Question

Lapack undefined reference

0

Entering edit mode

10.6 years ago

Carl ▴ 40

Hi guys,

I am having trouble installing this software called Shellfish which looks very helpful and a good alternative to EIGENSTRAT. When I try to make all, it gives me this endless error:

$ make all
cc -O2 -I . -lm    lines.c   -o lines
cc -O2 -I . -lm    columns.c   -o columns
cc -O2 -I . -lm    columns-split.c   -o columns-split
cc -O2 -I . -c -o io.o io.c
cc -O2 -I .  -c -o iogeno.o iogeno.c
cc -O2 -I .  -c -o dan.o dan.c
cc -O2 -I . -lm    sstat.c io.o iogeno.o dan.o   -o sstat
cc -O2 -I . -lm    istat.c io.o iogeno.o dan.o   -o istat
cc -O2 -I . -lm    flipind.c io.o iogeno.o dan.o   -o flipind
cc -O2 -I . -lm    flipgen.c io.o iogeno.o dan.o   -o flipgen
cc -O2 -I . -lm    flipgeno.c io.o iogeno.o dan.o   -o flipgeno
cc -O2 -I . -lm    gen2geno.c io.o iogeno.o dan.o   -o gen2geno
cc -O2 -I . -lm    geno2gen.c io.o iogeno.o dan.o   -o geno2gen
cc -O2 -I .  -c -o blas-lapack-dan.o blas-lapack-dan.c
cc -O2 -I . -lm    project.c io.o iogeno.o dan.o blas-lapack-dan.o /lib/libblas.a /lib/liblapack.a lib64/libcblas.a   -o project
/lib/libblas.a(xerbla.f.o): In function `xerbla_':
/usr/src/debug/lapack-3.5.0-1/BLAS/SRC/xerbla.f:80: undefined reference to `_gfortran_st_write'
/usr/src/debug/lapack-3.5.0-1/BLAS/SRC/xerbla.f:80: undefined reference to `_gfortran_string_len_trim'
/usr/src/debug/lapack-3.5.0-1/BLAS/SRC/xerbla.f:80: undefined reference to `_gfortran_transfer_character_write'
/usr/src/debug/lapack-3.5.0-1/BLAS/SRC/xerbla.f:80: undefined reference to `_gfortran_transfer_integer_write'
/usr/src/debug/lapack-3.5.0-1/BLAS/SRC/xerbla.f:80: undefined reference to `_gfortran_st_write_done'
/usr/src/debug/lapack-3.5.0-1/BLAS/SRC/xerbla.f:82: undefined reference to `_gfortran_stop_string'
/lib/liblapack.a(dsyevr.f.o): In function `dsyevr_':
/usr/src/debug/lapack-3.5.0-1/SRC/dsyevr.f:493: undefined reference to `dscal_'
/usr/src/debug/lapack-3.5.0-1/SRC/dsyevr.f:658: undefined reference to `dswap_'
/usr/src/debug/lapack-3.5.0-1/SRC/dsyevr.f:556: undefined reference to `dcopy_'
/usr/src/debug/lapack-3.5.0-1/SRC/dsyevr.f:557: undefined reference to `dcopy_'
/usr/src/debug/lapack-3.5.0-1/SRC/dsyevr.f:636: undefined reference to `dscal_'
/usr/src/debug/lapack-3.5.0-1/SRC/dsyevr.f:497: undefined reference to `dscal_'
/usr/src/debug/lapack-3.5.0-1/SRC/dsyevr.f:560: undefined reference to `dcopy_'
/usr/src/debug/lapack-3.5.0-1/SRC/dsyevr.f:561: undefined reference to `dcopy_'
/lib/liblapack.a(ilaenv.f.o): In function `ilaenv_':
/usr/src/debug/lapack-3.5.0-1/SRC/ilaenv.f:272: undefined reference to `_gfortran_compare_string'
/usr/src/debug/lapack-3.5.0-1/SRC/ilaenv.f:273: undefined reference to `_gfortran_compare_string'
/usr/src/debug/lapack-3.5.0-1/SRC/ilaenv.f:279: undefined reference to `_gfortran_compare_string'
/usr/src/debug/lapack-3.5.0-1/SRC/ilaenv.f:279: undefined reference to `_gfortran_compare_string'
/usr/src/debug/lapack-3.5.0-1/SRC/ilaenv.f:279: undefined reference to `_gfortran_compare_string'
/lib/liblapack.a(ilaenv.f.o):/usr/src/debug/lapack-3.5.0-1/SRC/ilaenv.f:279: more undefined references to `_gfortran_compare_string' follow
/lib/liblapack.a(dsytrd.f.o): In function `dsytrd_':
