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
Hi,
I did as suggested by @annebiton-7817. Yet, when running "runAn" I have the following error:
It seems related to the params variable. How can I fix this error please?
Thank you in advance