Re: [Rd] packageDate() segfaults, if used without argument
> Rainer Hurling > on Sun, 15 Apr 2018 11:01:59 +0200 writes: > Out of curiosity, I played a bit with the new function > packageDate() from April, 4th. All works fine, except > using it without any argument. In this case, it > segfaults: Thank you, Rainer, for the report -- about the *development* version of R Note that the segfault would not have happened in 'R 3.5.0 beta' (today turning to be 'R 3.5.0 RC' : RC := Release Candidate ) which we'd be very happy if you used extensively. > #> packageDate() Error in packageDescription(pkg, lib.loc > = lib.loc, fields = date.fields) : argument "pkg" is > missing, with no default > *** caught segfault *** address 0x77bc3c0, cause 'memory > not mapped' Segmentation fault (core dumped) > My system is FreeBSD 12.0-CURRENT amd64 with R-devel > (r74601). It was a lapsus -- of mine -- not at all related to packageDate(), corrected yesterday (svn r 74604). Martin __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] packageDate() segfaults, if used without argument
Hi Martin, Am 16.04.2018 um 09:03 schrieb Martin Maechler: Rainer Hurling on Sun, 15 Apr 2018 11:01:59 +0200 writes: > Out of curiosity, I played a bit with the new function > packageDate() from April, 4th. All works fine, except > using it without any argument. In this case, it > segfaults: Thank you, Rainer, for the report -- about the *development* version of R Yupp. Note that the segfault would not have happened in 'R 3.5.0 beta' (today turning to be 'R 3.5.0 RC' : RC := Release Candidate ) which we'd be very happy if you used extensively. Ah, interesting news, that this does not occur with beta and RC. > #> packageDate() Error in packageDescription(pkg, lib.loc > = lib.loc, fields = date.fields) : argument "pkg" is > missing, with no default > *** caught segfault *** address 0x77bc3c0, cause 'memory > not mapped' Segmentation fault (core dumped) > My system is FreeBSD 12.0-CURRENT amd64 with R-devel > (r74601). It was a lapsus -- of mine -- not at all related to packageDate(), corrected yesterday (svn r 74604). Nice to here. Thanks for the fast response and greetings, Rainer Martin __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] alpha transparency doesn't work for lines when xpd=TRUE
Dear R-devel, I think I've found a bug - the alpha transparency doesn't work when plotting lines with xpd = TRUE. #works plot(1:20, col="#1874CD", xpd=T, type="l") #works plot(1:20, col="#1874CD50", xpd=F, type="l") #doesn't work plot(1:20, col="#1874CD50", xpd=T, type="l") Thank you. Jim [[alternative HTML version deleted]] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] alpha transparency doesn't work for lines when xpd=TRUE
> On Apr 16, 2018, at 10:41 AM, Jiaxuan Chen > wrote: > > Dear R-devel, > > I think I've found a bug - the alpha transparency doesn't work when plotting > lines with xpd = TRUE. > > #works > plot(1:20, col="#1874CD", xpd=T, type="l") > > #works > plot(1:20, col="#1874CD50", xpd=F, type="l") > > #doesn't work > plot(1:20, col="#1874CD50", xpd=T, type="l") It's behaving as expected (last two lines light blue) on a Mac (El Capitan) and R 3.4.3. (I did check to see if T and F were still TRUE and FALSE at the time. It's possible that they were not in your session. Only TRUE and FALSE are reserved words.) > > Thank you. > > Jim > > > [[alternative HTML version deleted]] All the R mailing lists are plain text. > > __ > R-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-devel David Winsemius Alameda, CA, USA 'Any technology distinguishable from magic is insufficiently advanced.' -Gehm's Corollary to Clarke's Third Law __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] alpha transparency doesn't work for lines when xpd=TRUE
The problem occurs in the Windows GUI with the 'windows()' graphics device.
In the following example the red diagonal line appears in 3 plots but not
in the one
with xpd=TRUE and alpha.f=0.9.
> par(mfrow=c(2,2))
> for(xpd in c(FALSE, TRUE)) for(alpha.f in c(.9, 1))
plot(0:1,xpd=xpd,type="l",col=adjustcolor("red",alpha.f=alpha.f),main=paste0("xpd=",xpd,",
alpha.f=",alpha.f))
> dev.cur()
windows
2
> sessionInfo()
R version 3.4.4 (2018-03-15)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 16299)
Matrix products: default
locale:
[1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United
States.1252
[3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C
[5] LC_TIME=English_United States.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] compiler_3.4.4
Bill Dunlap
TIBCO Software
wdunlap tibco.com
On Mon, Apr 16, 2018 at 12:14 PM, David Winsemius
wrote:
>
> > On Apr 16, 2018, at 10:41 AM, Jiaxuan Chen
> wrote:
> >
> > Dear R-devel,
> >
> > I think I've found a bug - the alpha transparency doesn't work when
> plotting lines with xpd = TRUE.
