[Bioc-devel] ptime ERROR

[Shepherd, Lori]

It might be a combination of both!  Thanks for the information.


Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263

________________________________
From: Andris Jankevics <A.Jankevics using bham.ac.uk>
Sent: Thursday, February 6, 2020 11:38 AM
To: Shepherd, Lori <Lori.Shepherd using RoswellPark.org>; chris.r.john86 using gmail.com <chris.r.john86 using gmail.com>; bioc-devel using r-project.org <bioc-devel using r-project.org>
Subject: Re: [Bioc-devel] ptime ERROR


My apologies for pointing in wrong direction, but I was getting the same error message in tests and it took me a while to figure out why.


https://github.com/r-lib/devtools/issues/2167

[https://avatars0.githubusercontent.com/u/22618716?s=400&v=4]<https://github.com/r-lib/devtools/issues/2167>
devtools:test() works, but devtools:check() fail on functions with if(class(x) == "type") conditional. · Issue #2167 · r-lib/devtools · GitHub<https://github.com/r-lib/devtools/issues/2167>
github.com
Hi. I and @grlloyd have stumbled across strange behaviour of the devtools package using R-devel (4.0.0) and the latest devtools package. I am using R command class to determine what data structure object belong to. Based on the object ty...
BW,

Andris

________________________________
From: Lori.Shepherd using RoswellPark.org <Lori.Shepherd using RoswellPark.org>
Sent: 06 February 2020 16:21:14
To: Andris Jankevics (Biosciences); chris.r.john86 using gmail.com; bioc-devel using r-project.org
Subject: Re: [Bioc-devel] ptime ERROR

Actually it looks like it has to do with having a conditional > 1 rather than a class() ==

There is this post:
https://stat.ethz.ch/pipermail/bioc-devel/2020-January/016081.html

And this:
http://bioconductor.org/developers/how-to/troubleshoot-build-report/

Cheers,


Lori Shepherd

Bioconductor Core Team

Roswell Park Comprehensive Cancer Center

Department of Biostatistics & Bioinformatics

Elm & Carlton Streets

Buffalo, New York 14263

________________________________
From: Bioc-devel <bioc-devel-bounces using r-project.org> on behalf of Andris Jankevics <A.Jankevics using bham.ac.uk>
Sent: Thursday, February 6, 2020 11:17 AM
To: chris.r.john86 using gmail.com <chris.r.john86 using gmail.com>; bioc-devel using r-project.org <bioc-devel using r-project.org>
Subject: Re: [Bioc-devel] ptime ERROR

Hi Chris,


Error message is caused by changes in R 4.0.0.

You can find more details here https://developer.r-project.org/Blog/public/2019/11/09/when-you-think-class.-think-again/index.html.


In short you have to check all cases where you are using `class()` in your code.


BW,

Andris

________________________________
From: Bioc-devel <bioc-devel-bounces using r-project.org> on behalf of chris.r.john86 using gmail.com <chris.r.john86 using gmail.com>
Sent: 06 February 2020 16:09:07
To: bioc-devel using r-project.org
Subject: Re: [Bioc-devel] ptime ERROR

This is the error, sorry my hand slipped when writing the last email. Thank you.
http://bioconductor.org/checkResults/devel/bioc-LATEST/M3C/malbec2-checksrc.html

checking examples ... ERROR

Running examples in �M3C-Ex.R� failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")


On Thu, 6 Feb 2020 at 16:07, Christopher John <chris.r.john86 using gmail.com>
wrote:

> Hi
>
> I was wondering will this error disappear by itself? Because I did not
> change the package.
>
> Thanks,
>
> Chris
>
>

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