[ Started: 2024-05-14 15:46:05 CEST ] [ OmnipathR v3.10.1 for BioC-3.18 from https://github.com/saezlab/OmnipathR@RELEASE_3_18 (b1b2bab 2023-10-25 17:47:10) ] * using log directory ‘/mnt/disk0/build/bioc-check/omnipathr/bioc-3.18/2024-05-14_1539/OmnipathR/OmnipathR.Rcheck’ * using R version 4.3.3 (2024-02-29) * using platform: x86_64-pc-linux-gnu (64-bit) * R was compiled by gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 * running under: Ubuntu 22.04.4 LTS * using session charset: UTF-8 * checking for file ‘OmnipathR/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘OmnipathR’ version ‘3.10.1’ * 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 5.9Mb sub-directories of 1Mb or more: doc 4.8Mb * 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 [2024-05-14 15:46:25] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-05-14 15:46:25] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-14 15:46:25] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2024-05-14 15:46:25] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2024-05-14 15:46:25] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2024-05-14 15:46:25] [TRACE] [OmnipathR] Contains 1 files. [2024-05-14 15:46:25] [TRACE] [OmnipathR] Cache is locked: FALSE. [2024-05-14 15:46:25] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-05-14 15:46:25] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-14 15:46:25] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2024-05-14 15:46:25] [TRACE] [OmnipathR] Pandoc version: `2.9.2.1`. [2024-05-14 15:46:25] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.18/2024-05-14_1539/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8). [2024-05-14 15:46:25] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-14 15:46:25] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.18/2024-05-14_1539/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2024-05-14 15:46:25] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-14 15:46:25] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.18/2024-05-14_1539/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8). [2024-05-14 15:46:25] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-14 15:46:25] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.18/2024-05-14_1539/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2024-05-14 15:46:25] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-14 15:46:25] [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 [2024-05-14 15:46:31] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-05-14 15:46:31] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-14 15:46:31] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`. [2024-05-14 15:46:31] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2024-05-14 15:46:31] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`. [2024-05-14 15:46:31] [TRACE] [OmnipathR] Contains 1 files. [2024-05-14 15:46:31] [TRACE] [OmnipathR] Cache is locked: FALSE. [2024-05-14 15:46:31] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-05-14 15:46:31] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-14 15:46:32] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`. [2024-05-14 15:46:32] [TRACE] [OmnipathR] Pandoc version: `2.9.2.1`. [2024-05-14 15:46:32] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.18/2024-05-14_1539/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8). [2024-05-14 15:46:32] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-14 15:46:32] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.18/2024-05-14_1539/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2024-05-14 15:46:32] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-14 15:46:32] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.18/2024-05-14_1539/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8). [2024-05-14 15:46:32] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-14 15:46:32] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.18/2024-05-14_1539/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2024-05-14 15:46:32] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-14 15:46:32] [TRACE] [OmnipathR] Cache locked: FALSE * 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 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: ensembl_id_mapping_table > ### Title: Identifier translation table from Ensembl > ### Aliases: ensembl_id_mapping_table > > ### ** Examples > > ensp_up <- ensembl_id_mapping_table("ensp") [2024-05-14 15:50:25] [TRACE] [OmnipathR] Creating ID mapping table from `uniprotswissprot` to `ensembl_peptide_id`, for organism hsapiens [2024-05-14 15:50:25] [TRACE] [OmnipathR] BioMart query: [2024-05-14 15:50:25] [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=%22hsapiens_gene_ensembl%22%20interface=%22default%22%20%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22uniprotswissprot%22/%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22ensembl_peptide_id%22/%3E%0A%20%20%20%20%3C/Dataset%3E%0A%3C/Query%3E%0A`. [2024-05-14 