===============================
BiocCheckGitClone('MetaProViz')
===============================
sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3967/016d117338b422dc8f7c12a4aee795fad4ccb9b6/MetaProViz
BiocVersion: 3.23
Package: MetaProViz
PackageVersion: 3.99.30
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3967/016d117338b422dc8f7c12a4aee795fad4ccb9b6/MetaProViz.BiocCheck
BiocCheckVersion: 1.47.1
sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3967/016d117338b422dc8f7c12a4aee795fad4ccb9b6/MetaProViz
installDir: NULL
isTarBall: FALSE
platform: unix
* Checking valid files...
* Checking individual file sizes...
* Checking for stray BiocCheck output folders...
* Checking for inst/doc folders...
* Checking if DESCRIPTION is well formatted...
* Checking NAMESPACE...
* Checking for valid maintainer...
* Checking CITATION...
* Checking that provided CITATION file is correctly formatted...
BiocCheck v1.47.1 results
0 ERRORS | 0 WARNINGS | i 0 NOTES
i For more details, run
browseVignettes(package = 'BiocCheck')
===============================
R CMD CHECK
===============================
* using log directory /home/pkgbuild/packagebuilder/workers/jobs/3967/016d117338b422dc8f7c12a4aee795fad4ccb9b6/MetaProViz.Rcheck
* using R Under development (unstable) (2025-10-20 r88955)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* using option --no-vignettes
* checking for file MetaProViz/DESCRIPTION ... OK
* checking extension type ... Package
* this is package MetaProViz version 3.99.30
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 38 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable. Move as many as possible to Suggests and
use conditionally.
* 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 MetaProViz can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for future file timestamps ... OK
* checking build directory ... OK
* checking DESCRIPTION meta-information ... NOTE
License stub is invalid DCF.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... [15s/15s] OK
* checking whether the package can be loaded with stated dependencies ... [15s/15s] OK
* checking whether the package can be unloaded cleanly ... [14s/14s] OK
* checking whether the namespace can be loaded with stated dependencies ... [14s/14s] OK
* checking whether the namespace can be unloaded cleanly ... [15s/15s] OK
* checking loading without being on the library search path ... [15s/15s] OK
* checking whether startup messages can be suppressed ... [14s/14s] OK
* checking use of S3 registration ... 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 ... [64s/64s] NOTE
equivalent_id: no visible binding for global variable OmnipathR
standard_ora: no visible binding for global variable top/Bottom
Undefined global functions or variables:
OmnipathR top/Bottom
* checking Rd files ... [1s/1s] OK
* checking Rd metadata ... OK
* checking Rd line widths ... 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 contents of data directory ... OK
* checking data for non-ASCII characters ... [7s/7s] OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in vignettes ... OK
* checking examples ... [85s/90s] ERROR
Running examples in MetaProViz-Ex.R failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: equivalent_id
> ### Title: Find additional potential IDs for "kegg", "pubchem", "chebi",
> ### "hmdb"
> ### Aliases: equivalent_id
>
> ### ** Examples
>
> data(cellular_meta)
> DetectedIDs <- cellular_meta %>% tidyr::drop_na()
> Res <- equivalent_id(
+ data = DetectedIDs,
+ metadata_info = c(InputID = "HMDB"),
+ from = "hmdb"
+ )
[2025-12-05 05:00:28] [WARN] [MetaProViz] OmnipathR version: 3.19.2
[2025-12-05 05:00:28] [INFO] [OmnipathR] Looking up in cache `https://omabrowser.org/All/oma-species.txt`: key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, latest version=1.
