install error

[zqr2008]

Hello and thanks for bringing up the package. I have issues in install the packages.

I used devtools as instructed:

library(devtools)   
install_github("efratmuller/MintTea")   

But there is a rare error in install R packages:

** using staged installation
** R
** data
*** moving datasets to lazyload DB
** byte-compile and prepare package for lazy loading
Warning: package 'readr' was built under R version 4.2.3
Warning: package 'usethis' was built under R version 4.2.3
Warning in path_file(base_path) :
  restarting interrupted promise evaluation
Error : Failed to evaluate glue component {ui_value(project_name())}
Caused by error:
! [EPERM] Failed to realize 'C:/Users/zqr20/AppData/Local/Temp/RtmpwnY8d4/R.INSTALL31d42f4d239a/MintTea': operation not permitted
Error: unable to load R code in package 'MintTea'
Execution halted
ERROR: lazy loading failed for package 'MintTea'
* removing 'C:/Users/zqr20/AppData/Local/R/win-library/4.2/MintTea'

My system info

R version 4.2.2 (2022-10-31 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 22631)

Matrix products: default

locale:
[1] LC_COLLATE=Chinese (Simplified)_China.utf8 
[2] LC_CTYPE=Chinese (Simplified)_China.utf8   
[3] LC_MONETARY=Chinese (Simplified)_China.utf8
[4] LC_NUMERIC=C                               
[5] LC_TIME=Chinese (Simplified)_China.utf8    

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

other attached packages:
[1] devtools_2.4.5 usethis_2.2.2 

loaded via a namespace (and not attached):
 [1] pbdZMQ_0.3-10         reticulate_1.34.0     tidyselect_1.2.1     
 [4] remotes_2.4.2.1       purrr_1.0.2           lattice_0.20-45      
 [7] basilisk.utils_1.10.0 generics_0.1.3        vctrs_0.6.5          
[10] miniUI_0.1.1.1        htmltools_0.5.7       utf8_1.2.2           
[13] rlang_1.1.3           pkgbuild_1.4.2        pillar_1.9.0         
[16] later_1.3.0           urlchecker_1.0.1      glue_1.7.0           
[19] sessioninfo_1.2.2     lifecycle_1.0.4       stringr_1.5.0        
[22] htmlwidgets_1.6.3     memoise_2.0.1         callr_3.7.3          
[25] fastmap_1.1.1         httpuv_1.6.8          ps_1.7.5             
[28] parallel_4.2.2        curl_5.1.0            fansi_1.0.4          
[31] Rcpp_1.0.10           xtable_1.8-4          promises_1.2.0.1     
[34] filelock_1.0.2        cachem_1.0.6          desc_1.4.2           
[37] pkgload_1.3.3         jsonlite_1.8.4        mime_0.12            
[40] fs_1.6.0              basilisk_1.10.2       dir.expiry_1.6.0     
[43] png_0.1-8             digest_0.6.31         stringi_1.7.12       
[46] processx_3.8.2        dplyr_1.1.4           shiny_1.8.0          
[49] grid_4.2.2            rprojroot_2.0.4       cli_3.6.2            
[52] tools_4.2.2           magrittr_2.0.3        tibble_3.2.1         
[55] profvis_0.3.8         pkgconfig_2.0.3       crayon_1.5.2         
[58] ellipsis_0.3.2        Matrix_1.6-4          prettyunits_1.2.0    
[61] rstudioapi_0.15.0     R6_2.5.1              compiler_4.2.2 

Please let me know if you have solutions. Many thanks ahead!

Best!

[efratmuller]

Hi @zqr2008 ,
I never encountered this kind of error. I found in another git issue that it might be related to the 'glue' package version. I see I have 1.6.2 installed, and you have 1.7.0. I'll try to look into it but in the meantime I would check if perhaps downgrading the glue package may solve the issue. Just as a first try.

[zqr2008]

Hi @zqr2008 , I never encountered this kind of error. I found in another git issue that it might be related to the 'glue' package version. I see I have 1.6.2 installed, and you have 1.7.0. I'll try to look into it but in the meantime I would check if perhaps downgrading the glue package may solve the issue. Just as a first try.

Many thanks for replying!

I tried to degrade glue to 1.6.2, and install MintTea again, however this error still exsits. Please see:

* installing *source* package 'MintTea' ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** byte-compile and prepare package for lazy loading
Warning: package 'readr' was built under R version 4.2.3
Warning: package 'usethis' was built under R version 4.2.3
Warning in path_file(base_path) :
  restarting interrupted promise evaluation
Error : [EPERM] Failed to realize 'C:/Users/zqr20/AppData/Local/Temp/Rtmpgrmsrl/R.INSTALL567428155b45/MintTea': operation not permitted
Error: unable to load R code in package 'MintTea'
Execution halted
ERROR: lazy loading failed for package 'MintTea'
* removing 'C:/Users/zqr20/AppData/Local/R/win-library/4.2/MintTea'

My current sessioninfo:

R version 4.2.2 (2022-10-31 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 22631)

