running ggplot2 in R 3.0.2

[Tristram Smith]

I upgraded to R 3.0.2 and now can't load ggplot2. I get this message:

Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) :
  there is no package called ‘colorspace’
Error: package or namespace load failed for ‘ggplot2’

I tried removing and re-installing the ggplot2 package, to no avail. Suggestions?

Thank you.

[Ista Zahn]

Hi Tristram,

This sounds strange... did you try

install.packages("ggplot2", dependencies=TRUE)

perhaps followed by

upgrade.packages(ask=FALSE, checkBuilt=TRUE)

?

If that doesn't solve it you could install colorspace manually, i.e.

install.packages("colorspace", dependencies=TRUE)

but you really shouldn't need to do that...

Best,
Ista

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[Tristram Smith]

I received very useful guidance from Ista and Dennis on re-installing ggplot2 in 3.0.2. I can now load it. However, it still doesn't seem to be running properly, and reverting to 3.0.1 didn't fix the problem, so now I'm stuck again. For example, I have a very simple file called iacc:

        Area Studies
1 Lifespan Issues      34
2    Epidemiology     108
3    Risk Factors     162
4       Diagnosis     166
5         Service     211
6       Treatment     277
7         Biology     409

I try to create a straightforward Cleveland dot plot:

ggplot(iacc,aes(x=Studies,y=Area))+geom_point()

Then I get the following error message:

 in scale$trans$breaks(limits) : lazy-load database 'P' is corrupt
In addition: Warning message:
In scale$trans$breaks(limits) : internal error -3 in R_decompress1

I appreciate any guidance the group can offer.

Tris

[Brandon Hurr]

What's your sessionInfo() after loading ggplot2? 

[Tristram Smith]

Hi Brandon,

Thank you for your quick reply. Here it is:

> library("ggplot2")
> sessionInfo()
R version 3.0.2 (2013-09-25)
Platform: i386-w64-mingw32/i386 (32-bit)

locale:
[1] LC_COLLATE=English_United States.1252
[2] LC_CTYPE=English_United States.1252  
[3] LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C                         
[5] LC_TIME=English_United States.1252   

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base    

other attached packages:
[1] ggplot2_0.9.3.1

loaded via a namespace (and not attached):
 [1] colorspace_1.2-3   dichromat_2.0-0    digest_0.6.3       grid_3.0.2       
 [5] gtable_0.1.2       labeling_0.2       MASS_7.3-29        munsell_0.4.2    
 [9] plyr_1.8           proto_0.3-10       RColorBrewer_1.0-5 reshape2_1.2.2   
[13] scales_0.2.3       stringr_0.6.2 

Tris

[Brandon Hurr]

Looks about the same as mine, but mine doesn't give me weird errors about lazy loading packages and I'm on Mac: 

> sessionInfo()

R version 3.0.2 (2013-09-25)

Platform: x86_64-apple-darwin10.8.0 (64-bit)

locale:

[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:

[1] stats     graphics  grDevices utils     datasets  methods  

[7] base     

other attached packages:

[1] ggplot2_0.9.3.1

loaded via a namespace (and not attached):

 [1] colorspace_1.2-3   dichromat_2.0-0    digest_0.6.3      

 [4] grid_3.0.2         gtable_0.1.2       labeling_0.2      

 [7] MASS_7.3-29        munsell_0.4.2      plyr_1.8          

[10] proto_0.3-10       RColorBrewer_1.0-5 reshape2_1.2.2    

[13] scales_0.2.3       stringr_0.6.2  

How did you install R? 

Did you get it from CRAN? http://cran.r-project.org/bin/windows/base/

Also, provide a dataset and code to reproduce exactly what is happening on your machine. 