[2025-12-05 05:00:28] [TRACE] [OmnipathR] Cache file path: /home/pkgbuild/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds
[2025-12-05 05:00:28] [WARN] [MetaProViz] Cache item for `OMA organisms table`: [number=1,path=/home/pkgbuild/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds,dl_started=2024-03-21 12:33:56,status=ready,dl_finished=2024-03-21 12:33:59]
[2025-12-05 05:00:28] [WARN] [MetaProViz] === === ===
[2025-12-05 05:00:28] [WARN] [MetaProViz] Complete cache content:
[2025-12-05 05:00:28] [WARN] [MetaProViz] Cache content: [/home/pkgbuild/.cache/OmnipathR/0bd054860c052a2ac0d7a3849b304d085f377df0-1.rds (2025-11-21 07:16-0500),/home/pkgbuild/.cache/OmnipathR/2e2b496d72e1686af2bd8a26a0b6d2f96d90e687-1.rds (2024-03-21 12:34-0400),/home/pkgbuild/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds (2024-03-21 12:33-0400),/home/pkgbuild/.cache/OmnipathR/41c8055b20002c0dbf8ddf485403332479b715a1-1.rds (2024-03-21 12:34-0400),/home/pkgbuild/.cache/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds (2025-11-21 07:24-0500),/home/pkgbuild/.cache/OmnipathR/6ed1bdfc7230bcb2925f9cb360e0b77190c82237-1.rds (2024-03-21 12:34-0400),/home/pkgbuild/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html (2024-03-21 12:33-0400),/home/pkgbuild/.cache/OmnipathR/855597ce84b494f3ef3ac5750c407848569a7f66-1.rds (2025-11-21 07:17-0500),/home/pkgbuild/.cache/OmnipathR/c6ff89c85308605f76b13b8b7eef2efc510fca11-1.rds (2025-11-21 07:16-0500),/home/pkgbuild/.cache/OmnipathR/cache.json (2025-11-21 07:24-0500),...]
[2025-12-05 05:00:28] [WARN] [MetaProViz] === === ===
[2025-12-05 05:00:28] [INFO] [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, latest version=1.
[2025-12-05 05:00:28] [TRACE] [OmnipathR] Cache file path: /home/pkgbuild/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html
[2025-12-05 05:00:28] [TRACE] [OmnipathR] Downloading by `generic_downloader`.
[2025-12-05 05:00:28] [TRACE] [OmnipathR] Looking up in cache: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`.
[2025-12-05 05:00:28] [TRACE] [OmnipathR] Loaded data from RDS `/home/pkgbuild/.cache/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`.
[2025-12-05 05:00:28] [TRACE] [OmnipathR] Downloading by `generic_downloader`.
[2025-12-05 05:00:28] [TRACE] [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`.
[2025-12-05 05:00:28] [TRACE] [OmnipathR] Loaded data from RDS `/home/pkgbuild/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2025-12-05 05:00:28] [WARN] [MetaProViz] DF: ensembl_o
[2025-12-05 05:00:28] [WARN] [MetaProViz] DF of size 317 x 4
[2025-12-05 05:00:28] [WARN] [MetaProViz] Columns: common_name <character>, latin_name <character>, ncbi_tax_id <integer>, ensembl_id <character>
[2025-12-05 05:00:28] [WARN] [MetaProViz] First 3 rows:
[2025-12-05 05:00:28] [WARN] [MetaProViz] Abingdon island giant tortoise|Chelonoidis abingdonii|106734|cabingdonii
[2025-12-05 05:00:28] [WARN] [MetaProViz] African ostrich|Struthio camelus australis|441894|scaustralis
[2025-12-05 05:00:28] [WARN] [MetaProViz] Agassiz's desert tortoise|Gopherus agassizii|38772|gagassizii
[2025-12-05 05:00:28] [WARN] [MetaProViz] DF: uniprot_o
[2025-12-05 05:00:28] [WARN] [MetaProViz] DF of size 27848 x 6
[2025-12-05 05:00:28] [WARN] [MetaProViz] Columns: code <character>, kingdom <character>, ncbi_tax_id <integer>, latin_name <character>, common_name <character>, synonym <character>
[2025-12-05 05:00:28] [WARN] [MetaProViz] First 3 rows:
[2025-12-05 05:00:28] [WARN] [MetaProViz] AADNV|V|648330|Aedes albopictus densovirus (isolate Boublik/1994)|AalDNV|NA
[2025-12-05 05:00:28] [WARN] [MetaProViz] AAV2|V|10804|Adeno-associated virus 2|AAV-2|NA
[2025-12-05 05:00:28] [WARN] [MetaProViz] AAV2S|V|648242|Adeno-associated virus 2 (isolate Srivastava/1982)|AAV-2|NA
[2025-12-05 05:00:28] [WARN] [MetaProViz] DF: oma_o
[2025-12-05 05:00:28] [WARN] [MetaProViz] DF of size 2851 x 7
[2025-12-05 05:00:28] [WARN] [MetaProViz] Columns: oma_code <character>, ncbi_tax_id <numeric>, latin_name <numeric>, genome_source <character>, oma_version <character>, X6 <character>, X7 <character>
[2025-12-05 05:00:28] [WARN] [MetaProViz] First 3 rows:
[2025-12-05 05:00:28] [WARN] [MetaProViz] ABSGL|4829|4829|n/a|Absidia glauca|EnsemblGenomes|Ensembl Fungi 48; AG_v1
[2025-12-05 05:00:28] [WARN] [MetaProViz] ACAM1|-644103924|329726|RS_GCF_000018105.1|Acaryochloris marina (strain MBIC 11017)|Genome Reviews|18-MAR-2008 (Rel. 88, Last updated, Version 2)
[2025-12-05 05:00:28] [WARN] [MetaProViz] ACAPL|133434|133434|n/a|Acanthaster planci|Refseq|Refseq; OKI-Apl_1.0; GCF_001949145.1; 08-AUG-2017
[2025-12-05 05:00:28] [WARN] [MetaProViz] Removing OMA organisms table from cache (/home/pkgbuild/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds)
[2025-12-05 05:00:28] [TRACE] [OmnipathR] Reading JSON from `/home/pkgbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-12-05 05:00:28] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-12-05 05:00:28] [TRACE] [OmnipathR] Removing cache entry 30e690cbb55dfc63b5903ab337f34ffc2f4be397 (https://omabrowser.org/All/oma-species.txt): no files available.
