[ Started: 2023-03-20 16:49:38 CET ] [ OmnipathR v3.7.3 for BioC-3.17 from https://github.com/saezlab/OmnipathR@master ] * using log directory ‘/mnt/disk0/build/bioc-check/omnipathr/bioc-3.17/2023-03-20_1626/OmnipathR/OmnipathR.Rcheck’ * using R Under development (unstable) (2023-03-16 r83996) * using platform: x86_64-pc-linux-gnu (64-bit) * R was compiled by gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0 GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0 * running under: Ubuntu 22.04.2 LTS * using session charset: UTF-8 * checking for file ‘OmnipathR/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘OmnipathR’ version ‘3.7.3’ * 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 executable files ... 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 ... NOTE installed size is 6.6Mb sub-directories of 1Mb or more: doc 5.6Mb * checking package 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 loading without being on the library search path ... OK * checking startup messages can be suppressed ... NOTE [2023-03-20 16:49:56] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2023-03-20 16:49:56] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-03-20 16:49:56] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2023-03-20 16:49:56] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2023-03-20 16:49:56] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2023-03-20 16:49:56] [TRACE] [OmnipathR] Contains 1 files. [2023-03-20 16:49:56] [TRACE] [OmnipathR] Cache is locked: FALSE. [2023-03-20 16:49:56] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2023-03-20 16:49:56] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-03-20 16:49:56] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2023-03-20 16:49:56] [TRACE] [OmnipathR] Pandoc version: `2.9.2.1`. [2023-03-20 16:49:56] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.17/2023-03-20_1626/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8). [2023-03-20 16:49:56] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-03-20 16:49:56] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.17/2023-03-20_1626/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2023-03-20 16:49:56] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-03-20 16:49:56] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.17/2023-03-20_1626/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8). [2023-03-20 16:49:56] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-03-20 16:49:56] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.17/2023-03-20_1626/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2023-03-20 16:49:56] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-03-20 16:49:56] [TRACE] [OmnipathR] Cache locked: FALSE It looks like this package (or a package it requires) has a startup message which cannot be suppressed: see ?packageStartupMessage. * 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 [2023-03-20 16:50:02] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2023-03-20 16:50:02] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-03-20 16:50:02] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2023-03-20 16:50:02] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2023-03-20 16:50:02] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2023-03-20 16:50:02] [TRACE] [OmnipathR] Contains 1 files. [2023-03-20 16:50:02] [TRACE] [OmnipathR] Cache is locked: FALSE. [2023-03-20 16:50:02] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2023-03-20 16:50:02] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-03-20 16:50:02] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2023-03-20 16:50:02] [TRACE] [OmnipathR] Pandoc version: `2.9.2.1`. [2023-03-20 16:50:02] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.17/2023-03-20_1626/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8). [2023-03-20 16:50:02] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-03-20 16:50:02] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.17/2023-03-20_1626/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2023-03-20 16:50:02] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-03-20 16:50:02] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.17/2023-03-20_1626/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8). [2023-03-20 16:50:02] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-03-20 16:50:02] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.17/2023-03-20_1626/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2023-03-20 16:50:02] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-03-20 16:50:02] [TRACE] [OmnipathR] Cache locked: FALSE build_index_impl: no visible binding for global variable ‘value’ complexes_search_index: no visible binding for global variable ‘name’ complexes_search_index: no visible binding for global variable ‘value’ complexes_search_index: no visible binding for global variable ‘resource’ enzsub_search_index: no visible binding for global variable ‘modification’ enzsub_search_index: no visible binding for global variable ‘resource’ interactions_search_index: no visible binding for global variable ‘attr_key’ interactions_search_index: no visible binding for global variable ‘value’ Undefined global functions or variables: attr_key modification name resource value * 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 ... WARNING Undocumented arguments in documentation object 'search_omnipath' ‘...’ Functions with \usage entries need to have the appropriate \alias entries, and all their arguments documented. The \usage entries must correspond to syntactically valid R code. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking R/sysdata.rda ... OK * checking installed files from ‘inst/doc’ ... OK * checking files in ‘vignettes’ ... OK * checking examples ... ERROR Running examples in ‘OmnipathR-Ex.R’ failed The error most likely occurred in: > ### Name: biomart_query > ### Title: Query the Ensembl BioMart web service > ### Aliases: biomart_query > > ### ** Examples > > cel_genes <- biomart_query( + attrs = c("external_gene_name", "start_position", "end_position"), + gene = TRUE, + dataset = "celegans_gene_ensembl" + ) [2023-03-20 16:51:11] [TRACE] [OmnipathR] BioMart query: [2023-03-20 16:51:11] [TRACE] [OmnipathR] Looking up in cache: `http://www.ensembl.org/biomart/martservice?query=%3C?xml%20version=%221.0%22%20encoding=%22UTF-8%22?