B

[Tristram Smith]

Hi Brandon,

 

Thank you once more. Yes, I installed R directly from http://cran.r-project.org/bin/windows/base/. I installed ggplot2 from my usual CRAN mirror (UCLA).I get the same error message with every plot I try to make, so, for simplicity, I use as an example a tiny dataset and straightforward code:

 

>iacc<-read.csv("IACC2.csv")

>iacc

Area Studies
1 Lifespan Issues      34
2    Epidemiology     108
3    Risk Factors     162
4       Diagnosis     166
5         Service     211
6       Treatment     277
7         Biology     409

I try to create a straightforward Cleveland dot plot:

>ggplot(iacc,aes(x=Studies,y=Area))+geom_point()

Then I get what I agree is a "crazy" error message:

 

 in scale$trans$breaks(limits) : lazy-load database 'P' is corrupt
In addition: Warning message:
In scale$trans$breaks(limits) : internal error -3 in R_decompress1

I've made my way through the R Cookbook and R Graphics Cookbook, so I can follow recipes but have very limited understanding of the underlying R system. I greatly appreciate your help.

Tris

[David Guy]

Tristram,

Try re-loading ggplot2 from a different CRAN mirror (other than UCLA). It happened to me in the past that changing mirrors solves the problem.

Use chooseCRANmirror() for making a different choice 

or the repos option as below:

install.packages('RMySQL', repos='http://cran.us.r-project.org')

HTH

David

David Guy, PhD

R Statistical Consulting Inc.

Flemington, NJ USA

www.RStatisticalConsulting.com

 

Office: 908-237-5107

Cell:    917-941-5890

Fax:    908-284-0356
Skype: david.guy1213

[Brandon Hurr]

Also, a quick google search indicates that you might have a corrupt session. Can you load a completely empty session? 

If not, start R and then:

rm (list = ls(all=TRUE)) 

quit()

# Save your "workspace", should be empty now

# Restart R

B

[Tristram Smith]

Thank you very much, everyone! Unfortunately, removing ggplot2 and installing from another CRAN didn't work (I tried Austria and New Zealand), nor did rm (list = ls(all=TRUE)). I also received a suggestion to search for help on LazyLoad (?lazyLoad), which may be the answer if I can figure out how to set the parameters. I'll keep investigating this.

[Brandon Hurr]

Hard for me to say... I only run windows rarely and I've never seen these errors. 

When's the last time you rebooted? 

Did you previously completely uninstall R previously? 

When's the last time you started with a fresh install of Windows? 

Have you got another machine you can try doing the same things on? 

Lastly, you need to probably go to r-help... as far as I can tell this isn't a ggplot-specific problem. 

B

[Felix Lankester]

HI All,

I seem to have 2 small problems:

1. how to get geom_points to appear on all lines on a plot, rather than just the ones from the first line of code (ie nsmeans2)

2. How to include the two dashed lines (ie the lines from nsmeans3) in the legend, with a title for each

Any help would be most appreciated,

Many thanks,

Felix

The code:

nsplot <- ggplot(data=nsmeans2[nsmeans2$trial==1,], aes(x = time,y = x, group = vacc, colour = vacc)) +
geom_line(size=0.8) +
geom_point(size = 2.0)+
geom_line(data=nsmeans3[nsmeans3$trial==1, ], linetype=4, linesize=0.9) +
xlab("Months post primary vaccination") + ylab("Titre") +
ggtitle("Mean nasal secretion titre in trial 1 - MRI & NMAIST ELISA RESULTS") +
scale_colour_discrete(name = "Vacc group", labels=c("Unvaccinated", "Vaccinated"))

The current plot:

[Tristram Smith]

I am immensely appreciative of all the detailed, helpful guidance I received. As suggested by Brandon and others, the program files on my computer somehow became corrupted. I expunged R and all related files with Revo Installer, permanently deleted them from my computer,  downloaded R into a different program file, and then downloaded ggplot2 again. Now both work. Laborious, but I learned a lot. Thank you!

Tris

[Tengiz]

Sorry for intruding: just used Ista's guidance to solve qplot problem - couldn't load until I manually installed colorspace.
Many thanks.
T.