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I understand that this has come up a lot, but I've looked through all the other answers and none of them are relevant to me.

I am trying to compile the neuroimaging software FSL from source (I have to, it's not supported on my Linux Distro). I've followed all the instructions listed here, and it's about 80% compiled. There are a few modules that have not been successful, however, and they all seem to trace back to a problem trying to compile CiftiLib-master.

Per the instructions, whenever I try to run the 'make' command, it returns:

Makefile:34: warning: overriding recipe for target 'clean'
/home/thosvarley/Desktop/fslbuild/fsl/config/common/rules.mk:32: warning: ignoring old recipe for target 'clean'
gcc -c -Wall -ansi -pedantic -Wno-long-long     -m64  -g -O3 -fexpensive-optimizations -m64  -I/home/thosvarley/Desktop/fslbuild/fsl/extras/include/boost -g -DCIFTILIB_USE_XMLPP -I/home/thosvarley/Desktop/fslbuild/fsl/extras/include -I/home/thosvarley/Desktop/fslbuild/fsl/extras/include/libxml2 -I/home/thosvarley/Desktop/fslbuild/fsl/extras/include/libxml++-2.6 -I/home/thosvarley/Desktop/fslbuild/fsl/extras/lib/libxml++-2.6/include -I/home/thosvarley/Desktop/fslbuild/fsl/extras/include/boost -I./Common -I./Nifti -I./Cifti  -I. -I/include -I/home/thosvarley/Desktop/fslbuild/fsl/include  -o Common/XmlAdapter.o Common/XmlAdapter.cxx
In file included from Common/XmlAdapter.cxx:28:0:
Common/XmlAdapter.h:56:10: fatal error: libxml++/libxml++.h: No such file or directory
 #include "libxml++/libxml++.h"
          ^~~~~~~~~~~~~~~~~~~~~
compilation terminated.
make: *** [Makefile:19: Common/XmlAdapter.o] Error 1

As I am not trying to compile one foo.c file, but rather, make a program a lot of the advice I've seen doesn't seem like it would apply to me. I've already installed all of the various libxml packages that get suggested in other posts (libxml2, libxslt1, etc).

I cannot make heads or tails of the error message: I'm not familiar with compiling C programs at all (this is my first serious foray into building from source). Apologies in advance if the answer is obvious and I just don't recognize it.

I'm on Antergos Linux (Arch kernel), which I think may be where the problem is coming from as all the other people who have asked after this seem to be on Debian or Ubuntu.

Thomas Varley
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1 Answers1

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I have been attempting to solve the same problem. It seems that libxml++ is bundled with FSL by default, and the bundled version fails to compile.

Solution #1: Install and use an older compiler (e.g. GCC 4.8), since the project's configurations are made to fit those old compilers

I cannot vouch for this solution, as I haven't tried it myself (because apparently, I like to make life difficult for myself), but it's probably your best bet.

Solution #2: Fix the problems manually

NOTE: This is not a comprehensive solution, but it might point you in the correct direction.

Your first problem is most likely that the compiler you're using by default uses a more recent C++ standard than the project is written to be compiled with. This causes the implicit conversion of input streams and output streams to booleans to fail. You might be able to solve it by messing around with compiler flags in the makefile configurations, but it's probably easier to just fix the problematic parts of the code. The relevant lines (FSL 5.0.11) are:

- extras/src/libxml++-2.34.0/libxml++/io/istreamparserinputbuffer.cc (line 42)
  return _input;
  SHOULD BE
  return static_cast<bool>(_input);

- extras/src/libxml++-2.34.0/libxml++/io/ostreamoutputbuffer.cc (line 32)
  return _output;
  SHOULD BE
  return static_cast<bool>(_output);

- extras/src/libxml++-2.34.0/libxml++/io/ostreamoutputbuffer.cc (line 39)
  return _output;
  SHOULD BE
  return static_cast<bool>(_output);

Depending on the version you're trying to install, the actual line numbers may be different, but they're probably in the same general area.

The next problem is that the include paths are not defined for INC_XML++, INC_XML++CONF and INC_XML2 in the generic makefile configuration. This is most likely the one your system defaults to, as there are no configurations for GCC versions > 4.8. Edit the config/generic/externallibs.mk file by adding the following lines (where exactly you add it is not important):

# XML++
LIB_XML++ = ${FSLEXTLIB}
INC_XML++ = ${FSLEXTINC}/libxml++-2.6
INC_XML++CONF = ${FSLEXTLIB}/libxml++-2.6/include
INC_XML2 = ${FSLEXTINC}/libxml2

(I addeed the LIB_XML++ for good measure, because the lib path was defined by other variables in the file, but I'm not 100% sure it's necessary.)

Again, this is what fixed it on my system. Depending on the version of the source code you downloaded, it might be different for you, but at least this is a starting point.

After fixing these errors, the CiftiLib-master target should compile. HOWEVER, if your system is anything like mine, this is far from the only error in the build process. Looking at the build.log file and searching for error: should give you a pretty good idea of which projects result in which errors, and what might be needed to fix them. The problems are likely to be similar in nature to the CiftiLib ones.

Final tip: If your libgd project fails to compile, look at the error: message. It probably complains about some undeclared identifiers (IMG_FMT_I420, PLANE_Y, PLANE_U, PLANE_V). If you prefix these identifiers with VPX_, it should work. The reason this fails is because of an update to the library that removes the definitions of the deprecated identifiers, forcing users to use the newer prefixed ones.

This is as far as I've come. I'm assuming you're not still troubled with this a year later, but I'm leaving this here for posterity.

winterweird
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