[2025-12-05 05:00:28] [TRACE] [OmnipathR] Downloading by `generic_downloader`.
[2025-12-05 05:00:28] [TRACE] [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`.
[2025-12-05 05:00:28] [INFO] [OmnipathR] Cache record does not exist: `https://omabrowser.org/All/oma-species.txt`
[2025-12-05 05:00:28] [TRACE] [OmnipathR] Could not find in cache, initiating download: `https://omabrowser.org/All/oma-species.txt`.
[2025-12-05 05:00:28] [TRACE] [OmnipathR] Reading JSON from `/home/pkgbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-12-05 05:00:28] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-12-05 05:00:28] [TRACE] [OmnipathR] Reading JSON from `/home/pkgbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-12-05 05:00:28] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-12-05 05:00:28] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `unknown` to `started`.
[2025-12-05 05:00:28] [TRACE] [OmnipathR] Exporting object to RDS: `/home/pkgbuild/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2025-12-05 05:00:28] [INFO] [OmnipathR] Retrieving URL: `https://omabrowser.org/All/oma-species.txt`
[2025-12-05 05:00:28] [TRACE] [OmnipathR] Attempt 1/3: `https://omabrowser.org/All/oma-species.txt`
[2025-12-05 05:00:28] [TRACE] [OmnipathR] HTTP request by `omnipath_curl`.
[2025-12-05 05:00:28] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-12-05 05:00:28] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-12-05 05:00:29] [TRACE] [OmnipathR] HTTP v2 GET: status 200.
[2025-12-05 05:00:29] [TRACE] [OmnipathR] Downloaded 10.1 Kb in 0.844979s from omabrowser.org (11.9 Kb/s); Redirect: 0s, DNS look up: 0.223043s, Connection: 0.223774s, Pretransfer: 0.653195s, First byte at: 0.753567s
[2025-12-05 05:00:29] [TRACE] [OmnipathR] HTTP headers: HTTP/2 200 ; date: Fri, 05 Dec 2025 10:00:29 GMT; server: nginx; strict-transport-security: max-age=31536000; includeSubDomains; content-type: text/plain; charset=UTF-8; last-modified: Wed, 20 Nov 2024 10:20:02 GMT; etag: W/"673db7d2-6517f"; access-control-allow-origin: *; content-encoding: gzip
[2025-12-05 05:00:31] [TRACE] [OmnipathR] Exported RDS to `/home/pkgbuild/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2025-12-05 05:00:31] [INFO] [OmnipathR] Download ready [key=30e690cbb55dfc63b5903ab337f34ffc2f4be397, version=1]
[2025-12-05 05:00:31] [TRACE] [OmnipathR] Reading JSON from `/home/pkgbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-12-05 05:00:31] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-12-05 05:00:31] [INFO] [OmnipathR] Cache item `30e690cbb55dfc63b5903ab337f34ffc2f4be397` version 1: status changed from `started` to `ready`.
