Compression issue when saving anR project

Question

I solved the problem by moving R installation directory out of disk C. Thanks Joris for the great suggestions! I think the R core team should also take this as a bug and do something against the protecting mechanism of windows xp.

Dear Community:

While using the BIOMOD packages in R, I always get the following problem:

Error in xzfile(file, "wb", compression = 9) : cannot open the connection In addition: Warning message: In xzfile(file, "wb", compression = 9) : cannot initialize lzma encoder, error 5

It was said by the author of the package and also in the help file of "save" that the problem should be caused by lack of permission to write. However, as I am logging in as administative account and have assess to all operations, I have no idea what the problem is. Can anybody help me out? I really need to run the package now. Thanks in advance~

Sincerely, Marco

Below is the illustration in the help file of "save":

The most common reason for failure is lack of write permission in the current directory. For 'save.image' and for saving at the end of a session this will shown by messages like

    Error in gzfile(file, "wb") : unable to open connection
     In addition: Warning message:
     In gzfile(file, "wb") :
       cannot open compressed file '.RDataTmp',
       probable reason 'Permission denied'
 The defaults were changed to use compressed saves for 'save' in
 2.3.0 and for 'save.image' in 2.4.0.  Any recent version of R can
 read compressed save files, and a compressed file can be
 uncompressed (by 'gzip -d') for use with very old versions of R.*

Sorry for the ommision of the information: Here is the sessionInfo():

> sessionInfo()
R version 2.12.2 (2011-02-25)
Platform: i386-pc-mingw32/i386 (32-bit)

locale:
[1] LC_COLLATE=Chinese_People's Republic of China.936 
[2] LC_CTYPE=Chinese_People's Republic of China.936   
[3] LC_MONETARY=Chinese_People's Republic of China.936
[4] LC_NUMERIC=C                                      
[5] LC_TIME=Chinese_People's Republic of China.936    

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

other attached packages:
 [1] BIOMOD_1.1-6.8     foreign_0.8-42     gam_1.04          
 [4] randomForest_4.6-2 mda_0.4-1          class_7.3-3       
 [7] gbm_1.6-3.1        lattice_0.19-17    MASS_7.3-11       
[10] Design_2.3-0       Hmisc_3.8-3        survival_2.36-5   
[13] rpart_3.1-48       nnet_7.3-1         ade4_1.4-16       
[16] rgdal_0.6-33       dismo_0.5-19       rJava_0.9-0       
[19] raster_1.7-47      sp_0.9-78         

    loaded via a namespace (and not attached):
    [1] cluster_1.13.3 grid_2.12.2    tools_2.12.2 

Now I found that the problem come form the lzma encoder in doing "save":

>  x<-runif(100)
>  save(x, file = "F:/test.gzip", compress='gzip')
>  save(x, file = "F:/test.xz", compress='xz')
Error in xzfile(file, "wb", compression = 9) : cannot open the connection
> 

Answer 1

I had a similar issue when trying to project to a new scenario (a tables containing columns corresponding to the predictor variables) after having run the modeling procedure using 8 models.

The first table (approx 250,000 rows) ran fine, and I was able to save the results as a .csv file. However the second one (approx 380,000 rows) resulted in the above error message, and some of the files were not written to the project folder.

I have since cut all the tables down to a maximum of 260,000 rows and I no longer recieve the error message. It was a bit of a pain doing it in multiple runs, but once I had written the script once, I just used find and replace in MS Word to change it for each run.