[R-pkg-devel] rcmdcheck reports wrong version of lattice
Dear all,
rcmdcheck::rcmdcheck() runs fine on my package. rcmdcheck::rcmdcheck(args
= c("--as-cran")) reports an error: package ‘lattice’ was installed before
R 4.0.0: please re-install it
The error persists, even when I reinstall lattice.
What am I missing?
Best regards,
Thierry
sessioninfo::session_info("lattice")
─ Session info
setting value
version R version 4.0.4 (2021-02-15)
os Ubuntu 18.04.5 LTS
system x86_64, linux-gnu
ui RStudio
language nl_BE:nl
collate nl_BE.UTF-8
ctypenl_BE.UTF-8
tz Europe/Brussels
date 2021-03-08
─ Packages
package * version date lib source
lattice 0.20-41 2020-04-02 [1] CRAN (R 4.0.4)
ir. Thierry Onkelinx
Statisticus / Statistician
Vlaamse Overheid / Government of Flanders
INSTITUUT VOOR NATUUR- EN BOSONDERZOEK / RESEARCH INSTITUTE FOR NATURE AND
FOREST
Team Biometrie & Kwaliteitszorg / Team Biometrics & Quality Assurance
thierry.onkel...@inbo.be
Havenlaan 88 bus 73, 1000 Brussel
www.inbo.be
///
To call in the statistician after the experiment is done may be no more
than asking him to perform a post-mortem examination: he may be able to say
what the experiment died of. ~ Sir Ronald Aylmer Fisher
The plural of anecdote is not data. ~ Roger Brinner
The combination of some data and an aching desire for an answer does not
ensure that a reasonable answer can be extracted from a given body of data.
~ John Tukey
///
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Re: [R-pkg-devel] rcmdcheck reports wrong version of lattice
On 08.03.2021 17:17, Thierry Onkelinx wrote:
Dear all,
rcmdcheck::rcmdcheck() runs fine on my package. rcmdcheck::rcmdcheck(args
= c("--as-cran")) reports an error: package ‘lattice’ was installed before
R 4.0.0: please re-install it
I have no idea how that package perfoms the checks, but I guess you have
an outdated version of lattice (or borken installtion of lattice) in
another library of packages that is used for these checks?
Best,
Uwe Ligges
The error persists, even when I reinstall lattice.
What am I missing?
Best regards,
Thierry
sessioninfo::session_info("lattice")
─ Session info
setting value
version R version 4.0.4 (2021-02-15)
os Ubuntu 18.04.5 LTS
system x86_64, linux-gnu
ui RStudio
language nl_BE:nl
collate nl_BE.UTF-8
ctypenl_BE.UTF-8
tz Europe/Brussels
date 2021-03-08
─ Packages
package * version date lib source
lattice 0.20-41 2020-04-02 [1] CRAN (R 4.0.4)
ir. Thierry Onkelinx
Statisticus / Statistician
Vlaamse Overheid / Government of Flanders
INSTITUUT VOOR NATUUR- EN BOSONDERZOEK / RESEARCH INSTITUTE FOR NATURE AND
FOREST
Team Biometrie & Kwaliteitszorg / Team Biometrics & Quality Assurance
thierry.onkel...@inbo.be
Havenlaan 88 bus 73, 1000 Brussel
www.inbo.be
///
To call in the statistician after the experiment is done may be no more
than asking him to perform a post-mortem examination: he may be able to say
what the experiment died of. ~ Sir Ronald Aylmer Fisher
The plural of anecdote is not data. ~ Roger Brinner
The combination of some data and an aching desire for an answer does not
ensure that a reasonable answer can be extracted from a given body of data.
~ John Tukey
///
[[alternative HTML version deleted]]
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Re: [R-pkg-devel] rcmdcheck reports wrong version of lattice
Hi,
If you think this is a bug in rcmdcheck, then please report an issue
here: https://github.com/r-lib/rcmdcheck/issues
My guess is that you have another version of lattice in another
library, and that version is used with `--as-cran`.
