.8' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: ../../phast/lib/libphast.a(subst_mods.o): relocation R_X86_64_32 against.rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: ../../phast/lib/libphast.a(eigen.o): relocation R_X86_64_32 against .rodata.str1.8' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: ../../phast/lib/liblapack.a(dgeev.o): relocation R_X86_64_32 against.rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: ../../phast/lib/liblapack.a(dgehrd.o): relocation R_X86_64_32 against .rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: ../../phast/lib/liblapack.a(dgesv.o): relocation R_X86_64_32 against.rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: ../../phast/lib/liblapack.a(dgetrf.o): relocation R_X86_64_32 against .rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: ../../phast/lib/liblapack.a(dgetri.o): relocation R_X86_64_32 against.rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: ../../phast/lib/liblapack.a(dgetrs.o): relocation R_X86_64_32 against .rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: ../../phast/lib/liblapack.a(dhseqr.o): relocation R_X86_64_32 against.rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: ../../phast/lib/liblapack.a(dlahqr.o): relocation R_X86_64_32 against .rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: ../../phast/lib/liblapack.a(dlahr2.o): relocation R_X86_64_32S against.data' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: ../../phast/lib/liblapack.a(dlange.o): relocation R_X86_64_32 against .rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: ../../phast/lib/liblapack.a(dlanv2.o): relocation R_X86_64_32 against.rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: ../../phast/lib/liblapack.a(dlaqr0.o): relocation R_X86_64_32 against .data' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: ../../phast/lib/liblapack.a(dlaqr3.o): relocation R_X86_64_32 against.rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: ../../phast/lib/liblapack.a(dlaqr4.o): relocation R_X86_64_32 against .data' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: ../../phast/lib/liblapack.a(dlaqr5.o): relocation R_X86_64_32 against.rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: ../../phast/lib/liblapack.a(dlarf.o): relocation R_X86_64_32 against .rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: ../../phast/lib/liblapack.a(dlarfb.o): relocation R_X86_64_32 against.rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: ../../phast/lib/liblapack.a(dlarfg.o): relocation R_X86_64_32 against .rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: ../../phast/lib/liblapack.a(dorghr.o): relocation R_X86_64_32 against.rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: ../../phast/lib/liblapack.a(dorgqr.o): relocation R_X86_64_32 against .rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: ../../phast/lib/liblapack.a(dormhr.o): relocation R_X86_64_32 against.rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: ../../phast/lib/liblapack.a(dormqr.o): relocation R_X86_64_32 against .rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: ../../phast/lib/liblapack.a(dtrevc.o): relocation R_X86_64_32 against.rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: ../../phast/lib/liblapack.a(dtrexc.o): relocation R_X86_64_32 against .rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: ../../phast/lib/liblapack.a(dtrtri.o): relocation R_X86_64_32 against.rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: ../../phast/lib/liblapack.a(dlacpy.o): relocation R_X86_64_32 against .rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: ../../phast/lib/liblapack.a(dlartg.o): relocation R_X86_64_32 against.rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: ../../phast/lib/liblapack.a(dlascl.o): relocation R_X86_64_32 against .rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: ../../phast/lib/liblapack.a(dlaset.o): relocation R_X86_64_32 against.rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: ../../phast/lib/liblapack.a(dlamch.o): relocation R_X86_64_32S against .bss' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: ../../phast/lib/liblapack.a(ilaenv.o): relocation R_X86_64_32S against.rodata' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: ../../phast/lib/liblapack.a(xerbla.o): relocation R_X86_64_32 against .rodata.str1.8' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: ../../phast/lib/liblapack.a(dgebak.o): relocation R_X86_64_32 against.rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: ../../phast/lib/liblapack.a(dgebal.o): relocation R_X86_64_32 against .rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: ../../phast/lib/liblapack.a(dgehd2.o): relocation R_X86_64_32 against.rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: ../../phast/lib/liblapack.a(dgetf2.o): relocation R_X86_64_32 against .rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: ../../phast/lib/liblapack.a(dlaexc.o): relocation R_X86_64_32 against.rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: ../../phast/lib/liblapack.a(dlaln2.o): relocation R_X86_64_32 against .rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: ../../phast/lib/liblapack.a(dlaqr2.o): relocation R_X86_64_32 against.rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: ../../phast/lib/liblapack.a(dlarft.o): relocation R_X86_64_32 against .rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: ../../phast/lib/liblapack.a(dlarfx.o): relocation R_X86_64_32 against.rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: ../../phast/lib/liblapack.a(dlasy2.o): relocation R_X86_64_32 against .rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: ../../phast/lib/liblapack.a(dorg2r.o): relocation R_X86_64_32 