[R-pkg-devel] Errors in r-devel (Linux) and r-patched (Solaris)
Dear all, I was notified about errors: https://cran.r-project.org/web/checks/check_results_replicateBE.html Since I don't have access to those operating systems, I'm a little bit lost. Here is what I get with 64bit R on Windows: library(replicateBE) x <- method.B(details = TRUE, print = FALSE, data = rds30, option = 1)[c(10, 19)] y <- c(17.86418, 92.73371) d <- as.numeric(signif(abs(x - y), 7)) With R 3.6.2 print(d) [1] 4.431372e-06 1.182994e-07 With R 3.6.3 print(d) [1] 1.078696e-05 1.182989e-07 x[10] are Satterthwaite's degrees of freedom obtained by package pbkrtest. In both R-versions I use its current version (0.4-8.6 of 2020-02-20). Any ideas / suggestions? As a workaround I could reduce the tolerance of testthat's expect_quivalent() from to currently 5e-7 to a higher (_which one?_) value. But I still want to know what might be going on the CRAN's linux/solaris devel/patched installations since the other R-versions on all operating systems passed the tests. Cheers, Helmut -- Ing. Helmut Schütz BEBAC – Consultancy Services for Bioequivalence and Bioavailability Studies Neubaugasse 36/11 1070 Vienna, Austria T +43 1 2311746 E helmut.schu...@bebac.at W https://bebac.at/ F https://forum.bebac.at/ __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] Errors in r-devel (Linux) and r-patched (Solaris)
Do both of your R installations use the same version of lme4 ? A new lme4 version has been published on CRAN yesterday and some changes regarding default numerical tolerances in optimizations could explain the difference in your results. See the NEWS here: https://cran.r-project.org/web/packages/lme4/news.html Best regards, Sebastian Meyer Am 08.04.20 um 13:43 schrieb Helmut Schütz: > Dear all, > > I was notified about errors: > https://cran.r-project.org/web/checks/check_results_replicateBE.html > > Since I don't have access to those operating systems, I'm a little bit > lost. > Here is what I get with 64bit R on Windows: > library(replicateBE) > x <- method.B(details = TRUE, print = FALSE, > data = rds30, option = 1)[c(10, 19)] > y <- c(17.86418, 92.73371) > d <- as.numeric(signif(abs(x - y), 7)) > > With R 3.6.2 > print(d) > [1] 4.431372e-06 1.182994e-07 > > With R 3.6.3 > print(d) > [1] 1.078696e-05 1.182989e-07 > > x[10] are Satterthwaite's degrees of freedom obtained by package > pbkrtest. In both R-versions I use its current version (0.4-8.6 of > 2020-02-20). > > Any ideas / suggestions? > As a workaround I could reduce the tolerance of testthat's > expect_quivalent() from to currently 5e-7 to a higher (_which one?_) > value. But I still want to know what might be going on the CRAN's > linux/solaris devel/patched installations since the other R-versions on > all operating systems passed the tests. > > Cheers, > Helmut > __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] Errors in r-devel (Linux) and r-patched (Solaris)
Dear Sebastian, Sebastian Meyer wrote on 2020-04-08 14:15: Do both of your R installations use the same version of lme4 ? THX, good point! On R3.6.2 I have lme4 1.1-21 (2019-03-05) and on R3.6.3 indeed yesterday's lme4 1.1-23. A new lme4 version has been published on CRAN yesterday and some changes regarding default numerical tolerances in optimizations could explain the difference in your results. See the NEWS here: https://cran.r-project.org/web/packages/lme4/news.html I see. Since the other 93 (!) tests passed, I will submit a fix only for _this_ data set. A little bit nasty since we recently published a paper about software validation: https://dx.doi.org/10.1208/s12248-020-0427-6 The supplementary material contains code for IQ (installation qualification). If a user on r-devel (Linux) or r-patched (Solaris) runs it – with the current lme4 - he/she will be slapped in the face and the suppl. material will tell him/her: "If a test fails […] the package did not pass IQ in the user’s computational environment (hardware, operating system, R-release) and _must not_ be used." Splendid. Cheers, Helmut -- Ing. Helmut Schütz BEBAC – Consultancy Services for Bioequivalence and Bioavailability Studies Neubaugasse 36/11 1070 Vienna, Austria T +43 1 2311746 E helmut.schu...@bebac.at W https://bebac.at/ F https://forum.bebac.at/ __ R-package-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] Error creating union class: object ‘.__C__compMatrix’ not found
> renozao
> on Mon, 30 Mar 2020 21:20:43 + writes:
> Hi,
> when R CMD check is run under R-devel (2020-03-29 r78108) I get the
following error at installation:
> Error in get(cname, envir = cwhere, inherits = FALSE) :
> object ‘.__C__compMatrix’ not found
> Error in setClassUnion("mMatrix", c("Matrix", "matrix")) :
> unable to create union class: could not set members "Matrix"
> This does not happen on R 3.6.3.
