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I am receiving an undefined reference error for every function used from the cfitsio library when compiling my code. Below is the relevant chunk of the make null command's output (Note that -L/usr/lib/ -lcfitsio is in the first line):

gcc -g -I../mdl/null   -DCHABRIER -DCHANGESOFT -DDENSITYU -DDENSITYUNOTP -DDIFFUSION -DDODVDS -DDTADJUST -DEPSACCH -DPARTICLESPLIT -DPROMOTE -DGASOLINE -DJEANSSOFT -DNSMOOTHINNER -DRTFORCE -DSETTRAPFPE -DSTARFORM -DTHERMALCOND -DTOPHATFEEDBACK -DTWOPHASE -DVSIGVISC -DWENDLAND -DRADIATION -DRADIATIONLUM -DDDSIMPLE -DR2PPBMAX -DCOOLING_METAL  -L/usr/lib/ -lcfitsio  -I/usr/include/fitsio.h -o gasoline.dfTest main.o master.o param.o outtype.o pkd.o pst.o grav.o ewald.o walk.o eccanom.o hypanom.o fdl.o htable.o smooth.o smoothfcn.o collision.o qqsmooth.o cooling_metal.o cosmo.o romberg.o starform.o feedback.o millerscalo.o supernova.o supernovaia.o startime.o stiff.o runge.o dumpframe.o dffuncs.o dumpvoxel.o rotbar.o special.o ssio.o   treezip.o log.o radiation.o erf.o v_sqrt1.o ../mdl/null/mdl.o -lm
dumpframe.o: In function `fitsError':
/.../dumpframe.c:2156: undefined reference to `ffrprt'
dumpframe.o: In function `dfFinishFrame':
/.../dumpframe.c:2175: undefined reference to `ffinit'
/.../dumpframe.c:2176: undefined reference to `ffcrim'
/.../dumpframe.c:2197: undefined reference to `ffppr'
/.../dumpframe.c:2198: undefined reference to `ffclos'
collect2: error: ld returned 1 exit status
Makefile:539: recipe for target 'gasoline.dfTest' failed
make[1]: *** [gasoline.dfTest] Error 1
make[1]: Leaving directory '/home/grondjj/Code/gasoline'
Makefile:457: recipe for target 'null' failed
make: *** [null] Error 2gcc -g -I../mdl/null   -DCHABRIER -DCHANGESOFT -DDENSITYU -DDENSITYUNOTP -DDIFFUSION -DDODVDS -DDTADJUST -DEPSACCH -DPARTICLESPLIT -DPROMOTE -DGASOLINE -DJEANSSOFT -DNSMOOTHINNER -DRTFORCE -DSETTRAPFPE -DSTARFORM -DTHERMALCOND -DTOPHATFEEDBACK -DTWOPHASE -DVSIGVISC -DWENDLAND -DRADIATION -DRADIATIONLUM -DDDSIMPLE -DR2PPBMAX -DCOOLING_METAL  -L/usr/lib/ -lcfitsio  -I/usr/include/fitsio.h -o gasoline.dfTest main.o master.o param.o outtype.o pkd.o pst.o grav.o ewald.o walk.o eccanom.o hypanom.o fdl.o htable.o smooth.o smoothfcn.o collision.o qqsmooth.o cooling_metal.o cosmo.o romberg.o starform.o feedback.o millerscalo.o supernova.o supernovaia.o startime.o stiff.o runge.o dumpframe.o dffuncs.o dumpvoxel.o rotbar.o special.o ssio.o   treezip.o log.o radiation.o erf.o v_sqrt1.o ../mdl/null/mdl.o -lm
dumpframe.o: In function `fitsError':
/.../dumpframe.c:2156: undefined reference to `ffrprt'
dumpframe.o: In function `dfFinishFrame':
/.../dumpframe.c:2175: undefined reference to `ffinit'
/.../dumpframe.c:2176: undefined reference to `ffcrim'
/.../dumpframe.c:2197: undefined reference to `ffppr'
/.../dumpframe.c:2198: undefined reference to `ffclos'
collect2: error: ld returned 1 exit status
Makefile:539: recipe for target 'gasoline.dfTest' failed
make[1]: *** [gasoline.dfTest] Error 1
make[1]: Leaving directory '/home/grondjj/Code/gasoline'
Makefile:457: recipe for target 'null' failed
make: *** [null] Error 2

Here are the relevant lines from the Makefile for make null

 FITS_LIB = -L/usr/lib/ -lcfitsio

 BASE_LD_FLAGS = $(PNG_LIB) $(GSL_LIB) $(FITS_LIB)

 NULL_LD_FLAGS   = $(BASE_LD_FLAGS) 

 null:
      cd $(NULL_MDL); make "CC=$(CC)" "CFLAGS=$(NULL_CFLAGS)"
      make $(EXE) "CFLAGS=$(NULL_CFLAGS)" "LD_FLAGS=$(NULL_LD_FLAGS)"\
           "MDL=$(NULL_MDL)" "XOBJ=$(NULL_XOBJ)" "LIBMDL=$(NULL_LIBMDL)"

In dumpframe.c I include the cfitsio header fitsio.h along with the other inlcudes at the top of the file:

 #ifndef GSS_DUMPFRAME
 #include <stdio.h>
 #include <stdlib.h>
 #include <math.h>
 #include <assert.h>
 #include <string.h>
 #include "fitsio.h"

The library was installed from source code. The source resides in /usr/local/src/cfitsio/, it was then installed via the following commands:

 $ ./configure --prefix=/usr
 $ make shared
 $ make install
 $ make clean

Which results in the libraries (libcfitsio.a, libcfitsio.so, libcfitsio.so.5, libcfitsio.so.5.3.39) being installed in /usr/lib/ and the auxiliary files (longnam.h, fitsio.h, fitsio2.h, drvrsmem.h) being installed in /usr/include/.

