freebayes: Missing external dependencies

Hello, I’m trying to switch from Cmake to meson build system and found several problems:

1. I have the same problem with tests which you described here #668 - so I will wait for you to fix it
2. I have missing dependencies - again - same as you:

Run-time dependency bz2lib found: NO (tried pkgconfig and cmake)
Run-time dependency htslib found: NO (tried pkgconfig and cmake)

But I have both installed in my system:

root@c653f49334a8:/soft/freebayes-1.3.3-src# bzip2 --version               
bzip2, a block-sorting file compressor.  Version 1.0.6, 6-Sept-2010.       
                                                                           
   Copyright (C) 1996-2010 by Julian Seward.                               
                                                                           
   This program is free software; you can redistribute it and/or modify    
   it under the terms set out in the LICENSE file, which is included       
   in the bzip2-1.0.6 source distribution.                                 
                                                                           
   This program is distributed in the hope that it will be useful,         
   but WITHOUT ANY WARRANTY; without even the implied warranty of          
   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the           
   LICENSE file for more details.                                          

root@c653f49334a8:/soft/freebayes-1.3.3-src# apt update && apt install libbz2-dev    
Hit:1 http://archive.ubuntu.com/ubuntu bionic InRelease                              
Hit:2 http://ppa.launchpad.net/openjdk-r/ppa/ubuntu bionic InRelease                 
Hit:3 http://archive.ubuntu.com/ubuntu bionic-updates InRelease                      
Hit:4 http://archive.ubuntu.com/ubuntu bionic-backports InRelease                    
Get:5 http://security.ubuntu.com/ubuntu bionic-security InRelease [88.7 kB]          
Fetched 88.7 kB in 1s (109 kB/s)                                                     
Reading package lists... Done                                                        
Building dependency tree                                                             
Reading state information... Done                                                    
1 package can be upgraded. Run 'apt list --upgradable' to see it.                    
Reading package lists... Done                                                        
Building dependency tree                                                             
Reading state information... Done                                                    
libbz2-dev is already the newest version (1.0.6-8.1ubuntu0.2).                       
0 upgraded, 0 newly installed, 0 to remove and 1 not upgraded.                       

root@c653f49334a8:/soft/freebayes-1.3.3-src# pkg-config --print-provides htslib 
htslib = 1.11                                                                   
root@c653f49334a8:/soft/freebayes-1.3.3-src# pkg-config --modversion htslib     
1.11                                                                            

I’ve found way to point meson to htslib - I’ve added its path to PKG_CONFIG_PATH:

root@c653f49334a8:/soft/freebayes-1.3.3-src# meson "$SOFT/freebayes-${FREEBAYES_VERSION}-src/build" --buildtype debug
Using 'PKG_CONFIG_PATH' from environment with value: '/soft/htslib-1.11/lib/pkgconfig'                               
Using 'PKG_CONFIG_PATH' from environment with value: '/soft/htslib-1.11/lib/pkgconfig'                               
The Meson build system                                                                                               
Version: 0.56.0                                                                                                      
Source dir: /soft/freebayes-1.3.3-src                                                                                
Build dir: /soft/freebayes-1.3.3-src/build                                                                           
Build type: native build                                                                                             
Project name: freebayes                                                                                              
Project version: 1.3.3                                                                                               
C compiler for the host machine: cc (gcc 7.5.0 "cc (Ubuntu 7.5.0-3ubuntu1~18.04) 7.5.0")                             
C linker for the host machine: cc ld.bfd 2.30                                                                        
C++ compiler for the host machine: c++ (gcc 7.5.0 "c++ (Ubuntu 7.5.0-3ubuntu1~18.04) 7.5.0")                         
C++ linker for the host machine: c++ ld.bfd 2.30                                                                     
Host machine cpu family: x86_64                                                                                      
Host machine cpu: x86_64                                                                                             
Dependency zlib found: YES 1.2.11 (cached)                                                                           
Dependency liblzma found: YES 5.2.2 (cached)                                                                         
Run-time dependency bz2lib found: NO (tried pkgconfig and cmake)
Dependency htslib found: YES 1.11 (cached)                                                                           
Dependency threads found: YES unknown (cached)                                                                       
Program prove found: YES (/usr/bin/prove)                                                                            
Build targets in project: 2                                                                                          

Cmake should find BZip2:

root@c653f49334a8:/soft/freebayes-1.3.3-src# find / -name 'Find*.cmake' | grep -i 'bzip2' 
/soft/cmake-3.19.2-Linux-x86_64/share/cmake-3.19/Modules/FindBZip2.cmake                  

But it’s not, and I cannot find any way to fix it. Additional proof that Cmake should find bz2 - part of vcflib install log in same container:

-- Found BZip2: /usr/lib/x86_64-linux-gnu/libbz2.so (found version "1.0.6")

Here are some links:

• https://github.com/libimobiledevice/sbmanager/issues/1 “libbz2 does not provide pkg-config”
• https://gitlab.freedesktop.org/gstreamer/gst-plugins-good/-/blob/16a70b58a6edd5927299406494544b5199e2e240/meson.build#L233

Should this be changed to something like: bzip2_dep = meson.get_compiler('c').find_library('bz2', required : false) or I’m wrong?