[2025-12-05 05:00:31] [WARN] [MetaProViz] Data frame after fresh download:
[2025-12-05 05:00:31] [WARN] [MetaProViz] DF: oma_o
[2025-12-05 05:00:31] [WARN] [MetaProViz] DF of size 2927 x 7
[2025-12-05 05:00:31] [WARN] [MetaProViz] Columns: oma_code <character>, oma_tax_id <numeric>, ncbi_tax_id <numeric>, genome_gtdb <character>, latin_name <character>, genome_source <character>, genome_version <character>
[2025-12-05 05:00:31] [WARN] [MetaProViz] First 3 rows:
[2025-12-05 05:00:31] [WARN] [MetaProViz] ABSGL|4829|4829|n/a|Absidia glauca|EnsemblGenomes|Ensembl Fungi 48; AG_v1
[2025-12-05 05:00:31] [WARN] [MetaProViz] ACACA|1257118|1257118|n/a|Acanthamoeba castellanii str. Neff|Genbank|Genbank; Acastellanii.strNEFF v1; GCF_000313135.1; 07-OCT-2021
[2025-12-05 05:00:31] [WARN] [MetaProViz] ACAM1|-644103924|329726|RS_GCF_000018105.1|Acaryochloris marina (strain MBIC 11017)|Genome Reviews|18-MAR-2008 (Rel. 88, Last updated, Version 2)
[2025-12-05 05:00:31] [WARN] [MetaProViz] DF: taxons_table
[2025-12-05 05:00:31] [WARN] [MetaProViz] DF of size 28160 x 13
[2025-12-05 05:00:31] [WARN] [MetaProViz] Columns: common_name_ensembl <character>, latin_name_ensembl <character>, ncbi_tax_id <numeric>, ensembl_id <character>, oma_code <character>, oma_tax_id <numeric>, genome_gtdb <character>, latin_name_oma <character>, uniprot_code <character>, kingdom <character>, latin_name_uniprot <character>, common_name_uniprot <character>, latin_name_synonym <character>
[2025-12-05 05:00:31] [WARN] [MetaProViz] First 3 rows:
[2025-12-05 05:00:31] [WARN] [MetaProViz] Abingdon island giant tortoise|Chelonoidis abingdonii|106734|cabingdonii|CHEAB|106734|n/a|Chelonoidis abingdonii|CHEAB|E|Chelonoidis abingdonii|Abingdon island giant tortoise|Testudo abingdonii
[2025-12-05 05:00:31] [WARN] [MetaProViz] African ostrich|Struthio camelus australis|441894|scaustralis|NA|NA|NA|NA|NA|NA|NA|NA|NA
[2025-12-05 05:00:31] [WARN] [MetaProViz] Agassiz's desert tortoise|Gopherus agassizii|38772|gagassizii|NA|NA|NA|NA|NA|NA|NA|NA|NA
[2025-12-05 05:00:31] [WARN] [MetaProViz] The following IDs are duplicated and removed: HMDB0000725, HMDB0000267, HMDB0000755
Warning in equivalent_id(data = DetectedIDs, metadata_info = c(InputID = "HMDB"), :
The following IDs are duplicated and removed: HMDB0000725, HMDB0000267, HMDB0000755
chebi is used to find additional potential IDs for hmdb.
[2025-12-05 05:00:31] [INFO] [OmnipathR] Loading database `Ensembl and OMA organism names`.
[2025-12-05 05:00:31] [INFO] [OmnipathR] Looking up in cache `https://www.ensembl.org/info/about/species.html`: key=7332486db7400730697234bad76ca0c8e4d00799, latest version=1.
[2025-12-05 05:00:31] [TRACE] [OmnipathR] Cache file path: /home/pkgbuild/.cache/OmnipathR/7332486db7400730697234bad76ca0c8e4d00799-1.html
[2025-12-05 05:00:31] [TRACE] [OmnipathR] Downloading by `generic_downloader`.
[2025-12-05 05:00:31] [TRACE] [OmnipathR] Looking up in cache: `https://omabrowser.org/All/oma-species.txt`.
[2025-12-05 05:00:31] [TRACE] [OmnipathR] Loaded data from RDS `/home/pkgbuild/.cache/OmnipathR/30e690cbb55dfc63b5903ab337f34ffc2f4be397-1.rds`.
[2025-12-05 05:00:31] [TRACE] [OmnipathR] Downloading by `generic_downloader`.
[2025-12-05 05:00:31] [TRACE] [OmnipathR] Looking up in cache: `https://ftp.expasy.org/databases/uniprot/current_release/knowledgebase/complete/docs/speclist.txt`.
[2025-12-05 05:00:31] [TRACE] [OmnipathR] Loaded data from RDS `/home/pkgbuild/.cache/OmnipathR/56ad6544dc07a2222fa6013d8d83e6e5a35fdf33-1.rds`.
[2025-12-05 05:00:31] [INFO] [OmnipathR] Loaded database `Ensembl and OMA organism names`.
