disable libcurl

[grenaud]

I tried to disable the libcurl dependency, I did the following:

git clone --recursive https://github.com/samtools/htslib.git cd htslib/ git submodule update --init --recursive autoreconf -i ./configure --disable-libcurl make

However, I am getting:
hfile.c:1084: undefined reference tohfile_plugin_init_libcurl' `

Which should not happen. This occurs on Ubuntu 20.04 but not on another machine running Ubuntu 18.04.

Any idea why?

[jkbonfield]

That code is around an ifdef:

#ifdef HAVE_LIBCURL
    init_add_plugin(NULL, hfile_plugin_init_libcurl, "libcurl");
#endif

So this implies your config.h somehow enabled that define still but didn't include the library on the link line.

I've tried to reproduce this and cannot. My config.h has /* #undef HAVE_LIBCURL */, so it's working as intended there. Can you check your config.h?

If your local config.h has the undef, then are you finding a copy of it from elsewhere? You can take your compilation line (it may differ to mine) and use -E to show the expanded code including or -M. Eg:

$ gcc -M -c -I. hfile.c|grep config
hfile.o: hfile.c /usr/include/stdc-predef.h config.h /usr/include/stdio.h \

$ gcc -E -I. hfile.c | grep config.h
# 1 "./config.h" 1

[grenaud]

my apologies about the formatting. I get different results, on the machine where it does not work:

htslib$ gcc -M -c -I. hfile.c|grep config
hfile.o: hfile.c /usr/include/stdc-predef.h /home/software/htslib/config.h \
htslib$  gcc -E -I. hfile.c | grep config.h
# 1 "/home/software/htslib/config.h" 1 3

/home/software/ is a directory where we keep a lot of software, I have no idea how htslib in my home dir knows about it.

on the machine where it works:

htslib$  gcc -M -c -I. hfile.c|grep config
hfile.o: hfile.c /usr/include/stdc-predef.h config.h /usr/include/stdio.h \
 /usr/include/x86_64-linux-gnu/bits/_G_config.h \

htslib$ gcc -E -I. hfile.c | grep config.h
# 1 "./config.h" 1
# 1 "/usr/include/x86_64-linux-gnu/bits/_G_config.h" 1 3 4
# 19 "/usr/include/x86_64-linux-gnu/bits/_G_config.h" 3 4
# 20 "/usr/include/x86_64-linux-gnu/bits/_G_config.h" 2 3 4
# 22 "/usr/include/x86_64-linux-gnu/bits/_G_config.h" 2 3 4

[jkbonfield]

This is probably something you have in your environment then. You do a "gcc -I." and yet it's using /home/software in preference. That to me smells like having a global search path such as CPATH or C_INCLUDE_PATH in your environment.

You can check with printenv | grep home/software to see what's pointing there.

Note it's generally a bad idea to have things in search paths defined in this way. At least globally. If it needs doing, put it in the build script for the specific packages.

[grenaud]

Dear James, my apologies for not getting back to you sooner! I have actually gone around the problem by disabling libcurl in the configure script. It seems that one cannot build a libcurl statically which is kind of annoying.