############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:OmnipathR.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings OmnipathR_3.2.9.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/OmnipathR.Rcheck’ * using R version 4.1.3 (2022-03-10) * using platform: x86_64-pc-linux-gnu (64-bit) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘OmnipathR/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘OmnipathR’ version ‘3.2.9’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘OmnipathR’ can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking R files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE [2022-04-12 08:32:56] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`. [2022-04-12 08:32:56] [INFO] [OmnipathR] Welcome to OmnipathR! [2022-04-12 08:32:56] [TRACE] [OmnipathR] Cache locked: FALSE get_connections: no visible binding for global variable ‘description’ get_connections: no visible binding for global variable ‘con_id’ Undefined global functions or variables: con_id description * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking R/sysdata.rda ... OK * checking files in ‘vignettes’ ... OK * checking examples ... ERROR Running examples in ‘OmnipathR-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: nichenet_lr_network > ### Title: Builds a NicheNet ligand-receptor network > ### Aliases: nichenet_lr_network > > ### ** Examples > > # load everything with the default parameters: > lr_network <- nichenet_lr_network() [2022-04-12 08:40:07] [SUCCESS] [OmnipathR] Starting to build NicheNet ligand-receptor network [2022-04-12 08:40:07] [INFO] [OmnipathR] Loading resource `omnipath`. [2022-04-12 08:40:08] [TRACE] [OmnipathR] Loaded data from RDS `/home/biocbuild/.cache/OmnipathR/3098404926bc0cf155d043ff0c6efe64e3424b74-1.rds`. [2022-04-12 08:40:08] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/interactions?genesymbols=yes&datasets=omnipath,pathwayextra,kinaseextra,ligrecextra&organisms=9606&fields=datasets,sources,references,curation_effort&license=academic` [2022-04-12 08:40:09] [SUCCESS] [OmnipathR] Loaded 80237 interactions from cache. [2022-04-12 08:40:09] [TRACE] [OmnipathR] Loaded data from RDS `/home/biocbuild/.cache/OmnipathR/1ac430724a20c137fc374a8499adabb468a12835-1.rds`. [2022-04-12 08:40:09] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/intercell?scope=generic&causality=trans&license=academic` [2022-04-12 08:40:09] [SUCCESS] [OmnipathR] Loaded 27928 intercellular communication role records from cache. [2022-04-12 08:40:10] [TRACE] [OmnipathR] Loaded data from RDS `/home/biocbuild/.cache/OmnipathR/552757063f9934c7b745a9c4247c3b5282a66c88-1.rds`. [2022-04-12 08:40:10] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/intercell?scope=generic&causality=rec&license=academic` [2022-04-12 08:40:10] [SUCCESS] [OmnipathR] Loaded 43967 intercellular communication role records from cache. [2022-04-12 08:41:01] [TRACE] [OmnipathR] Loaded data from RDS `/home/biocbuild/.cache/OmnipathR/88868f24833199a6a4a8e27980fa32cd50c1c600-1.rds`. [2022-04-12 08:41:01] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/intercell?license=academic` [2022-04-12 08:41:02] [SUCCESS] [OmnipathR] Loaded 323572 intercellular communication role records from cache. [2022-04-12 08:41:02] [TRACE] [OmnipathR] Loaded data from RDS `/home/biocbuild/.cache/OmnipathR/9ecbbba7b7129c316d69501f7af5c2aced05a498-1.rds`. [2022-04-12 08:41:02] [INFO] [OmnipathR] Loaded from cache: `https://omnipathdb.org/intercell?aspect=locational&parent=secreted,plasma_membrane_transmembrane,plasma_membrane_peripheral&license=academic` [2022-04-12 08:41:02] [SUCCESS] [OmnipathR] Loaded 21325 intercellular communication role records from cache. [2022-04-12 08:41:04] [INFO] [OmnipathR] Loading resource `guide2pharma`. [2022-04-12 08:41:04] [TRACE] [OmnipathR] Looking up in cache: `https://www.guidetopharmacology.org/DATA/interactions.tsv`. [2022-04-12 08:41:04] [TRACE] [OmnipathR] Loaded data from RDS `/home/biocbuild/.cache/OmnipathR/6b853e2c431d0829466878e2e619ca4ec878523b-1.rds`. [2022-04-12 08:41:04] [SUCCESS] [OmnipathR] Unknown source: downloaded 21146 records Error in `filter()`: ! Problem while computing `..1 = target_species == "Human" & ligand_species == "Human"`. ✖ Input `..1` must be of size 21146 or 1, not size 0. Backtrace: ▆ 1. ├─OmnipathR::nichenet_lr_network() 2. │ └─... %>% do.call(nichenet_network, .) 3. ├─base::do.call(nichenet_network, .) 4. ├─OmnipathR ``(...) 5. │ └─... %T>% ... 6. ├─tibble::as_tibble(.) 7. ├─dplyr::filter(., !is.na(from) & !is.na(to)) 8. ├─dplyr::filter(., from != to) 9. ├─dplyr::bind_rows(.) 10. │ └─rlang::list2(...) 11. ├─purrr::map2(...) 12. │ └─OmnipathR .f(.x[[i]], .y[[i]], ...) 13. │ └─... %>% do.call(args) 14. ├─base::do.call(., args) 15. ├─OmnipathR ``() 16. │ └─... %>% ... 17. ├─OmnipathR:::nichenet_common_postprocess(...) 18. │ └─... %>% mutate(source = source, database = database) 19. ├─dplyr::mutate(., source = source, database = database) 20. ├─dplyr::distinct(.) 21. ├─dplyr::select(., from = !!from_col, to = !!to_col) 22. ├─dplyr::filter(...) 23. ├─dplyr:::filter.data.frame(...) 24. │ └─dplyr:::filter_rows(.data, ..., caller_env = caller_env()) 25. │ └─dplyr:::filter_eval(dots, mask = mask, error_call = error_call) 26. │ ├─base::withCallingHandlers(...) 27. │ └─mask$eval_all_filter(dots, env_filter) 28. ├─dplyr:::dplyr_internal_error(...) 29. │ └─rlang::abort(class = c(class, "dplyr:::internal_error"), dplyr_error_data = data) 30. │ └─rlang:::signal_abort(cnd, .file) 31. │ └─base::signalCondition(cnd) 32. └─dplyr ``(``) 33. └─rlang::abort(bullets, call = error_call, parent = skip_internal_condition(e)) Execution halted * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes in ‘inst/doc’ ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 1 ERROR, 1 NOTE See ‘/home/biocbuild/bbs-3.14-bioc/meat/OmnipathR.Rcheck/00check.log’ for details.