/usr/src/debug/lapack-3.5.0-1/SRC/dsytrd.f:322: undefined reference to `dsyr2k_'
/usr/src/debug/lapack-3.5.0-1/SRC/dsytrd.f:354: undefined reference to `dsyr2k_'
/lib/liblapack.a(dstein.f.o): In function `dstein_':
/usr/src/debug/lapack-3.5.0-1/SRC/dstein.f:353: undefined reference to `dcopy_'
/usr/src/debug/lapack-3.5.0-1/SRC/dstein.f:354: undefined reference to `dcopy_'
/usr/src/debug/lapack-3.5.0-1/SRC/dstein.f:355: undefined reference to `dcopy_'
/usr/src/debug/lapack-3.5.0-1/SRC/dstein.f:375: undefined reference to `dasum_'
/usr/src/debug/lapack-3.5.0-1/SRC/dstein.f:376: undefined reference to `dscal_'
/usr/src/debug/lapack-3.5.0-1/SRC/dstein.f:394: undefined reference to `ddot_'
/usr/src/debug/lapack-3.5.0-1/SRC/dstein.f:396: undefined reference to `daxpy_'
/usr/src/debug/lapack-3.5.0-1/SRC/dstein.f:403: undefined reference to `idamax_'
/usr/src/debug/lapack-3.5.0-1/SRC/dstein.f:427: undefined reference to `dnrm2_'
/usr/src/debug/lapack-3.5.0-1/SRC/dstein.f:428: undefined reference to `idamax_'
/usr/src/debug/lapack-3.5.0-1/SRC/dstein.f:431: undefined reference to `dscal_'
/lib/liblapack.a(dormtr.f.o): In function `dormtr_':
/usr/src/debug/lapack-3.5.0-1/SRC/dormtr.f:245: undefined reference to `_gfortran_concat_string'
/usr/src/debug/lapack-3.5.0-1/SRC/dormtr.f:253: undefined reference to `_gfortran_concat_string'
/usr/src/debug/lapack-3.5.0-1/SRC/dormtr.f:248: undefined reference to `_gfortran_concat_string'
/usr/src/debug/lapack-3.5.0-1/SRC/dormtr.f:256: undefined reference to `_gfortran_concat_string'
/lib/liblapack.a(dstemr.f.o): In function `dstemr_':
/usr/src/debug/lapack-3.5.0-1/SRC/dstemr.f:748: undefined reference to `dswap_'
/usr/src/debug/lapack-3.5.0-1/SRC/dstemr.f:718: undefined reference to `dscal_'
/usr/src/debug/lapack-3.5.0-1/SRC/dstemr.f:615: undefined reference to `dcopy_'
/usr/src/debug/lapack-3.5.0-1/SRC/dstemr.f:578: undefined reference to `dscal_'
/usr/src/debug/lapack-3.5.0-1/SRC/dstemr.f:579: undefined reference to `dscal_'
/lib/liblapack.a(dlatrd.f.o): In function `dlatrd_':
/usr/src/debug/lapack-3.5.0-1/SRC/dlatrd.f:298: undefined reference to `dgemv_'
/usr/src/debug/lapack-3.5.0-1/SRC/dlatrd.f:300: undefined reference to `dgemv_'
/usr/src/debug/lapack-3.5.0-1/SRC/dlatrd.f:314: undefined reference to `dsymv_'
/usr/src/debug/lapack-3.5.0-1/SRC/dlatrd.f:316: undefined reference to `dgemv_'
/usr/src/debug/lapack-3.5.0-1/SRC/dlatrd.f:318: undefined reference to `dgemv_'
/usr/src/debug/lapack-3.5.0-1/SRC/dlatrd.f:320: undefined reference to `dgemv_'
/usr/src/debug/lapack-3.5.0-1/SRC/dlatrd.f:322: undefined reference to `dgemv_'
/usr/src/debug/lapack-3.5.0-1/SRC/dlatrd.f:323: undefined reference to `dscal_'
/usr/src/debug/lapack-3.5.0-1/SRC/dlatrd.f:325: undefined reference to `ddot_'
/usr/src/debug/lapack-3.5.0-1/SRC/dlatrd.f:326: undefined reference to `daxpy_'
/usr/src/debug/lapack-3.5.0-1/SRC/dlatrd.f:269: undefined reference to `dsymv_'
/usr/src/debug/lapack-3.5.0-1/SRC/dlatrd.f:282: undefined reference to `dscal_'
/usr/src/debug/lapack-3.5.0-1/SRC/dlatrd.f:284: undefined reference to `ddot_'
/usr/src/debug/lapack-3.5.0-1/SRC/dlatrd.f:285: undefined reference to `daxpy_'
/usr/src/debug/lapack-3.5.0-1/SRC/dlatrd.f:253: undefined reference to `dgemv_'