> >
> > #works
> > plot(1:20, col="#1874CD", xpd=T, type="l")
> >
> > #works
> > plot(1:20, col="#1874CD50", xpd=F, type="l")
> >
> > #doesn't work
> > plot(1:20, col="#1874CD50", xpd=T, type="l")
>
> It's behaving as expected (last two lines light blue) on a Mac (El
> Capitan) and R 3.4.3. (I did check to see if T and F were still TRUE and
> FALSE at the time. It's possible that they were not in your session. Only
> TRUE and FALSE are reserved words.)
> >
> > Thank you.
> >
> > Jim
> >
> >
> > [[alternative HTML version deleted]]
>
> All the R mailing lists are plain text.
>
> >
> > __
> > R-devel@r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/r-devel
>
> David Winsemius
> Alameda, CA, USA
>
> 'Any technology distinguishable from magic is insufficiently advanced.'
> -Gehm's Corollary to Clarke's Third Law
>
> __
> R-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
>
[[alternative HTML version deleted]]
__
R-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel
[Rd] strange warning: data() error?
A user asked me about this and I can't figure it out. tmt% R R Under development (unstable) (2018-04-09 r74565) -- "Unsuffered Consequences" Copyright (C) 2018 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu (64-bit) > library(survival) > data(cgd0) Warning message: In data(cgd0) : data set ‘cgd0’ not found The data set is present and can be manipulated: data() is not required. Other data sets in the survival package don't generate this message. Terry T. __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] strange warning: data() error?
> On Apr 16, 2018, at 2:58 PM, Therneau, Terry M., Ph.D. via R-devel
> wrote:
>
> A user asked me about this and I can't figure it out.
>
> tmt% R
> R Under development (unstable) (2018-04-09 r74565) -- "Unsuffered
> Consequences"
> Copyright (C) 2018 The R Foundation for Statistical Computing
> Platform: x86_64-pc-linux-gnu (64-bit)
>
> > library(survival)
> > data(cgd0)
> Warning message:
> In data(cgd0) : data set ‘cgd0’ not found
>
>
>
> The data set is present and can be manipulated: data() is not required.
> Other data sets in the survival package don't generate this message.
On a Mac the Data Manager panel lists that dataset as "cgd0 (cgd)" and I get
the same warning with any dataset that has a similar appearance of , even the `state.abb` vector that is displayed "state.abb
(state)" (without the quotes.)
> data('state.abb')
Warning message:
In data("state.abb") : data set ‘state.abb’ not found
> str(state.abb)
chr [1:50] "AL" "AK" "AZ" "AR" "CA" "CO" "CT" "DE" "FL" "GA" "HI" "ID" "IL"
"IN" "IA" "KS" "KY" "LA" "ME" "MD" "MA" ...
> data(stack.loss)
Warning message:
In data(stack.loss) : data set ‘stack.loss’ not found
So I guess the message is don't feel picked upon. It seems to be an infelicity
shared by many other datasets even those in the canonical 'datasets' package.
>
> Terry T.
>
> __
> R-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
David Winsemius
Alameda, CA, USA
'Any technology distinguishable from magic is insufficiently advanced.'
-Gehm's Corollary to Clarke's Third Law
__
R-devel@r-project.org mailing list
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Re: [Rd] strange warning: data() error?
