[R-pkg-devel] NOTE regarding dependencies in R code: Missing or unexported object
--- Begin Message ---
Hi,
I have sent my package "clickR" to CRAN and was asked to fix the following NOTE:
* checking dependencies in R code ... NOTE
Missing or unexported object: 'lmerTest::summary'
I'm not sure what's going on, here is the Imports section of my DESCRIPTION
file:
Imports: beeswarm, boot, lme4, lmerTest, methods, ReporteRs, xtable
Here are the first lines of the function causing this NOTE:
report.merModLmerTest<-function(x, file=NULL, type="word", digits=3,
digitspvals=3, font=ifelse(Sys.info()["sysname"]
== "Windows", "Arial",
"Helvetica")[[1]], pointsize=11, info=TRUE, ...){ sx <- lmerTest::summary(x)
cor <- as.data.frame(lme4::VarCorr(x)) ...
And here is the output from getNamespaceExports("lmerTest") where "summary" is
listed at position [23]
[1] "lmer" "lsmeansLT" ".__T__is.infinite:base"
[4] ".__T__as.integer:base" ".__T__as.numeric:base" ".__T__%*%:base"
[7] ".__T__dim:base" ".__T__summary:base" ".__T__$<-:base"
[10] ".__T__^:base" ".__T__sum:base" ".__T__rep:base"
[13] ".__T__*:base" ".__T__[<-:base" ".__T__as.logical:base"
[16] ".__T__dimnames:base" ".__T__%/%:base" ".__T__prod:base"
[19] ".__T__[[<-:base" ".__T__/:base" "step"
[22] "calcSatterth" "summary" ".__T__anova:stats"
[25] ".__T__is.finite:base" ".__T__anyNA:base" ".__T__!:base"
[28] ".__T__all:base" ".__T__+:base" ".__T__any:base"
[31] ".__T__dim<-:base" ".__T__-:base" ".__T__[:base"
[34] "anova" "difflsmeans" "lsmeans"
[37] "rand" ".__C__merModLmerTest" ".__T__length:base"
[40] ".__T__is.na:base" ".__T__dimnames<-:base" ".__T__&:base"
[43] ".__T__%%:base" ".__T__$:base"
I have tried to reproduce this problem in my computer with different versions
of R (3.4.4, 3.5 RC and R-devel) and only get the NOTE when performing the
check with R-devel.
What should I do to fix this?
[[alternative HTML version deleted]]
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Re: [R-pkg-devel] NOTE regarding dependencies in R code: Missing or unexported object
I don't think 'summary' is actually exported by lmerTest (version >= 3.0-0):
library(lmerTest)
fm <- lmer(Informed.liking ~ Gender + Information * Product + (1 | Consumer) +
(1 | Consumer:Product), data=ham)
lmerTest::summary(fm) # gives: Error: 'summary' is not an exported
object from 'namespace:lmerTest'
On the other hand
summary(fm)
works just fine. lmerTest defines the S3 method 'summary' for
'lmerModLmerTest' objects, so if you change sx <-
lmerTest::summary(x) to sx <- summary(x) you should be fine assuming
that x is of class 'lmerModLmerTest'.
For more details see
https://stat.ethz.ch/pipermail/r-sig-mixed-models/2018q1/026596.html
and perhaps
https://github.com/runehaubo/lmerTestR/blob/master/pkg_notes/new_lmerTest.pdf
(which you were also pointed to previously).
Best regards
Rune
On 20 April 2018 at 21:53, David Hervás via R-package-devel
wrote:
> __
> R-package-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-package-devel
>
>
> -- Forwarded message --
> From: "David Hervás"
> To: "r-package-devel@r-project.org"
> Cc:
> Bcc:
> Date: Fri, 20 Apr 2018 19:53:50 + (UTC)
> Subject: NOTE regarding dependencies in R code: Missing or unexported object
> Hi,
> I have sent my package "clickR" to CRAN and was asked to fix the following
> NOTE:
> * checking dependencies in R code ... NOTE
> Missing or unexported object: 'lmerTest::summary'
> I'm not sure what's going on, here is the Imports section of my DESCRIPTION
> file:
> Imports: beeswarm, boot, lme4, lmerTest, methods, ReporteRs, xtable
>
>
>
> Here are the first lines of the function causing this NOTE:
> report.merModLmerTest<-function(x, file=NULL, type="word", digits=3,
> digitspvals=3,
> font=ifelse(Sys.info()["sysname"] == "Windows", "Arial",
> "Helvetica")[[1]], pointsize=11, info=TRUE, ...){ sx
> <- lmerTest::summary(x) cor <- as.data.frame(lme4::VarCorr(x)) ...