/usr/src/debug/lapack-3.5.0-1/SRC/dlatrd.f:255: undefined reference to `dgemv_'
/usr/src/debug/lapack-3.5.0-1/SRC/dlatrd.f:272: undefined reference to `dgemv_'
/usr/src/debug/lapack-3.5.0-1/SRC/dlatrd.f:275: undefined reference to `dgemv_'
/usr/src/debug/lapack-3.5.0-1/SRC/dlatrd.f:277: undefined reference to `dgemv_'
/lib/liblapack.a(dlatrd.f.o):/usr/src/debug/lapack-3.5.0-1/SRC/dlatrd.f:280: more undefined references to `dgemv_' follow
/lib/liblapack.a(dsytd2.f.o): In function `dsytd2_':
/usr/src/debug/lapack-3.5.0-1/SRC/dsytd2.f:256: undefined reference to `dsymv_'
/usr/src/debug/lapack-3.5.0-1/SRC/dsytd2.f:260: undefined reference to `ddot_'
/usr/src/debug/lapack-3.5.0-1/SRC/dsytd2.f:261: undefined reference to `daxpy_'
/usr/src/debug/lapack-3.5.0-1/SRC/dsytd2.f:267: undefined reference to `dsyr2_'
/usr/src/debug/lapack-3.5.0-1/SRC/dsytd2.f:297: undefined reference to `dsymv_'
/usr/src/debug/lapack-3.5.0-1/SRC/dsytd2.f:302: undefined reference to `ddot_'
/usr/src/debug/lapack-3.5.0-1/SRC/dsytd2.f:303: undefined reference to `daxpy_'
/usr/src/debug/lapack-3.5.0-1/SRC/dsytd2.f:309: undefined reference to `dsyr2_'
/lib/liblapack.a(dormqr.f.o): In function `dormqr_':
/usr/src/debug/lapack-3.5.0-1/SRC/dormqr.f:252: undefined reference to `_gfortran_concat_string'
/usr/src/debug/lapack-3.5.0-1/SRC/dormqr.f:278: undefined reference to `_gfortran_concat_string'
/lib/liblapack.a(dormql.f.o): In function `dormql_':
/usr/src/debug/lapack-3.5.0-1/SRC/dormql.f:253: undefined reference to `_gfortran_concat_string'
/usr/src/debug/lapack-3.5.0-1/SRC/dormql.f:283: undefined reference to `_gfortran_concat_string'
/lib/liblapack.a(dlarre.f.o): In function `dlarre_':
/usr/src/debug/lapack-3.5.0-1/SRC/dlarre.f:753: undefined reference to `dcopy_'
/usr/src/debug/lapack-3.5.0-1/SRC/dlarre.f:754: undefined reference to `dcopy_'
/lib/liblapack.a(dlarrv.f.o): In function `dlarrv_':
/usr/src/debug/lapack-3.5.0-1/SRC/dlarrv.f:467: undefined reference to `dcopy_'
/usr/src/debug/lapack-3.5.0-1/SRC/dlarrv.f:542: undefined reference to `dcopy_'
/usr/src/debug/lapack-3.5.0-1/SRC/dlarrv.f:544: undefined reference to `dcopy_'
/usr/src/debug/lapack-3.5.0-1/SRC/dlarrv.f:985: undefined reference to `dscal_'
/lib/liblapack.a(dlarfg.f.o): In function `dlarfg_':
/usr/src/debug/lapack-3.5.0-1/SRC/dlarfg.f:149: undefined reference to `dnrm2_'
/usr/src/debug/lapack-3.5.0-1/SRC/dlarfg.f:170: undefined reference to `dscal_'
/usr/src/debug/lapack-3.5.0-1/SRC/dlarfg.f:178: undefined reference to `dnrm2_'
/usr/src/debug/lapack-3.5.0-1/SRC/dlarfg.f:182: undefined reference to `dscal_'
/lib/liblapack.a(dlarfb.f.o): In function `dlarfb_':
/usr/src/debug/lapack-3.5.0-1/SRC/dlarfb.f:260: undefined reference to `dcopy_'
/usr/src/debug/lapack-3.5.0-1/SRC/dlarfb.f:266: undefined reference to `dtrmm_'
/usr/src/debug/lapack-3.5.0-1/SRC/dlarfb.f:279: undefined reference to `dtrmm_'
/usr/src/debug/lapack-3.5.0-1/SRC/dlarfb.f:295: undefined reference to `dtrmm_'
/usr/src/debug/lapack-3.5.0-1/SRC/dlarfb.f:490: undefined reference to `dcopy_'
/usr/src/debug/lapack-3.5.0-1/SRC/dlarfb.f:496: undefined reference to `dtrmm_'
/usr/src/debug/lapack-3.5.0-1/SRC/dlarfb.f:509: undefined reference to `dtrmm_'