> I tried with Matrix listed in Depends but I still get the same error.
> Is this linked to some changes in union classes or the Matrix package?
> Thank you.
> Bests,
> Renaud
Hi Renaud,
One reason you got no response here, is because we don't even
know about which package you are talking.
So there's nothing, anybody can reproduce from your posting.
There have been changes in R's dealing with class unions etc,
notably even *relating* to an earlier bug report on class unions
exactly for such a case which was *triggered* when people built
on such Matrix classes.
But we would really want to be able to reproduce what you are seeing..
Best regards,
Martin Maechler
ETH Zurich, R Core Team *and* maintainer("Matrix")
__
R-package-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-package-devel
Re: [R-pkg-devel] Error creating union class: object ‘.__C__compMatrix’ not found
Use trace() to get a bit more detail - .__C_compMatrix is looked for in the
wrong environment with inherits=FALSE.
> setClassUnion("mMatrix", c("Matrix", "matrix"))
Tracing get(name, envir = env) on entry
x=".AllMTable", envir="", topenv="", inherits=TRUE
Tracing get(name, envir = env) on entry
x=".MTable", envir="", topenv="", inherits=TRUE
Tracing get(name, envir = env) on entry
x=".AllMTable", envir="", topenv="", inherits=TRUE
Tracing get("#HAS_DUPLICATE_CLASS_NAMES", envir = .classTable) on entry
x="#HAS_DUPLICATE_CLASS_NAMES", envir="",
topenv="", inherits=TRUE
Tracing get(name, envir = env) on entry
x=".AllMTable", envir="", topenv="", inherits=TRUE
Tracing get(name, envir = env) on entry
x=".MTable", envir="", topenv="", inherits=TRUE
Tracing get(name, envir = env) on entry
x=".MTable", envir="", topenv="", inherits=TRUE
Tracing get(".SigLength", envir = env) on entry
x=".SigLength", envir="", topenv="", inherits=TRUE
Tracing get(".SigLength", envir = env) on entry
x=".SigLength", envir="", topenv="", inherits=TRUE
Tracing get(name, envir = env) on entry
x=".MTable", envir="", topenv="", inherits=TRUE
Tracing get(".SigLength", envir = env) on entry
x=".SigLength", envir="", topenv="", inherits=TRUE
Tracing get(".SigLength", envir = env) on entry
x=".SigLength", envir="", topenv="", inherits=TRUE
Tracing get(cname, envir = cwhere, inherits = FALSE) on entry
x=".__C__compMatrix", envir="",
topenv="", inherits=FALSE
Error in get(cname, envir = cwhere, inherits = FALSE) :
object '.__C__compMatrix' not found
...
Bill Dunlap
TIBCO Software
wdunlap tibco.com
On Wed, Apr 8, 2020 at 7:52 AM William Dunlap wrote:
> % R-devel --vanilla --quiet
> > library(Matrix)
> > setClassUnion("mMatrix", c("Matrix", "matrix"))
> Error in get(cname, envir = cwhere, inherits = FALSE) :
> object '.__C__compMatrix' not found
> Error in setClassUnion("mMatrix", c("Matrix", "matrix")) :
> unable to create union class: could not set members "Matrix"
> > sessionInfo()
> R Under development (unstable) (2020-04-07 r78175)
> Platform: x86_64-pc-linux-gnu (64-bit)
> Running under: Ubuntu 16.04.6 LTS
>
> Matrix products: default
> BLAS/LAPACK: /usr/lib/libopenblasp-r0.2.18.so
>
> locale:
> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
> [3] LC_TIME=en_US.UTF-8LC_COLLATE=en_US.UTF-8
> [5] LC_MONETARY=en_US.UTF-8LC_MESSAGES=en_US.UTF-8
> [7] LC_PAPER=en_US.UTF-8 LC_NAME=C
> [9] LC_ADDRESS=C LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats graphics grDevices utils datasets methods base
>
> other attached packages:
> [1] Matrix_1.2-18
>
> loaded via a namespace (and not attached):
> [1] compiler_4.1.0 grid_4.1.0 lattice_0.20-41
>
> Bill Dunlap
> TIBCO Software
> wdunlap tibco.com
>
>
> On Wed, Apr 8, 2020 at 7:35 AM Martin Maechler
> wrote:
>
>> > renozao
>> > on Mon, 30 Mar 2020 21:20:43 + writes:
>>
>> > Hi,
>> > when R CMD check is run under R-devel (2020-03-29 r78108) I get the
>> following error at installation:
>>
>> > Error in get(cname, envir = cwhere, inherits = FALSE) :
>> > object ‘.__C__compMatrix’ not found
>> > Error in setClassUnion("mMatrix", c("Matrix", "matrix")) :
>> > unable to create union class: could not set members "Matrix"
>>
>> > This does not happen on R 3.6.3.
