I'm trying to run the krushkalmc method after running kruskal.test as part of my analysis with the Kruskal-Wallis rank sum test.
However, I've run into difficulties trying to install the pgirmess package that contains krushkalmc.
trying to install it from inside R:
install.packages("pgirmess")
package ‘pgirmess’ is available as a source package but not as a binary
so then I downloaded it and tried to install it manually:
install.packages("pgirmess", repos = NULL, type="source")
Warning: invalid package ‘pgirmess’
Error: ERROR: no packages specified
Warning in install.packages :
installation of package ‘pgirmess’ had non-zero exit status
and here is my sessionInfo()
> sessionInfo()
R version 3.1.2 (2014-10-31)
Platform: x86_64-apple-darwin13.4.0 (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_1.0.0
loaded via a namespace (and not attached):
[1] colorspace_1.2-4 digest_0.6.8 grid_3.1.2
[4] gtable_0.1.2 labeling_0.3 MASS_7.3-35
[7] munsell_0.4.2 plyr_1.8.1 proto_0.3-10
[10] Rcpp_0.11.4 reshape2_1.4.1 scales_0.2.4
[13] stringr_0.6.2 tools_3.1.2
I've tried to determine if any other package has the kruskalmc but don't see any.
Do you have any recommendations on a replacement package that I can use that has a test to dive deeper into the results of Kruskal-Wallis rank sum test?
Is there a debug mode on an install.packages to see what might be the problem?
Thanks for your help
I am moving this question over to cross-validated (aka stats.stackoverflow.com) as it is probably a more suitable location for this question. I don't think I have the ability to actually close it here, though. Thanks
Related
I have been running a bash script (under Ubuntu) that calls and runs some R scripts to plot some maps with ggplot2. As it is a production system I don't update any new R or package releases. But recently I tried to install plotly with an error message output.
Now, when trying to run the script (calling a php webpage trhough a browser; that was running fine for a lot of time) an error with crayon package halts and exits the script without plotting the maps.
'/usr/lib/R/bin/R --slave --no-restore --no-save --no-restore --file=./RAMS-mapa-onades-zones-manual.R'
Loading required package: sp
Loading required package: methods
Checking rgeos availability: TRUE
Error : .onLoad failed in loadNamespace() for 'pillar', details:
call: loadNamespace(name)
error: there is no package called 'crayon'
Error: package or namespace load failed for 'ggplot2'
Execution halted
But if I run from a terminal or with RStudio server crayon package is loaded, ggplot2 is also properly loaded, and the maps are produced.
crayon package (located at /home/meteo/R/i686-pc-linux-gnu-library/3.1) called as
library("crayon", lib.loc= c("/home/meteo/R/i686-pc-linux-gnu-library/3.1", "/usr/local/lib/R/site-library", "/usr/lib/R/library"))
R session info on Rstudio Server:
> sessionInfo()
R version 3.2.2 (2015-08-14)
Platform: i686-pc-linux-gnu (32-bit)
Running under: Ubuntu precise (12.04.5 LTS)
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=C LC_COLLATE=C LC_MONETARY=C LC_MESSAGES=C
[7] LC_PAPER=C LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=C LC_IDENTIFICATION=C
attached base packages:
[1] grid stats graphics grDevices utils datasets methods base
other attached packages:
[1] crayon_1.3.4 rgdal_0.9-1 rgeos_0.3-8 raster_2.3-24 gpclib_1.5-5 mapproj_1.2-2 maps_2.3-9
[8] stringr_0.6.2 plyr_1.8.1 ggplot2_3.2.0 maptools_0.8-34 sp_1.2-3
loaded via a namespace (and not attached):
[1] Rcpp_1.0.1 magrittr_1.5 tidyselect_0.2.5 munsell_0.5.0 colorspace_1.2-4 lattice_0.20-33 R6_2.4.0
[8] rlang_0.3.4 dplyr_0.8.1 tools_3.2.2 gtable_0.1.2 withr_2.1.2 digest_0.6.8 lazyeval_0.2.2
[15] assertthat_0.2.1 tibble_2.1.3 purrr_0.3.2 glue_1.3.1 labeling_0.3 pillar_1.4.1 scales_1.0.0
[22] foreign_0.8-66 pkgconfig_2.0.2
Maybe there is a version conflict? How do I check?
what version of R is in /usr/lib/R/bin/R? Basically it appears you are in a slight "dependency hell" I would run /usr/lib/R/bin/R and check to see if crayon is installed there. #Alexis is correct though, it is not wise to mix versions like that. Let R handle library location unless you are trying to separate packages. Check the libraries for 3.2.2 and see if crayon is installed. you may have switched your R version since plotly depends on R >=3.2.0 https://cran.r-project.org/web/packages/plotly/
I think the easy fix would be to correct your .libpaths() i.e not call the 3.1 library and install the correct version of the packages you need.