/usr/src/debug/lapack-3.5.0-1/SRC/dlarfb.f:525: undefined reference to `dtrmm_'
/usr/src/debug/lapack-3.5.0-1/SRC/dlarfb.f:376: undefined reference to `dcopy_'
/usr/src/debug/lapack-3.5.0-1/SRC/dlarfb.f:382: undefined reference to `dtrmm_'
/usr/src/debug/lapack-3.5.0-1/SRC/dlarfb.f:394: undefined reference to `dtrmm_'
/usr/src/debug/lapack-3.5.0-1/SRC/dlarfb.f:409: undefined reference to `dtrmm_'
/usr/src/debug/lapack-3.5.0-1/SRC/dlarfb.f:606: undefined reference to `dcopy_'
/usr/src/debug/lapack-3.5.0-1/SRC/dlarfb.f:612: undefined reference to `dtrmm_'
/usr/src/debug/lapack-3.5.0-1/SRC/dlarfb.f:624: undefined reference to `dtrmm_'
/usr/src/debug/lapack-3.5.0-1/SRC/dlarfb.f:639: undefined reference to `dtrmm_'
/usr/src/debug/lapack-3.5.0-1/SRC/dlarfb.f:658: undefined reference to `dcopy_'
/usr/src/debug/lapack-3.5.0-1/SRC/dlarfb.f:664: undefined reference to `dtrmm_'
/usr/src/debug/lapack-3.5.0-1/SRC/dlarfb.f:676: undefined reference to `dtrmm_'
/usr/src/debug/lapack-3.5.0-1/SRC/dlarfb.f:691: undefined reference to `dtrmm_'
/usr/src/debug/lapack-3.5.0-1/SRC/dlarfb.f:544: undefined reference to `dcopy_'
/usr/src/debug/lapack-3.5.0-1/SRC/dlarfb.f:550: undefined reference to `dtrmm_'
/usr/src/debug/lapack-3.5.0-1/SRC/dlarfb.f:563: undefined reference to `dtrmm_'
/usr/src/debug/lapack-3.5.0-1/SRC/dlarfb.f:579: undefined reference to `dtrmm_'
/usr/src/debug/lapack-3.5.0-1/SRC/dlarfb.f:314: undefined reference to `dcopy_'
/usr/src/debug/lapack-3.5.0-1/SRC/dlarfb.f:320: undefined reference to `dtrmm_'
/usr/src/debug/lapack-3.5.0-1/SRC/dlarfb.f:333: undefined reference to `dtrmm_'
/usr/src/debug/lapack-3.5.0-1/SRC/dlarfb.f:349: undefined reference to `dtrmm_'
/usr/src/debug/lapack-3.5.0-1/SRC/dlarfb.f:428: undefined reference to `dcopy_'
/usr/src/debug/lapack-3.5.0-1/SRC/dlarfb.f:434: undefined reference to `dtrmm_'
/usr/src/debug/lapack-3.5.0-1/SRC/dlarfb.f:446: undefined reference to `dtrmm_'
/usr/src/debug/lapack-3.5.0-1/SRC/dlarfb.f:461: undefined reference to `dtrmm_'
/lib/liblapack.a(dlarft.f.o): In function `dlarft_':
/usr/src/debug/lapack-3.5.0-1/SRC/dlarft.f:231: undefined reference to `dgemv_'
/usr/src/debug/lapack-3.5.0-1/SRC/dlarft.f:252: undefined reference to `dtrmv_'
/usr/src/debug/lapack-3.5.0-1/SRC/dlarft.f:246: undefined reference to `dgemv_'
/usr/src/debug/lapack-3.5.0-1/SRC/dlarft.f:290: undefined reference to `dgemv_'
/usr/src/debug/lapack-3.5.0-1/SRC/dlarft.f:311: undefined reference to `dtrmv_'
/usr/src/debug/lapack-3.5.0-1/SRC/dlarft.f:305: undefined reference to `dgemv_'
/lib/liblapack.a(dlarrf.f.o): In function `dlarrf_':
/usr/src/debug/lapack-3.5.0-1/SRC/dlarrf.f:479: undefined reference to `dcopy_'
/usr/src/debug/lapack-3.5.0-1/SRC/dlarrf.f:480: undefined reference to `dcopy_'
/lib/liblapack.a(dlarf.f.o): In function `dlarf_':
/usr/src/debug/lapack-3.5.0-1/SRC/dlarf.f:201: undefined reference to `dgemv_'
/usr/src/debug/lapack-3.5.0-1/SRC/dlarf.f:205: undefined reference to `dger_'
/usr/src/debug/lapack-3.5.0-1/SRC/dlarf.f:216: undefined reference to `dgemv_'
/usr/src/debug/lapack-3.5.0-1/SRC/dlarf.f:220: undefined reference to `dger_'
collect2: error: ld returned 1 exit status
<builtin>: recipe for target 'project' failed
make: *** [project] Error 1