>>
>> > I tried with Matrix listed in Depends but I still get the same
>> error.
>>
>> > Is this linked to some changes in union classes or the Matrix
>> package?
>>
>> > Thank you.
>>
>> > Bests,
>> > Renaud
>>
>> Hi Renaud,
>> One reason you got no response here, is because we don't even
>> know about which package you are talking.
>>
>> So there's nothing, anybody can reproduce from your posting.
>>
>> There have been changes in R's dealing with class unions etc,
>> notably even *relating* to an earlier bug report on class unions
>> exactly for such a case which was *triggered* when people built
>> on such Matrix classes.
>>
>> But we would really want to be able to reproduce what you are seeing..
>>
>> Best regards,
>> Martin Maechler
>>
>> ETH Zurich, R Core Team *and* maintainer("Matrix")
>>
>> __
>> 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
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Re: [R-pkg-devel] Error creating union class: object ‘.__C__compMatrix’ not found
% R-devel --vanilla --quiet
> library(Matrix)
> setClassUnion("mMatrix", c("Matrix", "matrix"))
Error in get(cname, envir = cwhere, inherits = FALSE) :
object '.__C__compMatrix' not found
Error in setClassUnion("mMatrix", c("Matrix", "matrix")) :
unable to create union class: could not set members "Matrix"
> sessionInfo()
R Under development (unstable) (2020-04-07 r78175)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.6 LTS
Matrix products: default
BLAS/LAPACK: /usr/lib/libopenblasp-r0.2.18.so
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] Matrix_1.2-18
loaded via a namespace (and not attached):
[1] compiler_4.1.0 grid_4.1.0 lattice_0.20-41
Bill Dunlap
TIBCO Software
wdunlap tibco.com
On Wed, Apr 8, 2020 at 7:35 AM Martin Maechler
wrote:
> > renozao
> > on Mon, 30 Mar 2020 21:20:43 + writes:
>
> > Hi,
> > when R CMD check is run under R-devel (2020-03-29 r78108) I get the
> following error at installation:
>
> > Error in get(cname, envir = cwhere, inherits = FALSE) :
> > object ‘.__C__compMatrix’ not found
> > Error in setClassUnion("mMatrix", c("Matrix", "matrix")) :
> > unable to create union class: could not set members "Matrix"
>
> > This does not happen on R 3.6.3.
>
> > I tried with Matrix listed in Depends but I still get the same error.
>
> > Is this linked to some changes in union classes or the Matrix
> package?
>
> > Thank you.
>
> > Bests,
> > Renaud
>
> Hi Renaud,
> One reason you got no response here, is because we don't even
> know about which package you are talking.
>
> So there's nothing, anybody can reproduce from your posting.
>
> There have been changes in R's dealing with class unions etc,
> notably even *relating* to an earlier bug report on class unions
> exactly for such a case which was *triggered* when people built
> on such Matrix classes.
>
> But we would really want to be able to reproduce what you are seeing..
>
> Best regards,
> Martin Maechler
>
> ETH Zurich, R Core Team *and* maintainer("Matrix")
>
> __
> 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
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Re: [R-pkg-devel] Error creating union class: object ‘.__C__compMatrix’ not found
Thank you William for the reproducible example.
Currently I using the following (same as in William's example):
setClassUnion("mMatrix", c("Matrix", "matrix"))
Martin, are the changes made in the union class handling affecting the way we
should declare them?
Thank you.
Bests,
Renaud
‐‐‐ Original Message ‐‐‐
On Wednesday, April 8, 2020 11:19 AM, William Dunlap wrote:
> Use trace() to get a bit more detail - .__C_compMatrix is looked for in the
> wrong environment with inherits=FALSE.
