runChicago.R is not able to parse input parameters

Issue #5 resolved
paulafp created an issue

When running the following command: "Rscript /bi/home/paulafp/CHiCAGOv2/chicagoTools/runChicago.R --features-only --en-feat-folder /bi/group/sysgen/SNP_Project/Blueprint/New/Macrophage_M0/ --en-feat-list /bi/group/sysgen/SNP_Project/Blueprint/New/Macrophage_M0/featureFiles.txt Mac0_13_14_15_merged_Step2.Rds Mac0_13_14_15_merged_Step"

We get the following error message:

"Error in preprocess_argv(argv, parser) : Insufficient number of arguments supplied for --features-only Calls: parse.args -> parse_args -> preprocess_argv "

sessionInfo() R version 3.2.1 (2015-06-18) Platform: x86_64-unknown-linux-gnu (64-bit) Running under: CentOS release 6.2 (Final)

locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

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

other attached packages: [1] argparser_0.3 Chicago_0.2.10 data.table_1.9.6

loaded via a namespace (and not attached): [1] Rcpp_0.12.2 matrixStats_0.50.1 lattice_0.20-33 Delaporte_2.2-3 Hmisc_3.17-1 MASS_7.3-45 chron_2.3-47 grid_3.2.1 plyr_1.8.3
[10] acepack_1.3-3.3 gtable_0.1.2 scales_0.3.0 ggplot2_2.0.0 latticeExtra_0.6-26 rpart_4.1-10 Formula_1.2-1 splines_3.2.1 RColorBrewer_1.1-2 [19] tools_3.2.1 foreign_0.8-66 munsell_0.4.2 survival_2.38-3 colorspace_1.2-6 cluster_2.0.3 nnet_7.3-11 gridExtra_2.0.0

Comments (2)

  1. Log in to comment