I would really appreciate your help.

lapack-package error unix • 8.2k views

ADD COMMENT • link updated 3.2 years ago by Ram 44k • written 10.6 years ago by Carl ▴ 40

Ram · Answer 1 · 2014-04-27

2

Entering edit mode

10.6 years ago

Neilfws 49k

First thing to check is whether libgfortran is installed; if not, install it.

Second: Google the first error, it seems to be a common issue with lots of potential causes.

I tried installation on my system (running Linux Mint 16) and had a different issue:

cc -O2 -I . -lm    sstat.c io.o iogeno.o dan.o   -o sstat
iogeno.o: In function `centre_and_zero_missing_and_scale':
iogeno.c:(.text+0x592): undefined reference to `sqrt'
iogeno.o: In function `bit_encode':
iogeno.c:(.text+0xdad): undefined reference to `pow'
collect2: error: ld returned 1 exit status
make: *** [sstat] Error 1

I also note from the Github repository that the software is not maintained and has not been updated for 4 years.

So I suspect this software is not as useful as you had hoped and is probably more trouble than it is worth. I'd suggest trying something else.

ADD COMMENT • link updated 4.9 years ago by Ram 44k • written 10.6 years ago by Neilfws 49k

2

Entering edit mode

I'll add that using -lgfortran is probably needed, as is -lblas. Anyway, the sailfish webpage even mentions that it's just trying make a single command replacement for doing PCA in R...so R would seem to be the obvious replacement.