Hi I was wondering will this error disappear by itself? Because I did not change the package. Thanks, Chris
[Bioc-devel] ptime ERROR
6 messages · Christopher John, Shepherd, Lori, Andris Jankevics
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 at gmail.com> wrote:
Hi I was wondering will this error disappear by itself? Because I did not change the package. Thanks, Chris
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 at r-project.org> on behalf of chris.r.john86 at gmail.com <chris.r.john86 at gmail.com>
Sent: 06 February 2020 16:09:07
To: bioc-devel at r-project.org
Subject: Re: [Bioc-devel] ptime ERROR
Sent: 06 February 2020 16:09:07
To: bioc-devel at 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 at gmail.com> wrote: > Hi > > I was wondering will this error disappear by itself? Because I did not > change the package. > > Thanks, > > Chris > > [[alternative HTML version deleted]] _______________________________________________ Bioc-devel at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
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 at r-project.org> on behalf of Andris Jankevics <A.Jankevics at bham.ac.uk>
Sent: Thursday, February 6, 2020 11:17 AM
To: chris.r.john86 at gmail.com <chris.r.john86 at gmail.com>; bioc-devel at r-project.org <bioc-devel at r-project.org>
Subject: Re: [Bioc-devel] ptime ERROR
Sent: Thursday, February 6, 2020 11:17 AM
To: chris.r.john86 at gmail.com <chris.r.john86 at gmail.com>; bioc-devel at r-project.org <bioc-devel at 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 at r-project.org> on behalf of chris.r.john86 at gmail.com <chris.r.john86 at gmail.com> Sent: 06 February 2020 16:09:07 To: bioc-devel at 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 at gmail.com> wrote: > Hi > > I was wondering will this error disappear by itself? Because I did not > change the package. > > Thanks, > > Chris > > [[alternative HTML version deleted]] _______________________________________________ Bioc-devel at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel [[alternative HTML version deleted]] This email message may contain legally privileged and/or confidential information. If you are not the intended recipient(s), or the employee or agent responsible for the delivery of this message to the intended recipient(s), you are hereby notified that any disclosure, copying, distribution, or use of this email message is prohibited. If you have received this message in error, please notify the sender immediately by e-mail and delete this email message from your computer. Thank you.
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 at RoswellPark.org <Lori.Shepherd at RoswellPark.org>
Sent: 06 February 2020 16:21:14
To: Andris Jankevics (Biosciences); chris.r.john86 at gmail.com; bioc-devel at r-project.org
Subject: Re: [Bioc-devel] ptime ERROR
Sent: 06 February 2020 16:21:14
To: Andris Jankevics (Biosciences); chris.r.john86 at gmail.com; bioc-devel at 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 at r-project.org> on behalf of Andris Jankevics <A.Jankevics at bham.ac.uk> Sent: Thursday, February 6, 2020 11:17 AM To: chris.r.john86 at gmail.com <chris.r.john86 at gmail.com>; bioc-devel at r-project.org <bioc-devel at 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 at r-project.org> on behalf of chris.r.john86 at gmail.com <chris.r.john86 at gmail.com> Sent: 06 February 2020 16:09:07 To: bioc-devel at 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 at gmail.com> wrote: > Hi > > I was wondering will this error disappear by itself? Because I did not > change the package. > > Thanks, > > Chris > > [[alternative HTML version deleted]] _______________________________________________ Bioc-devel at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel [[alternative HTML version deleted]] This email message may contain legally privileged and/or confidential information. If you are not the intended recipient(s), or the employee or agent responsible for the delivery of this message to the intended recipient(s), you are hereby notified that any disclosure, copying, distribution, or use of this email message is prohibited. If you have received this message in error, please notify the sender immediately by e-mail and delete this email message from your computer. Thank you.
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 at bham.ac.uk>
Sent: Thursday, February 6, 2020 11:38 AM
To: Shepherd, Lori <Lori.Shepherd at RoswellPark.org>; chris.r.john86 at gmail.com <chris.r.john86 at gmail.com>; bioc-devel at r-project.org <bioc-devel at r-project.org>
Subject: Re: [Bioc-devel] ptime ERROR
Sent: Thursday, February 6, 2020 11:38 AM
To: Shepherd, Lori <Lori.Shepherd at RoswellPark.org>; chris.r.john86 at gmail.com <chris.r.john86 at gmail.com>; bioc-devel at r-project.org <bioc-devel at 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 at RoswellPark.org <Lori.Shepherd at RoswellPark.org> Sent: 06 February 2020 16:21:14 To: Andris Jankevics (Biosciences); chris.r.john86 at gmail.com; bioc-devel at 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 at r-project.org> on behalf of Andris Jankevics <A.Jankevics at bham.ac.uk> Sent: Thursday, February 6, 2020 11:17 AM To: chris.r.john86 at gmail.com <chris.r.john86 at gmail.com>; bioc-devel at r-project.org <bioc-devel at 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 at r-project.org> on behalf of chris.r.john86 at gmail.com <chris.r.john86 at gmail.com> Sent: 06 February 2020 16:09:07 To: bioc-devel at 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 at gmail.com> wrote: > Hi > > I was wondering will this error disappear by itself? Because I did not > change the package. > > Thanks, > > Chris > > [[alternative HTML version deleted]] _______________________________________________ Bioc-devel at r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel [[alternative HTML version deleted]] This email message may contain legally privileged and/or confidential information. If you are not the intended recipient(s), or the employee or agent responsible for the delivery of this message to the intended recipient(s), you are hereby notified that any disclosure, copying, distribution, or use of this email message is prohibited. If you have received this message in error, please notify the sender immediately by e-mail and delete this email message from your computer. Thank you. This email message may contain legally privileged and/or confidential information. If you are not the intended recipient(s), or the employee or agent responsible for the delivery of this message to the intended recipient(s), you are hereby notified that any disclosure, copying, distribution, or use of this email message is prohibited. If you have received this message in error, please notify the sender immediately by e-mail and delete this email message from your computer. Thank you.