[R] segfault from systemfonts::system_fonts
R 4.0.3
OS X 10.15.7
Colleagues
When I run flextable, it generates a segfault. I traced the problem to
systemfonts::system_fonts()
> > require("systemfonts")
> Loading required package: systemfonts
> > system_fonts()
>
> *** caught segfault ***
> address 0x0, cause 'memory not mapped'
>
> Traceback:
> 1: system_fonts_c()
> 2: system_fonts()
>
> Possible actions:
> 1: abort (with core dump, if enabled)
> 2: normal R exit
> 3: exit R without saving workspace
> 4: exit R saving workspace
>
I updated my OS and R, deleted and reinstalled the systemfonts package --
problem persists.
I also opened Apple's font application and "validated" all font files (I have
never installed any special fonts nor is there anything non-standard (e.g.,
Homebrew) on my system.
Of note, I can run other functions in systemfonts without problems -- only
system_fonts triggers the segfault.
Another similar setup on OS X does not trigger the same problem, so the problem
is more likely something in my system rather than a problem in R.
Does anyone have any ideas on how one might address this?
Dennis
Dennis Fisher MD
P < (The "P Less Than" Company)
Phone / Fax: 1-866-PLessThan (1-866-753-7784)
www.PLessThan.com
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Re: [R] segfault from systemfonts::system_fonts
On 03/11/2020 3:43 p.m., Dennis Fisher wrote:
R 4.0.3
OS X 10.15.7
Colleagues
When I run flextable, it generates a segfault. I traced the problem to
systemfonts::system_fonts()
require("systemfonts")
Loading required package: systemfonts
system_fonts()
*** caught segfault ***
address 0x0, cause 'memory not mapped'
Traceback:
1: system_fonts_c()
2: system_fonts()
Possible actions:
1: abort (with core dump, if enabled)
2: normal R exit
3: exit R without saving workspace
4: exit R saving workspace
I updated my OS and R, deleted and reinstalled the systemfonts package --
problem persists.
I also opened Apple's font application and "validated" all font files (I have
never installed any special fonts nor is there anything non-standard (e.g., Homebrew) on
my system.
Of note, I can run other functions in systemfonts without problems -- only
system_fonts triggers the segfault.
Another similar setup on OS X does not trigger the same problem, so the problem
is more likely something in my system rather than a problem in R.
Does anyone have any ideas on how one might address this?
For what it's worth, I have the same R version and macOS version, and it
works fine. Debugging it will be hard: all the work happens in a
function called using
.Call("_systemfonts_system_fonts_c")
If I could reproduce the bug and wanted to track it down, I think I'd do
it by adding a bunch of Rprintf() commands into the source of
_systemfonts_system_fonts_c and rebuilding the package. It would be
really tedious; I'm glad I'm not doing this!
Duncan Murdoch
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Re: [R] segfault from systemfonts::system_fonts
Duncan
Thanks for responding -- but your response did not help my mood.
Executing:
.Call("_systemfonts_system_fonts_c")
triggered the segfault (as you proposed).
Dennis
Dennis Fisher MD
P < (The "P Less Than" Company)
Phone / Fax: 1-866-PLessThan (1-866-753-7784)
www.PLessThan.com
> On Nov 3, 2020, at 1:00 PM, Duncan Murdoch wrote:
>
> On 03/11/2020 3:43 p.m., Dennis Fisher wrote:
>> R 4.0.3
>> OS X 10.15.7
>> Colleagues
>> When I run flextable, it generates a segfault. I traced the problem to
>> systemfonts::system_fonts()
require("systemfonts")
>>> Loading required package: systemfonts
system_fonts()
>>>
>>> *** caught segfault ***
>>> address 0x0, cause 'memory not mapped'
>>>
>>> Traceback:
>>> 1: system_fonts_c()
>>> 2: system_fonts()
>>>
>>> Possible actions:
>>> 1: abort (with core dump, if enabled)
>>> 2: normal R exit
>>> 3: exit R without saving workspace
>>> 4: exit R saving workspace
>>>
>> I updated my OS and R, deleted and reinstalled the systemfonts package --
>> problem persists.
>> I also opened Apple's font application and "validated" all font files (I
>> have never installed any special fonts nor is there anything non-standard
>> (e.g., Homebrew) on my system.
>> Of note, I can run other functions in systemfonts without problems -- only
>> system_fonts triggers the segfault.
>> Another similar setup on OS X does not trigger the same problem, so the
>> problem is more likely something in my system rather than a problem in R.
>> Does anyone have any ideas on how one might address this?
>
> For what it's worth, I have the same R version and macOS version, and it
> works fine. Debugging it will be hard: all the work happens in a function
> called using
>
>.Call("_systemfonts_system_fonts_c")
>
> If I could reproduce the bug and wanted to track it down, I think I'd do it
> by adding a bunch of Rprintf() commands into the source of
> _systemfonts_system_fonts_c and rebuilding the package. It would be really
> tedious; I'm glad I'm not doing this!