>
>> setClassUnion("mMatrix", c("Matrix", "matrix"))
> Tracing get(name, envir = env) on entry
> x=".AllMTable", envir="", topenv=" namespace:methods>", inherits=TRUE
> Tracing get(name, envir = env) on entry
> x=".MTable", envir="", topenv=" namespace:methods>", inherits=TRUE
> Tracing get(name, envir = env) on entry
> x=".AllMTable", envir="", topenv=" namespace:methods>", inherits=TRUE
> Tracing get("#HAS_DUPLICATE_CLASS_NAMES", envir = .classTable) on entry
> x="#HAS_DUPLICATE_CLASS_NAMES", envir="",
> topenv="", inherits=TRUE
> Tracing get(name, envir = env) on entry
> x=".AllMTable", envir="", topenv=" namespace:methods>", inherits=TRUE
> Tracing get(name, envir = env) on entry
> x=".MTable", envir="", topenv=" namespace:methods>", inherits=TRUE
> Tracing get(name, envir = env) on entry
> x=".MTable", envir="", topenv=" namespace:methods>", inherits=TRUE
> Tracing get(".SigLength", envir = env) on entry
> x=".SigLength", envir="", topenv=" namespace:methods>", inherits=TRUE
> Tracing get(".SigLength", envir = env) on entry
> x=".SigLength", envir="", topenv=" namespace:methods>", inherits=TRUE
> Tracing get(name, envir = env) on entry
> x=".MTable", envir="", topenv=" namespace:methods>", inherits=TRUE
> Tracing get(".SigLength", envir = env) on entry
> x=".SigLength", envir="", topenv=" namespace:methods>", inherits=TRUE
> Tracing get(".SigLength", envir = env) on entry
> x=".SigLength", envir="", topenv=" namespace:methods>", inherits=TRUE
> Tracing get(cname, envir = cwhere, inherits = FALSE) on entry
> x=".__C__compMatrix", envir="",
> topenv="", inherits=FALSE
> Error in get(cname, envir = cwhere, inherits = FALSE) :
> object '.__C__compMatrix' not found
> ...
>
> Bill Dunlap
> TIBCO Software
> wdunlap tibco.com
>
> On Wed, Apr 8, 2020 at 7:52 AM William Dunlap wrote:
>
>> % R-devel --vanilla --quiet
>>> library(Matrix)
>>> setClassUnion("mMatrix", c("Matrix", "matrix"))
>> Error in get(cname, envir = cwhere, inherits = FALSE) :
>> object '.__C__compMatrix' not found
>> Error in setClassUnion("mMatrix", c("Matrix", "matrix")) :
>> unable to create union class: could not set members "Matrix"
>>> sessionInfo()
>> R Under development (unstable) (2020-04-07 r78175)
>> Platform: x86_64-pc-linux-gnu (64-bit)
>> Running under: Ubuntu 16.04.6 LTS
>>
>> Matrix products: default
>> BLAS/LAPACK: /usr/lib/libopenblasp-r0.2.18.so
>>
>> locale:
>> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
>> [3] LC_TIME=en_US.UTF-8LC_COLLATE=en_US.UTF-8
>> [5] LC_MONETARY=en_US.UTF-8LC_MESSAGES=en_US.UTF-8
>> [7] LC_PAPER=en_US.UTF-8 LC_NAME=C
>> [9] LC_ADDRESS=C LC_TELEPHONE=C
>> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>>
>> attached base packages:
>> [1] stats graphics grDevices utils datasets methods base
>>
>> other attached packages:
>> [1] Matrix_1.2-18
>>
>> loaded via a namespace (and not attached):
>> [1] compiler_4.1.0 grid_4.1.0 lattice_0.20-41
>>
>> Bill Dunlap
>> TIBCO Software
>> wdunlap tibco.com
>>
>> On Wed, Apr 8, 2020 at 7:35 AM Martin Maechler
>> wrote:
>>
renozao
on Mon, 30 Mar 2020 21:20:43 + writes:
>>>
>>> > Hi,
>>> > when R CMD check is run under R-devel (2020-03-29 r78108) I get the
>>> following error at installation:
>>>
>>> > Error in get(cname, envir = cwhere, inherits = FALSE) :
>>> > object ‘.__C__compMatrix’ not found
>>> > Error in setClassUnion("mMatrix", c("Matrix", "matrix")) :
>>> > unable to create union class: could not set members "Matrix"
>>>
>>> > This does not happen on R 3.6.3.
>>>
>>> > I tried with Matrix listed in Depends but I still get the same error.
>>>
>>> > Is this linked to some changes in union classes or the Matrix package?
>>>
>>> > Thank you.
>>>
>>> > Bests,
>>> > Renaud
>>>
>>> Hi Renaud,
>>> One reason you got no response here, is because we don't even
>>> know about which package you are talking.
>>>
>>> So there's nothing, anybody can reproduce from your posting.
>>>
>>> There have been changes in R's dealing with class unions etc,
>>> notably even *relating* to an earlier bug report on class unions
>>> exactly for such a case which was *triggered* when people built
>>> on such Matrix classes.
>>>
>>> But we would really want to be able to reproduce what you are seeing..
>>>
>>> Best regards,
>>> Martin Maechler
>>>
>>> ETH Zurich, R Core Team *and* maintainer("Ma