Matrix products: default

locale:
[1] LC_COLLATE=Chinese (Simplified)_China.utf8 
[2] LC_CTYPE=Chinese (Simplified)_China.utf8   
[3] LC_MONETARY=Chinese (Simplified)_China.utf8
[4] LC_NUMERIC=C                               
[5] LC_TIME=Chinese (Simplified)_China.utf8    

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

other attached packages:
[1] devtools_2.4.5 usethis_2.2.2 

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.10                 dir.expiry_1.6.0           
 [3] lattice_0.20-45             prettyunits_1.2.0          
 [5] png_0.1-8                   ps_1.7.5                   
 [7] rprojroot_2.0.4             digest_0.6.31              
 [9] mime_0.12                   R6_2.5.1                   
[11] GenomeInfoDb_1.34.9         stats4_4.2.2               
[13] basilisk_1.10.2             zlibbioc_1.44.0            
[15] rlang_1.1.3                 curl_5.1.0                 
[17] rstudioapi_0.15.0           miniUI_0.1.1.1             
[19] urlchecker_1.0.1            callr_3.7.3                
[21] S4Vectors_0.36.2            Matrix_1.6-4               
[23] reticulate_1.34.0           desc_1.4.2                 
[25] BiocParallel_1.32.6         stringr_1.5.0              
[27] htmlwidgets_1.6.3           RCurl_1.98-1.13            
[29] shiny_1.8.1.1               DelayedArray_0.23.2        
[31] compiler_4.2.2              httpuv_1.6.8               
[33] BiocGenerics_0.44.0         pkgbuild_1.4.2             
[35] htmltools_0.5.7             SummarizedExperiment_1.28.0
[37] GenomeInfoDbData_1.2.9      gss_2.2-7                  
[39] IRanges_2.32.0              codetools_0.2-19           
[41] matrixStats_1.1.0           crayon_1.5.2               
[43] later_1.3.0                 bitops_1.0-7               
[45] basilisk.utils_1.10.0       grid_4.2.2                 
[47] jsonlite_1.8.4              xtable_1.8-4               
[49] lifecycle_1.0.4             magrittr_2.0.3             
[51] stringi_1.7.12              cli_3.6.2                  
[53] cachem_1.0.6                XVector_0.38.0             
[55] remotes_2.4.2.1             fs_1.6.0                   
[57] promises_1.2.0.1            ellipsis_0.3.2             
[59] filelock_1.0.2              generics_0.1.3             
[61] vctrs_0.6.5                 tools_4.2.2                
[63] Biobase_2.58.0              glue_1.6.2                 
[65] purrr_1.0.2                 MatrixGenerics_1.10.0      
[67] processx_3.8.2              pkgload_1.3.3              
[69] parallel_4.2.2              fastmap_1.1.1              
[71] sessioninfo_1.2.2           GenomicRanges_1.50.2       
[73] memoise_2.0.1               pbdZMQ_0.3-10              
[75] profvis_0.3.8 

[efratmuller]

Is this your own computer? No permission issues expected right?
Another thing we can try is to change the temporary directory where the repository is currently being downloaded by default. For this I think you need to run both of these lines before you execute install_github command:

Sys.setenv(TMPDIR="C:/Users/zqr20/<some directory of your choice>")
configure.vars="TMPDIR=C:/Users/zqr20/<some directory of your choice>"

[zqr2008]

Is this your own computer? No permission issues expected right? Another thing we can try is to change the temporary directory where the repository is currently being downloaded by default. For this I think you need to run both of these lines before you execute install_github command:

Sys.setenv(TMPDIR="C:/Users/zqr20/<some directory of your choice>") configure.vars="TMPDIR=C:/Users/zqr20/<some directory of your choice>"

Thanks for the suggestion. I also tried this config you provide. It did not work. I have permissions and installed many developmental packages before, and I successfully today use devtools in building other developing packages, like this one:

devtools::install_github("irinagain/SLIDE")

So, I suspect that the temp directory was not correctly created. But I can not figure out why.

Many many thanks for your time.

[efratmuller]

You can also just clone the repository, and then install the package. If you use RStudio you should open a "R package" project based on the cloned repository, and then click "install" on the right.

[zqr2008]

You can also just clone the repository, and then install the package. If you use RStudio you should open a "R package" project based on the cloned repository, and then click "install" on the right.

Many thanks for suggestion. It did not work. But I manage to install your package on another computer with different version of a R base. I guess it is a basic systemic error.

Anyway, I already used this package for our own data. It went well. Many many thanks for your hard work in developing it!!!

[zqr2008]

Also another little issue for your tutorial in README.md,
(for example: 'T_' for taxonomy, 'P_' for pathways, 'M_' for metabolites, etc.);

It can be better if you write
(for example: 'T__' for taxonomy, 'P__' for pathways, 'M__' for metabolites, etc.);
Because I spend some time finding that "__" is what you want in column names instead of "_"

[efratmuller]

I updated the tutorial, thanks for letting me know.
Best regards!
Efrat