[2025-12-05 05:00:31] [TRACE] [OmnipathR] ID translation table: from `hmdb` to `chebi`, using RaMP
[2025-12-05 05:00:31] [TRACE] [OmnipathR] Looking up in cache: `ramp_id_mapping_table`.
[2025-12-05 05:00:31] [TRACE] [OmnipathR] Not found in cache, rebuilding: `ramp_id_mapping_table`.
[2025-12-05 05:00:31] [TRACE] [OmnipathR] Reading JSON from `/home/pkgbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-12-05 05:00:31] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-12-05 05:00:31] [TRACE] [OmnipathR] Reading JSON from `/home/pkgbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-12-05 05:00:31] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-12-05 05:00:31] [INFO] [OmnipathR] Cache item `6cb5231204c9a7caf10d9a19e01e0ac86ff85b0c` version 1: status changed from `unknown` to `started`.
[2025-12-05 05:00:31] [TRACE] [OmnipathR] Exporting object to RDS: `/home/pkgbuild/.cache/OmnipathR/6cb5231204c9a7caf10d9a19e01e0ac86ff85b0c-1.rds`.
[2025-12-05 05:00:31] [TRACE] [OmnipathR] Reading JSON from `/home/pkgbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-12-05 05:00:31] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-12-05 05:00:31] [INFO] [OmnipathR] Looking up in cache `ramp_2.5.4.sqlite`: key=2792c9a0814e66fa86fadf2c9f613c4075a3145c, no version available.
[2025-12-05 05:00:31] [TRACE] [OmnipathR] Reading JSON from `/home/pkgbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-12-05 05:00:31] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-12-05 05:00:31] [INFO] [OmnipathR] Created new version for cache record 2792c9a0814e66fa86fadf2c9f613c4075a3145c: version 1.
[2025-12-05 05:00:31] [TRACE] [OmnipathR] Cache file path: /home/pkgbuild/.cache/OmnipathR/2792c9a0814e66fa86fadf2c9f613c4075a3145c-1
[2025-12-05 05:00:31] [TRACE] [OmnipathR] Reading JSON from `/home/pkgbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-12-05 05:00:31] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-12-05 05:00:31] [INFO] [OmnipathR] Looking up in cache `https://media.githubusercontent.com/media/ncats/RaMP-DB/main/db/RaMP_SQLite_v2.5.4.sqlite.gz`: key=3c92c86840bbbe428e793c4f683167ceaa139e9d, no version available.
[2025-12-05 05:00:31] [TRACE] [OmnipathR] Reading JSON from `/home/pkgbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-12-05 05:00:31] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-12-05 05:00:31] [INFO] [OmnipathR] Created new version for cache record 3c92c86840bbbe428e793c4f683167ceaa139e9d: version 1.
[2025-12-05 05:00:31] [TRACE] [OmnipathR] Cache file path: /home/pkgbuild/.cache/OmnipathR/3c92c86840bbbe428e793c4f683167ceaa139e9d-1.gz
[2025-12-05 05:00:31] [INFO] [OmnipathR] Retrieving URL: `https://media.githubusercontent.com/media/ncats/RaMP-DB/main/db/RaMP_SQLite_v2.5.4.sqlite.gz`
[2025-12-05 05:00:31] [TRACE] [OmnipathR] Downloading by `httr2` in `download_base`.
[2025-12-05 05:00:31] [TRACE] [OmnipathR] Attempt 1/3: `https://media.githubusercontent.com/media/ncats/RaMP-DB/main/db/RaMP_SQLite_v2.5.4.sqlite.gz`
[2025-12-05 05:00:31] [TRACE] [OmnipathR] Preparing httr2 request to URL `https://media.githubusercontent.com/media/ncats/RaMP-DB/main/db/RaMP_SQLite_v2.5.4.sqlite.gz`.
[2025-12-05 05:00:31] [TRACE] [OmnipathR] HTTP headers: <NULL>
[2025-12-05 05:00:31] [TRACE] [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-12-05 05:00:32] [TRACE] [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=10,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=1,ssl_verifyhost=2]
[2025-12-05 05:00:32] [TRACE] [OmnipathR] HTTP headers: []
[2025-12-05 05:00:32] [TRACE] [OmnipathR] Sending HTTP request.
[2025-12-05 05:00:37] [TRACE] [OmnipathR] HTTP 200 (OK)
[2025-12-05 05:00:37] [TRACE] [OmnipathR] HTTP v2 GET: status 200.
