Dear List,
I am trying to get R's terminal output to a file and to the terminal
at the same time, so that I can walk through some tests and keep a log
concurrently. The function 'sink' with the option split=TRUE seems to
do just that. It works fine for most output but for objects of class
htest, the terminal output is incomplete (the lines are there but
empty). Here is an example session which shows the problem:
> sink("textout.txt", type="output", split=T)
> b=bartlett.test(runif(10),c(1,1,1,1,2,2,2,2,2,2))
> class(b)
[1] "htest"
> b
data: runif(10) and c(1, 1, 1, 1, 2, 2, 2, 2, 2, 2)
> t=t.test(runif(10),c(1,1,1,1,2,2,2,2,2,2))
> t
data: runif(10) and c(1, 1, 1, 1, 2, 2, 2, 2, 2, 2)
alternative hypothesis: true difference in means is not equal to 0
95 percent confidence interval:
-1.5807338 -0.7316803
sample estimates:
mean of x mean of y
0.4437929 1.6000000
> sink() # output in the file is complete
> b
Bartlett test of homogeneity of variances
data: runif(10) and c(1, 1, 1, 1, 2, 2, 2, 2, 2, 2)
Bartlett's K-squared = 0.9959, df = 1, p-value = 0.3183
> t
Welch Two Sample t-test
data: runif(10) and c(1, 1, 1, 1, 2, 2, 2, 2, 2, 2)
t = -5.7659, df = 16.267, p-value = 2.712e-05
alternative hypothesis: true difference in means is not equal to 0
95 percent confidence interval:
-1.5807338 -0.7316803
sample estimates:
mean of x mean of y
0.4437929 1.6000000
>
Is this a known bug (I'm using R 2.6.1 on OS X and Linux - FC8)? Is
there an inherent reason why some portions of this output are not
redirected?
Thank you in advance for your help.
JiHO
---
http://jo.irisson.free.fr/
you could use the unix function 'script' before invoking the R interpreter. example session: $ script Script started, file is typescript [x86_64|alex at riki:~] $ R --quiet --vanilla > 1:10 [1] 1 2 3 4 5 6 7 8 9 10 > q() [x86_64|alex at riki:~] $ exit exit Script done, file is typescript contents of file typescript: ==========Script started on Tue Feb 5 19:01:32 2008 [x86_64|alex at riki:~] $ R --quiet --vanilla > 1:10 [1] 1 2 3 4 5 6 7 8 9 10 > q() [x86_64|alex at riki:~] $ exit exit Script done on Tue Feb 5 19:01:45 2008 [x86_64|alex at riki:~] =========== -Alex On 5 Feb 2008, at 16:12, jiho wrote:> Dear List, > > I am trying to get R's terminal output to a file and to the terminal > at the same time, so that I can walk through some tests and keep a log > concurrently. The function 'sink' with the option split=TRUE seems to > do just that. It works fine for most output but for objects of class > htest, the terminal output is incomplete (the lines are there but > empty). Here is an example session which shows the problem: > >> sink("textout.txt", type="output", split=T) >> b=bartlett.test(runif(10),c(1,1,1,1,2,2,2,2,2,2)) >> class(b) > [1] "htest" >> b > > > data: runif(10) and c(1, 1, 1, 1, 2, 2, 2, 2, 2, 2) > >> t=t.test(runif(10),c(1,1,1,1,2,2,2,2,2,2)) >> t > > > data: runif(10) and c(1, 1, 1, 1, 2, 2, 2, 2, 2, 2) > alternative hypothesis: true difference in means is not equal to 0 > 95 percent confidence interval: > -1.5807338 -0.7316803 > sample estimates: > mean of x mean of y > 0.4437929 1.6000000 > >> sink() # output in the file is complete >> b > > Bartlett test of homogeneity of variances > > data: runif(10) and c(1, 1, 1, 1, 2, 2, 2, 2, 2, 2) > Bartlett's K-squared = 0.9959, df = 1, p-value = 0.3183 > >> t > > Welch Two Sample t-test > > data: runif(10) and c(1, 1, 1, 1, 2, 2, 2, 2, 2, 2) > t = -5.7659, df = 16.267, p-value = 2.712e-05 > alternative hypothesis: true difference in means is not equal to 0 > 95 percent confidence interval: > -1.5807338 -0.7316803 > sample estimates: > mean of x mean of y > 0.4437929 1.6000000 > >> > > Is this a known bug (I'm using R 2.6.1 on OS X and Linux - FC8)? Is > there an inherent reason why some portions of this output are not > redirected? > > Thank you in advance for your help. > > JiHO > --- > http://jo.irisson.free.fr/ > > ______________________________________________ > R-help at r-project.org mailing list > 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.
On 2/5/2008 11:12 AM, jiho wrote:> Dear List, > > I am trying to get R's terminal output to a file and to the terminal > at the same time, so that I can walk through some tests and keep a log > concurrently. The function 'sink' with the option split=TRUE seems to > do just that. It works fine for most output but for objects of class > htest, the terminal output is incomplete (the lines are there but > empty). Here is an example session which shows the problem:stats:::print.htest() uses writeLines to write some of its output to stdout(), and it looks as though sink(split=T) misses those bits. I'll change print.htest to use cat(), but it is probably a sign of a bigger problem in sink(), and it's too late in the schedule to touch that for 2.6.2. Duncan Murdoch> > > sink("textout.txt", type="output", split=T) > > b=bartlett.test(runif(10),c(1,1,1,1,2,2,2,2,2,2)) > > class(b) > [1] "htest" > > b > > > data: runif(10) and c(1, 1, 1, 1, 2, 2, 2, 2, 2, 2) > > > t=t.test(runif(10),c(1,1,1,1,2,2,2,2,2,2)) > > t > > > data: runif(10) and c(1, 1, 1, 1, 2, 2, 2, 2, 2, 2) > alternative hypothesis: true difference in means is not equal to 0 > 95 percent confidence interval: > -1.5807338 -0.7316803 > sample estimates: > mean of x mean of y > 0.4437929 1.6000000 > > > sink() # output in the file is complete > > b > > Bartlett test of homogeneity of variances > > data: runif(10) and c(1, 1, 1, 1, 2, 2, 2, 2, 2, 2) > Bartlett's K-squared = 0.9959, df = 1, p-value = 0.3183 > > > t > > Welch Two Sample t-test > > data: runif(10) and c(1, 1, 1, 1, 2, 2, 2, 2, 2, 2) > t = -5.7659, df = 16.267, p-value = 2.712e-05 > alternative hypothesis: true difference in means is not equal to 0 > 95 percent confidence interval: > -1.5807338 -0.7316803 > sample estimates: > mean of x mean of y > 0.4437929 1.6000000 > > > > > Is this a known bug (I'm using R 2.6.1 on OS X and Linux - FC8)? Is > there an inherent reason why some portions of this output are not > redirected? > > Thank you in advance for your help. > > JiHO > --- > http://jo.irisson.free.fr/ > > ______________________________________________ > R-help at r-project.org mailing list > 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.