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Sambamba has remaining references to libbiod #484
Comments
meson should be fixed, but I did not do a release yet. Do you mind
trying the latest commit?
…On Wed, Jan 12, 2022 at 08:06:37AM -0800, Andreas Tille wrote:
Hi,
when I try to build Sambamba, I get
[4/34] ldc2 -I=sambamba.p -I=. -I=.. -enable-color -wi -O -g -release -wi -O3 -r
elease -enable-inlining -boundscheck=off -J../ -J. -makedeps=sambamba.p/sambamba
_fixbins.d.o.deps -of=sambamba.p/sambamba_fixbins.d.o -c ../sambamba/fixbins.d
FAILED: sambamba.p/sambamba_fixbins.d.o
ldc2 -I=sambamba.p -I=. -I=.. -enable-color -wi -O -g -release -wi -O3 -release
-enable-inlining -boundscheck=off -J../ -J. -makedeps=sambamba.p/sambamba_fixbin
s.d.o.deps -of=sambamba.p/sambamba_fixbins.d.o -c ../sambamba/fixbins.d
../sambamba/fixbins.d(25): Error: module `reader` is in file 'bio/std/hts/bam/re
ader.d' which cannot be read
So there seem to be some remaining references to BioD which are not yet
taken over in the source base of Sambamba.
BTW, ***@***.*** I tried to send this via e-mail to you but your mail
address is bouncing.
Kind regards, Andreas.
—
Reply to this email directly, [2]view it on GitHub, or [3]unsubscribe.
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References
1. https://github.com/pjotrp
2. #484
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|
Am Wed, Jan 12, 2022 at 09:01:28PM -0800 schrieb Pjotr Prins:
meson should be fixed, but I did not do a release yet. Do you mind
trying the latest commit?
Do you mean just releasing current HEAD or just using a specific commit as a patch (link to that actual patch would be welcome).
A single patch would be OK but switching from release tags to HEAD is a bit more invasive and I'm not really in a hurry to force this.
Kind regards, Andreas.
|
I am working on a release. It would be good if someone could *test*
the meson build before we release.
Other than that I am trying to remove deprecation warnings and update
the docs a bit.
…On Wed, Jan 12, 2022 at 10:33:43PM -0800, Andreas Tille wrote:
Am Wed, Jan 12, 2022 at 09:01:28PM -0800 schrieb Pjotr Prins:
> meson should be fixed, but I did not do a release yet. Do you mind
> trying the latest commit?
Do you mean just releasing current HEAD or just using a specific commit
as a patch (link to that actual patch would be welcome).
A single patch would be OK but switching from release tags to HEAD is a
bit more invasive and I'm not really in a hurry to force this.
Kind regards, Andreas.
—
Reply to this email directly, [1]view it on GitHub, or [2]unsubscribe.
Triage notifications on the go with GitHub Mobile for [3]iOS or
[4]Android.
You are receiving this because you were mentioned. Message ID:
***@***.***>
References
1. #484 (comment)
2. https://github.com/notifications/unsubscribe-auth/AAADJ34N2ZNCXMIY33ABOVTUVZW4PANCNFSM5LZLVBLQ
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|
OK, when trying to build current HEAD locally I get:
Seems you are lacking a linker flag to libz. BTW, I'm wondering whether you want to apply this patch before doing the next release. Kind regards, Andreas. |
Thinks, I'll take a look. I think the python3 patch is applied pretty
much.
|
Oh, for libz4 we don't use the one that comes with Debian because it
lacks a few functions. The meson build should pick up a local version.
I'll check.
|
I just built the latest checkout on a Debian system. @tillea do you mind checking before I do a release? |
We have a new 0.8.2 release. @tillea if you use meson with buildtype=release we should have an optimal version of sambamba. Please give it a shot. |
I think this can be closed. |
Hi,
when I try to build Sambamba, I get
So there seem to be some remaining references to BioD which are not yet taken over in the source base of Sambamba.
BTW, @pjotrp I tried to send this via e-mail to you but your mail address is bouncing.
Kind regards, Andreas.
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