Am Tue, Mar 15, 2022 at 09:01:12AM -0700 schrieb Chris Chang:
> Just a heads-up, today's release contains a fix for an
> infinite-loop-instead-of-error bug in the previous release.
Thanks a lot for the headsup - just uploaded the updated version to Debian.
> On Sun, Feb 20, 2022 at 12:36 PM
Just a heads-up, today's release contains a fix for an
infinite-loop-instead-of-error bug in the previous release.
On Sun, Feb 20, 2022 at 12:36 PM Andreas Tille wrote:
> Cool! This finally works. Thanks a lot for your patience, Andreas.
>
> Am Sun, Feb 20, 2022 at 09:43:10AM -0800 schrieb
Cool! This finally works. Thanks a lot for your patience, Andreas.
Am Sun, Feb 20, 2022 at 09:43:10AM -0800 schrieb Chris Chang:
> Hmm. Ordinarily, that download link would be fine. I had not updated it
> this time because the issue only affects gcc 11+, so it did not affect any
> of the
Hmm. Ordinarily, that download link would be fine. I had not updated it
this time because the issue only affects gcc 11+, so it did not affect any
of the precompiled binaries and I wanted to keep the posted source
identical to that used to compile those binaries.
On the other hand, the only
Hi Chris,
Am Sat, Feb 19, 2022 at 11:37:34PM -0800 schrieb Chris Chang:
> To elaborate: when I look at
> https://salsa.debian.org/med-team/plink2/-/tree/master , I can see that
> plink2.cc, include/plink2_base.h, and include/plink2_base.cc don't have the
> same contents as the v2.00a3-20220218
To elaborate: when I look at
https://salsa.debian.org/med-team/plink2/-/tree/master , I can see that
plink2.cc, include/plink2_base.h, and include/plink2_base.cc don't have the
same contents as the v2.00a3-20220218 GitHub tag/release. So I don't know
where you grabbed the code from this time, but
If you build off the current head, the version string should say "18 Feb
2022", not "17 Feb 2022".
On Sat, Feb 19, 2022 at 7:02 AM Andreas Tille wrote:
> Hi again,
>
> Am Sat, Feb 19, 2022 at 12:28:21AM -0800 schrieb Chris Chang:
> > Ok, new release/tag created.
>
> I've built the new version
Hi again,
Am Sat, Feb 19, 2022 at 12:28:21AM -0800 schrieb Chris Chang:
> Ok, new release/tag created.
I've built the new version now. The bad news is that it keeps on
SEGFAULTing for me:
...
(gdb) run
Starting program: /usr/lib/plink2/plink2-sse3 --debug --pfile tmp_data --export
vcf
Ok, new release/tag created.
On Fri, Feb 18, 2022 at 10:55 PM Andreas Tille wrote:
> Hi Chris,
>
> Am Fri, Feb 18, 2022 at 07:27:20PM -0800 schrieb Chris Chang:
> > I have confirmed that the original code segfaults when compiled with gcc
> > 11.2 on my Debian instance, and that it runs to
Hi Chris,
Am Fri, Feb 18, 2022 at 07:27:20PM -0800 schrieb Chris Chang:
> I have confirmed that the original code segfaults when compiled with gcc
> 11.2 on my Debian instance, and that it runs to completion after the latest
> patch. I have also confirmed that, after the latest patch, all other
I have confirmed that the original code segfaults when compiled with gcc
11.2 on my Debian instance, and that it runs to completion after the latest
patch. I have also confirmed that, after the latest patch, all other tests
pass.
On Fri, Feb 18, 2022 at 1:27 PM Chris Chang wrote:
> I am
I am installing gcc-11 on my Debian instance now, and will be running more
extensive tests today searching for other things that may have stopped
working for the same reason.
On Fri, Feb 18, 2022 at 1:22 PM Andreas Tille wrote:
> I confirm its gcc-11. I'll check tomorrow. Thanks a lot for
I confirm its gcc-11. I'll check tomorrow. Thanks a lot for your quick and
helpful responses, Andreas.
Am Fri, Feb 18, 2022 at 12:53:58PM -0800 schrieb Chris Chang:
> I have posted an update under the provisional assumption that it's gcc 11's
> new ipa-modref pass that is causing this code to
I have posted an update under the provisional assumption that it's gcc 11's
new ipa-modref pass that is causing this code to fail, since it does seem
to break some similar code.
On Fri, Feb 18, 2022 at 11:49 AM Chris Chang wrote:
> What compiler version are you using? This implies that the
What compiler version are you using? This implies that the pgl_malloc
inline function is not being compiled to the expected code; there is an
existing non-inlined version that is used for very old gcc versions, but it
looks like it may also be needed here.
On Fri, Feb 18, 2022 at 11:40 AM
Hi again,
I applied this patch and now I get:
(gdb) run
Starting program: /usr/lib/plink2/plink2-sse2 --debug --pfile tmp_data --export
vcf vcf-dosage=DS --out tmp_data2
[Thread debugging using libthread_db enabled]
Using host libthread_db library "/lib/x86_64-linux-gnu/libthread_db.so.1".
[New
Ok, I don't know why that particular line would fail, but I've added
another debug-print before it on GitHub.
On Fri, Feb 18, 2022 at 4:24 AM Andreas Tille wrote:
> Hi Chris,
>
> Am Thu, Feb 17, 2022 at 07:13:49PM -0800 schrieb Chris Chang:
> > I was unable to replicate this issue on a Debian
Hi Chris,
Am Thu, Feb 17, 2022 at 07:13:49PM -0800 schrieb Chris Chang:
> I was unable to replicate this issue on a Debian EC2 instance. However,
> there are very few things that happen between printing "End time:" and
> program exit, so I have added a bunch of debug-prints (active when the
>
I was unable to replicate this issue on a Debian EC2 instance. However,
there are very few things that happen between printing "End time:" and
program exit, so I have added a bunch of debug-prints (active when the
--debug flag is passed in) to the latest GitHub commit that should reveal
which of
Am Thu, Feb 17, 2022 at 11:39:30AM -0800 schrieb Chris Chang:
> Haven't yet replicated this on any of my usual non-Debian test machines,
> but I will spin up a Debian EC2 instance within the next two days and try
> to replicate the crash there.
Thanks a lot, Andreas.
--
http://fam-tille.de
Haven't yet replicated this on any of my usual non-Debian test machines,
but I will spin up a Debian EC2 instance within the next two days and try
to replicate the crash there.
On Wed, Feb 16, 2022 at 11:30 PM Andreas Tille wrote:
> PS to last mail: Here
>
>
PS to last mail: Here
https://salsa.debian.org/med-team/plink2/-/jobs/2479769
is a full test log in our Gitlab CI for the latest version which I just
injected into the packaging Git repository but did not upload yet.
Kind regards
Andreas.
--
http://fam-tille.de
Control: reopen -1
Control: tags -1 confirmed
Control: tags -1 upstream
Control: forwarded -1 Christopher Chang
Hi Christopher (and Dylan),
I verified the latest version (29 Jan 2022) of plink2 with the same
result for the CI test we are doing in Debian (which was written by
Dylan):
$ plink2
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