[R-pkg-devel] package test returns error when R version 4.1.0
Murray Efford
murr@y@e||ord @end|ng |rom ot@go@@c@nz
Tue Jul 6 23:18:59 CEST 2021
I also get from Winbuilder:
** byte-compile and prepare package for lazy loading
ERROR: lazy loading failed for package 'secr'
even for the tar.gz of the version secr 4.4.4 that currently passes all checks on CRAN. Perhaps it is significant that secr also imports from raster that had a new version on CRAN 18th June.
Murray Efford
________________________________________
From: R-package-devel <r-package-devel-bounces using r-project.org> on behalf of Duncan Murdoch <murdoch.duncan using gmail.com>
Sent: 07 July 2021 08:28
To: Alex Chubaty
Cc: r-package-devel using r-project.org
Subject: Re: [R-pkg-devel] package test returns error when R version 4.1.0
On 06/07/2021 4:15 p.m., Alex Chubaty wrote:
> Thanks for the suggestion Duncan.
>
> The same code version ran on winbuilder last week, but it's broken this
> week.
If that happened with a released version of R, then it could be that
some new package version is causing the problem, or it could be a
transient problem on Winbuilder.
Devel versions of R change every day, so there are more possibilities
for origins of the problem there.
Duncan Murdoch
>
> I'll compare the dependencies between the two packages and focus on
> those used by both for now, to see if it's caused by a broken dependency.
>
> Alex
>
>
> On Tue, Jul 6, 2021 at 2:08 PM Duncan Murdoch <murdoch.duncan using gmail.com
> <mailto:murdoch.duncan using gmail.com>> wrote:
>
> Both NegLogoR and movecost have a lot of hard dependencies -- so many
> that I'm unwilling to install them with the limited bandwidth that I
> have right now. I suspect that's related to the problem: some
> dependency install is failing, and that causes something else to fail,
> and that leads to the not-very-informative failure messages.
>
> This kind of problem is quite a lot of work to debug. If I were going
> to attempt to do it, I would go for a bisection strategy:
>
> - Do you have any old revision which succeeds? If so, use bisection
> on the revisions until you find the change which first triggers the
> error.
>
> - Perhaps no versions succeed, because something external to your
> package has triggered the error. In this case, bisection would work on
> the dependencies: cut out half of the dependencies and all the code
> that depends on those. Have you fixed the error? If so, add back half
> of the dependencies, otherwise cut out half of the remaining ones.
>
> - If you're still getting the errors after cutting out all of the
> dependencies, then start cutting out code and data. Etc.
>
> In any case, try to find a version of the package that doesn't trigger
> the error, and a minimal change to it that does. Then perhaps you'll
> understand the root cause of the error.
>
> Duncan Murdoch
>
> On 06/07/2021 3:11 p.m., Alex Chubaty wrote:
> > FWIW I'm having the same issue with package NetLogoR (
> > https://apc01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2FPredictiveEcology%2FNetLogoR%2F&data=04%7C01%7Cmurray.efford%40otago.ac.nz%7C0215a2eac18a47b8f63108d940bcd5d9%7C0225efc578fe4928b1579ef24809e9ba%7C1%7C0%7C637612003078338060%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=5XPRhpw3sUyHbOiiupslC%2BZ0pCxcvNekFmWzmZkQPig%3D&reserved=0
> <https://apc01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2FPredictiveEcology%2FNetLogoR%2F&data=04%7C01%7Cmurray.efford%40otago.ac.nz%7C0215a2eac18a47b8f63108d940bcd5d9%7C0225efc578fe4928b1579ef24809e9ba%7C1%7C0%7C637612003078348021%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=faXwrXOP1RHKEsPrqjmOhg4O8MWayRou6%2B1Y%2BPIj%2FuY%3D&reserved=0>)
> >
> > Passing windows tests locally but code can't be lazy loaded on
> winbuilder,
> > except for oldrel.
> >
> > Alex
> >
> >
> >
> >
> >
> > On Tue, Jul 6, 2021 at 10:18 AM Gianmarco Alberti <
> > gianmarcoalberti using gmail.com <mailto:gianmarcoalberti using gmail.com>>
> wrote:
> >
> >> Thank you all. I appreciate your help and discussion so far.
> >>
> >> To complicate the matter further, I have done an experiment. I
> have tried
> >> to test a new version which is 99.9% identical to the last
> official one on
> >> CRAN because I wanted to understand if the issue was with some
> new code
> >> added to the version I have been testing in the last couple of days.
> >>
> >> The new version 1.2 (virtually identical to the 1.1 on CRAN) did
> not pass
> >> the tests as per my earlier description. Same errors. The only
> Ok is on my
> >> computer and with devtools’ winoldrealeases()
> >>
> >> I really don’t know that to do next.