I am not sure what causes this, as the compiler does not complain about missing libraries or a missing fitsio.h header file.

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1 Answer 1

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Put the library after the object files, not before.

Wrong:

gcc -g -I../mdl/null -DCHABRIER -DCHANGESOFT -DDENSITYU -DDENSITYUNOTP \
    -DDIFFUSION -DDODVDS -DDTADJUST -DEPSACCH -DPARTICLESPLIT -DPROMOTE \
   -DGASOLINE -DJEANSSOFT -DNSMOOTHINNER -DRTFORCE -DSETTRAPFPE -DSTARFORM \
   -DTHERMALCOND -DTOPHATFEEDBACK -DTWOPHASE -DVSIGVISC -DWENDLAND -DRADIATION \
   -DRADIATIONLUM -DDDSIMPLE -DR2PPBMAX -DCOOLING_METAL \
   -L/usr/lib/ -lcfitsio  -I/usr/include/fitsio.h \
   -o gasoline.dfTest main.o master.o param.o outtype.o pkd.o pst.o grav.o ewald.o \
   walk.o eccanom.o hypanom.o fdl.o htable.o smooth.o smoothfcn.o collision.o \
   qqsmooth.o cooling_metal.o cosmo.o romberg.o starform.o feedback.o millerscalo.o \
   supernova.o supernovaia.o startime.o stiff.o runge.o dumpframe.o dffuncs.o \
   dumpvoxel.o rotbar.o special.o ssio.o treezip.o log.o radiation.o erf.o v_sqrt1.o \
   ../mdl/null/mdl.o -lm

Right:

gcc -g -I../mdl/null -DCHABRIER -DCHANGESOFT -DDENSITYU -DDENSITYUNOTP \
    -DDIFFUSION -DDODVDS -DDTADJUST -DEPSACCH -DPARTICLESPLIT -DPROMOTE \
   -DGASOLINE -DJEANSSOFT -DNSMOOTHINNER -DRTFORCE -DSETTRAPFPE -DSTARFORM \
   -DTHERMALCOND -DTOPHATFEEDBACK -DTWOPHASE -DVSIGVISC -DWENDLAND -DRADIATION \
   -DRADIATIONLUM -DDDSIMPLE -DR2PPBMAX -DCOOLING_METAL \
   -o gasoline.dfTest main.o master.o param.o outtype.o pkd.o pst.o grav.o ewald.o \
   walk.o eccanom.o hypanom.o fdl.o htable.o smooth.o smoothfcn.o collision.o \
   qqsmooth.o cooling_metal.o cosmo.o romberg.o starform.o feedback.o millerscalo.o \
   supernova.o supernovaia.o startime.o stiff.o runge.o dumpframe.o dffuncs.o \
   dumpvoxel.o rotbar.o special.o ssio.o treezip.o log.o radiation.o erf.o v_sqrt1.o \
   ../mdl/null/mdl.o -lcfitsio -lm

Note that the -I/usr/include/cfitsio.h option does no good, though it also does no harm given that the header is in /usr/include. The -I option takes a directory name, not a file name. Similarly, the -L/usr/lib option does no good, though it too does no harm either. The /usr/lib library is searched automatically.

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3 Comments

I am a little confused as to why the order needs to be changed. I am currently editing a Makefile given to me, and the order things get put in are "predefined", meaning the template wants to have -lcfitsio before the object files. I am aware that the library with the .a extension might cause problems, as apposed to the .so extensions.
Given the makefile, the problem is probably that the LD_FLAGS macro contains library information but is listed before the object files in the linker command line. If you're in charge of the makefile, one way around this is to use LDFLAGS to set library directories (-L/opt/whatever/lib) a separate LDLIBS or LDLIBES macro to specify the libraries (-lwhatever) which is then listed after the object files in the linker command. This is mostly traditional. Without knowing what is in the relevant bits of your makefile(s) — which you aren't in charge of — it's hard to help much more.
Some systems allow you to list libraries anywhere on the command line; it appears that the system this makefile originated on is one such system. It also appears you're using a system that doesn't afford you the luxury of allowing libraries anywhere — welcome to the majority of the 'real world'. See the duplicate Q&A for information about --as-needed and see whether that helps you. Yes, it's a nuisance. Well designed (or previously ported) packages compile correctly on both types of system, by listing libraries after objects. Apparently, this package hasn't encountered this problem before.

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