>
> And here is the output from getNamespaceExports("lmerTest") where "summary"
> is listed at position [23]
>
> [1] "lmer" "lsmeansLT"
> ".__T__is.infinite:base" [4] ".__T__as.integer:base" ".__T__as.numeric:base"
> ".__T__%*%:base" [7] ".__T__dim:base" ".__T__summary:base"
> ".__T__$<-:base"[10] ".__T__^:base" ".__T__sum:base"
>".__T__rep:base"[13] ".__T__*:base" ".__T__[<-:base"
> ".__T__as.logical:base" [16] ".__T__dimnames:base"".__T__%/%:base"
> ".__T__prod:base" [19] ".__T__[[<-:base"".__T__/:base"
> "step" [22] "calcSatterth" "summary"
>".__T__anova:stats" [25] ".__T__is.finite:base"
> ".__T__anyNA:base" ".__T__!:base" [28] ".__T__all:base"
> ".__T__+:base" ".__T__any:base"[31] ".__T__dim<-:base"
> ".__T__-:base" ".__T__[:base" [34] "anova"
>"difflsmeans""lsmeans" [37] "rand"
> ".__C__merModLmerTest" ".__T__length:base" [40] ".__T__is.na:base"
> ".__T__dimnames<-:base" ".__T__&:base" [43] ".__T__%%:base"
> ".__T__$:base"
This seems to be from an older version of lmerTest.
>
>
> I have tried to reproduce this problem in my computer with different versions
> of R (3.4.4, 3.5 RC and R-devel) and only get the NOTE when performing the
> check with R-devel.
Have you checked that you are using a recent version of lmerTest with
3.4.4 and 3.5 RC? I think that might explain the diff.
> What should I do to fix this?
> [[alternative HTML version deleted]]
>
>
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Re: [R-pkg-devel] NOTE regarding dependencies in R code: Missing or unexported object
On 20/04/2018 3:53 PM, David Hervás via R-package-devel wrote:
Hi,
I have sent my package "clickR" to CRAN and was asked to fix the following NOTE:
* checking dependencies in R code ... NOTE
Missing or unexported object: 'lmerTest::summary'
I'm not sure what's going on, here is the Imports section of my DESCRIPTION
file:
Imports: beeswarm, boot, lme4, lmerTest, methods, ReporteRs, xtable
Here are the first lines of the function causing this NOTE:
report.merModLmerTest<-function(x, file=NULL, type="word", digits=3, digitspvals=3,
font=ifelse(Sys.info()["sysname"] == "Windows", "Arial",
"Helvetica")[[1]], pointsize=11, info=TRUE, ...){ sx <- lmerTest::summary(x) cor <- as.data.frame(lme4::VarCorr(x)) ...
And here is the output from getNamespaceExports("lmerTest") where "summary" is
listed at position [23]
[1] "lmer" "lsmeansLT" ".__T__is.infinite:base" [4] ".__T__as.integer:base" ".__T__as.numeric:base" ".__T__%*%:base" [7] ".__T__dim:base" ".__T__summary:base" ".__T__$<-:base" [10] ".__T__^:base" ".__T__sum:base" ".__T__rep:base" [13] ".__T__*:base" ".__T__[<-:base"
".__T__as.logical:base" [16] ".__T__dimnames:base" ".__T__%/%:base" ".__T__prod:base" [19] ".__T__[[<-:base" ".__T__/:base" "step" [22] "calcSatterth" "summary" ".__T__anova:stats" [25] ".__T__is.finite:base" ".__T__anyNA:base" ".__T__!:base" [28] ".__T__all:base" ".__T__+:base"
".__T__any:base" [31] ".__T__dim<-:base" ".__T__-:base" ".__T__[:base" [34] "anova" "difflsmeans" "lsmeans" [37] "rand" ".__C__merModLmerTest" ".__T__length:base" [40] ".__T__is.na:base" ".__T__dimnames<-:base" ".__T__&:base" [43] ".__T__%%:base"
".__T__$:base"
I have tried to reproduce this problem in my computer with different versions
of R (3.4.4, 3.5 RC and R-devel) and only get the NOTE when performing the
check with R-devel.
