[R-pkg-devel] package test returns error when R version 4.1.0

[Murray Efford]

Likewise: secr now passes on Winbuilder for R-release.
Thanks
Murray

________________________________________
From: Gianmarco Alberti <gianmarcoalberti using gmail.com>
Sent: 08 July 2021 08:21
To: r-package-devel using r-project.org
Cc: Murray Efford; Duncan Murdoch; Alex Chubaty; Uwe Ligges
Subject: Re: [R-pkg-devel] package test returns error when R version 4.1.0

Dear All,
Thanks for the useful discussion.

After Uwe’s prompt, I have tested the package again, and everything is fine now.
Was it a CRAN issue?

Whatever the issue was, I am glad my new version is bound to be on CRAN soon (I have just submitted it).

Best
Gianmarco

************************************************
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
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Correspondence Analysis website
http://cainarchaeology.weebly.com/<https://apc01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fcainarchaeology.weebly.com%2F&data=04%7C01%7Cmurray.efford%40otago.ac.nz%7Cc4dbf78cce0a48d0d11708d94184c644%7C0225efc578fe4928b1579ef24809e9ba%7C1%7C0%7C637612862130933658%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=CsvmSG6H6Hdo32dt95ylIXFJL80zBFKpwp8Jck5awns%3D&reserved=0>

R packages on CRAN:
CAinterprTools
https://cran.r-project.org/web/packages/CAinterprTools/index.html<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%7Cc4dbf78cce0a48d0d11708d94184c644%7C0225efc578fe4928b1579ef24809e9ba%7C1%7C0%7C637612862130943618%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=LAeqHw6HR8j99IxLlt142lRP9Zr0OHvQuaRSMgE6tz4%3D&reserved=0>

GmAMisc
https://cran.r-project.org/package=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%7Cc4dbf78cce0a48d0d11708d94184c644%7C0225efc578fe4928b1579ef24809e9ba%7C1%7C0%7C637612862130943618%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=0g8Doj4UduPhPihoTd0M5i8UkHEAu526hW8bw%2FLqW2A%3D&reserved=0>

movecost
https://cran.r-project.org/web/packages/movecost/index.html<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%7Cc4dbf78cce0a48d0d11708d94184c644%7C0225efc578fe4928b1579ef24809e9ba%7C1%7C0%7C637612862130953573%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=NTlgzW0PBh7RvbhNWb9ZCWsUG8Fh2NcVIqX%2Flta9%2FJ4%3D&reserved=0>
************************************************
On 7 Jul 2021, 16:47 +0200, Uwe Ligges <ligges using statistik.tu-dortmund.de>, wrote:
Can you pls try again now.

Best,
Uwe Ligges

On 06.07.2021 23:18, Murray Efford wrote:
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

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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
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movecost
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<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.

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