[2025-12-05 05:00:37] [TRACE] [OmnipathR] Downloaded 295.2 Mb in 5.130179s from media.githubusercontent.com (57.5 Mb/s); Redirect: 0s, DNS look up: 0.078991s, Connection: 0.122582s, Pretransfer: 0.17362s, First byte at: 0.524428s
[2025-12-05 05:00:37] [TRACE] [OmnipathR] HTTP headers: HTTP/2 200 ; cache-control: max-age=300; content-security-policy: default-src 'none'; content-type: application/octet-stream; etag: "528eb01837a518d21f51092080b40a6646de00342c1ac0fae436abbc3024a5c7"; last-modified: Fri, 05 Dec 2025 10:00:32 GMT; strict-transport-security: max-age=31557600; timing-allow-origin: https://github.com; x-content-type-options: nosniff; x-frame-options: deny; x-github-tenant: ; x-xss-protection: 1; mode=block; x-github-request-id: B526:7A22C:15D2C6:1AB26F:6932AD3B; accept-ranges: bytes; date: Fri, 05 Dec 2025 10:00:32 GMT; via: 1.1 varnish; x-served-by: cache-iad-kcgs7200065-IAD; x-cache: MISS; x-cache-hits: 0; x-timer: S1764928832.203494,VS0,VE307; access-control-allow-origin: *; cross-origin-resource-policy: cross-origin; x-fastly-request-id: 9cfbbc5d44c926dc8a586f7734496e4c5ba3859a; expires: Fri, 05 Dec 2025 10:05:32 GMT; source-age: 0; vary: Authorization,Accept-Encoding; content-length: 309499334
[2025-12-05 05:00:37] [TRACE] [OmnipathR] Response headers: [cache-control=max-age=300,content-security-policy=default-src 'none',content-type=application/octet-stream,etag="528eb01837a518d21f51092080b40a6646de00342c1ac0fae436abbc3024a5c7",last-modified=Fri, 05 Dec 2025 10:00:32 GMT,strict-transport-security=max-age=31557600,timing-allow-origin=https://github.com,x-content-type-options=nosniff,x-frame-options=deny,x-github-tenant=,x-xss-protection=1; mode=block,x-github-request-id=B526:7A22C:15D2C6:1AB26F:6932AD3B,accept-ranges=bytes,date=Fri, 05 Dec 2025 10:00:32 GMT,via=1.1 varnish,x-served-by=cache-iad-kcgs7200065-IAD,x-cache=MISS,x-cache-hits=0,x-timer=S1764928832.203494,VS0,VE307,access-control-allow-origin=*,cross-origin-resource-policy=cross-origin,x-fastly-request-id=9cfbbc5d44c926dc8a586f7734496e4c5ba3859a,expires=Fri, 05 Dec 2025 10:05:32 GMT,source-age=0,vary=Authorization,Accept-Encoding,content-length=309499334]
[2025-12-05 05:00:38] [INFO] [OmnipathR] Download ready [key=3c92c86840bbbe428e793c4f683167ceaa139e9d, version=1]
[2025-12-05 05:00:38] [TRACE] [OmnipathR] Reading JSON from `/home/pkgbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-12-05 05:00:38] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-12-05 05:00:38] [INFO] [OmnipathR] Cache item `3c92c86840bbbe428e793c4f683167ceaa139e9d` version 1: status changed from `unknown` to `ready`.
[2025-12-05 05:00:45] [INFO] [OmnipathR] Download ready [key=2792c9a0814e66fa86fadf2c9f613c4075a3145c, version=1]
[2025-12-05 05:00:45] [TRACE] [OmnipathR] Reading JSON from `/home/pkgbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-12-05 05:00:45] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-12-05 05:00:45] [INFO] [OmnipathR] Cache item `2792c9a0814e66fa86fadf2c9f613c4075a3145c` version 1: status changed from `unknown` to `ready`.
[2025-12-05 05:00:58] [TRACE] [OmnipathR] Exported RDS to `/home/pkgbuild/.cache/OmnipathR/6cb5231204c9a7caf10d9a19e01e0ac86ff85b0c-1.rds`.
[2025-12-05 05:00:58] [INFO] [OmnipathR] Download ready [key=6cb5231204c9a7caf10d9a19e01e0ac86ff85b0c, version=1]
[2025-12-05 05:00:58] [TRACE] [OmnipathR] Reading JSON from `/home/pkgbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-12-05 05:00:58] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-12-05 05:00:58] [INFO] [OmnipathR] Cache item `6cb5231204c9a7caf10d9a19e01e0ac86ff85b0c` version 1: status changed from `started` to `ready`.
