Arch Linux User Repository

They are provided by the base package, which is implicit. It is assumed you have it installed. There has been much discussion on forums/IRC over the years about this with no official stance. As such, I choose to not list dependencies that should already be installed.

Hello, why were deps removed in commit https://aur.archlinux.org/cgit/aur.git/commit/?h=htslib&id=5c2e86016ef129cc785920946478d4bb8631c253 ?
These are still direct link dependencies.

Please add zlib, openssl and glibc to depends.

Thank you @meanjollies, it is working now.

$> pacman -Ql htslib | grep -P 'hts.+a$' htslib /usr/lib/libhts.a 

@magno can you try again? By default, makepkg will clean up any static libs. I've enabled the option to keep it here, so you should be good to go now.

Hi Andrew,

I tried to install htslib-git but got this error about the htscodecs submodule...

Motivation for installing htslib-git is to check whether the newest version provides the static library libhts.a required by SHAPEIT4, please see https://github.com/odelaneau/shapeit4/issues/74.

$> yay -S htslib-git :: Checking for conflicts... :: Checking for inner conflicts...  ->  Package conflicts found:  -> Installing htslib-git will remove: htslib  -> Conflicting packages will have to be confirmed manually [Aur:1]  htslib-git-1.10.2.r134.ge9447f86-2  :: (1/1) Downloaded PKGBUILD: htslib-git   1 htslib-git                       (Build Files Exist) ==> Diffs to show? ==> [N]one [A]ll [Ab]ort [I]nstalled [No]tInstalled or (1 2 3, 1-3, ^4) ==>  :: (1/1) Parsing SRCINFO: htslib-git ==> Making package: htslib-git 1.10.2.r134.ge9447f86-2 (Thu 19 May 2022 04:27:55 PM WEST) ==> Retrieving sources...   -> Cloning htslib git repo... Cloning into bare repository '/home/rmagno/.cache/yay/htslib-git/htslib'... remote: Enumerating objects: 19249, done. remote: Counting objects: 100% (1187/1187), done. remote: Compressing objects: 100% (511/511), done. remote: Total 19249 (delta 835), reused 845 (delta 676), pack-reused 18062 Receiving objects: 100% (19249/19249), 13.17 MiB | 3.21 MiB/s, done. Resolving deltas: 100% (13927/13927), done. ==> Validating source files with sha256sums...     htslib ... Skipped ==> Making package: htslib-git 1.10.2.r134.ge9447f86-2 (Thu 19 May 2022 04:28:03 PM WEST) ==> Checking runtime dependencies... ==> Checking buildtime dependencies... ==> Retrieving sources...   -> Updating htslib git repo... Fetching origin ==> Validating source files with sha256sums...     htslib ... Skipped ==> Removing existing $srcdir/ directory... ==> Extracting sources...   -> Creating working copy of htslib git repo... Cloning into 'htslib'... done. ==> Starting pkgver()... ==> Updated version: htslib-git 1.15.1.r20.g46c56fcc-1 ==> Sources are ready. ==> Making package: htslib-git 1.15.1.r20.g46c56fcc-1 (Thu 19 May 2022 04:28:10 PM WEST) ==> Checking runtime dependencies... ==> Checking buildtime dependencies... ==> WARNING: Using existing $srcdir/ tree ==> Starting pkgver()... ==> Starting build()... checking for 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 ranlib... ranlib checking for grep that handles long lines and -e... /usr/bin/grep checking for C compiler warning flags... -Wall checking for pkg-config... /usr/bin/pkg-config checking pkg-config is at least version 0.9.0... yes checking for special C compiler options needed for large files... no checking for _FILE_OFFSET_BITS value needed for large files... no checking shared library type for unknown-Linux... plain .so checking whether the compiler accepts -fvisibility=hidden... yes checking build system type... x86_64-pc-linux-gnu checking host system type... x86_64-pc-linux-gnu checking for stdio.h... yes checking for stdlib.h... yes checking for string.h... yes checking for inttypes.h... yes checking for stdint.h... yes checking for strings.h... yes checking for sys/stat.h... yes checking for sys/types.h... yes checking for unistd.h... yes checking for sys/param.h... yes checking for getpagesize... yes checking for working mmap... yes checking for gmtime_r... yes checking for fsync... yes checking for drand48... yes checking for srand48_deterministic... no checking for gcc options needed to detect all undeclared functions... none needed checking whether fdatasync is declared... yes checking for fdatasync... yes checking for library containing dlsym... -ldl checking whether the compiler accepts -rdynamic... yes checking for library containing log... -lm checking for zlib.h... yes checking for inflate in -lz... yes checking for library containing recv... none required checking for bzlib.h... yes checking for BZ2_bzBuffToBuffCompress in -lbz2... yes checking for lzma.h... yes checking for lzma_easy_buffer_encode in -llzma... yes checking whether htscodecs files are present... no configure: error: htscodecs submodule files not present.  HTSlib uses some functions from the htscodecs project, which is normally included as a submodule.  Try running:    git submodule update --init --recursive  in  the top-level htslib directory to update it, and then re-run configure.  ==> ERROR: A failure occurred in build().     Aborting...  -> error making: htslib-git 

No worries - I got it.

Hi, I can maintain it. I maintain htslib/samtools elsewhere on an HPC and I use Arch locally so I have an interest in having this be available. Cheers...

I no longer have time to maintain this package and am disowning it.

Hey @viralstitch, would you be able to update this to 1.13?