OR
switch from R 3.2 back to R 3.1
Since yesterday, I cannot load some common used packages, e.g. reshape2 and stringr through library command.
Step to reproduce my problem:
1) Start a new session in Rstudio server (Version 0.99.467). I also kill the active-sessions in Rstudio server.
2) Run these codes
library(ggplot2)
library(stringr)
3) Get an error message:
Error in unloadNamespace(package) :
namespace ‘stringr’ is imported by ‘reshape2’ so cannot be unloaded
Show Traceback
Rerun with Debug
Error in library(stringr) : “stringr” version 0.6.2 cannot be unloaded.
But I don't get error if stringr is loaded before ggplot2. How should I fix this problem. Thanks for any suggestions.
I may have to update R to 3.2
My R session info:
R version 3.1.3 (2015-03-09)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu precise (12.04.5 LTS)
locale:
[1] LC_CTYPE=en_AU.UTF-8 LC_NUMERIC=C LC_TIME=en_AU.UTF-8 LC_COLLATE=en_AU.UTF-8
[5] LC_MONETARY=en_AU.UTF-8 LC_MESSAGES=en_AU.UTF-8 LC_PAPER=en_AU.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=en_AU.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] ggplot2_1.0.0
loaded via a namespace (and not attached):
[1] colorspace_1.2-4 digest_0.6.4 grid_3.1.3 gtable_0.1.2 MASS_7.3-39 munsell_0.4.2 plyr_1.8.1
[8] proto_0.3-10 Rcpp_0.11.2 reshape2_1.4 scales_0.2.4 stringr_0.6.2 tools_3.1.3
I resolved my problem through updating R and all R packages.
I guess the problem is caused by old version of stringr or reshape2 as I install the same packages in different places (system folder or personal library). R tried to load a old version of package.
Even though it is a good practice to update R for me it was not necessary to solve the same issue. The problem can result from few .libPaths(). With .libPaths("C:/Program Files/R/R-3.4.3patched/library") you can point out one folder. After that just reinstall of packages, and it should work.
My code:
> .libPaths()
[1] "L:/My Documents/R/win-library/3.4" "C:/Program Files/R/R-3.4.3patched/library"
> .libPaths("C:/Program Files/R/R-3.4.3patched/library")
> packages<-c('ggplot2','data.table','knitr','xtable')
> install.packages(packages)
> lapply(packages,library,character.only=T)
Even though the issue is solved I hope it will help someone.
I was able to use pander successfully this morning on one computer, but now I am trying to do it on my own computer, and I am having some weird issues.
Here is my very elementary R Pander code:
library("pander")
library("knitr")
test<-Pandoc$new("My Name","Test")
test$add.paragraph('# Welcome to Test')
test$add.paragraph('*****')
#works so far but here it won't work
test$add(3+3)
#here I get error in dev.control(displaylist = "enable"):
# dev.control() called without an open grpahics device
# In addition: Warning message:
#In png("plots/....png", width=480,height=480,res=72, : failed to load cairo DLL
I literally can't use $add to add R code, and I don't understand why. I would greatly appreciate if someone could help.
Regards
edit:
R version 3.2.1 (2015-06-18)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.10.4 (Yosemite)
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] knitr_1.10.5 rmarkdown_0.7 rapport_0.51 yaml_2.1.13 plyr_1.8.3 lattice_0.20-33 pander_0.5.2 brew_1.0-6
loaded via a namespace (and not attached):
[1] htmltools_0.2.6 tools_3.2.1 Rcpp_0.12.0 reshape_0.8.5 grid_3.2.1 digest_0.6.8
It appears I did not have XQuartz installed. I installed it and everything works so thank you and köszönöm for the help.
I have a data frame "df1" of the following kind:
set.seed(2)
df1 = data.frame(Var1=rep(c('a','b','c','d'),3),
Var2=rep(c('aa','bb','cc'),each=4),
value=rnorm(12))
I try to create this plot:
ggplot(df1) + geom_bar(aes(x=Var2,y=value),stat="identity") + facet_wrap(~Var1)
and I get the following error message that I don't understand:
formal classes cannot be used without the methods package
What's wrong ? I can't find a package called methods by the way.