[2025-12-05 05:00:58] [TRACE] [OmnipathR] Translating complexes: 0 complexes in data.
[2025-12-05 05:00:59] [TRACE] [OmnipathR] 0 complexes after removing the ones mapping to more than 1 items in target identifier space.
[2025-12-05 05:00:59] [TRACE] [OmnipathR] Translated 0 complexes to 0.
[2025-12-05 05:00:59] [TRACE] [OmnipathR] 157 rows before translation, 157 hmdb IDs in column `HMDB`.
[2025-12-05 05:00:59] [TRACE] [OmnipathR] Translation ambiguity between columns `HMDB` and `chebi`
[2025-12-05 05:00:59] [TRACE] [OmnipathR] 157 rows after translation; translated 157 `hmdb` IDs in column `HMDB` to 305 `chebi` IDs in column `chebi`.
[2025-12-05 05:00:59] [TRACE] [OmnipathR] ID translation table: from `chebi` to `hmdb`, using RaMP
[2025-12-05 05:00:59] [TRACE] [OmnipathR] Looking up in cache: `ramp_id_mapping_table`.
[2025-12-05 05:00:59] [TRACE] [OmnipathR] Not found in cache, rebuilding: `ramp_id_mapping_table`.
[2025-12-05 05:00:59] [TRACE] [OmnipathR] Reading JSON from `/home/pkgbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-12-05 05:00:59] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-12-05 05:00:59] [TRACE] [OmnipathR] Reading JSON from `/home/pkgbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-12-05 05:00:59] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-12-05 05:00:59] [INFO] [OmnipathR] Cache item `f146d4b534dee110286529915961eeee2c69843a` version 1: status changed from `unknown` to `started`.
[2025-12-05 05:00:59] [TRACE] [OmnipathR] Exporting object to RDS: `/home/pkgbuild/.cache/OmnipathR/f146d4b534dee110286529915961eeee2c69843a-1.rds`.
[2025-12-05 05:00:59] [INFO] [OmnipathR] Looking up in cache `ramp_2.5.4.sqlite`: key=2792c9a0814e66fa86fadf2c9f613c4075a3145c, latest version=1.
[2025-12-05 05:00:59] [TRACE] [OmnipathR] Cache file path: /home/pkgbuild/.cache/OmnipathR/2792c9a0814e66fa86fadf2c9f613c4075a3145c-1
[2025-12-05 05:01:07] [TRACE] [OmnipathR] Exported RDS to `/home/pkgbuild/.cache/OmnipathR/f146d4b534dee110286529915961eeee2c69843a-1.rds`.
[2025-12-05 05:01:07] [INFO] [OmnipathR] Download ready [key=f146d4b534dee110286529915961eeee2c69843a, version=1]
[2025-12-05 05:01:07] [TRACE] [OmnipathR] Reading JSON from `/home/pkgbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-12-05 05:01:07] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2025-12-05 05:01:07] [INFO] [OmnipathR] Cache item `f146d4b534dee110286529915961eeee2c69843a` version 1: status changed from `started` to `ready`.
[2025-12-05 05:01:08] [TRACE] [OmnipathR] Translating complexes: 0 complexes in data.
[2025-12-05 05:01:08] [TRACE] [OmnipathR] 0 complexes after removing the ones mapping to more than 1 items in target identifier space.
[2025-12-05 05:01:08] [TRACE] [OmnipathR] Translated 0 complexes to 0.
[2025-12-05 05:01:08] [TRACE] [OmnipathR] 305 rows before translation, 305 chebi IDs in column `chebi`.
[2025-12-05 05:01:08] [TRACE] [OmnipathR] Translation ambiguity between columns `chebi` and `hmdb`
[2025-12-05 05:01:08] [TRACE] [OmnipathR] 305 rows after translation; translated 305 `chebi` IDs in column `chebi` to 241 `hmdb` IDs in column `hmdb`.
[2025-12-05 05:01:09] [ERROR] [MetaProViz] Interrupting R CMD check to see stderr in BioC SPB.
Error in equivalent_id(data = DetectedIDs, metadata_info = c(InputID = "HMDB"), :
Interrupting R CMD check to see stderr in BioC SPB.
Execution halted
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
dma 18.238 1.577 19.778
* checking for unstated dependencies in tests ... OK
* checking tests ...