against.rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: ../../phast/lib/liblapack.a(dorm2r.o): relocation R_X86_64_32 against .rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: ../../phast/lib/liblapack.a(dtrti2.o): relocation R_X86_64_32 against.rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: ../../phast/lib/libblaswr.a(dgemv.o): relocation R_X86_64_32 against .rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: ../../phast/lib/libblaswr.a(dtrmv.o): relocation R_X86_64_32 against.rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: ../../phast/lib/libblaswr.a(dger.o): relocation R_X86_64_32 against .rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: ../../phast/lib/libblaswr.a(dgemm.o): relocation R_X86_64_32 against.rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: ../../phast/lib/libblaswr.a(dtrmm.o): relocation R_X86_64_32 against .rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: ../../phast/lib/libblaswr.a(dtrsm.o): relocation R_X86_64_32 against.rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: ../../clapack/F2CLIBS/libf2c.a(s_cat.o): relocation R_X86_64_32 against .rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: ../../clapack/F2CLIBS/libf2c.a(fmt.o): relocation R_X86_64_32S against.bss' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: ../../clapack/F2CLIBS/libf2c.a(sfe.o): relocation R_X86_64_32S against undefined symbol f__units' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: ../../clapack/F2CLIBS/libf2c.a(wsfe.o): relocation R_X86_64_32S against symbolx_putc' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: ../../clapack/F2CLIBS/libf2c.a(sig_die.o): relocation R_X86_64_32 against .rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: ../../clapack/F2CLIBS/libf2c.a(f77_aloc.o): relocation R_X86_64_32 against.rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: ../../clapack/F2CLIBS/libf2c.a(close.o): relocation R_X86_64_32S against undefined symbol f__units' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: ../../clapack/F2CLIBS/libf2c.a(endfile.o): relocation R_X86_64_32S against undefined symbolf__units' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: ../../clapack/F2CLIBS/libf2c.a(err.o): relocation R_X86_64_32 against .rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: ../../clapack/F2CLIBS/libf2c.a(open.o): relocation R_X86_64_32S against.bss' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: ../../clapack/F2CLIBS/libf2c.a(wrtfmt.o): relocation R_X86_64_32S against .rodata' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: ../../clapack/F2CLIBS/libf2c.a(fmtlib.o): relocation R_X86_64_32 against.bss' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: ../../clapack/F2CLIBS/libf2c.a(wref.o): relocation R_X86_64_32 against .rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: final link failed: nonrepresentable section on output collect2: error: ld returned 1 exit status make[1]: *** [../rules.mk:32: ../bin/halPhyloP] Error 1 make[1]: Leaving directory '/shared/home/mf485/software/hal/phyloP' make: *** [Makefile:17: phyloP.progs] Error 2

diekhans commented 3 years ago

The problem here is that HAL and sonLib are compiled with -fPIC and PHAST is not. This is defined in sonLib/include.mk. I have no idea why.

It is fine to link a program without -fPIC against module built with -fPIC, but not the other way around. So if you remove -fPIC from the sonLib/include.mk, it should link fine.

Marta Farré notifications@github.com writes:

Hi Mark,

Thanks. I just tried with phast-1.4 but now I get this error. Any ideas of what might be wrong?

cd phyloP && make progs make[1]: Entering directory '/shared/home/mf485/software/hal/phyloP' h5c++ -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -D_GLIBCXX_USE_CXX11_ABI=1 -std=c++11 -Wno-sign-compare -DENABLE_PHYLOP -I../../phast/include -I../../phast/src/lib/pcre -I../../clapack/INCLUDE -I../../clapack/F2CLIBS -I../api/inc -Iimpl -Iinc -I../liftover/inc -I../liftover/inc -I tests -o ../bin/halPhyloP ../objs/phyloP/impl/halPhyloPMain.o ../objs/phyloP/impl/halPhyloPBed.o ../objs/phyloP/impl/halPhyloP.o ../lib/libHalLiftover.a ../lib/libHal.a ../../sonLib/lib/sonLib.a ../../sonLib/lib/cuTest.a -L../../phast/lib -lphast -L../../clapack -L../../clapack/F2CLIBS -llapack -ltmg -lblaswr -lf2c /shared/home/mf485/anaconda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: ../../phast/lib/libphast.a(lists.o): relocation R_X86_64_32 against.rodata.str1.8' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: ../../phast/lib/libphast.a(numerical_opt.o): relocation R_X86_64_32 against .rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: ../../phast/lib/libphast.a(vector.o): relocation R_X86_64_32 against.rodata.str1.8' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: ../../phast/lib/libphast.a(stringsplus.o): relocation R_X86_64_32 against .rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: ../../phast/lib/libphast.a(hashtable.o): relocation R_X86_64_32 against symbolequal' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: ../../phast/lib/libphast.a(matrix.o): relocation R_X86_64_32 against .rodata.str1.8' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: ../../phast/lib/libphast.a(misc.o): relocation R_X86_64_32 against.rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: ../../phast/lib/libphast.a(sufficient_stats.o): relocation R_X86_64_32 against .rodata.str1.8' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: ../../phast/lib/libphast.a(maf.o): relocation R_X86_64_32 against.rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: ../../phast/lib/libphast.a(msa.o): relocation R_X86_64_32S against .rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: ../../phast/lib/libphast.a(category_map.o): relocation