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Kjetil brinchmann Halvorsen

2019-Apr-08 12:19 UTC

[R-sig-Debian] debian testing: Problems with R function vignette()

Hola!

I am on debian testing, all updates up to date. I am running R via emacs
and ess, so I canot know if this is an R or emacs/ess problem.  What
happens is that I want to read an vignette, and calls something like
    vignette("mle2", package="bbmle")

the pdf file opens (for me in Foxit reader), no problem, but then emacs
starts to spew a lot of spam, interfering with the use of ess/R.  A small
sample:

ScheduleTimerQuery called
GetDntDataTotal sql exec success
GetDntDataQueue sql exec success
SchedulePriorTracktype called
GetDntDataPriorQueue sql exec success
SchedulePriorTracktype called
GetDntDataPriorQueue sql exec success
SchedulePriorTracktype called
GetDntDataPriorQueue sql exec success
ScheduleTimerQuery called
GetDntDataTotal sql exec success
GetDntDataQueue sql exec success
SchedulePriorTracktype called
GetDntDataPriorQueue sql exec success
SchedulePriorTracktype called
GetDntDataPriorQueue sql exec success
SchedulePriorTracktype called
GetDntDataPriorQueue sql exec success
ScheduleTimerQuery called
GetDntDataTotal sql exec success
GetDntDataQueue sql exec success
SchedulePriorTracktype called
GetDntDataPriorQueue sql exec success
SchedulePriorTracktype called
GetDntDataPriorQueue sql exec success
ScheduleTimerQuery called
GetDntDataTotal sql exec success
GetDntDataQueue sql exec success
SchedulePriorTracktype called
GetDntDataPriorQueue sql exec success
SchedulePriorTracktype called
GetDntDataPriorQueue sql exec success
SchedulePriorTracktype called
GetDntDataPriorQueue sql exec success
ScheduleTimerQuery called
GetDntDataTotal sql exec success
GetDntDataQueue sql exec success
SchedulePriorTracktype called

....  continuing like that without stop.  To get a prompt I have to send
(from emacs "Signals" menu) the EOF signal, and then choosing
"cancel".
Then I can continue issuing commands, which get interrupted by the noise
above ... What is happening?

Now I try the same with R running in a Mate terminal, lets see what happens:
vignette("mle2", package="bbmle")> [TimeStamp]-----main-----beginsendMessage

Well, ... nothing happens---no problems & no pdf!

Thanks,
Kjetil
This is the output of sessionInfo() at start of session:
sessionInfo()
R version 3.5.2 (2018-12-20)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Debian GNU/Linux buster/sid

Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/openblas/libblas.so.3
LAPACK: /usr/lib/x86_64-linux-gnu/libopenblasp-r0.3.5.so

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
 [5] LC_MONETARY=en_US.UTF-8    LC_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] MASS_7.3-51.3

loaded via a namespace (and not attached):
[1] compiler_3.5.2 fortunes_1.5-4

	[[alternative HTML version deleted]]

Dirk Eddelbuettel

2019-Apr-18 10:29 UTC

head link

[R-sig-Debian] debian testing: Problems with R function vignette()

On 8 April 2019 at 14:19, Kjetil brinchmann Halvorsen wrote:
| Hola!
| 
| I am on debian testing, all updates up to date. I am running R via emacs
| and ess, so I canot know if this is an R or emacs/ess problem.  What

So separate it out. Do it outside emacs, if it persists report to the ESS list.

Dirk

| happens is that I want to read an vignette, and calls something like
|     vignette("mle2", package="bbmle")
| 
| the pdf file opens (for me in Foxit reader), no problem, but then emacs
| starts to spew a lot of spam, interfering with the use of ess/R.  A small
| sample:
| 
| ScheduleTimerQuery called
| GetDntDataTotal sql exec success
| GetDntDataQueue sql exec success
| SchedulePriorTracktype called
| GetDntDataPriorQueue sql exec success
| SchedulePriorTracktype called
| GetDntDataPriorQueue sql exec success
| SchedulePriorTracktype called
| GetDntDataPriorQueue sql exec success
| ScheduleTimerQuery called
| GetDntDataTotal sql exec success
| GetDntDataQueue sql exec success
| SchedulePriorTracktype called
| GetDntDataPriorQueue sql exec success
| SchedulePriorTracktype called
| GetDntDataPriorQueue sql exec success
| SchedulePriorTracktype called
| GetDntDataPriorQueue sql exec success
| ScheduleTimerQuery called
| GetDntDataTotal sql exec success
| GetDntDataQueue sql exec success
| SchedulePriorTracktype called
| GetDntDataPriorQueue sql exec success
| SchedulePriorTracktype called
| GetDntDataPriorQueue sql exec success
| ScheduleTimerQuery called
| GetDntDataTotal sql exec success
| GetDntDataQueue sql exec success
| SchedulePriorTracktype called
| GetDntDataPriorQueue sql exec success
| SchedulePriorTracktype called
| GetDntDataPriorQueue sql exec success
| SchedulePriorTracktype called
| GetDntDataPriorQueue sql exec success
| ScheduleTimerQuery called
| GetDntDataTotal sql exec success
| GetDntDataQueue sql exec success
| SchedulePriorTracktype called
| 
| ....  continuing like that without stop.  To get a prompt I have to send
| (from emacs "Signals" menu) the EOF signal, and then choosing
"cancel".
| Then I can continue issuing commands, which get interrupted by the noise
| above ... What is happening?
| 
| Now I try the same with R running in a Mate terminal, lets see what happens:
| vignette("mle2", package="bbmle")
| > [TimeStamp]-----main-----begin
| sendMessage
| 
| Well, ... nothing happens---no problems & no pdf!
| 
| Thanks,
| Kjetil
| This is the output of sessionInfo() at start of session:
| sessionInfo()
| R version 3.5.2 (2018-12-20)
| Platform: x86_64-pc-linux-gnu (64-bit)
| Running under: Debian GNU/Linux buster/sid
| 
| Matrix products: default
| BLAS: /usr/lib/x86_64-linux-gnu/openblas/libblas.so.3
| LAPACK: /usr/lib/x86_64-linux-gnu/libopenblasp-r0.3.5.so
| 
| locale:
|  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
|  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
|  [5] LC_MONETARY=en_US.UTF-8    LC_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] MASS_7.3-51.3
| 
| loaded via a namespace (and not attached):
| [1] compiler_3.5.2 fortunes_1.5-4
| 
| 	[[alternative HTML version deleted]]
| 
| _______________________________________________
| R-SIG-Debian mailing list
| R-SIG-Debian at r-project.org
| https://stat.ethz.ch/mailman/listinfo/r-sig-debian

-- 
http://dirk.eddelbuettel.com | @eddelbuettel | edd at debian.org

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