Comments (6)
Hi @DylanPostmus ,
Could you please try to install the latest version of OmnipathR
and try again?
devtools::install_github('saezlab/OmnipathR')
from omnipathr.
Works now! Many thanks.
from omnipathr.
The error in your previous comment is the same as in #57, and has been fixed some weeks ago. The next error that you experience is not a problem with this package, but an issue with the installation or loading on your system, and most likely can be addressed by simply restarting R.
from omnipathr.
Well this is weird. I restarted R and my computer and the problem was solved. I wonder why this issue occurred.
Thanks a lot.
from omnipathr.
I am having similar issue. can you please help. Thanks
net <- get_dorothea(organism='human', levels=c('A', 'B', 'C'))
Error in
mutate()
:
ℹ In argument:n_references = ifelse(...)
.
Caused by error inmap()
:
ℹ In index: 1.
Caused by error in.f()
:
! Arguments in...
must be passed by position, not name.
✖ Problematic argument:
• outsep = outsep
Runrlang::last_trace()
to see where the error occurred.
sessionInfo()
R version 4.2.3 (2023-03-15 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19045)Matrix products: default
locale:
[1] LC_COLLATE=English_United States.utf8 LC_CTYPE=English_United States.utf8
[3] LC_MONETARY=English_United States.utf8 LC_NUMERIC=C
[5] LC_TIME=English_United States.utf8attached base packages:
[1] stats graphics grDevices utils datasets methods baseother attached packages:
[1] pheatmap_1.0.12 ggplot2_3.4.2 patchwork_1.1.2 tidyr_1.3.0 tibble_3.2.1
[6] dplyr_1.1.1 decoupleR_2.4.0 SeuratObject_4.1.3 Seurat_4.3.0loaded via a namespace (and not attached):
[1] Rtsne_0.16 colorspace_2.1-0 deldir_1.0-6 ellipsis_0.3.2
[5] ggridges_0.5.4 rstudioapi_0.14 spatstat.data_3.0-1 leiden_0.4.3
[9] listenv_0.9.0 farver_2.1.1 bit64_4.0.5 ggrepel_0.9.3
[13] fansi_1.0.4 xml2_1.3.3 codetools_0.2-19 splines_4.2.3
[17] knitr_1.42 polyclip_1.10-4 jsonlite_1.8.4 ica_1.0-3
[21] cluster_2.1.4 png_0.1-8 uwot_0.1.14 shiny_1.7.4
[25] sctransform_0.3.5 spatstat.sparse_3.0-1 readr_2.1.4 compiler_4.2.3
[29] httr_1.4.5 backports_1.4.1 Matrix_1.5-3 fastmap_1.1.1
[33] lazyeval_0.2.2 cli_3.6.1 later_1.3.0 prettyunits_1.1.1
[37] htmltools_0.5.5 tools_4.2.3 igraph_1.4.2 gtable_0.3.3
[41] glue_1.6.2 RANN_2.6.1 reshape2_1.4.4 rappdirs_0.3.3
[45] Rcpp_1.0.10 scattermore_0.8 cellranger_1.1.0 vctrs_0.6.1
[49] spatstat.explore_3.1-0 nlme_3.1-162 progressr_0.13.0 lmtest_0.9-40
[53] spatstat.random_3.1-4 xfun_0.38 OmnipathR_3.6.0 stringr_1.5.0
[57] globals_0.16.2 rvest_1.0.3 mime_0.12 miniUI_0.1.1.1
[61] lifecycle_1.0.3 irlba_2.3.5.1 goftest_1.2-3 future_1.32.0
[65] MASS_7.3-58.3 zoo_1.8-12 scales_1.2.1 vroom_1.6.1
[69] hms_1.1.3 promises_1.2.0.1 spatstat.utils_3.0-2 parallel_4.2.3
[73] RColorBrewer_1.1-3 yaml_2.3.7 curl_5.0.0 reticulate_1.28
[77] pbapply_1.7-0 gridExtra_2.3 stringi_1.7.12 checkmate_2.1.0
[81] rlang_1.1.0 pkgconfig_2.0.3 matrixStats_0.63.0 evaluate_0.20
[85] lattice_0.20-45 ROCR_1.0-11 purrr_1.0.1 tensor_1.5
[89] htmlwidgets_1.6.2 labeling_0.4.2 bit_4.0.5 cowplot_1.1.1
[93] tidyselect_1.2.0 parallelly_1.35.0 RcppAnnoy_0.0.20 plyr_1.8.8
[97] logger_0.2.2 magrittr_2.0.3 R6_2.5.1 generics_0.1.3
[101] pillar_1.9.0 withr_2.5.0 fitdistrplus_1.1-8 survival_3.5-5
[105] abind_1.4-5 sp_1.6-0 future.apply_1.10.0 crayon_1.5.2
[109] KernSmooth_2.23-20 utf8_1.2.3 spatstat.geom_3.1-0 plotly_4.10.1
[113] rmarkdown_2.21 tzdb_0.3.0 progress_1.2.2 readxl_1.4.2
[117] grid_4.2.3 data.table_1.14.8 digest_0.6.31 xtable_1.8-4
[121] httpuv_1.6.9 munsell_0.5.0 viridisLite_0.4.1
from omnipathr.
After running
devtools::install_github('saezlab/OmnipathR')
net <- get_dorothea(organism='human', levels=c('A', 'B', 'C'))
Error in original_appender_console(lines) :
lazy-load database 'C:/xxxR/win-library/4.2/OmnipathR/R/OmnipathR.rdb' is corrupt
In addition: Warning messages:
1: 'OmnipathR::import_dorothea_interactions' is deprecated.
Use 'dorothea' instead.
See help("Deprecated")
2: In original_appender_console(lines) :
restarting interrupted promise evaluation
3: In original_appender_console(lines) :
internal error -3 in R_decompress1
from omnipathr.
Related Issues (20)
- CellPhoneDB Version HOT 2
- error when run import_omnipath_annotations HOT 1
- Clarification about commercial licenses HOT 3
- TIME OUT for import_intercell_network HOT 6
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- loading package failed HOT 1
- import_all_interactions only shows transcriptional HOT 2
- connection problem HOT 2
- cannot open the connection to 'https://omnipathdb.org/resources' HOT 2
- Error: Error installing package 'OmnipathR': when trying to install LianaR HOT 17
- Omnipath failing to install in GitHub actions. HOT 3
- Installation error HOT 3
- wrong TGFB1-SMAD7 interaction
- Error in get_collectri()
- Orthology translation does not work: `oma_pairwise` fails with HTTP 503 HOT 8
- OmniPath failling to install in GH action HOT 2
- kegg_pathways_download returns fewer pathways HOT 1
- 500 Internal server error HOT 1
- Error in import_omnipath_annotations HOT 1
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