R_X86_64_32 against.rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: ../../phast/lib/libphast.a(gff.o): relocation R_X86_64_32 against .rodata.str1.8' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: ../../phast/lib/libphast.a(fit_column.o): relocation R_X86_64_32 against.rodata.str1.8' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: ../../phast/lib/libphast.a(trees.o): relocation R_X86_64_32 against .rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: ../../phast/lib/libphast.a(tree_model.o): relocation R_X86_64_32 against.rodata.str1.8' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: ../../phast/lib/libphast.a(pcre_exec.o): relocation R_X86_64_32S against .rodata' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: ../../phast/lib/libphast.a(pcre_compile.o): relocation R_X86_64_32S against.rodata' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: ../../phast/lib/libphast.a(complex_matrix.o): relocation R_X86_64_32 against .rodata.str1.8' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: ../../phast/lib/libphast.a(memory_handler.o): relocation R_X86_64_32 against.rodata.str1.8' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: ../../phast/lib/libphast.a(prob_vector.o): relocation R_X86_64_32 against .rodata.str1.8' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: ../../phast/lib/libphast.a(complex_vector.o): relocation R_X86_64_32 against.rodata.str1.8' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: ../../phast/lib/libphast.a(markov_matrix.o): relocation R_X86_64_32 against .rodata.str1.8' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: ../../phast/lib/libphast.a(local_alignment.o): relocation R_X86_64_32 against.rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: ../../phast/lib/libphast.a(bed.o): relocation R_X86_64_32 against .rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: ../../phast/lib/libphast.a(wig.o): relocation R_X86_64_32 against.rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: ../../phast/lib/libphast.a(genepred.o): relocation R_X86_64_32 against .rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: ../../phast/lib/libphast.a(dgamma.o): relocation R_X86_64_32 against.rodata.str1.8' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: ../../phast/lib/libphast.a(tree_likelihoods.o): relocation R_X86_64_32 against .rodata.str1.8' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: ../../phast/lib/libphast.a(subst_mods.o): relocation R_X86_64_32 against.rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: ../../phast/lib/libphast.a(eigen.o): relocation R_X86_64_32 against .rodata.str1.8' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: ../../phast/lib/liblapack.a(dgeev.o): relocation R_X86_64_32 against.rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: ../../phast/lib/liblapack.a(dgehrd.o): relocation R_X86_64_32 against .rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: ../../phast/lib/liblapack.a(dgesv.o): relocation R_X86_64_32 against.rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: ../../phast/lib/liblapack.a(dgetrf.o): relocation R_X86_64_32 against .rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: ../../phast/lib/liblapack.a(dgetri.o): relocation R_X86_64_32 against.rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: ../../phast/lib/liblapack.a(dgetrs.o): relocation R_X86_64_32 against .rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: ../../phast/lib/liblapack.a(dhseqr.o): relocation R_X86_64_32 against.rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: ../../phast/lib/liblapack.a(dlahqr.o): relocation R_X86_64_32 against .rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: ../../phast/lib/liblapack.a(dlahr2.o): relocation R_X86_64_32S against.data' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: ../../phast/lib/liblapack.a(dlange.o): relocation R_X86_64_32 against .rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: ../../phast/lib/liblapack.a(dlanv2.o): relocation R_X86_64_32 against.rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: ../../phast/lib/liblapack.a(dlaqr0.o): relocation R_X86_64_32 against .data' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: ../../phast/lib/liblapack.a(dlaqr3.o): relocation R_X86_64_32 against.rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: ../../phast/lib/liblapack.a(dlaqr4.o): relocation R_X86_64_32 against .data' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: ../../phast/lib/liblapack.a(dlaqr5.o): relocation R_X86_64_32 against.rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: ../../phast/lib/liblapack.a(dlarf.o): relocation R_X86_64_32 against .rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: ../../phast/lib/liblapack.a(dlarfb.o): relocation R_X86_64_32 against.rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: ../../phast/lib/liblapack.a(dlarfg.o): relocation R_X86_64_32 against .rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: ../../phast/lib/liblapack.a(dorghr.o): relocation R_X86_64_32 against.rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: ../../phast/lib/liblapack.a(dorgqr.o): relocation R_X86_64_32 against .rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: ../../phast/lib/liblapack.a(dormhr.o): relocation R_X86_64_32 against.rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: ../../phast/lib/liblapack.a(dormqr.o): relocation R_X86_64_32 against .rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: ../../phast/lib/liblapack.a(dtrevc.o): relocation R_X86_64_32 against.rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: ../../phast/lib/liblapack.a(dtrexc.o): relocation R_X86_64_32 against .rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: ../../phast/lib/liblapack.a(dtrtri.o): relocation R_X86_64_32 against.rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: ../../phast/lib/liblapack.a(dlacpy.o): relocation R_X86_64_32 against .rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: ../../phast/lib/liblapack.a(dlartg.o): relocation R_X86_64_32 against.rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: ../../phast/lib/liblapack.a(dlascl.o): relocation R_X86_64_32 against .rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: ../../phast/lib/liblapack.a(dlaset.o): relocation R_X86_64_32 against.rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: ../../phast/lib/liblapack.a(dlamch.o): relocation R_X86_64_32S against .bss' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: ../../phast/lib/liblapack.a(ilaenv.o): relocation R_X86_64_32S against.rodata' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: ../../phast/lib/liblapack.a(xerbla.o): relocation R_X86_64_32 against .rodata.str1.8' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: ../../phast/lib/liblapack.a(dgebak.o): relocation R_X86_64_32 against.rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: ../../phast/lib/liblapack.a(dgebal.o): relocation R_X86_64_32 against .rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: ../../phast/lib/liblapack.a(dgehd2.o): relocation R_X86_64_32 against.rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: ../../phast/lib/liblapack.a(dgetf2.o): relocation R_X86_64_32 against .rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: ../../phast/lib/liblapack.a(dlaexc.o): relocation R_X86_64_32 against.rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: ../../phast/lib/liblapack.a(dlaln2.o): relocation R_X86_64_32 against .rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: ../../phast/lib/liblapack.a(dlaqr2.o): relocation R_X86_64_32 against.rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: ../../phast/lib/liblapack.a(dlarft.o): relocation R_X86_64_32 against .rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: ../../phast/lib/liblapack.a(dlarfx.o): relocation R_X86_64_32 against.rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: ../../phast/lib/liblapack.a(dlasy2.o): relocation R_X86_64_32 against .rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: ../../phast/lib/liblapack.a(dorg2r.o): relocation R_X86_64_32 against.rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: ../../phast/lib/liblapack.a(dorm2r.o): relocation R_X86_64_32 against .rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: ../../phast/lib/liblapack.a(dtrti2.o): relocation R_X86_64_32 against.rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: ../../phast/lib/libblaswr.a(dgemv.o): relocation R_X86_64_32 against .rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: ../../phast/lib/libblaswr.a(dtrmv.o): relocation R_X86_64_32 against.rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: ../../phast/lib/libblaswr.a(dger.o): relocation R_X86_64_32 against .rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: ../../phast/lib/libblaswr.a(dgemm.o): relocation R_X86_64_32 against.rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: ../../phast/lib/libblaswr.a(dtrmm.o): relocation R_X86_64_32 against .rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: ../../phast/lib/libblaswr.a(dtrsm.o): relocation R_X86_64_32 against.rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: ../../clapack/F2CLIBS/libf2c.a(s_cat.o): relocation R_X86_64_32 against .rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: ../../clapack/F2CLIBS/libf2c.a(fmt.o): relocation R_X86_64_32S against.bss' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: ../../clapack/F2CLIBS/libf2c.a(sfe.o): relocation R_X86_64_32S against undefined symbol f__units' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: ../../clapack/F2CLIBS/libf2c.a(wsfe.o): relocation R_X86_64_32S against symbolx_putc' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: ../../clapack/F2CLIBS/libf2c.a(sig_die.o): relocation R_X86_64_32 against .rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: ../../clapack/F2CLIBS/libf2c.a(f77_aloc.o): relocation R_X86_64_32 against.rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: ../../clapack/F2CLIBS/libf2c.a(close.o): relocation R_X86_64_32S against undefined symbol f__units' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: ../../clapack/F2CLIBS/libf2c.a(endfile.o): relocation R_X86_64_32S against undefined symbolf__units' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: ../../clapack/F2CLIBS/libf2c.a(err.o): relocation R_X86_64_32 against .rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: ../../clapack/F2CLIBS/libf2c.a(open.o): relocation R_X86_64_32S against.bss' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: ../../clapack/F2CLIBS/libf2c.a(wrtfmt.o): relocation R_X86_64_32S against .rodata' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: ../../clapack/F2CLIBS/libf2c.a(fmtlib.o): relocation R_X86_64_32 against.bss' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: ../../clapack/F2CLIBS/libf2c.a(wref.o): relocation R_X86_64_32 against .rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ld: final link failed: nonrepresentable section on output collect2: error: ld returned 1 exit status make[1]: *** [../rules.mk:32: ../bin/halPhyloP] Error 1 make[1]: Leaving directory '/shared/home/mf485/software/hal/phyloP' make: *** [Makefile:17: phyloP.progs] Error 2

-- You are receiving this because you commented. Reply to this email directly or view it on GitHub: https://github.com/ComparativeGenomicsToolkit/hal/issues/178#issuecomment-742764434 Hi Mark,

Thanks. I just tried with phast-1.4 but now I get this error. Any ideas of what might be wrong?

