Tena Sakai
2009-May-07 04:22 UTC
[R] I updated/reinstalled ggplot2 and the trouble started...
Hi Ian,
Per your suggestion, I reinstalled R 2.9.0, then
I reinstalled ggplot2 on top. The problem persists.
Here's the what happens after the installation:
> qplot (carat, price, data = diamonds, alpha = I(1/10))
Warning message:
In grid.Call.graphics("L_points", x$x, x$y, x$pch, x$size) :
semi-transparency is not supported on this device: reported only once per
page
The entire record of installing ggplot2 package, ending
up with the line above is in the attached file. I would
think this should be reproducible with anybody else.
If you have any other suggestion, I am all ears.
Regards,
Tena Sakai
tsakai at gallo.ucsf.edu
-----Original Message-----
From: Ian Fellows [mailto:ifellows at gmail.com]
Sent: Tue 5/5/2009 11:43 PM
To: Tena Sakai
Subject: Re: I updated/reinstalled ggplot2 and the trouble started...
Tena,
May I suggest that you do a full clean install of R 2.9.0, then install
ggplot2 from cran. See if the problem persists after that.
Ian
On Tue, May 5, 2009 at 11:13 PM, tena <tsakai at gallo.ucsf.edu> wrote:
>
> Hi Hadley,
>
> Many thanks for your reply.
>
> I followed your instruction and got past the point where I
> was stuck at. Namely, I was able to generate a few plots.
> But as I came to the second half of section 2.4, where I
> wanted to see the behavior of alpha paramter, which I
> had apparently misspelled, I encountered another hindrance:
> > qplot (carat, price, data = diamonds, alpha = I(1/10))
> Warning message:
> In grid.Call.graphics("L_points", x$x, x$y, x$pch, x$size) :
> semi-transparency is not supported on this device: reported only
> once per page
>
> A plot was generated, but there are tic marks and labels on
> each direction, but no plot at all.
>
> I wonder if this is yet another (hidden) package to be updated...
> The warning message suggests grid, but I am hesitant to do
> something without knowing what is what. I would appreciate
> your instruction.
>
> Regards,
>
> Tena Sakai
>
>
> On May 5, 5:24 pm, hadley wickham <h.wick... at gmail.com> wrote:
> > Hi Tena,
> >
> > R isn't very good at detecting when package dependencies also need
to
> > be updated, so you probably need to do:
> >
> > install.packages(c("reshape","plyr"))
> >
> > And you want
> >
> > qplot (carat, price, data=diamonds, alpha = I(1/10))
> >
> > not
> >
> > qplot (carat, price, data=diamonds, slpha = i(1/10))
> >
> > Hadley
> >
> > On Tue, May 5, 2009 at 6:27 PM, tena <tsa... at gallo.ucsf.edu>
wrote:
> >
> > > Hi Folks,
> >
> > > I am pretty new to R and I am even newer to ggplot.
> >
> > > I am using R 2.7.1, 2.8.1, and 2.9.0 on linux host and
> > > what I am experiencing holds for all three.
> >
> > > I was just typing a few examples from the chapter 2 of
> > > the book, ggplot2 --Elegant graphics for data analysis.
> >
> > > I typed 3 qplot lines on page 13:
> > > > qplot (carat, price, data=diamonds, slpha = i(1/10))
> > > > qplot (carat, price, data=diamonds, slpha = i(1/100))
> > > > qplot (carat, price, data=diamonds, slpha = i(1/200))
> >
> > > To me, the plot looked identical. I went to my R library
> > > directory and looked at the date on the ggplot2 directory,
> > > which was April of 2008. I decided to update the library.
> > > In R, I issued:
> > > > install.packages ('ggplot2',
'/usr/local/Gallo/R')
> > > and there was a complaint as to permission denied for
> > > saving the current version (or something). I reissued
> > > the command as root and this time it gave me a normal
> > > return.
> >
> > > I was ready to retrace my steps with the book. I only got
> > > to page 11 this time. Here's what happened (in all three
> > > versions):
> > > > set.seed (1410)
> > > > dsmall <- diamonds [sample (nrow(diamonds), 100), ]
> > > >
> > > > qplot (carat, price, data = diamonds)
> > > Error in get("new", env = FacetGrid, inherits = TRUE)
> > > (FacetGrid, ...) :
> > > could not find function "is.formula"
> > > >
> >
> > > Can somebody please clue me in as to what's happening,
> > > what I am doing wrong, etc?
> >
> > > Regards,
> >
> > > Tena Sakai
> > > tsa... at gallo.ucsf.edu
> >
> > --http://had.co.nz/
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>
>
ONKELINX, Thierry
2009-May-07 08:01 UTC
[R] I updated/reinstalled ggplot2 and the trouble started...
What device are you using to plot the graph? According to the warning,
the device is causing the problem.
HTH,
Thierry
------------------------------------------------------------------------
----
ir. Thierry Onkelinx
Instituut voor natuur- en bosonderzoek / Research Institute for Nature
and Forest
Cel biometrie, methodologie en kwaliteitszorg / Section biometrics,
methodology and quality assurance
Gaverstraat 4
9500 Geraardsbergen
Belgium
tel. + 32 54/436 185
Thierry.Onkelinx at inbo.be
www.inbo.be
To call in the statistician after the experiment is done may be no more
than asking him to perform a post-mortem examination: he may be able to
say what the experiment died of.
~ Sir Ronald Aylmer Fisher
The plural of anecdote is not data.