Running testthat.R [15s/15s]
[15s/15s] OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... [4s/4s] OK
* DONE
Status: 1 ERROR, 2 NOTEs
See
/home/pkgbuild/packagebuilder/workers/jobs/3967/016d117338b422dc8f7c12a4aee795fad4ccb9b6/MetaProViz.Rcheck/00check.log
for details.
===============================
BiocCheck('MetaProViz_3.99.30.tar.gz')
===============================
Installing MetaProViz
Package installed successfully
MetaProViz session metadata
sourceDir: /tmp/Rtmp4NMrkK/filee0d096dc2cc58/MetaProViz
BiocVersion: 3.23
Package: MetaProViz
PackageVersion: 3.99.30
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3967/016d117338b422dc8f7c12a4aee795fad4ccb9b6/MetaProViz.BiocCheck
BiocCheckVersion: 1.47.1
sourceDir: /tmp/Rtmp4NMrkK/filee0d096dc2cc58/MetaProViz
installDir: /tmp/Rtmp4NMrkK/filee0d095afe7b9f
isTarBall: TRUE
platform: unix
Running BiocCheck on MetaProViz
* Checking for deprecated package usage...
* Checking for remote package usage...
* Checking for 'LazyData: true' usage...
* Checking version number...
* Checking for version number mismatch...
* Checking new package version number...
! WARNING: New package x version starting with non-zero value (e.g., 1.y.z,
2.y.z); got 3.99.30.
* Checking R version dependency...
i NOTE: Update R version dependency from 4.4 to 4.6.0
* Checking package size...
* Checking individual file sizes...
* Checking biocViews...
* Checking that biocViews are present...
* Checking package type based on biocViews...
Software
* Checking for non-trivial biocViews...
* Checking that biocViews come from the same category...
* Checking biocViews validity...
* Checking for recommended biocViews...
i NOTE: Consider adding these automatically suggested biocViews: Reactome
i Search 'biocViews' at https://contributions.bioconductor.org
* Checking build system compatibility...
* Checking for proper Description: field...
* Checking if DESCRIPTION is well formatted...
* Checking for whitespace in DESCRIPTION field names...
* Checking that Package field matches directory/tarball name...
* Checking for Version: field...
* Checking License: for restrictive use...
* Checking for recommended DESCRIPTION fields...
* Checking for Bioconductor software dependencies...
i Bioconductor dependencies found in Imports & Depends (17%).
* Checking for pinned package versions in DESCRIPTION...
* Checking for 'fnd' role in Authors@R...
* Checking NAMESPACE...
* Checking .Rbuildignore...
* Checking for stray BiocCheck output folders...
* Checking vignette directory...
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of MetaProViz...
* Checking coding practice...
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
i NOTE: The recommended function length is 50 lines or less. There are 60
functions greater than 50 lines.
The longest 5 functions are:
mca_core() (R/MetaboliteClusteringAnalysis.R): 1686 lines
...
mapping_ambiguity() (R/RefactorPriorKnoweldge.R): 574 lines
* Checking man page documentation...
i NOTE: Consider adding runnable examples to man pages that document exported
objects.
checkmatch_pk_to_data.Rd
...
translate_id.Rd
i NOTE: Usage of dontrun / donttest tags found in man page examples. 9% of man
pages use at least one of these tags.
Found in files:
checkmatch_pk_to_data.Rd
...
translate_id.Rd
i NOTE: Use donttest instead of dontrun.
Found in files:
checkmatch_pk_to_data.Rd
...
translate_id.Rd
* Checking package NEWS...
* Checking unit tests...
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source, and
vignette source...
i NOTE: Consider shorter lines; 1263 lines (6%) are > 80 characters long.
First few lines:
R/DifferentialMetaboliteAnalysis.R#L38 #' @param metadata_info Named
character ...
...
vignettes/quick-start.Rmd#L471 For a detailed example of the visualisat ...
i See https://contributions.bioconductor.org/r-code.html
i See styler package: https://cran.r-project.org/package=styler as described in
the BiocCheck vignette.
* Checking if package already exists in CRAN...
* Checking if new package already exists in Bioconductor...
* Checking for bioc-devel mailing list subscription...
i Maintainer is subscribed to bioc-devel.
* Checking for support site registration...
i Maintainer is registered at support site.
i Package is in the Support Site Watched Tags.
BiocCheck v1.47.1 results
0 ERRORS | 1 WARNINGS | i 7 NOTES
i See the MetaProViz.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.