>
> Duncan Murdoch
[[alternative HTML version deleted]]
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Re: [R] How to correct my error message
Dear All, Many thanks for your responses. I got it ! Best, Le mardi 27 octobre 2020 à 21:16:50 UTC+1, Md. Moyazzem Hossain a écrit : Dear Varin, I think the following code will solve your problem. n <- 60 b <- runif(n, 0, 5) a <- runif(n, 0, 5) z1 <- data.frame(x0=1:57, x1=rnorm(n*0.95,2,3)) z2 <- data.frame(x0=58:60, x1=rnorm(n*0.05,2,9)) combined=rbind(z1,z2) z=combined[,2] y_model <- 0.1 * b - 0.5 * z - a + 10 y_obs <- y_model +c( rnorm(n*0.95, 0, 0.1), rnorm(n*0.05, 0, 0.5) ) df<-data.frame(b,a,z,y_obs) Thanks. Md On Tue, Oct 27, 2020 at 7:21 PM Sarah Goslee wrote: > Hi, > > a is of length 60. > b is of length 60. > z is of length 57. > > What do you expect to have happen when you create y_model ? What > happens to those other 3 observations? > > Sarah > > On Tue, Oct 27, 2020 at 3:07 PM varin sacha via R-help > wrote: >> >> Dear R-experts, >> >> Here below my R code. The warning message is not a problem to me but there >> is an error message more problematic. I understand the error message but I >> don't know if it is possible to correct the error and if yes, how to correct >> it. >> >> Many thanks. >> >> >> n <- 60 >> b <- runif(n, 0, 5) >> a <- runif(n, 0, 5) >> z <- rnorm(n*0.95,2,3) + rnorm(n*0.05,2,9) >> y_model <- 0.1 * b - 0.5 * z - a + 10 >> y_obs <- y_model +c( rnorm(n*0.95, 0, 0.1), rnorm(n*0.05, 0, 0.5) ) >> df<-data.frame(b,a,z,y_obs) >> >> __ >> R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see >> https://stat.ethz.ch/mailman/listinfo/r-help >> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html >> and provide commented, minimal, self-contained, reproducible code. > > > > -- > Sarah Goslee (she/her) > http://www.numberwright.com > > > __ > R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. > > -- Best Regards, Md. Moyazzem Hossain Associate Professor Department of Statistics Jahangirnagar University Savar, Dhaka-1342 Bangladesh Website: http://www.juniv.edu/teachers/hossainmm Research: Google Scholar; ResearchGate; ORCID iD __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] How to correct my error message
Many thanks Duncan, It works ! Best. Le mardi 27 octobre 2020 à 20:49:25 UTC+1, Duncan Murdoch a écrit : On 27/10/2020 3:06 p.m., varin sacha via R-help wrote: > Dear R-experts, > > Here below my R code. The warning message is not a problem to me but there is > an error message more problematic. I understand the error message but I don't > know if it is possible to correct the error and if yes, how to correct it. > > Many thanks. > > > n <- 60 > b <- runif(n, 0, 5) > a <- runif(n, 0, 5) > z <- rnorm(n*0.95,2,3) + rnorm(n*0.05,2,9) > y_model <- 0.1 * b - 0.5 * z - a + 10 > y_obs <- y_model +c( rnorm(n*0.95, 0, 0.1), rnorm(n*0.05, 0, 0.5) ) > df<-data.frame(b,a,z,y_obs) > I suspect you intended to concatenate the two parts of z, i.e. z <- c(rnorm(n*0.95,2,3), rnorm(n*0.05,2,9)) You shouldn't ignore the warning. By the way, it's not true for every n that my expression for z will always give something of length n. It would be safer to do the calculation as m <- round(n*0.95) z <- c(rnorm(m,2,3), rnorm(n-m,2,9) Duncan Murdoch __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] nlcor package
Dear R-helpers,
Here below my R code showing warnings and error messages I don't understand.
What is going wrong ?
install.packages("devtools")
library(devtools)
install_github("ProcessMiner/nlcor")
library(nlcor)
A=c(505, 530, 419, 486, 608, 468, 519, 486, 532, 289, 529, 474, 571, 546, 458,
476, 376, 474, 598, 419, 479, 615, 507, 473, 532, 392, 496, 426, 480, 583, 490,
499, 513, 444, 542)
B=c(508, 516, 390, 520, 375, 499, 478, 534, 553, 485, 405, 478, 542, 523, 491,
363, 456, 498, 506, 529, 574, 478, 411, 571, 512, 487, 518, 515, 467, 513, 536,
555, 508, 507, 535)
c<-nlcor(A,B,refine=0.5,plt=T)
c$cor.estimate
c$adjusted.p.value
print(c$cor.plot)
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Re: [R] nlcor package
Someone may investigate this for you anyway, but technically this request is
outside of the scope of this mailing list (which is the R programming language,
not the theory of use nor possible bugs in the current version of random
packages not even registered in CRAN). Do read the Posting Guide and consider
corresponding with the package author as directed by the package DESCRIPTION
file.
On November 3, 2020 1:23:50 PM PST, varin sacha via R-help
wrote:
>Dear R-helpers,
>
>Here below my R code showing warnings and error messages I don't
>understand.
>What is going wrong ?
>
>
>install.packages("devtools")
>library(devtools)
>install_github("ProcessMiner/nlcor")
>library(nlcor)
>
>A=c(505, 530, 419, 486, 608, 468, 519, 486, 532, 289, 529, 474, 571,
>546, 458, 476, 376, 474, 598, 419, 479, 615, 507, 473, 532, 392, 496,
>426, 480, 583, 490, 499, 513, 444, 542)
>B=c(508, 516, 390, 520, 375, 499, 478, 534, 553, 485, 405, 478, 542,
>523, 491, 363, 456, 498, 506, 529, 574, 478, 411, 571, 512, 487, 518,
>515, 467, 513, 536, 555, 508, 507, 535)
>
>c<-nlcor(A,B,refine=0.5,plt=T)
>c$cor.estimate
>c$adjusted.p.value
>print(c$cor.plot)
>
>
>__
>R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
>https://stat.ethz.ch/mailman/listinfo/r-help
>PLEASE do read the posting guide
>http://www.R-project.org/posting-guide.html
>and provide commented, minimal, self-contained, reproducible code.
--
Sent from my phone. Please excuse my brevity.
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