[Bioc-devel] error on riesling1 but not on palomino3

Oleksii Nikolaienko o|ek@||@n|ko|@|enko @end|ng |rom gm@||@com
Fri Mar 4 22:56:03 CET 2022

Thanks for the confirmation, Jennifer.


On Fri, 4 Mar 2022 at 21:28, Jennifer Wokaty <Jennifer.Wokaty using sph.cuny.edu>

> Hi Oleksii,
> Although it's marked as failing on the devel package page when viewing the
> short report, if you click on the long report (top right), it's only
> because of the errors on Riesling. I can confirm that that the issues on
> Riesling are not a problem for the next Bioconductor release as we will
> only be looking for errors on Palomino3 (as well as Nebbiolo1 and Merida1).
> This machine has the new R tool chain for R that we must use going forward
> for the Windows builds. ​
> Jennifer Wokaty
> Bioconductor Core Team
> ------------------------------
> *From:* Oleksii Nikolaienko <oleksii.nikolaienko using gmail.com>
> *Sent:* Thursday, February 24, 2022 5:05 AM
> *To:* Jennifer Wokaty
> *Cc:* bioc-devel using r-project.org
> *Subject:* Re: [Bioc-devel] error on riesling1 but not on palomino3
> Thanks Jennifer,
> I tried to fix it and now ran into another (known?) issue because of lack
> of proper support for “snprintf”. I would like to disregard this error, but
> could you please confirm that it won’t be a problem for a coming Bioc
> release? Package is marked as failing its build on the dev package page…
> Best,
> Oleksii
> On Wed, 23 Feb 2022 at 15:14, Jennifer Wokaty <
> Jennifer.Wokaty using sph.cuny.edu> wrote:
>> Hi Oleksii,
>> Palomino3, which has the new UCRT toolchain to allow native support of
>> UTF-8 and non-European languages, will replace Riesling1 soon, so please
>> disregard the error on Riesling1, which is only running for historical
>> reference.
>> We're also working on a way to help troubleshoot issues related to
>> Windows environments.
>> Jennifer Wokaty
>> Bioconductor Core Team
>> ________________________________________
>> From: Bioc-devel <bioc-devel-bounces using r-project.org> on behalf of Oleksii
>> Nikolaienko <oleksii.nikolaienko using gmail.com>
>> Sent: Wednesday, February 23, 2022 4:44 AM
>> To: bioc-devel using r-project.org
>> Subject: [Bioc-devel] error on riesling1 but not on palomino3
>> ***ATTENTION: This email came from an external source. Do not open
>> attachments or click on links from unknown senders or unexpected emails.***
>> Dear Bioc team,
>> my package (epiallleleR) currently fails tests on riesling1, but not on
>> the
>> other hosts. Wrong results are produced by compiled c++ code, and at the
>> moment I don't understand why. I can see that both Windows hosts use GCC
>> 8.3.0, but the compiler flags are different. I don't have access to
>> Windows, but I wasn't able to reproduce this error on my Linux with GCC
>> 7.5.0 when tried to set "-fno-reorder-blocks-and-partition" in my
>> Makevars,
>> or did "pkgbuild::with_debug(devtools::check())".
>> What are the other differences between riesling1 and palomino3? Is, for
>> example, sizeof(int)<4? And what can I do to debug it if I don't have
>> Windows around?
>> Best regards,
>> Oleksii
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