Gabor
On Mon, Mar 8, 2021 at 5:18 PM Thierry Onkelinx
wrote:
>
> Dear all,
>
> rcmdcheck::rcmdcheck() runs fine on my package. rcmdcheck::rcmdcheck(args
> = c("--as-cran")) reports an error: package ‘lattice’ was installed before
> R 4.0.0: please re-install it
> The error persists, even when I reinstall lattice.
>
> What am I missing?
>
> Best regards,
>
> Thierry
>
> sessioninfo::session_info("lattice")
> ─ Session info
>
> setting value
> version R version 4.0.4 (2021-02-15)
> os Ubuntu 18.04.5 LTS
> system x86_64, linux-gnu
> ui RStudio
> language nl_BE:nl
> collate nl_BE.UTF-8
> ctypenl_BE.UTF-8
> tz Europe/Brussels
> date 2021-03-08
>
> ─ Packages
>
> package * version date lib source
> lattice 0.20-41 2020-04-02 [1] CRAN (R 4.0.4)
>
>
> ir. Thierry Onkelinx
> Statisticus / Statistician
>
> Vlaamse Overheid / Government of Flanders
> INSTITUUT VOOR NATUUR- EN BOSONDERZOEK / RESEARCH INSTITUTE FOR NATURE AND
> FOREST
> Team Biometrie & Kwaliteitszorg / Team Biometrics & Quality Assurance
> thierry.onkel...@inbo.be
> Havenlaan 88 bus 73, 1000 Brussel
> www.inbo.be
>
> ///
> To call in the statistician after the experiment is done may be no more
> than asking him to perform a post-mortem examination: he may be able to say
> what the experiment died of. ~ Sir Ronald Aylmer Fisher
> The plural of anecdote is not data. ~ Roger Brinner
> The combination of some data and an aching desire for an answer does not
> ensure that a reasonable answer can be extracted from a given body of data.
> ~ John Tukey
> ///
>
>
>
> [[alternative HTML version deleted]]
>
> __
> R-package-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-package-devel
__
R-package-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] rcmdcheck reports wrong version of lattice
Yes, This was the problem. The recent version of lattice was in my home
folder ~/R/x86_64-pc-linux-gnu-library/4.0 (first element of .libPaths()).
An older version of lattice was in /usr/lib/R/library (last element of
.libPaths()).
install.packages("lattice", lib = "/usr/lib/R/library") solved the problem.
So it looks like rcmdcheck ignored the first element of .libPaths(). I'm
not sure if that is a bug of rcmdcheck. Shall I report an issue?
Best regards,
Thierry
ir. Thierry Onkelinx
Statisticus / Statistician
Vlaamse Overheid / Government of Flanders
INSTITUUT VOOR NATUUR- EN BOSONDERZOEK / RESEARCH INSTITUTE FOR NATURE AND
FOREST
Team Biometrie & Kwaliteitszorg / Team Biometrics & Quality Assurance
thierry.onkel...@inbo.be
Havenlaan 88 bus 73, 1000 Brussel
www.inbo.be
///
To call in the statistician after the experiment is done may be no more
than asking him to perform a post-mortem examination: he may be able to say
what the experiment died of. ~ Sir Ronald Aylmer Fisher
The plural of anecdote is not data. ~ Roger Brinner
The combination of some data and an aching desire for an answer does not
ensure that a reasonable answer can be extracted from a given body of data.
~ John Tukey
///
Op ma 8 mrt. 2021 om 17:28 schreef Gábor Csárdi :
> Hi,
>
> If you think this is a bug in rcmdcheck, then please report an issue
> here: https://github.com/r-lib/rcmdcheck/issues
>
> My guess is that you have another version of lattice in another
> library, and that version is used with `--as-cran`.