What should I do to fix this?
getNamespaceExports() is described on its help page as an internal
function, not intended for users. If you want to see the exports of a
package, look at its NAMESPACE file. For example,
file.show(system.file("NAMESPACE", package="lmerTest"))
which lists these lines as exports:
export(as_lmerModLmerTest)
export(calcSatterth)
export(contest)
export(contest1D)
export(contestMD)
export(difflsmeans)
export(get_model)
export(lmer)
export(ls_means)
export(lsmeansLT)
export(ranova)
export(show_tests)
export(step)
The summary() function isn't listed there, as Rune demonstrated.
Duncan Murdoch
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Re: [R-pkg-devel] NOTE regarding dependencies in R code: Missing or unexported object
--- Begin Message ---
My fault, just noticed I had downloaded the wrong version of lmerTest from
github (lmerTest instead of lmerTestR). Fixed now. Thank you
Regards,
David
En sábado, 21 de abril de 2018 16:27:45 CEST, Rune Haubo
escribió:
I don't think 'summary' is actually exported by lmerTest (version >= 3.0-0):
library(lmerTest)
fm <- lmer(Informed.liking ~ Gender + Information * Product + (1 | Consumer) +
(1 | Consumer:Product), data=ham)
lmerTest::summary(fm) # gives: Error: 'summary' is not an exported
object from 'namespace:lmerTest'
On the other hand
summary(fm)
works just fine. lmerTest defines the S3 method 'summary' for
'lmerModLmerTest' objects, so if you change sx <-
lmerTest::summary(x) to sx <- summary(x) you should be fine assuming
that x is of class 'lmerModLmerTest'.
For more details see
https://stat.ethz.ch/pipermail/r-sig-mixed-models/2018q1/026596.html
and perhaps
https://github.com/runehaubo/lmerTestR/blob/master/pkg_notes/new_lmerTest.pdf
(which you were also pointed to previously).
Best regards
Rune
On 20 April 2018 at 21:53, David Hervás via R-package-devel
wrote:
> __
> R-package-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-package-devel
>
>
> -- Forwarded message --
> From: "David Hervás"
> To: "r-package-devel@r-project.org"
> Cc:
> Bcc:
> Date: Fri, 20 Apr 2018 19:53:50 + (UTC)
> Subject: NOTE regarding dependencies in R code: Missing or unexported object
> Hi,
> I have sent my package "clickR" to CRAN and was asked to fix the following
> NOTE:
> * checking dependencies in R code ... NOTE
> Missing or unexported object: 'lmerTest::summary'
> I'm not sure what's going on, here is the Imports section of my DESCRIPTION
> file:
> Imports: beeswarm, boot, lme4, lmerTest, methods, ReporteRs, xtable
>
>
>
> Here are the first lines of the function causing this NOTE:
> report.merModLmerTest<-function(x, file=NULL, type="word", digits=3,
> digitspvals=3,
> font=ifelse(Sys.info()["sysname"] == "Windows", "Arial",
> "Helvetica")[[1]], pointsize=11, info=TRUE, ...){ sx
> <- lmerTest::summary(x) cor <- as.data.frame(lme4::VarCorr(x)) ...
>
> And here is the output from getNamespaceExports("lmerTest") where "summary"
> is listed at position [23]
>
> [1] "lmer" "lsmeansLT"
>".__T__is.infinite:base" [4] ".__T__as.integer:base" ".__T__as.numeric:base"
>".__T__%*%:base" [7] ".__T__dim:base" ".__T__summary:base"
>".__T__$<-:base" [10] ".__T__^:base" ".__T__sum:base"
>".__T__rep:base" [13] ".__T__*:base" ".__T__[<-:base"
>".__T__as.logical:base" [16] ".__T__dimnames:base" ".__T__%/%:base"
>".__T__prod:base" [19] ".__T__[[<-:base" ".__T__/:base"
>"step" [22] "calcSatterth" "summary"
>".__T__anova:stats" [25] ".__T__is.finite:base" ".__T__anyNA:base"
>".__T__!:base" [28] ".__T__all:base" ".__T__+:base"
>".__T__any:base" [31] ".__T__dim<-:base" ".__T__-:base"
>".__T__[:base" [34] "anova" "difflsmeans"
>"lsmeans" [37] "rand" ".__C__merModLmerTest"
>".__T__length:base" [40] ".__T__is.na:base" ".__T__dimnames<-:base"
>".__T__&:base" [43] ".__T__%%:base" ".__T__$:base"
This seems to be from an older version of lmerTest.