Here is my sessionInfo()
R version 3.0.1 (2013-05-16)
Platform: x86_64-apple-darwin10.8.0 (64-bit)
locale:
[1] fr_CH.UTF-8/fr_CH.UTF-8/fr_CH.UTF-8/C/fr_CH.UTF-8/fr_CH.UTF-8
attached base packages:
[1] utils graphics methods stats base
other attached packages:
[1] agricolae_1.1-4 reshape2_1.2.2 lattice_0.20-15 ggplot2_0.9.3.1 data.table_1.8.8
loaded via a namespace (and not attached):
[1] colorspace_1.2-2 datasets_3.0.1 dichromat_2.0-0 digest_0.6.3 grDevices_3.0.1 grid_3.0.1 gtable_0.1.2
[8] labeling_0.1 lme4_0.999999-2 MASS_7.3-26 Matrix_1.0-12 munsell_0.4 nlme_3.1-109 plyr_1.8
[15] proto_0.3-10 RColorBrewer_1.0-5 scales_0.2.3 stats4_3.0.1 stringr_0.6.2 tools_3.0.1
Thank you
I encountered the same error message and found a solution but in a different context.
The error happened while running an R script on a cluster. Interestingly the same script worked fine on a laptop (during testing with a subset of the data).
The solution in my context was to import the package with which the data was preprocessed. What I mean is that I previously saved an RDS file created using the package "Seurat". When reading the RDS file in a new session the package "Seurat" would load automatically when ran on a local machine. However on the cluster I had to specifically load the package with the library() command, before reading the RDS file. This is what solved the problem and stopped the obfuscated error message.
I ´ve tried to install some packages from Rmetrics, but it looks I am doing something wrong.
For
https://r-forge.r-project.org/scm/viewvc.php/pkg/fPortfolioBacktest/?logsort=cvs&root=rmetrics&pathrev=4948
I simply used
install.packages("fPortfolioBacktest", repos="http://R-Forge.R-project.org")
but
> install.packages("fPortfolioBacktest", repos="http://R-Forge.R-project.org")
Warning: unable to access index for repository http://R-Forge.R-project.org/bin/windows/contrib/2.12
Warning message:
In getDependencies(pkgs, dependencies, available, lib) :
package ‘fPortfolioBacktest’ is not available
Exactly the same problem is with
https://r-forge.r-project.org/scm/viewvc.php/pkg/Rsocp/?root=rmetrics&pathrev=3690
> sessionInfo()
R version 2.12.0 (2010-10-15)
Platform: i386-pc-mingw32/i386 (32-bit)
locale:
[1] LC_COLLATE=Slovak_Slovakia.1250 LC_CTYPE=Slovak_Slovakia.1250 LC_MONETARY=Slovak_Slovakia.1250 LC_NUMERIC=C
[5] LC_TIME=Slovak_Slovakia.1250
attached base packages:
[1] splines stats graphics grDevices utils datasets methods base
other attached packages:
[1] corpcor_1.5.7 fPortfolio_2130.80 fAssets_2100.78 fCopulae_2110.78 sn_0.4-16
[6] mnormt_1.4-3 robustbase_0.7-0 xlsx_0.3.0 xlsxjars_0.3.0 rJava_0.8-8
[11] ttrTests_1.5 PerformanceAnalytics_1.0.3.2 fTrading_2110.77 fBasics_2110.80 timeSeries_2130.90
[16] timeDate_2130.91 dynlm_0.3-0 car_2.0-8 survival_2.36-3 nnet_7.3-1
[21] MASS_7.3-8 lmtest_0.9-27 tseries_0.10-24 quadprog_1.5-3 quantmod_0.3-15
[26] TTR_0.20-2 xts_0.8-0 zoo_1.6-4 Defaults_1.1-1
loaded via a namespace (and not attached):
[1] grid_2.12.0 lattice_0.19-13 Rglpk_0.3-5 slam_0.1-22 strucchange_1.4-2 tools_2.12.0
Is there a fast way how to install them with all the dependencies? I am using Windows XP
Thanks,
Alex
Thanks for adding the error and your sessionInfo.
As I said in my comment, you're running an old version of R (2.12.0). R-forge only builds binaries for the most recent major revision (2.13.X). You need to either upgrade R or build from source. To build from source on Windows, you will need the Windows toolset.