data(package="survival") gives, in part, cgd Chronic Granulotomous Disease data cgd0 (cgd) Chronic Granulotomous Disease data colon Chemotherapy for Stage B/C colon cancer flchain Assay of serum free light chain for 7874 subjects. genfan Generator fans heart Stanford Heart Transplant data jasa (heart)Stanford Heart Transplant data jasa1 (heart) Stanford Heart Transplant data The 'name1 (name2)' entries indicate that 'name'; is in the file labelled name2. If you run data(cgd) you get both cgd and cdg0 in .GlobalEnv; if you run data(heart) you get heart, jasa, and jasa1. I don't think this has changed recently, although it might be nice if the names were handled more symmetrically, like alias entries in help files. Bill Dunlap TIBCO Software wdunlap tibco.com On Mon, Apr 16, 2018 at 2:58 PM, Therneau, Terry M., Ph.D. via R-devel < r-devel@r-project.org> wrote: > A user asked me about this and I can't figure it out. > > tmt% R > R Under development (unstable) (2018-04-09 r74565) -- "Unsuffered > Consequences" > Copyright (C) 2018 The R Foundation for Statistical Computing > Platform: x86_64-pc-linux-gnu (64-bit) > > > library(survival) > > data(cgd0) > Warning message: > In data(cgd0) : data set ‘cgd0’ not found > > > > The data set is present and can be manipulated: data() is not required. > Other data sets in the survival package don't generate this message. > > Terry T. > > __ > R-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-devel > [[alternative HTML version deleted]] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
Re: [Rd] strange warning: data() error?
> On Apr 16, 2018, at 3:20 PM, David Winsemius wrote:
>
>>
>> On Apr 16, 2018, at 2:58 PM, Therneau, Terry M., Ph.D. via R-devel
>> wrote:
>>
>> A user asked me about this and I can't figure it out.
>>
>> tmt% R
>> R Under development (unstable) (2018-04-09 r74565) -- "Unsuffered
>> Consequences"
>> Copyright (C) 2018 The R Foundation for Statistical Computing
>> Platform: x86_64-pc-linux-gnu (64-bit)
>>
>>> library(survival)
>>> data(cgd0)
>> Warning message:
>> In data(cgd0) : data set ‘cgd0’ not found
>>
>>
>>
>> The data set is present and can be manipulated: data() is not required.
>> Other data sets in the survival package don't generate this message.
>
> On a Mac the Data Manager panel lists that dataset as "cgd0 (cgd)" and I get
> the same warning with any dataset that has a similar appearance of paren-name-paren> , even the `state.abb` vector that is displayed "state.abb
> (state)" (without the quotes.)
>
>> data('state.abb')
> Warning message:
> In data("state.abb") : data set ‘state.abb’ not found
>> str(state.abb)
> chr [1:50] "AL" "AK" "AZ" "AR" "CA" "CO" "CT" "DE" "FL" "GA" "HI" "ID" "IL"
> "IN" "IA" "KS" "KY" "LA" "ME" "MD" "MA" ...
>> data(stack.loss)
> Warning message:
> In data(stack.loss) : data set ‘stack.loss’ not found
>
> So I guess the message is don't feel picked upon. It seems to be an
> infelicity shared by many other datasets even those in the canonical
> 'datasets' package.
> survival_Rdata <-
> readRDS("/Library/Frameworks/R.framework/Versions/3.4/Resources/library/survival/data/Rdata.rds")
> survival_Rdata
$bladder
[1] "bladder" "bladder1" "bladder2"
$cancer
[1] "cancer"
$cgd
[1] "cgd" "cgd0"
$colon
[1] "colon"
$flchain
[1] "flchain"
$genfan
[1] "genfan"
$heart
[1] "heart" "jasa" "jasa1"
--- snip
data(bladder2)
# Warning message:
# In data(bladder2) : data set ‘bladder2’ not found
data(mgus1)
# Warning message:
# In data(mgus1) : data set ‘mgus1’ not found
> data(mgus1)
Warning message:
In data(mgus1) : data set ‘mgus1’ not found
> data("survexp.mn")
Warning message:
In data("survexp.mn") : data set ‘survexp.mn’ not found
Hypothesis: datasets in a ..library/data/Rdata.rds file whose listing does
not match the name of the dataset from which it is derived will cause the
behavior in question.
And Terry; After executing `data(package-"survival")` I must mention that the
spelling of "Granulomatous" is not "Granulotomous", and neither is the spelling
of "gammapathy", "gammapothy".
--
David Winsemius
Alameda, CA, USA
'Any technology distinguishable from magic is insufficiently advanced.'
-Gehm's Corollary to Clarke's Third Law
__
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[Rd] Experimental package for asan-usan checks
I've been trying to replicate Brian's excellent work on sanity checks so we can get that information before submitting. I've put together an experimental package here: https://github.com/thk686/sanitycheckr It uses a modified rocker r-devel-san image and attempts to install all dependencies before running a check. This would probably be better integrated into TravisCI, et al. It was nonetheless a good opportunity to learn a bit about docker + asan/usan. Happy to have people kick the tires, make suggestions or make pull requests. THK http://www.keittlab.org/ [[alternative HTML version deleted]] __ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