>
>
> I have tried to reproduce this problem in my computer with different versions
> of R (3.4.4, 3.5 RC and R-devel) and only get the NOTE when performing the
> check with R-devel.
Have you checked that you are using a recent version of lmerTest with
3.4.4 and 3.5 RC? I think that might explain the diff.
> What should I do to fix this?
> [[alternative HTML version deleted]]
>
>
[[alternative HTML version deleted]]
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Re: [R-pkg-devel] Fwd: [CRAN-pretest-archived] CRAN submission Boom 0.8
No word from the maintainers. I submitted a revised version of the package just now (with an updated date in DESCRIPTION). If someone could look at it in the next few days I'd appreciate it. Thanks. On Wed, Apr 4, 2018 at 3:01 PM, Steven Scott wrote: > Thanks Dirk. IMO the package is in good shape otherwise. I'll wait hear > from the CRAN maintainers. > S > > On Wed, Apr 4, 2018 at 2:53 PM, Dirk Eddelbuettel wrote: > >> >> On 4 April 2018 at 14:15, Steven Scott wrote: >> | These appear to be caused by an ill formed std::set or std::function in >> the >> | STL implementation of the host machine. If I'm reading that wrong >> someone >> | please let me know. >> >> AFAICT it needs C++11 explicitly set which that machine (with a new >> clang-6.0 >> installation) did not provide by default. This has bitten a few other >> compilations lately as well but should get sorted out in due course. >> >> Dirk >> >> -- >> http://dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org >> > > [[alternative HTML version deleted]] __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] Fwd: [CRAN-pretest-archived] CRAN submission Boom 0.8
On 21.04.2018 20:06, Steven Scott wrote: No word from the maintainers. Only one maintainer is reading this list. I submitted a revised version of the package just now (with an updated date in DESCRIPTION). Thanks. If someone could look at it in the next few days I'd appreciate it. Thanks. We will do. Best, Uwe Ligges On Wed, Apr 4, 2018 at 3:01 PM, Steven Scott wrote: Thanks Dirk. IMO the package is in good shape otherwise. I'll wait hear from the CRAN maintainers. S On Wed, Apr 4, 2018 at 2:53 PM, Dirk Eddelbuettel wrote: On 4 April 2018 at 14:15, Steven Scott wrote: | These appear to be caused by an ill formed std::set or std::function in the | STL implementation of the host machine. If I'm reading that wrong someone | please let me know. AFAICT it needs C++11 explicitly set which that machine (with a new clang-6.0 installation) did not provide by default. This has bitten a few other compilations lately as well but should get sorted out in due course. Dirk -- http://dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org [[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] Fwd: [CRAN-pretest-archived] CRAN submission Boom 0.8
Thanks Uwe. On Sat, Apr 21, 2018 at 3:02 PM, Uwe Ligges wrote: > > > On 21.04.2018 20:06, Steven Scott wrote: > >> No word from the maintainers. >> > > Only one maintainer is reading this list. > > > I submitted a revised version of the package >> just now (with an updated date in DESCRIPTION). >> > > Thanks. > > If someone could look at it in the next few days I'd appreciate it. >> Thanks. >> > > We will do. > > Best, > Uwe Ligges > >> On Wed, Apr 4, 2018 at 3:01 PM, Steven Scott < >> steve.the.bayes...@gmail.com> >> wrote: >> >> Thanks Dirk. IMO the package is in good shape otherwise. I'll wait hear >>> from the CRAN maintainers. >>> S >>> >>> On Wed, Apr 4, 2018 at 2:53 PM, Dirk Eddelbuettel >>> wrote: >>> >>> On 4 April 2018 at 14:15, Steven Scott wrote: | These appear to be caused by an ill formed std::set or std::function in the | STL implementation of the host machine. If I'm reading that wrong someone | please let me know. AFAICT it needs C++11 explicitly set which that machine (with a new clang-6.0 installation) did not provide by default. This has bitten a few other compilations lately as well but should get sorted out in due course. Dirk -- http://dirk.eddelbuettel.com | @eddelbuettel | e...@debian.org >>> >>> >> [[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