15:50:25] [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=%22hsapiens_gene_ensembl%22%20interface=%22default%22%20%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22uniprotswissprot%22/%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22ensembl_peptide_id%22/%3E%0A%20%20%20%20%3C/Dataset%3E%0A%3C/Query%3E%0A` [2024-05-14 15:50:25] [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=%22hsapiens_gene_ensembl%22%20interface=%22default%22%20%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22uniprotswissprot%22/%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22ensembl_peptide_id%22/%3E%0A%20%20%20%20%3C/Dataset%3E%0A%3C/Query%3E%0A`. [2024-05-14 15:50:25] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-05-14 15:50:25] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-14 15:50:25] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-05-14 15:50:25] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-14 15:50:25] [INFO] [OmnipathR] Cache item `5146291739ab7fee3dd9b2830721d4357888383d` version 1: status changed from `unknown` to `started`. [2024-05-14 15:50:25] [TRACE] [OmnipathR] Exporting object to RDS: `/home/omnipath/.cache/OmnipathR/5146291739ab7fee3dd9b2830721d4357888383d-1.rds`. [2024-05-14 15:50:25] [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=%22hsapiens_gene_ensembl%22%20interface=%22default%22%20%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22uniprotswissprot%22/%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22ensembl_peptide_id%22/%3E%0A%20%20%20%20%3C/Dataset%3E%0A%3C/Query%3E%0A` [2024-05-14 15:50:25] [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=%22hsapiens_gene_ensembl%22%20interface=%22default%22%20%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22uniprotswissprot%22/%3E%0A%20%20%20%20%20%20%20%20%3CAttribute%20name=%22ensembl_peptide_id%22/%3E%0A%20%20%20%20%3C/Dataset%3E%0A%3C/Query%3E%0A` [2024-05-14 15:50:25] [TRACE] [OmnipathR] Exported RDS to `/home/omnipath/.cache/OmnipathR/5146291739ab7fee3dd9b2830721d4357888383d-1.rds`. [2024-05-14 15:50:25] [INFO] [OmnipathR] Download ready [key=5146291739ab7fee3dd9b2830721d4357888383d, version=1] [2024-05-14 15:50:25] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-05-14 15:50:25] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-14 15:50:25] [INFO] [OmnipathR] Cache item `5146291739ab7fee3dd9b2830721d4357888383d` version 1: status changed from `started` to `ready`. [2024-05-14 15:50:25] [WARN] [OmnipathR] BioMart: missing success flag, data might be incomplete or contain error message! [2024-05-14 15:50:25] [WARN] [OmnipathR] Query ERROR: caught BioMart::Exception::Database: Error during query execution: Table 'ensembl_mart_112.hsapiens_gene_ensembl__ox_uniprotswissprot__dm' doesn't exist [2024-05-14 15:50:25] [SUCCESS] [OmnipathR] www.ensembl.org: downloaded 1 records Error in `set_names()`: ! The size of `nm` (2) must be compatible with the size of `x` (1). Backtrace: ▆ 1. ├─OmnipathR::ensembl_id_mapping_table("ensp") 2. │ └─... %>% trim_and_distinct 3. ├─OmnipathR:::trim_and_distinct(.) 4. │ └─d %>% mutate(across(everything(), str_trim)) %>% distinct 5. ├─dplyr::distinct(.) 6. ├─dplyr::mutate(., across(everything(), str_trim)) 7. ├─rlang::set_names(., c("From", "To")) 8. └─rlang::abort(message = message) 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’... failed ‘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 ERROR Errors in running code in vignettes: when running code in ‘bioc_workshop.Rmd’ ... [2024-05-14 15:51:03] [INFO] [OmnipathR] Cache item `07dc3ca232cbc620ab6be7d21a3a41bfc7b2d3e1` version 1: status changed from `started` to `ready`. [2024-05-14 15:51:03] [SUCCESS] [OmnipathR] Downloaded 0 annotation records. > uniprot_loc <- import_omnipath_annotations(resuorces = "UniProt_location", + wide = TRUE) [2024-05-14 15:51:03] [FATAL] [OmnipathR] Downloading the entire annotations database is not allowed by default because of its huge size (>1GB). If you really want to do that, you find static files at https://archive.omnipathdb.org/. However we recommend to query a set of proteins or a few resources, depending on your interest. When sourcing ‘bioc_workshop.R’: Error: Downloading the entire annotations database is not allowed by default because of its huge size (>1GB). If you really want to do that, you find static files at https://archive.omnipathdb.org/. However we recommend to query a set of proteins or a few resources, depending on your interest. Execution halted * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 2 ERRORs, 3 NOTEs See ‘/mnt/disk0/build/bioc-check/omnipathr/bioc-3.18/2024-05-14_1539/OmnipathR/OmnipathR.Rcheck/00check.log’ for details. [ Finished: 2024-05-14 16:02:41 CEST ]