Package Details: allelecount 4.3.0-4

Git Clone URL: https://aur.archlinux.org/allelecount.git (read-only, click to copy)
Package Base: allelecount
Description: program for estimating the NGS copy number
Upstream URL: http://cancerit.github.io/alleleCount/
Licenses: AGPL-3.0-or-later
Submitter: kbipinkumar
Maintainer: kbipinkumar (BioArchLinuxBot)
Last Packager: BioArchLinuxBot
Votes: 0
Popularity: 0.000000
First Submitted: 2023-05-09 09:51 (UTC)
Last Updated: 2025-08-23 18:03 (UTC)

Latest Comments

kbipinkumar commented on 2025-08-23 18:13 (UTC)

@micwoj92 the PKGBUILD has been updated to fix the build issues. you can check the log for package being built with revised PKGBUILD here.

Alternatively you can install the prebuilt package from BioArchlinux repo

micwoj92 commented on 2025-08-23 00:23 (UTC)

Build fails:

/usr/src/debug/allelecount/alleleCount-4.3.0/c/tests/bam_access_tests.c:43:(.text+0x65): undefined reference to `bam_access_openhts'
/usr/bin/ld: /usr/src/debug/allelecount/alleleCount-4.3.0/c/tests/bam_access_tests.c:45:(.text+0x10f): undefined reference to `bam_access_get_position_base_counts'
/usr/bin/ld: /usr/src/debug/allelecount/alleleCount-4.3.0/c/tests/bam_access_tests.c:58:(.text+0x296): undefined reference to `bam_access_min_base_qual'
/usr/bin/ld: /usr/src/debug/allelecount/alleleCount-4.3.0/c/tests/bam_access_tests.c:59:(.text+0x2b1): undefined reference to `bam_access_get_position_base_counts'
/usr/bin/ld: /usr/src/debug/allelecount/alleleCount-4.3.0/c/tests/bam_access_tests.c:72:(.text+0x50e): undefined reference to `bam_access_min_map_qual'
/usr/bin/ld: /usr/src/debug/allelecount/alleleCount-4.3.0/c/tests/bam_access_tests.c:73:(.text+0x529): undefined reference to `bam_access_get_position_base_counts'
/usr/bin/ld: /usr/src/debug/allelecount/alleleCount-4.3.0/c/tests/bam_access_tests.c:79:(.text+0x692): undefined reference to `bam_access_closehts'
/usr/bin/ld: /usr/src/debug/allelecount/alleleCount-4.3.0/c/tests/bam_access_tests.c:83:(.text+0x69d): undefined reference to `bam_access_min_base_qual'
/usr/bin/ld: /usr/src/debug/allelecount/alleleCount-4.3.0/c/tests/bam_access_tests.c:84:(.text+0x6a8): undefined reference to `bam_access_min_map_qual'
/usr/bin/ld: /usr/src/debug/allelecount/alleleCount-4.3.0/c/tests/bam_access_tests.c:85:(.text+0x6b0): undefined reference to `bam_access_inc_flag'
/usr/bin/ld: /usr/src/debug/allelecount/alleleCount-4.3.0/c/tests/bam_access_tests.c:86:(.text+0x6b8): undefined reference to `bam_access_exc_flag'
/usr/bin/ld: /usr/src/debug/allelecount/alleleCount-4.3.0/c/tests/bam_access_tests.c:87:(.text+0x6cc): undefined reference to `bam_access_openhts'
/usr/bin/ld: /usr/src/debug/allelecount/alleleCount-4.3.0/c/tests/bam_access_tests.c:100:(.text+0x7c2): undefined reference to `bam_access_get_multi_position_base_counts'
/usr/bin/ld: /usr/src/debug/allelecount/alleleCount-4.3.0/c/tests/bam_access_tests.c:118:(.text+0x910): undefined reference to `bam_access_closehts'
collect2: error: ld returned 1 exit status
make: *** [<builtin>: tests/bam_access_tests] Error 1
make: *** Waiting for unfinished jobs....
==> ERROR: A failure occurred in build().
    Aborting...