%3E%0A%3C!DOCTYPE%20Query%3E%0A%3CQuery%20%20virtualSchemaName=%22default%22%20formatter=%22TSV%22%20header=%220%22%20uniqueRows=%220%22%20count=%22%22%20datasetConfigVersion=%220.6%22%20completionStamp=%221%22%20%3E%0A%20%20%20%20%3CDataset%20name=%22celegans_gene_ensembl%22%20interface=%22default%22%20%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22ensembl_gene_id%22/%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22external_gene_name%22/%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22start_position%22/%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22end_position%22/%3E%0A%20%20%20%20%3C/Dataset%3E%0A%3C/Query%3E%0A`. [2023-03-20 16:51:11] [INFO] [OmnipathR] Cache record does not exist: `http://www.ensembl.org/biomart/martservice?query=%3C?xml%20version=%221.0%22%20encoding=%22UTF-8%22?%3E%0A%3C!DOCTYPE%20Query%3E%0A%3CQuery%20%20virtualSchemaName=%22default%22%20formatter=%22TSV%22%20header=%220%22%20uniqueRows=%220%22%20count=%22%22%20datasetConfigVersion=%220.6%22%20completionStamp=%221%22%20%3E%0A%20%20%20%20%3CDataset%20name=%22celegans_gene_ensembl%22%20interface=%22default%22%20%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22ensembl_gene_id%22/%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22external_gene_name%22/%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22start_position%22/%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22end_position%22/%3E%0A%20%20%20%20%3C/Dataset%3E%0A%3C/Query%3E%0A` [2023-03-20 16:51:11] [TRACE] [OmnipathR] Could not find in cache, initiating download: `http://www.ensembl.org/biomart/martservice?query=%3C?xml%20version=%221.0%22%20encoding=%22UTF-8%22?%3E%0A%3C!DOCTYPE%20Query%3E%0A%3CQuery%20%20virtualSchemaName=%22default%22%20formatter=%22TSV%22%20header=%220%22%20uniqueRows=%220%22%20count=%22%22%20datasetConfigVersion=%220.6%22%20completionStamp=%221%22%20%3E%0A%20%20%20%20%3CDataset%20name=%22celegans_gene_ensembl%22%20interface=%22default%22%20%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22ensembl_gene_id%22/%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22external_gene_name%22/%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22start_position%22/%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22end_position%22/%3E%0A%20%20%20%20%3C/Dataset%3E%0A%3C/Query%3E%0A`. [2023-03-20 16:51:11] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2023-03-20 16:51:11] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-03-20 16:51:11] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2023-03-20 16:51:11] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-03-20 16:51:11] [INFO] [OmnipathR] Cache item `a8b90a9acba0cd1c9f3efeb7eded4b5cd3d3303c` version 1: status changed from `unknown` to `started`. [2023-03-20 16:51:11] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/a8b90a9acba0cd1c9f3efeb7eded4b5cd3d3303c-1.rds`. [2023-03-20 16:51:11] [INFO] [OmnipathR] Retrieving URL: `http://www.ensembl.org/biomart/martservice?query=%3C?xml%20version=%221.0%22%20encoding=%22UTF-8%22?%3E%0A%3C!DOCTYPE%20Query%3E%0A%3CQuery%20%20virtualSchemaName=%22default%22%20formatter=%22TSV%22%20header=%220%22%20uniqueRows=%220%22%20count=%22%22%20datasetConfigVersion=%220.6%22%20completionStamp=%221%22%20%3E%0A%20%20%20%20%3CDataset%20name=%22celegans_gene_ensembl%22%20interface=%22default%22%20%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22ensembl_gene_id%22/%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22external_gene_name%22/%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22start_position%22/%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22end_position%22/%3E%0A%20%20%20%20%3C/Dataset%3E%0A%3C/Query%3E%0A` [2023-03-20 16:51:11] [TRACE] [OmnipathR] Attempt 1/3: `http://www.ensembl.org/biomart/martservice?query=%3C?xml%20version=%221.0%22%20encoding=%22UTF-8%22?%3E%0A%3C!DOCTYPE%20Query%3E%0A%3CQuery%20%20virtualSchemaName=%22default%22%20formatter=%22TSV%22%20header=%220%22%20uniqueRows=%220%22%20count=%22%22%20datasetConfigVersion=%220.6%22%20completionStamp=%221%22%20%3E%0A%20%20%20%20%3CDataset%20name=%22celegans_gene_ensembl%22%20interface=%22default%22%20%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22ensembl_gene_id%22/%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22external_gene_name%22/%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22start_position%22/%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22end_position%22/%3E%0A%20%20%20%20%3C/Dataset%3E%0A%3C/Query%3E%0A` [2023-03-20 16:51:13] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/a8b90a9acba0cd1c9f3efeb7eded4b5cd3d3303c-1.rds`. [2023-03-20 16:51:13] [INFO] [OmnipathR] Download ready [key=a8b90a9acba0cd1c9f3efeb7eded4b5cd3d3303c, version=1] [2023-03-20 16:51:13] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2023-03-20 16:51:13] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-03-20 16:51:13] [INFO] [OmnipathR] Cache item `a8b90a9acba0cd1c9f3efeb7eded4b5cd3d3303c` version 1: status changed from `started` to `ready`. Error in if (slice_tail(., n = 1L) %>% first %>% equals("[success]")) slice_head(., : the condition has length > 1 Calls: biomart_query ... is_from_cache -> %>% -> type_convert -> stopifnot -> is.data.frame 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 ... ‘bioc_workshop.Rmd’ using ‘UTF-8’... OK ‘db_manager.Rmd’ using ‘UTF-8’... OK ‘drug_targets.Rmd’ using ‘UTF-8’... OK ‘extra_attrs.Rmd’ using ‘UTF-8’... OK ‘nichenet.Rmd’ using ‘UTF-8’... OK ‘omnipath_intro.Rmd’ using ‘UTF-8’... OK ‘paths.Rmd’ using ‘UTF-8’... OK NONE * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 1 ERROR, 1 WARNING, 3 NOTEs See ‘/mnt/disk0/build/bioc-check/omnipathr/bioc-3.17/2023-03-20_1626/OmnipathR/OmnipathR.Rcheck/00check.log’ for details. [ Finished: 2023-03-20 17:13:25 CET ]