egeulgen
commented
3 years ago hey @aberral,
You are currently using pathfindR v1.4.0, please update to the latest version (v1.6.1).
If this doesn't resolve the issue,
Can you load the package via library(pathfindR) and try running run_pathfindR() and can you share the input data frame as an RDS file so that I can try to reproduce the issue?
-E
aberral
Describe the bug Error executing "run_pathfindR" function with default parameters.
To Reproduce I have a matrix with values like this:
and when executing the function, this error is given as an output:
I can provide the used data if you are interested.
Desktop (please complete the following information):
R Session Information: R version 4.0.4 (2021-02-15) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 20.04.2 LTS
Matrix products: default BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.9.0 LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.9.0
locale: [1] LC_CTYPE=es_ES.UTF-8 LC_NUMERIC=C LC_TIME=es_ES.UTF-8
[4] LC_COLLATE=es_ES.UTF-8 LC_MONETARY=es_ES.UTF-8 LC_MESSAGES=es_ES.UTF-8
[7] LC_PAPER=es_ES.UTF-8 LC_NAME=C LC_ADDRESS=C
[10] LC_TELEPHONE=C LC_MEASUREMENT=es_ES.UTF-8 LC_IDENTIFICATION=C
attached base packages: [1] stats graphics grDevices utils datasets methods base
other attached packages: [1] forcats_0.5.1 stringr_1.4.0 dplyr_1.0.5 purrr_0.3.4 readr_1.4.0 tidyr_1.1.3
[7] tibble_3.1.0 ggplot2_3.3.3 tidyverse_1.3.0 pathfindR_1.4.0
loaded via a namespace (and not attached): [1] bitops_1.0-6 fs_1.5.0 lubridate_1.7.10 bit64_4.0.5
[5] doParallel_1.0.16 httr_1.4.2 tools_4.0.4 backports_1.2.1
[9] utf8_1.1.4 R6_2.5.0 DBI_1.1.1 BiocGenerics_0.36.0 [13] colorspace_2.0-0 withr_2.4.1 tidyselect_1.1.0 gridExtra_2.3
[17] curl_4.3 bit_4.0.4 compiler_4.0.4 graph_1.68.0
[21] cli_2.3.1 rvest_1.0.0 Biobase_2.50.0 pacman_0.5.1
[25] xml2_1.3.2 KEGGgraph_1.50.0 scales_1.1.1 digest_0.6.27
[29] rmarkdown_2.7 XVector_0.30.0 pkgconfig_2.0.3 htmltools_0.5.1.1
[33] dbplyr_2.1.0 fastmap_1.1.0 rlang_0.4.10 readxl_1.3.1
[37] rstudioapi_0.13 RSQLite_2.2.3 farver_2.1.0 generics_0.1.0
[41] jsonlite_1.7.2 RCurl_1.98-1.2 magrittr_2.0.1 Rcpp_1.0.6
[45] munsell_0.5.0 S4Vectors_0.28.1 fansi_0.4.2 viridis_0.5.1
[49] lifecycle_1.0.0 stringi_1.5.3 ggraph_2.0.5 zlibbioc_1.36.0
[53] debugme_1.1.0 MASS_7.3-53.1 org.Hs.eg.db_3.12.0 grid_4.0.4
[57] blob_1.2.1 parallel_4.0.4 ggrepel_0.9.1 crayon_1.4.1
[61] Biostrings_2.58.0 graphlayouts_0.7.1 haven_2.3.1 KEGGREST_1.30.1
[65] hms_1.0.0 knitr_1.31 pillar_1.5.1 igraph_1.2.6
[69] codetools_0.2-18 stats4_4.0.4 XML_3.99-0.5 reprex_1.0.0
[73] glue_1.4.2 evaluate_0.14 modelr_0.1.8 png_0.1-7
[77] vctrs_0.3.6 tweenr_1.0.1 foreach_1.5.1 cellranger_1.1.0
[81] gtable_0.3.0 polyclip_1.10-0 assertthat_0.2.1 cachem_1.0.4
[85] xfun_0.21 ggforce_0.3.3 broom_0.7.5 tidygraph_1.2.0
[89] viridisLite_0.3.0 iterators_1.0.13 AnnotationDbi_1.52.0 memoise_2.0.0
[93] IRanges_2.24.1 ellipsis_0.3.1