Problem with input files

gspirito commented 4 years ago

Hello, I installed SAKE on Ubuntu 16.04.6 LTS, R version 3.6.1. When I start SAKE I get to the correct page with the GUI on firefox. However it seems like I am not able to input any data: if I select "Upload raw data" from the drop down menù and try to upload a matrix of gene counts nothing happens; also if I select "Select from preloaded data" and select a dataset nothing happens. What could be causing this issue?

Thanks in advance.

naikai commented 4 years ago

Hi, can you please provide an example input data set so that I can reproduce the problem on my end. Thanks.

zhaoxi10 commented 3 years ago

Hi, I have the same problem. Even the preload dataset dose not work.

naikai commented 3 years ago

Hi,

Sorry for the late reply. I just tried installing sake on my end, and these functions seem to work fine. Please see attached sessionInfo for your references.

For Upload raw data, please make sure to select the correct Separator that matches your data file.
- Comma for .csv file
- Tab for .txt, .tsv file
For Upload saved NMF run, please try downloading precomputed [data] (https://github.com/naikai/sake/tree/master/data) and run it again
For Select from preloaded data, all of them should work.

@gspirito and @zhaoxi10 Can you please send me the data you are working on so that I can help you solve the issues?

Thank you.

> sessionInfo()
R version 3.6.3 (2020-02-29)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Catalina 10.15.7

Matrix products: default
BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib

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] stats4    tools     parallel  stats     graphics  grDevices utils     datasets 
 [9] methods   base     

other attached packages:
 [1] Rtsne_0.15           doParallel_1.0.16    iterators_1.0.13    
 [4] foreach_1.5.1        pathview_1.26.0      org.Hs.eg.db_3.10.0 
 [7] AnnotationDbi_1.48.0 IRanges_2.20.2       S4Vectors_0.24.4    
[10] gageData_2.24.0      gage_2.36.0          snowfall_1.84-6.1   
[13] snow_0.4-3           matrixStats_0.58.0   RColorBrewer_1.1-2  
[16] AnnotationHub_2.18.0 BiocFileCache_1.10.2 dbplyr_2.1.0        
[19] BiocParallel_1.20.1  biomaRt_2.42.1       corrplot_0.84       
[22] magrittr_2.0.1       data.table_1.13.6    DT_0.16             
[25] shinydashboard_0.7.1 shinythemes_1.2.0    htmltools_0.5.1.1   
[28] d3heatmap_0.6.1.3    plotly_4.9.2.1       ggplot2_3.3.3       
[31] shinyBS_0.61         networkD3_0.4        sake_0.4.0          
[34] dplyr_1.0.5          NMF_0.22.0           Biobase_2.46.0      
[37] BiocGenerics_0.32.0  cluster_2.1.0        rngtools_1.5        
[40] pkgmaker_0.32.2.900  registry_0.5-1       shiny_1.6.0

awsreview commented 3 years ago

Hello, I am having the same problem. Ubuntu 18 LTS and R 3.6.3 and unable to view or load any datasets. Thanks

naikai commented 3 years ago

As suggested by multiple users. We figure out a tentative solution to successfully install the package. It is related to bf3a2970e839ebfe290fdbfea0d3746550c003ad

Posted steps here for references:

Quick update 2021-03-25 (inputs from Jarrett Eshima jarrettbryceeshima@gmail.com)

Installed RTools40, Devtools, pkgmaker, and SAKE (and dependencies) according to the README rmarkdown file
I removed the following dependent packages from my R library: plotly, shiny, shinydashboard, htmltools, htmlwidgets, promises, crosstalk and DT
I reinstalled older versions of the packages: plotly 4.9.2, shiny 1.5.0, shinydashboard 0.6.1, htmltools 0.5.0, htmlwidgets 1.5.2, promises 1.1.1, crosstalk 1.1.0.1, and DT 0.16 (SessionInfo() output screenshots attached to this email).
Loaded SAKE library and ran shiny::runApp(system.file("sake",package="sake"))
Software was back to normal

User Zig Zag also confirms on his end, with his sessionInfo()

> sessionInfo()
R version 4.0.4 (2021-02-15)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19042)

Matrix products: default

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

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

other attached packages:
[1] sake_0.4.0          dplyr_1.0.5         NMF_0.30.1          Biobase_2.50.0      BiocGenerics_0.36.0 cluster_2.1.0      
[7] rngtools_1.5        pkgmaker_0.32.2.900 registry_0.5-1    