> >>
> >> Best
> >> Gm
> >>
> >> ************************************************
> >> Dr Gianmarco Alberti (PhD Udine)
> >> Lecturer in Spatial Forensics
> >> Coordinator of the BA dissertations
> >> Department of Criminology
> >> Faculty for Social Wellbeing
> >> Room 332, Humanities B (FEMA)
> >> University of Malta, Msida, Malta (Europe) - MSD 2080
> >> tel +356 2340 3718
> >>
> >> Academic profiles
> >> https://apc01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.researchgate.net%2Fprofile%2FGianmarco_Alberti4&data=04%7C01%7Cmurray.efford%40otago.ac.nz%7C0215a2eac18a47b8f63108d940bcd5d9%7C0225efc578fe4928b1579ef24809e9ba%7C1%7C0%7C637612003078348021%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=03qtEfvqo6lqgqCe7QRBIOLM%2BSHSNDAEFqOwPT25pnc%3D&reserved=0
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> >> https://apc01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmalta.academia.edu%2FGianmarcoAlberti&data=04%7C01%7Cmurray.efford%40otago.ac.nz%7C0215a2eac18a47b8f63108d940bcd5d9%7C0225efc578fe4928b1579ef24809e9ba%7C1%7C0%7C637612003078348021%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=S9uUT6rfFrnB2Fhic84eYMuhA3qZ23HMhbYXANLCEbI%3D&reserved=0
> <https://apc01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmalta.academia.edu%2FGianmarcoAlberti&data=04%7C01%7Cmurray.efford%40otago.ac.nz%7C0215a2eac18a47b8f63108d940bcd5d9%7C0225efc578fe4928b1579ef24809e9ba%7C1%7C0%7C637612003078348021%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=S9uUT6rfFrnB2Fhic84eYMuhA3qZ23HMhbYXANLCEbI%3D&reserved=0>
> >>
> >> Google Scholar profile
> >> https://apc01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fscholar.google.com%2Fcitations%3Fuser%3DtFrJKQ0AAAAJ%26hl%3Den&data=04%7C01%7Cmurray.efford%40otago.ac.nz%7C0215a2eac18a47b8f63108d940bcd5d9%7C0225efc578fe4928b1579ef24809e9ba%7C1%7C0%7C637612003078348021%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=ktVjpaYkTtPx0%2BniHOTrq8Bz2FkegI8QMWkpcU%2B%2BY1s%3D&reserved=0
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> >>
> >> Correspondence Analysis website
> >> https://apc01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fcainarchaeology.weebly.com%2F&data=04%7C01%7Cmurray.efford%40otago.ac.nz%7C0215a2eac18a47b8f63108d940bcd5d9%7C0225efc578fe4928b1579ef24809e9ba%7C1%7C0%7C637612003078348021%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=y5f2wO8GCmbcuACuiIjhvlmnczh3N096S%2BLfXUMnG9g%3D&reserved=0
> <https://apc01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fcainarchaeology.weebly.com%2F&data=04%7C01%7Cmurray.efford%40otago.ac.nz%7C0215a2eac18a47b8f63108d940bcd5d9%7C0225efc578fe4928b1579ef24809e9ba%7C1%7C0%7C637612003078348021%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=y5f2wO8GCmbcuACuiIjhvlmnczh3N096S%2BLfXUMnG9g%3D&reserved=0>
> >>
> >> R packages on CRAN:
> >> CAinterprTools
> >>
> https://apc01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fcran.r-project.org%2Fweb%2Fpackages%2FCAinterprTools%2Findex.html&data=04%7C01%7Cmurray.efford%40otago.ac.nz%7C0215a2eac18a47b8f63108d940bcd5d9%7C0225efc578fe4928b1579ef24809e9ba%7C1%7C0%7C637612003078348021%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=DkyH2A6ZVY4BAwEw%2BxVxEp6xVCN1fZWvxKqH7nR3OFI%3D&reserved=0
> <https://apc01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fcran.r-project.org%2Fweb%2Fpackages%2FCAinterprTools%2Findex.html&data=04%7C01%7Cmurray.efford%40otago.ac.nz%7C0215a2eac18a47b8f63108d940bcd5d9%7C0225efc578fe4928b1579ef24809e9ba%7C1%7C0%7C637612003078348021%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=DkyH2A6ZVY4BAwEw%2BxVxEp6xVCN1fZWvxKqH7nR3OFI%3D&reserved=0>
> >>
> >> GmAMisc
> >> https://apc01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fcran.r-project.org%2Fpackage%3DGmAMisc&data=04%7C01%7Cmurray.efford%40otago.ac.nz%7C0215a2eac18a47b8f63108d940bcd5d9%7C0225efc578fe4928b1579ef24809e9ba%7C1%7C0%7C637612003078348021%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=SKhC8DWY62W2hmb%2BSSnu7yQ49ysHRKW1o6M1DXq3XeU%3D&reserved=0
