Question

Error in MineICA parameter build

0

Entering edit mode

Udi Landau ▴ 30

@udi-landau-9726

Last seen 4.2 years ago

Hi, I am tring to run the demo data in the MineICA package: https://bioconductor.org/packages/release/bioc/vignettes/MineICA/inst/doc/MineICA.pdf

however the comamnd buildMineICAParams give me an error.

> params <- buildMineICAParams(resPath = "mainz/", selCutoff = 3, pvalCutoff = 0.05)
Error in system("echo $HOME", intern = TRUE) : 'echo' not found

maybe it is because I on a windows machine? appreciate the help.

> sessionInfo()
R version 3.6.2 (2019-12-12)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows >= 8 x64 (build 9200)

Matrix products: default

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

attached base packages:
 [1] grid      stats4    parallel  stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] breastCancerMAINZ_1.24.0 MineICA_1.26.0           JADE_2.0-2               fastICA_1.2-2           
 [5] Hmisc_4.3-0              Formula_1.2-3            survival_3.1-8           lattice_0.20-38         
 [9] annotate_1.64.0          XML_3.98-1.20            Rgraphviz_2.30.0         igraph_1.2.4.2          
[13] colorspace_1.4-1         RColorBrewer_1.1-2       mclust_5.4.5             marray_1.64.0           
[17] limma_3.42.0             cluster_2.1.0            GOstats_2.52.0           graph_1.64.0            
[21] Category_2.52.1          Matrix_1.2-18            AnnotationDbi_1.48.0     IRanges_2.16.0          
[25] S4Vectors_0.20.1         biomaRt_2.42.0           xtable_1.8-4             foreach_1.4.7           
[29] ggplot2_3.2.1            plyr_1.8.5               Biobase_2.42.0           BiocGenerics_0.32.0     
[33] gtools_3.8.1             scales_1.1.0            

loaded via a namespace (and not attached):
 [1] bitops_1.0-6           bit64_0.9-7            progress_1.2.2         httr_1.4.1            
 [5] tools_3.6.2            backports_1.1.5        R6_2.4.1               rpart_4.1-15          
 [9] DBI_1.1.0              lazyeval_0.2.2         nnet_7.3-12            withr_2.1.2           
[13] tidyselect_0.2.5       gridExtra_2.3          prettyunits_1.1.0      bit_1.1-14            
[17] curl_4.3               compiler_3.6.2         htmlTable_1.13.3       checkmate_1.9.4       
[21] genefilter_1.68.0      RBGL_1.62.1            askpass_1.1            rappdirs_0.3.1        
[25] stringr_1.4.0          digest_0.6.23          foreign_0.8-74         AnnotationForge_1.28.0
[29] htmltools_0.4.0        base64enc_0.1-3        jpeg_0.1-8.1           pkgconfig_2.0.3       
[33] dbplyr_1.4.2           htmlwidgets_1.5.1      rlang_0.4.2            rstudioapi_0.10       
[37] RSQLite_2.2.0          acepack_1.4.1          dplyr_0.8.3            RCurl_1.95-4.13       
[41] magrittr_1.5           GO.db_3.7.0            Rcpp_1.0.3             munsell_0.5.0         
[45] lifecycle_0.1.0        stringi_1.4.4          yaml_2.2.0             BiocFileCache_1.10.2  
[49] blob_1.2.1             crayon_1.3.4           splines_3.6.2          hms_0.5.3             
[53] knitr_1.27             zeallot_0.1.0          pillar_1.4.3           codetools_0.2-16      
[57] glue_1.3.1             latticeExtra_0.6-29    data.table_1.12.8      BiocManager_1.30.10   
[61] vctrs_0.2.1            png_0.1-7              gtable_0.3.0           openssl_1.4.1         
[65] purrr_0.3.3            clue_0.3-57            assertthat_0.2.1       xfun_0.12             
[69] tibble_2.1.3           iterators_1.0.12       memoise_1.1.0          GSEABase_1.48.0

MineICA • 643 views

ADD COMMENT • link updated 17 months ago by Masa • 0 • written 4.2 years ago by Udi Landau ▴ 30

score 0 · Answer 1 · 2020-02-03

0

Entering edit mode

anne.biton ▴ 20

@annebiton-7817

Last seen 6.2 years ago

United States

Hi,

Sorry I missed this, is it still a problem ? it is indeed because of Windows, i will rewrite this function. A temporary work-around would be to use resPath="" which would use the current directory to store the output files for now but this is not ideal.

best, Anne

Le mer. 22 janv. 2020 à 14:07, Udi Landau [bioc] noreply@bioconductor.org a écrit :

ADD COMMENT • link 4.2 years ago anne.biton ▴ 20

0

Entering edit mode

Hi,

I did as suggested by @annebiton-7817. Yet, when running "runAn" I have the following error:

runAn(params=params, icaSet=icaSet_RNAseq, writeGenesByComp = TRUE,
           keepVar=keepVar)
The detected qualitative variables are: Genotype
No quantitative variable is found in pheno data.
..Write gene contributions..
Error in { : task 1 failed - "cannot open the connection"
In addition: There were 21 warnings (use warnings() to see them)

It seems related to the params variable. How can I fix this error please?