>
> Gabor
>
> On Mon, Mar 8, 2021 at 5:18 PM Thierry Onkelinx
> wrote:
> >
> > Dear all,
> >
> > rcmdcheck::rcmdcheck() runs fine on my package.
> rcmdcheck::rcmdcheck(args
> > = c("--as-cran")) reports an error: package ‘lattice’ was installed
> before
> > R 4.0.0: please re-install it
> > The error persists, even when I reinstall lattice.
> >
> > What am I missing?
> >
> > Best regards,
> >
> > Thierry
> >
> > sessioninfo::session_info("lattice")
> > ─ Session info
> >
>
> > setting value
> > version R version 4.0.4 (2021-02-15)
> > os Ubuntu 18.04.5 LTS
> > system x86_64, linux-gnu
> > ui RStudio
> > language nl_BE:nl
> > collate nl_BE.UTF-8
> > ctypenl_BE.UTF-8
> > tz Europe/Brussels
> > date 2021-03-08
> >
> > ─ Packages
> >
>
> > package * version date lib source
> > lattice 0.20-41 2020-04-02 [1] CRAN (R 4.0.4)
> >
> >
> > ir. Thierry Onkelinx
> > Statisticus / Statistician
> >
> > Vlaamse Overheid / Government of Flanders
> > INSTITUUT VOOR NATUUR- EN BOSONDERZOEK / RESEARCH INSTITUTE FOR NATURE
> AND
> > FOREST
> > Team Biometrie & Kwaliteitszorg / Team Biometrics & Quality Assurance
> > thierry.onkel...@inbo.be
> > Havenlaan 88 bus 73, 1000 Brussel
> > www.inbo.be
> >
> >
> ///
> > To call in the statistician after the experiment is done may be no more
> > than asking him to perform a post-mortem examination: he may be able to
> say
> > what the experiment died of. ~ Sir Ronald Aylmer Fisher
> > The plural of anecdote is not data. ~ Roger Brinner
> > The combination of some data and an aching desire for an answer does not
> > ensure that a reasonable answer can be extracted from a given body of
> data.
> > ~ John Tukey
> >
> ///
> >
> >
> >
> > [[alternative HTML version deleted]]
> >
> > __
> > R-package-devel@r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-package-devel
>
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__
R-package-devel@r-project.org mailing list
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Re: [R-pkg-devel] rcmdcheck reports wrong version of lattice
On Mon, Mar 8, 2021 at 5:45 PM Thierry Onkelinx
wrote:
> Yes, This was the problem. The recent version of lattice was in my home
> folder ~/R/x86_64-pc-linux-gnu-library/4.0 (first element of .libPaths()).
> An older version of lattice was in /usr/lib/R/library (last element of
> .libPaths()).
>
> install.packages("lattice", lib = "/usr/lib/R/library") solved the problem.
>
> So it looks like rcmdcheck ignored the first element of .libPaths(). I'm
> not sure if that is a bug of rcmdcheck. Shall I report an issue?
>
If you suspect that this behavior is different from running `R CMD check`
directly, then yes, please do.
Thanks,
Gabor
[...]
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Re: [R-pkg-devel] rcmdcheck reports wrong version of lattice
I haven't followed all the code branches in tools:::.check_packages(),
but some of them use --vanilla when running the R subprocess that does
the checking. I think that would mean that libraries in ~/R would not
be in the search path.
-BIll
On Mon, Mar 8, 2021 at 8:45 AM Thierry Onkelinx
wrote:
>
> Yes, This was the problem. The recent version of lattice was in my home
> folder ~/R/x86_64-pc-linux-gnu-library/4.0 (first element of .libPaths()).
> An older version of lattice was in /usr/lib/R/library (last element of
> .libPaths()).
>
> install.packages("lattice", lib = "/usr/lib/R/library") solved the problem.
>
> So it looks like rcmdcheck ignored the first element of .libPaths(). I'm
> not sure if that is a bug of rcmdcheck. Shall I report an issue?