cd phyloP && make progs make[1]: Entering directory '/shared/home/mf485/ software/hal/phyloP' h5c++ -fPIC -D_GLIBCXX_USE_CXX11_ABI=1 -O3 -g -Wall -funroll-loops -DNDEBUG -I../../sonLib/lib -D_GLIBCXX_USE_CXX11_ABI=1 -std= c++11 -Wno-sign-compare -DENABLE_PHYLOP -I../../phast/include -I../../phast/src /lib/pcre -I../../clapack/INCLUDE -I../../clapack/F2CLIBS -I../api/inc -Iimpl -Iinc -I../liftover/inc -I../liftover/inc -I tests -o ../bin/halPhyloP ../objs/ phyloP/impl/halPhyloPMain.o ../objs/phyloP/impl/halPhyloPBed.o ../objs/phyloP/ impl/halPhyloP.o ../lib/libHalLiftover.a ../lib/libHal.a ../../sonLib/lib/ sonLib.a ../../sonLib/lib/cuTest.a -L../../phast/lib -lphast -L../../clapack -L../../clapack/F2CLIBS -llapack -ltmg -lblaswr -lf2c /shared/home/mf485/ anaconda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../ x86_64-conda_cos6-linux-gnu/bin/ld: ../../phast/lib/libphast.a(lists.o): relocation R_X86_64_32 against .rodata.str1.8' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/.. /../../../x86_64-conda_cos6-linux-gnu/bin/ld: ../../phast/lib/libphast.a (numerical_opt.o): relocation R_X86_64_32 against .rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda /bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../ x86_64-conda_cos6-linux-gnu/bin/ld: ../../phast/lib/libphast.a(vector.o): relocation R_X86_64_32 against .rodata.str1.8' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/.. /../../../x86_64-conda_cos6-linux-gnu/bin/ld: ../../phast/lib/libphast.a (stringsplus.o): relocation R_X86_64_32 against .rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin /../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../ x86_64-conda_cos6-linux-gnu/bin/ld: ../../phast/lib/libphast.a(hashtable.o): relocation R_X86_64_32 against symbol equal' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/.. /../../../x86_64-conda_cos6-linux-gnu/bin/ld: ../../phast/lib/libphast.a (matrix.o): relocation R_X86_64_32 against .rodata.str1.8' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../ lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../ x86_64-conda_cos6-linux-gnu/bin/ld: ../../phast/lib/libphast.a(misc.o): relocation R_X86_64_32 against .rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/.. /../../../x86_64-conda_cos6-linux-gnu/bin/ld: ../../phast/lib/libphast.a (sufficient_stats.o): relocation R_X86_64_32 against .rodata.str1.8' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda /bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../ x86_64-conda_cos6-linux-gnu/bin/ld: ../../phast/lib/libphast.a(maf.o): relocation R_X86_64_32 against .rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/.. /../../../x86_64-conda_cos6-linux-gnu/bin/ld: ../../phast/lib/libphast.a (msa.o): relocation R_X86_64_32S against .rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../ lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../ x86_64-conda_cos6-linux-gnu/bin/ld: ../../phast/lib/libphast.a(category_map.o): relocation R_X86_64_32 against .rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/.. /../../../x86_64-conda_cos6-linux-gnu/bin/ld: ../../phast/lib/libphast.a (gff.o): relocation R_X86_64_32 against .rodata.str1.8' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../ lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../ x86_64-conda_cos6-linux-gnu/bin/ld: ../../phast/lib/libphast.a(fit_column.o): relocation R_X86_64_32 against .rodata.str1.8' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/.. /../../../x86_64-conda_cos6-linux-gnu/bin/ld: ../../phast/lib/libphast.a (trees.o): relocation R_X86_64_32 against .rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../ lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../ x86_64-conda_cos6-linux-gnu/bin/ld: ../../phast/lib/libphast.a(tree_model.o): relocation R_X86_64_32 against .rodata.str1.8' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/.. /../../../x86_64-conda_cos6-linux-gnu/bin/ld: ../../phast/lib/libphast.a (pcre_exec.o): relocation R_X86_64_32S against .rodata' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../ lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../ x86_64-conda_cos6-linux-gnu/bin/ld: ../../phast/lib/libphast.a(pcre_compile.o): relocation R_X86_64_32S against .rodata' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/.. /../../../x86_64-conda_cos6-linux-gnu/bin/ld: ../../phast/lib/libphast.a (complex_matrix.o): relocation R_X86_64_32 against .rodata.str1.8' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda /bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../ x86_64-conda_cos6-linux-gnu/bin/ld: ../../phast/lib/libphast.a (memory_handler.o): relocation R_X86_64_32 against .rodata.str1.8' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/.. /../../../x86_64-conda_cos6-linux-gnu/bin/ld: ../../phast/lib/libphast.a (prob_vector.o): relocation R_X86_64_32 against .rodata.str1.8' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin /../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../ x86_64-conda_cos6-linux-gnu/bin/ld: ../../phast/lib/libphast.a (complex_vector.o): relocation R_X86_64_32 against .rodata.str1.8' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/.. /../../../x86_64-conda_cos6-linux-gnu/bin/ld: ../../phast/lib/libphast.a (markov_matrix.o): relocation R_X86_64_32 against .rodata.str1.8' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda /bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../ x86_64-conda_cos6-linux-gnu/bin/ld: ../../phast/lib/libphast.a (local_alignment.o): relocation R_X86_64_32 against .rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/.. /../../../x86_64-conda_cos6-linux-gnu/bin/ld: ../../phast/lib/libphast.a (bed.o): relocation R_X86_64_32 against .rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../ lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../ x86_64-conda_cos6-linux-gnu/bin/ld: ../../phast/lib/libphast.a(wig.o): relocation R_X86_64_32 against .rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/.. /../../../x86_64-conda_cos6-linux-gnu/bin/ld: ../../phast/lib/libphast.a (genepred.o): relocation R_X86_64_32 against .rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin /../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../ x86_64-conda_cos6-linux-gnu/bin/ld: ../../phast/lib/libphast.a(dgamma.o): relocation R_X86_64_32 against .rodata.str1.8' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/.. /../../../x86_64-conda_cos6-linux-gnu/bin/ld: ../../phast/lib/libphast.a (tree_likelihoods.o): relocation R_X86_64_32 against .rodata.str1.8' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda /bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../ x86_64-conda_cos6-linux-gnu/bin/ld: ../../phast/lib/libphast.a(subst_mods.o): relocation R_X86_64_32 against .rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/.. /../../../x86_64-conda_cos6-linux-gnu/bin/ld: ../../phast/lib/libphast.a (eigen.o): relocation R_X86_64_32 against .rodata.str1.8' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../ lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../ x86_64-conda_cos6-linux-gnu/bin/ld: ../../phast/lib/liblapack.a(dgeev.o): relocation R_X86_64_32 against .rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/.. /../../../x86_64-conda_cos6-linux-gnu/bin/ld: ../../phast/lib/liblapack.a (dgehrd.o): relocation R_X86_64_32 against .rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../ lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../ x86_64-conda_cos6-linux-gnu/bin/ld: ../../phast/lib/liblapack.a(dgesv.o): relocation R_X86_64_32 against .rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/.. /../../../x86_64-conda_cos6-linux-gnu/bin/ld: ../../phast/lib/liblapack.a (dgetrf.o): relocation R_X86_64_32 against .rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../ lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../ x86_64-conda_cos6-linux-gnu/bin/ld: ../../phast/lib/liblapack.a(dgetri.o): relocation R_X86_64_32 against .rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/.. /../../../x86_64-conda_cos6-linux-gnu/bin/ld: ../../phast/lib/liblapack.a (dgetrs.o): relocation R_X86_64_32 against .rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../ lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../ x86_64-conda_cos6-linux-gnu/bin/ld: ../../phast/lib/liblapack.a(dhseqr.o): relocation R_X86_64_32 against .rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/.. /../../../x86_64-conda_cos6-linux-gnu/bin/ld: ../../phast/lib/liblapack.a (dlahqr.o): relocation R_X86_64_32 against .rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../ lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../ x86_64-conda_cos6-linux-gnu/bin/ld: ../../phast/lib/liblapack.a(dlahr2.o): relocation R_X86_64_32S against .data' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/.. /../../../x86_64-conda_cos6-linux-gnu/bin/ld: ../../phast/lib/liblapack.a (dlange.o): relocation R_X86_64_32 against .rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../ lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../ x86_64-conda_cos6-linux-gnu/bin/ld: ../../phast/lib/liblapack.a(dlanv2.o): relocation R_X86_64_32 against .rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/.. /../../../x86_64-conda_cos6-linux-gnu/bin/ld: ../../phast/lib/liblapack.a (dlaqr0.o): relocation R_X86_64_32 against .data' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../lib/gcc/ x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ ld: ../../phast/lib/liblapack.a(dlaqr3.o): relocation R_X86_64_32 against .rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/.. /../../../x86_64-conda_cos6-linux-gnu/bin/ld: ../../phast/lib/liblapack.a (dlaqr4.o): relocation R_X86_64_32 against .data' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../lib/gcc/ x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ ld: ../../phast/lib/liblapack.a(dlaqr5.o): relocation R_X86_64_32 against .rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/.. /../../../x86_64-conda_cos6-linux-gnu/bin/ld: ../../phast/lib/liblapack.a (dlarf.o): relocation R_X86_64_32 against .rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../ lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../ x86_64-conda_cos6-linux-gnu/bin/ld: ../../phast/lib/liblapack.a(dlarfb.o): relocation R_X86_64_32 against .rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/.. /../../../x86_64-conda_cos6-linux-gnu/bin/ld: ../../phast/lib/liblapack.a (dlarfg.o): relocation R_X86_64_32 against .rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../ lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../ x86_64-conda_cos6-linux-gnu/bin/ld: ../../phast/lib/liblapack.a(dorghr.o): relocation R_X86_64_32 against .rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/.. /../../../x86_64-conda_cos6-linux-gnu/bin/ld: ../../phast/lib/liblapack.a (dorgqr.o): relocation R_X86_64_32 against .rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../ lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../ x86_64-conda_cos6-linux-gnu/bin/ld: ../../phast/lib/liblapack.a(dormhr.o): relocation R_X86_64_32 against .rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/.. /../../../x86_64-conda_cos6-linux-gnu/bin/ld: ../../phast/lib/liblapack.a (dormqr.o): relocation R_X86_64_32 against .rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../ lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../ x86_64-conda_cos6-linux-gnu/bin/ld: ../../phast/lib/liblapack.a(dtrevc.o): relocation R_X86_64_32 against .rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/.. /../../../x86_64-conda_cos6-linux-gnu/bin/ld: ../../phast/lib/liblapack.a (dtrexc.o): relocation R_X86_64_32 against .rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../ lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../ x86_64-conda_cos6-linux-gnu/bin/ld: ../../phast/lib/liblapack.a(dtrtri.o): relocation R_X86_64_32 against .rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/.. /../../../x86_64-conda_cos6-linux-gnu/bin/ld: ../../phast/lib/liblapack.a (dlacpy.o): relocation R_X86_64_32 against .rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../ lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../ x86_64-conda_cos6-linux-gnu/bin/ld: ../../phast/lib/liblapack.a(dlartg.o): relocation R_X86_64_32 against .rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/.. /../../../x86_64-conda_cos6-linux-gnu/bin/ld: ../../phast/lib/liblapack.a (dlascl.o): relocation R_X86_64_32 against .rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../ lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../ x86_64-conda_cos6-linux-gnu/bin/ld: ../../phast/lib/liblapack.a(dlaset.o): relocation R_X86_64_32 against .rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/.. /../../../x86_64-conda_cos6-linux-gnu/bin/ld: ../../phast/lib/liblapack.a (dlamch.o): relocation R_X86_64_32S against .bss' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../lib/gcc/ x86_64-conda_cos6-linux-gnu/7.3.0/../../../../x86_64-conda_cos6-linux-gnu/bin/ ld: ../../phast/lib/liblapack.a(ilaenv.o): relocation R_X86_64_32S against .rodata' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/.. /../../../x86_64-conda_cos6-linux-gnu/bin/ld: ../../phast/lib/liblapack.a (xerbla.o): relocation R_X86_64_32 against .rodata.str1.8' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../ lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../ x86_64-conda_cos6-linux-gnu/bin/ld: ../../phast/lib/liblapack.a(dgebak.o): relocation R_X86_64_32 against .rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/.. /../../../x86_64-conda_cos6-linux-gnu/bin/ld: ../../phast/lib/liblapack.a (dgebal.o): relocation R_X86_64_32 against .rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../ lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../ x86_64-conda_cos6-linux-gnu/bin/ld: ../../phast/lib/liblapack.a(dgehd2.o): relocation R_X86_64_32 against .rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/.. /../../../x86_64-conda_cos6-linux-gnu/bin/ld: ../../phast/lib/liblapack.a (dgetf2.o): relocation R_X86_64_32 against .rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../ lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../ x86_64-conda_cos6-linux-gnu/bin/ld: ../../phast/lib/liblapack.a(dlaexc.o): relocation R_X86_64_32 against .rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/.. /../../../x86_64-conda_cos6-linux-gnu/bin/ld: ../../phast/lib/liblapack.a (dlaln2.o): relocation R_X86_64_32 against .rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../ lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../ x86_64-conda_cos6-linux-gnu/bin/ld: ../../phast/lib/liblapack.a(dlaqr2.o): relocation R_X86_64_32 against .rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/.. /../../../x86_64-conda_cos6-linux-gnu/bin/ld: ../../phast/lib/liblapack.a (dlarft.o): relocation R_X86_64_32 against .rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../ lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../ x86_64-conda_cos6-linux-gnu/bin/ld: ../../phast/lib/liblapack.a(dlarfx.o): relocation R_X86_64_32 against .rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/.. /../../../x86_64-conda_cos6-linux-gnu/bin/ld: ../../phast/lib/liblapack.a (dlasy2.o): relocation R_X86_64_32 against .rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../ lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../ x86_64-conda_cos6-linux-gnu/bin/ld: ../../phast/lib/liblapack.a(dorg2r.o): relocation R_X86_64_32 against .rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/.. /../../../x86_64-conda_cos6-linux-gnu/bin/ld: ../../phast/lib/liblapack.a (dorm2r.o): relocation R_X86_64_32 against .rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../ lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../ x86_64-conda_cos6-linux-gnu/bin/ld: ../../phast/lib/liblapack.a(dtrti2.o): relocation R_X86_64_32 against .rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/.. /../../../x86_64-conda_cos6-linux-gnu/bin/ld: ../../phast/lib/libblaswr.a (dgemv.o): relocation R_X86_64_32 against .rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../ lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../ x86_64-conda_cos6-linux-gnu/bin/ld: ../../phast/lib/libblaswr.a(dtrmv.o): relocation R_X86_64_32 against .rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/.. /../../../x86_64-conda_cos6-linux-gnu/bin/ld: ../../phast/lib/libblaswr.a (dger.o): relocation R_X86_64_32 against .rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../ lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../ x86_64-conda_cos6-linux-gnu/bin/ld: ../../phast/lib/libblaswr.a(dgemm.o): relocation R_X86_64_32 against .rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/.. /../../../x86_64-conda_cos6-linux-gnu/bin/ld: ../../phast/lib/libblaswr.a (dtrmm.o): relocation R_X86_64_32 against .rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../ lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../ x86_64-conda_cos6-linux-gnu/bin/ld: ../../phast/lib/libblaswr.a(dtrsm.o): relocation R_X86_64_32 against .rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/.. /../../../x86_64-conda_cos6-linux-gnu/bin/ld: ../../clapack/F2CLIBS/libf2c.a (s_cat.o): relocation R_X86_64_32 against .rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../ lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../ x86_64-conda_cos6-linux-gnu/bin/ld: ../../clapack/F2CLIBS/libf2c.a(fmt.o): relocation R_X86_64_32S against .bss' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/.. /../../../x86_64-conda_cos6-linux-gnu/bin/ld: ../../clapack/F2CLIBS/libf2c.a (sfe.o): relocation R_X86_64_32S against undefined symbol funits' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda /bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../ x86_64-conda_cos6-linux-gnu/bin/ld: ../../clapack/F2CLIBS/libf2c.a(wsfe.o): relocation R_X86_64_32S against symbol x_putc' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/.. /../../../x86_64-conda_cos6-linux-gnu/bin/ld: ../../clapack/F2CLIBS/libf2c.a (sig_die.o): relocation R_X86_64_32 against .rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin /../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../ x86_64-conda_cos6-linux-gnu/bin/ld: ../../clapack/F2CLIBS/libf2c.a(f77_aloc.o): relocation R_X86_64_32 against .rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/.. /../../../x86_64-conda_cos6-linux-gnu/bin/ld: ../../clapack/F2CLIBS/libf2c.a (close.o): relocation R_X86_64_32S against undefined symbol f__units' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/ anaconda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../ x86_64-conda_cos6-linux-gnu/bin/ld: ../../clapack/F2CLIBS/libf2c.a(endfile.o): relocation R_X86_64_32S against undefined symbol funits' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/.. /../../../x86_64-conda_cos6-linux-gnu/bin/ld: ../../clapack/F2CLIBS/libf2c.a (err.o): relocation R_X86_64_32 against .rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../ lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../ x86_64-conda_cos6-linux-gnu/bin/ld: ../../clapack/F2CLIBS/libf2c.a(open.o): relocation R_X86_64_32S against .bss' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/.. /../../../x86_64-conda_cos6-linux-gnu/bin/ld: ../../clapack/F2CLIBS/libf2c.a (wrtfmt.o): relocation R_X86_64_32S against .rodata' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../ lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../ x86_64-conda_cos6-linux-gnu/bin/ld: ../../clapack/F2CLIBS/libf2c.a(fmtlib.o): relocation R_X86_64_32 against .bss' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/.. /../../../x86_64-conda_cos6-linux-gnu/bin/ld: ../../clapack/F2CLIBS/libf2c.a (wref.o): relocation R_X86_64_32 against .rodata.str1.1' can not be used when making a PIE object; recompile with -fPIC /shared/home/mf485/anaconda/bin/../ lib/gcc/x86_64-conda_cos6-linux-gnu/7.3.0/../../../../ x86_64-conda_cos6-linux-gnu/bin/ld: final link failed: nonrepresentable section on output collect2: error: ld returned 1 exit status make[1]: [../ rules.mk:32: ../bin/halPhyloP] Error 1 make[1]: Leaving directory '/shared/home /mf485/software/hal/phyloP' make: [Makefile:17: phyloP.progs] Error 2

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