Thank you in advance

> sessionInfo()
R version 4.2.1 (2022-06-23 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 22621)

Matrix products: default


attached base packages:
[1] grid      stats4    stats     graphics  grDevices utils     datasets  methods  
[9] base     

other attached packages:
 [1] seewave_2.2.0        edgeR_3.38.4         MineICA_1.36.1       JADE_2.0-3          
 [5] fastICA_1.2-3        Hmisc_4.7-1          Formula_1.2-4        survival_3.3-1      
 [9] lattice_0.20-45      annotate_1.74.0      XML_3.99-0.12        Rgraphviz_2.40.0    
[13] igraph_1.3.5         colorspace_2.0-3     RColorBrewer_1.1-3   mclust_6.0.0        
[17] marray_1.74.0        limma_3.52.4         cluster_2.1.3        GOstats_2.62.0      
[21] graph_1.74.0         Category_2.62.0      Matrix_1.5-3         AnnotationDbi_1.58.0
[25] IRanges_2.30.1       S4Vectors_0.34.0     gtools_3.9.3         biomaRt_2.52.0      
[29] xtable_1.8-4         foreach_1.5.2        scales_1.2.1         ggplot2_3.4.0       
[33] plyr_1.8.8           Biobase_2.56.0       BiocGenerics_0.42.0 

loaded via a namespace (and not attached):
 [1] backports_1.4.1             BiocFileCache_2.4.0         GSEABase_1.58.0            
 [4] splines_4.2.1               GenomeInfoDb_1.32.4         digest_0.6.30              
 [7] htmltools_0.5.3             GO.db_3.15.0                fansi_1.0.3                
[10] checkmate_2.1.0             magrittr_2.0.3              memoise_2.0.1              
[13] Biostrings_2.64.1           matrixStats_0.62.0          prettyunits_1.1.1          
[16] jpeg_0.1-9                  signal_0.7-7                blob_1.2.3                 
[19] rappdirs_0.3.3              xfun_0.34                   dplyr_1.0.10               
[22] crayon_1.5.2                RCurl_1.98-1.9              genefilter_1.78.0          
[25] iterators_1.0.14            glue_1.6.2                  gtable_0.3.1               
[28] zlibbioc_1.42.0             XVector_0.36.0              DelayedArray_0.22.0        
[31] DBI_1.1.3                   Rcpp_1.0.9                  htmlTable_2.4.1            
[34] progress_1.2.2              clue_0.3-62                 foreign_0.8-82             
[37] bit_4.0.4                   preprocessCore_1.58.0       tuneR_1.4.1                
[40] AnnotationForge_1.38.1      htmlwidgets_1.5.4           httr_1.4.4                 
[43] ellipsis_0.3.2              ff_4.0.7                    pkgconfig_2.0.3            
[46] nnet_7.3-17                 deldir_1.0-6                dbplyr_2.2.1               
[49] locfit_1.5-9.6              utf8_1.2.2                  tidyselect_1.2.0           
[52] rlang_1.0.6                 munsell_0.5.0               tools_4.2.1                
[55] cachem_1.0.6                cli_3.3.0                   generics_0.1.3             
[58] RSQLite_2.2.18              stringr_1.4.1               fastmap_1.1.0              
[61] knitr_1.41                  bit64_4.0.5                 oligoClasses_1.58.0        
[64] purrr_0.3.5                 KEGGREST_1.36.3             RBGL_1.72.0                
[67] xml2_1.3.3                  compiler_4.2.1              rstudioapi_0.14            
[70] filelock_1.0.2              curl_4.3.3                  png_0.1-7                  
[73] affyio_1.66.0               tibble_3.1.8                stringi_1.7.8              
[76] vctrs_0.5.0                 pillar_1.8.1                lifecycle_1.0.3            
[79] BiocManager_1.30.18         data.table_1.14.4           bitops_1.0-7               
[82] GenomicRanges_1.48.0        R6_2.5.1                    latticeExtra_0.6-30        
[85] gridExtra_2.3               affxparser_1.68.1           codetools_0.2-18           
[88] MASS_7.3-57                 assertthat_0.2.1            SummarizedExperiment_1.26.1
[91] withr_2.5.0                 GenomeInfoDbData_1.2.8      hms_1.1.2                  
[94] rpart_4.1.16                MatrixGenerics_1.8.1        base64enc_0.1-3            
[97] interp_1.1-3

ADD REPLY • link 17 months ago Masa • 0