>
> Best regards,
>
> Thierry
>
> ir. Thierry Onkelinx
> Statisticus / Statistician
>
> Vlaamse Overheid / Government of Flanders
> INSTITUUT VOOR NATUUR- EN BOSONDERZOEK / RESEARCH INSTITUTE FOR NATURE AND
> FOREST
> Team Biometrie & Kwaliteitszorg / Team Biometrics & Quality Assurance
> thierry.onkel...@inbo.be
> Havenlaan 88 bus 73, 1000 Brussel
> www.inbo.be
>
> ///
> To call in the statistician after the experiment is done may be no more
> than asking him to perform a post-mortem examination: he may be able to say
> what the experiment died of. ~ Sir Ronald Aylmer Fisher
> The plural of anecdote is not data. ~ Roger Brinner
> The combination of some data and an aching desire for an answer does not
> ensure that a reasonable answer can be extracted from a given body of data.
> ~ John Tukey
> ///
>
>
>
>
> Op ma 8 mrt. 2021 om 17:28 schreef Gábor Csárdi :
>
> > Hi,
> >
> > If you think this is a bug in rcmdcheck, then please report an issue
> > here: https://github.com/r-lib/rcmdcheck/issues
> >
> > My guess is that you have another version of lattice in another
> > library, and that version is used with `--as-cran`.
> >
> > Gabor
> >
> > On Mon, Mar 8, 2021 at 5:18 PM Thierry Onkelinx
> > wrote:
> > >
> > > Dear all,
> > >
> > > rcmdcheck::rcmdcheck() runs fine on my package.
> > rcmdcheck::rcmdcheck(args
> > > = c("--as-cran")) reports an error: package ‘lattice’ was installed
> > before
> > > R 4.0.0: please re-install it
> > > The error persists, even when I reinstall lattice.
> > >
> > > What am I missing?
> > >
> > > Best regards,
> > >
> > > Thierry
> > >
> > > sessioninfo::session_info("lattice")
> > > ─ Session info
> > >
> >
> > > setting value
> > > version R version 4.0.4 (2021-02-15)
> > > os Ubuntu 18.04.5 LTS
> > > system x86_64, linux-gnu
> > > ui RStudio
> > > language nl_BE:nl
> > > collate nl_BE.UTF-8
> > > ctypenl_BE.UTF-8
> > > tz Europe/Brussels
> > > date 2021-03-08
> > >
> > > ─ Packages
> > >
> >
> > > package * version date lib source
> > > lattice 0.20-41 2020-04-02 [1] CRAN (R 4.0.4)
> > >
> > >
> > > ir. Thierry Onkelinx
> > > Statisticus / Statistician
> > >
> > > Vlaamse Overheid / Government of Flanders
> > > INSTITUUT VOOR NATUUR- EN BOSONDERZOEK / RESEARCH INSTITUTE FOR NATURE
> > AND
> > > FOREST
> > > Team Biometrie & Kwaliteitszorg / Team Biometrics & Quality Assurance
> > > thierry.onkel...@inbo.be
> > > Havenlaan 88 bus 73, 1000 Brussel
> > > www.inbo.be
> > >
> > >
> > ///
> > > To call in the statistician after the experiment is done may be no more
> > > than asking him to perform a post-mortem examination: he may be able to
> > say
> > > what the experiment died of. ~ Sir Ronald Aylmer Fisher
> > > The plural of anecdote is not data. ~ Roger Brinner
> > > The combination of some data and an aching desire for an answer does not
> > > ensure that a reasonable answer can be extracted from a given body of
> > data.
> > > ~ John Tukey
> > >
> > ///
> > >
> > >
> > >
> > > [[alternative HTML version deleted]]
> > >
> > > __
> > > R-package-devel@r-project.org mailing list
> > > https://stat.ethz.ch/mailman/listinfo/r-package-devel
> >
>
> [[alternative HTML version deleted]]
>
> __
> R-package-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-package-devel