loaded via a namespace (and not attached):
 [1] viridis_0.5.1       pkgload_1.2.0       viridisLite_0.3.0   foreach_1.5.1       shiny_1.5.0         assertthat_0.2.1  
 [7] BiocManager_1.30.12 remotes_2.2.0       sessioninfo_1.1.1   pillar_1.5.1        glue_1.4.2          digest_0.6.27      
[13] RColorBrewer_1.1-2  promises_1.1.1      colorspace_2.0-0    htmltools_0.5.1.1   httpuv_1.5.5        plyr_1.8.6        
[19] pkgconfig_2.0.3     devtools_2.3.2      purrr_0.3.4         xtable_1.8-4        scales_1.1.1        processx_3.5.0    
[25] later_1.1.0.1       tibble_3.1.0        generics_0.1.0      ggplot2_3.3.3       usethis_2.0.1       ellipsis_0.3.1    
[31] cachem_1.0.4        withr_2.4.1         cli_2.3.1           magrittr_2.0.1      crayon_1.4.1        mime_0.10          
[37] memoise_2.0.0       ps_1.6.0            fs_1.5.0            fansi_0.4.2         doParallel_1.0.16   pkgbuild_1.2.0    
[43] tools_4.0.4         data.table_1.14.0   prettyunits_1.1.1   lifecycle_1.0.0     matrixStats_0.58.0  gridBase_0.4-7    
[49] stringr_1.4.0       munsell_0.5.0       callr_3.6.0         compiler_4.0.4      rlang_0.4.10        grid_4.0.4        
[55] iterators_1.0.13    rstudioapi_0.13     testthat_3.0.2      gtable_0.3.0        codetools_0.2-18    DBI_1.1.1          
[61] curl_4.3            reshape2_1.4.4      R6_2.5.0            gridExtra_2.3       fastmap_1.1.0       utf8_1.2.1        
[67] rprojroot_2.0.2     dendextend_1.14.0   desc_1.3.0          stringi_1.5.3       Rcpp_1.0.6          vctrs_0.3.6        
[73] tidyselect_1.1.0  
> shiny::runApp(system.file("sake", package="sake"))

zhaoxi10 commented 3 years ago

Hi,

Sorry for the late reply. I just tried installing sake on my end, and these functions seem to work fine. Please see attached sessionInfo for your references.

For Upload raw data, please make sure to select the correct Separator that matches your data file.

Comma for .csv file

Tab for .txt, .tsv file

For Upload saved NMF run, please try downloading precomputed [data] (https://github.com/naikai/sake/tree/master/data) and run it again

For Select from preloaded data, all of them should work.

@gspirito and @zhaoxi10 Can you please send me the data you are working on so that I can help you solve the issues?

Thank you.
> sessionInfo()
R version 3.6.3 (2020-02-29)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Catalina 10.15.7

Matrix products: default
BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib

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] stats4    tools     parallel  stats     graphics  grDevices utils     datasets 
 [9] methods   base     

other attached packages:
 [1] Rtsne_0.15           doParallel_1.0.16    iterators_1.0.13    
 [4] foreach_1.5.1        pathview_1.26.0      org.Hs.eg.db_3.10.0 
 [7] AnnotationDbi_1.48.0 IRanges_2.20.2       S4Vectors_0.24.4    
[10] gageData_2.24.0      gage_2.36.0          snowfall_1.84-6.1   
[13] snow_0.4-3           matrixStats_0.58.0   RColorBrewer_1.1-2  
[16] AnnotationHub_2.18.0 BiocFileCache_1.10.2 dbplyr_2.1.0        
[19] BiocParallel_1.20.1  biomaRt_2.42.1       corrplot_0.84       
[22] magrittr_2.0.1       data.table_1.13.6    DT_0.16             
[25] shinydashboard_0.7.1 shinythemes_1.2.0    htmltools_0.5.1.1   
[28] d3heatmap_0.6.1.3    plotly_4.9.2.1       ggplot2_3.3.3       
[31] shinyBS_0.61         networkD3_0.4        sake_0.4.0          
[34] dplyr_1.0.5          NMF_0.22.0           Biobase_2.46.0      
[37] BiocGenerics_0.32.0  cluster_2.1.0        rngtools_1.5        
[40] pkgmaker_0.32.2.900  registry_0.5-1       shiny_1.6.0         
Hello, I am having the same problem. Ubuntu 18 LTS and R 3.6.3 and unable to view or load any datasets. Thanks

did you figure out how to upload the data. I reinstalled and the preload dataset still dose not work.

zhaoxi10 commented 3 years ago

Hi,

Sorry for the late reply. I just tried installing sake on my end, and these functions seem to work fine. Please see attached sessionInfo for your references.

For Upload raw data, please make sure to select the correct Separator that matches your data file.

Comma for .csv file

Tab for .txt, .tsv file

For Upload saved NMF run, please try downloading precomputed [data] (https://github.com/naikai/sake/tree/master/data) and run it again

For Select from preloaded data, all of them should work.

@gspirito and @zhaoxi10 Can you please send me the data you are working on so that I can help you solve the issues?

Thank you.

This what it was shown when I try to use the preload data. The downloaded data also dose not work.

nickhir commented 2 years ago

I have the same issue. Did anyone gain some new insights in the meantime?

naikai / sake

Problem with input files #79