{2025.06}[2024a] SAMtools 1.21

[PetrKralCZ]

1 out of 8 required modules missing:

* SAMtools/1.21-GCC-13.3.0 (SAMtools-1.21-GCC-13.3.0.eb)

The build fails for me under EESSI:

checking for gawk... gawk
checking for x86_64-pc-linux-gnu-gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether the compiler supports GNU C... yes
checking whether gcc accepts -g... yes
checking for gcc option to enable C11 features... none needed
checking for grep that handles long lines and -e... /cvmfs/software.eessi.io/versions/2025.06/compat/linux/x86_64/bin/grep
checking for C compiler warning flags... -Wall
checking for gcc option to enable large file support... none needed
checking location of HTSlib source tree... htslib-1.21
checking for NcursesW wide-character library... yes
checking for working ncursesw/curses.h... no
checking for working ncursesw.h... no
checking for working ncurses.h... no
checking for working ncurses/curses.h... no
configure: WARNING: could not find a working ncursesw/curses.h, ncursesw.h or ncurses.h
checking for Ncurses library... yes
checking for working ncurses/curses.h... no
checking for working ncurses.h... no
configure: WARNING: could not find a working ncurses/curses.h or ncurses.h
checking for Curses library... no
configure: error: curses development files not found

The 'samtools tview' command uses the curses text user interface library.
Building samtools with tview requires curses/ncurses/etc development files
to be installed on the build machine; you may need to ensure a package such
as libncurses5-dev (on Debian or Ubuntu Linux) or ncurses-devel (on RPM-based
Linux distributions) is installed.

FAILED.  Either configure --without-curses or resolve this error to build
samtools successfully.

[boegel]

@PetrKralCZ Can you check the config.log file for hints on why it's failing to pick up on the ncurses headers?

[boegel]

ncurses is a filtered dependency in the EasyBuild configuration used in EESSI 2023.06, so if an ncurses is found, it will be the one from the EESSI compay layer, which may be too new/old, or missing stuff

config.log should tell us more...

[bedroge]

Looks like it's a bit of a mixture of issues, depending on which ncurses library it's trying to use (ncurses or ncursesw). Linking against ncursesw seems to fail due to:

/cvmfs/software.eessi.io/versions/2025.06/compat/linux/x86_64/usr/bin/ld: /cvmfs/software.eessi.io/versions/2025.06/compat/linux/x86_64/usr/lib/../lib64/libtinfo.so.6: error adding symbols: DSO missing from command line

and that's apparently because it also needs libtinfow (see for instance https://bugs.gentoo.org/457530)? This can be done by setting CURSES_LIB="-lncursesw -ltinfow" in preconfigopts (can also be determined dynamically using pkgconf --libs ncursesw).

Not sure how specific this is to Gentoo, and hence, if we should add this to the easyconfig of SAMtools or solve it specifically for EESSI using a hook.