~ Roger Brinner
The combination of some data and an aching desire for an answer does not
ensure that a reasonable answer can be extracted from a given body of
data.
~ John Tukey
-----Oorspronkelijk bericht-----
Van: r-help-bounces at r-project.org [mailto:r-help-bounces at r-project.org]
Namens Tena Sakai
Verzonden: donderdag 7 mei 2009 6:22
Aan: Ian Fellows; r-help at r-project.org
Onderwerp: Re: [R] I updated/reinstalled ggplot2 and the trouble
started...
Hi Ian,
Per your suggestion, I reinstalled R 2.9.0, then
I reinstalled ggplot2 on top. The problem persists.
Here's the what happens after the installation:
> qplot (carat, price, data = diamonds, alpha = I(1/10))
Warning message:
In grid.Call.graphics("L_points", x$x, x$y, x$pch, x$size) :
semi-transparency is not supported on this device: reported only
once per page
The entire record of installing ggplot2 package, ending
up with the line above is in the attached file. I would
think this should be reproducible with anybody else.
If you have any other suggestion, I am all ears.
Regards,
Tena Sakai
tsakai at gallo.ucsf.edu
-----Original Message-----
From: Ian Fellows [mailto:ifellows at gmail.com]
Sent: Tue 5/5/2009 11:43 PM
To: Tena Sakai
Subject: Re: I updated/reinstalled ggplot2 and the trouble started...
Tena,
May I suggest that you do a full clean install of R 2.9.0, then install
ggplot2 from cran. See if the problem persists after that.
Ian
On Tue, May 5, 2009 at 11:13 PM, tena <tsakai at gallo.ucsf.edu> wrote:
>
> Hi Hadley,
>
> Many thanks for your reply.
>
> I followed your instruction and got past the point where I
> was stuck at. Namely, I was able to generate a few plots.
> But as I came to the second half of section 2.4, where I
> wanted to see the behavior of alpha paramter, which I
> had apparently misspelled, I encountered another hindrance:
> > qplot (carat, price, data = diamonds, alpha = I(1/10))
> Warning message:
> In grid.Call.graphics("L_points", x$x, x$y, x$pch, x$size) :
> semi-transparency is not supported on this device: reported only
> once per page
>
> A plot was generated, but there are tic marks and labels on
> each direction, but no plot at all.
>
> I wonder if this is yet another (hidden) package to be updated...
> The warning message suggests grid, but I am hesitant to do
> something without knowing what is what. I would appreciate
> your instruction.
>
> Regards,
>
> Tena Sakai
>
>
> On May 5, 5:24 pm, hadley wickham <h.wick... at gmail.com> wrote:
> > Hi Tena,
> >
> > R isn't very good at detecting when package dependencies also need
to> > be updated, so you probably need to do:
> >
> > install.packages(c("reshape","plyr"))
> >
> > And you want
> >
> > qplot (carat, price, data=diamonds, alpha = I(1/10))
> >
> > not
> >
> > qplot (carat, price, data=diamonds, slpha = i(1/10))
> >
> > Hadley
> >
> > On Tue, May 5, 2009 at 6:27 PM, tena <tsa... at gallo.ucsf.edu>
wrote:
> >
> > > Hi Folks,
> >
> > > I am pretty new to R and I am even newer to ggplot.
> >
> > > I am using R 2.7.1, 2.8.1, and 2.9.0 on linux host and
> > > what I am experiencing holds for all three.
> >
> > > I was just typing a few examples from the chapter 2 of
> > > the book, ggplot2 --Elegant graphics for data analysis.
> >
> > > I typed 3 qplot lines on page 13:
> > > > qplot (carat, price, data=diamonds, slpha = i(1/10))
> > > > qplot (carat, price, data=diamonds, slpha = i(1/100))
> > > > qplot (carat, price, data=diamonds, slpha = i(1/200))
> >
> > > To me, the plot looked identical. I went to my R library
> > > directory and looked at the date on the ggplot2 directory,
> > > which was April of 2008. I decided to update the library.
> > > In R, I issued:
> > > > install.packages ('ggplot2',
'/usr/local/Gallo/R')
> > > and there was a complaint as to permission denied for
> > > saving the current version (or something). I reissued
> > > the command as root and this time it gave me a normal
> > > return.
> >
> > > I was ready to retrace my steps with the book. I only got
> > > to page 11 this time. Here's what happened (in all three
> > > versions):
> > > > set.seed (1410)
> > > > dsmall <- diamonds [sample (nrow(diamonds), 100), ]
> > > >
> > > > qplot (carat, price, data = diamonds)
> > > Error in get("new", env = FacetGrid, inherits = TRUE)
> > > (FacetGrid, ...) :
> > > could not find function "is.formula"
> > > >
> >
> > > Can somebody please clue me in as to what's happening,
> > > what I am doing wrong, etc?
> >
> > > Regards,
> >
> > > Tena Sakai
> > > tsa... at gallo.ucsf.edu
> >
> > --http://had.co.nz/
> --~--~---------~--~----~------------~-------~--~----~
> You received this message because you are subscribed to the ggplot2
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> To post to this group, send email to ggplot2 at googlegroups.com
> To unsubscribe from this group, send email to
>
ggplot2+unsubscribe at googlegroups.com<ggplot2%2Bunsubscribe at
googlegroups.
com>> For more options, visit this group at
> http://groups.google.com/group/ggplot2
> -~----------~----~----~----~------~----~------~--~---
>
>
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