> <https://apc01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fcran.r-project.org%2Fpackage%3DGmAMisc&data=04%7C01%7Cmurray.efford%40otago.ac.nz%7C0215a2eac18a47b8f63108d940bcd5d9%7C0225efc578fe4928b1579ef24809e9ba%7C1%7C0%7C637612003078348021%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=SKhC8DWY62W2hmb%2BSSnu7yQ49ysHRKW1o6M1DXq3XeU%3D&reserved=0>
> >>
> >> movecost
> >> https://apc01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fcran.r-project.org%2Fweb%2Fpackages%2Fmovecost%2Findex.html&data=04%7C01%7Cmurray.efford%40otago.ac.nz%7C0215a2eac18a47b8f63108d940bcd5d9%7C0225efc578fe4928b1579ef24809e9ba%7C1%7C0%7C637612003078348021%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=ZoZci%2FxGKJPeWZsLFfjR5wC0nlqKMc4BUguMRoKdctI%3D&reserved=0
> <https://apc01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fcran.r-project.org%2Fweb%2Fpackages%2Fmovecost%2Findex.html&data=04%7C01%7Cmurray.efford%40otago.ac.nz%7C0215a2eac18a47b8f63108d940bcd5d9%7C0225efc578fe4928b1579ef24809e9ba%7C1%7C0%7C637612003078348021%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=ZoZci%2FxGKJPeWZsLFfjR5wC0nlqKMc4BUguMRoKdctI%3D&reserved=0>
> >> ************************************************
> >> Il 6 lug 2021, 14:53 +0200, brodie gaslam via R-package-devel <
> >> r-package-devel using r-project.org
> <mailto:r-package-devel using r-project.org>>, ha scritto:
> >>>
> >>>> On Tuesday, July 6, 2021, 8:09:18 AM EDT, dbosak01 using gmail.com
> <mailto:dbosak01 using gmail.com> <
> >> dbosak01 using gmail.com <mailto:dbosak01 using gmail.com>> wrote:
> >>>>
> >>>> Martin:
> >>>>
> >>>> What I suggested was he remove the LazyData entry from the
> description
> >> file
> >>>> if he was NOT lazy loading data. If someone is lazy loading data,
> >> then that
> >>>> is a different situation, and they obviously need to set the
> entry.
> >>>>
> >>>> But clearly Gm has a different problem. He has now tried
> "LazyData:
> >> true",
> >>>> "LazyData: false", and removing the LazyData entry entirely.
> And he is
> >>>> still getting this error:
> >>>>
> >>>> * installing *source* package 'movecost' ...
> >>>> ** using staged installation
> >>>> ** R
> >>>> ** data
> >>>> ** byte-compile and prepare package for lazy loading
> >>>> ERROR: lazy loading failed for package 'movecost'
> >>>> * removing 'd:/RCompile/CRANguest/R-release/lib/movecost'
> >>>
> >>> FWIW I think this is lazy loading of the code, which I think is
> >>> different to what LazyData controls. This is described in
> >>> R-Internals:
> >>>
> >>> https://apc01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fcran.r-project.org%2Fdoc%2Fmanuals%2FR-ints.html%23Lazy-loading&data=04%7C01%7Cmurray.efford%40otago.ac.nz%7C0215a2eac18a47b8f63108d940bcd5d9%7C0225efc578fe4928b1579ef24809e9ba%7C1%7C0%7C637612003078348021%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=h%2FGUwYdqUFaP7y2R9r%2BD40xKGAQ3A7igBm0PWP9%2BlpM%3D&reserved=0
> <https://apc01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fcran.r-project.org%2Fdoc%2Fmanuals%2FR-ints.html%23Lazy-loading&data=04%7C01%7Cmurray.efford%40otago.ac.nz%7C0215a2eac18a47b8f63108d940bcd5d9%7C0225efc578fe4928b1579ef24809e9ba%7C1%7C0%7C637612003078348021%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=h%2FGUwYdqUFaP7y2R9r%2BD40xKGAQ3A7igBm0PWP9%2BlpM%3D&reserved=0>
> >>>
> >>> I know nothing about it so I will not comment further.
> >>>
> >>> Best,
> >>>
> >>> B.
> >>>
> >>> ______________________________________________
> >>> R-package-devel using r-project.org
> <mailto:R-package-devel using r-project.org> mailing list
> >>> https://apc01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fr-package-devel&data=04%7C01%7Cmurray.efford%40otago.ac.nz%7C0215a2eac18a47b8f63108d940bcd5d9%7C0225efc578fe4928b1579ef24809e9ba%7C1%7C0%7C637612003078357978%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=qdOZZ66nPru98mfJQfM6X2A5dJ71uGdmfuqdgaMTd0c%3D&reserved=0
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> >>
> >> [[alternative HTML version deleted]]
> >>
> >> ______________________________________________
> >> R-package-devel using r-project.org
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> >>
> >
> > [[alternative HTML version deleted]]
> >
> > ______________________________________________
> > R-package-devel using r-project.org
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