Multiple platform build/check report for BioC 3.21 - BUILD results for wppi on nebbiolo1

Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo1	Linux (Ubuntu 24.04.1 LTS)	x86_64	R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences"	4719
palomino7	Windows Server 2022 Datacenter	x64	R Under development (unstable) (2025-01-21 r87610 ucrt) -- "Unsuffered Consequences"	4480
lconway	macOS 12.7.1 Monterey	x86_64	R Under development (unstable) (2025-01-22 r87618) -- "Unsuffered Consequences"	4491
kjohnson3	macOS 13.7.1 Ventura	arm64	R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences"	4444
Click on any hostname to see more info about the system (e.g. compilers) () as reported by 'uname -p', except on Windows and Mac OS X*

BUILD results for wppi on nebbiolo1

To the developers/maintainers of the wppi package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/wppi.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results

Summary

Package: wppi

Version: 1.15.0

Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data wppi

StartedAt: 2025-02-10 19:55:02 -0500 (Mon, 10 Feb 2025)

EndedAt: 2025-02-10 19:55:36 -0500 (Mon, 10 Feb 2025)

EllapsedTime: 34.0 seconds

RetCode: 1

Status: ERROR

PackageFile: None

PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data wppi
###
##############################################################################
##############################################################################


* checking for file ‘wppi/DESCRIPTION’ ... OK
* preparing ‘wppi’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘wppi_workflow.Rmd’ using rmarkdown
[2025-02-10 19:55:19] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-10 19:55:19] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-10 19:55:19] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2025-02-10 19:55:19] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2025-02-10 19:55:19] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2025-02-10
[2025-02-10 19:55:19] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-02-10 20:17:41 UTC; unix
[2025-02-10 19:55:19] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.15.6
[2025-02-10 19:55:19] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.21
[2025-02-10 19:55:19] [INFO]    [OmnipathR] Session info: [version=R Under development (unstable) (2025-01-20 r87609); os=Ubuntu 24.04.1 LTS; system=x86_64, linux-gnu; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-02-10; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.5.57 @ /usr/local/bin/quarto]
[2025-02-10 19:55:19] [INFO]    [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.52.1; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6.14; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/home/biocbuild/bbs-3.21-bioc/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0]
[2025-02-10 19:55:19] [INFO]    [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: OpenSSL/3.0.13; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE
[2025-02-10 19:55:19] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-02-10 19:55:19] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2025-02-10 19:55:19] [TRACE]   [OmnipathR] Contains 1 files.
[2025-02-10 19:55:19] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-02-10 19:55:19] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-10 19:55:19] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-10 19:55:19] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2025-02-10 19:55:19] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2025-02-10 19:55:19] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-02-10 19:55:19] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-10 19:55:19] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-02-10 19:55:19] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-10 19:55:19] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-02-10 19:55:19] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-10 19:55:19] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.21-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-02-10 19:55:19] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-10 19:55:19] [TRACE]   [OmnipathR] Cache locked: FALSE
[2025-02-10 19:55:20] [INFO]    [wppi] Executing WPPI workflow.
[2025-02-10 19:55:20] [INFO]    [wppi] Collecting database knowledge.
[2025-02-10 19:55:20] [TRACE]   [OmnipathR] Downloading by `generic_downloader`.
[2025-02-10 19:55:20] [TRACE]   [OmnipathR] Looking up in cache: `http://purl.obolibrary.org/obo/hp/hpoa/genes_to_phenotype.txt`.
[2025-02-10 19:55:20] [INFO]    [OmnipathR] Cache record does not exist: `http://purl.obolibrary.org/obo/hp/hpoa/genes_to_phenotype.txt`
[2025-02-10 19:55:20] [TRACE]   [OmnipathR] Could not find in cache, initiating download: `http://purl.obolibrary.org/obo/hp/hpoa/genes_to_phenotype.txt`.
[2025-02-10 19:55:20] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-10 19:55:20] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-10 19:55:20] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-10 19:55:20] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-10 19:55:20] [INFO]    [OmnipathR] Cache item `17e608c86c1284f1d80eb7aae56c9a652906c66e` version 1: status changed from `unknown` to `started`.
[2025-02-10 19:55:20] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/17e608c86c1284f1d80eb7aae56c9a652906c66e-1.rds`.
[2025-02-10 19:55:20] [INFO]    [OmnipathR] Retrieving URL: `http://purl.obolibrary.org/obo/hp/hpoa/genes_to_phenotype.txt`
[2025-02-10 19:55:20] [TRACE]   [OmnipathR] Attempt 1/3: `http://purl.obolibrary.org/obo/hp/hpoa/genes_to_phenotype.txt`
[2025-02-10 19:55:20] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-02-10 19:55:20] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=13,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=TRUE,ssl_verifyhost=TRUE]
[2025-02-10 19:55:21] [TRACE]   [OmnipathR] Downloaded 18.8 Mb in 0.786633s from purl.obolibrary.org (23.9 Mb/s); Redirect: 0.325387s, DNS look up: 0.012479s, Connection: 0.03329s, Pretransfer: 0.182737s, First byte at: 0.465007s
[2025-02-10 19:55:23] [TRACE]   [OmnipathR] Exported RDS to `/home/biocbuild/.cache/OmnipathR/17e608c86c1284f1d80eb7aae56c9a652906c66e-1.rds`.
[2025-02-10 19:55:23] [INFO]    [OmnipathR] Download ready [key=17e608c86c1284f1d80eb7aae56c9a652906c66e, version=1]
[2025-02-10 19:55:23] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-10 19:55:23] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-10 19:55:23] [INFO]    [OmnipathR] Cache item `17e608c86c1284f1d80eb7aae56c9a652906c66e` version 1: status changed from `started` to `ready`.
[2025-02-10 19:55:23] [SUCCESS] [OmnipathR] Human Phenotype Ontology (purl.obolibrary.org): downloaded 316589 records
[2025-02-10 19:55:23] [TRACE]   [OmnipathR] Downloading by `generic_downloader`.
[2025-02-10 19:55:23] [TRACE]   [OmnipathR] Looking up in cache: `http://current.geneontology.org/annotations/goa_human.gaf.gz`.
[2025-02-10 19:55:23] [INFO]    [OmnipathR] Cache record does not exist: `http://current.geneontology.org/annotations/goa_human.gaf.gz`
[2025-02-10 19:55:23] [TRACE]   [OmnipathR] Could not find in cache, initiating download: `http://current.geneontology.org/annotations/goa_human.gaf.gz`.
[2025-02-10 19:55:23] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-10 19:55:23] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-10 19:55:23] [TRACE]   [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-10 19:55:23] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-10 19:55:23] [INFO]    [OmnipathR] Cache item `4dccec1f0141d8846ba49e6f0eada25ebf0253fa` version 1: status changed from `unknown` to `started`.
[2025-02-10 19:55:23] [TRACE]   [OmnipathR] Exporting object to RDS: `/home/biocbuild/.cache/OmnipathR/4dccec1f0141d8846ba49e6f0eada25ebf0253fa-1.rds`.
[2025-02-10 19:55:23] [INFO]    [OmnipathR] Retrieving URL: `http://current.geneontology.org/annotations/goa_human.gaf.gz`
[2025-02-10 19:55:23] [TRACE]   [OmnipathR] Attempt 1/3: `http://current.geneontology.org/annotations/goa_human.gaf.gz`
[2025-02-10 19:55:23] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-02-10 19:55:23] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=13,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=TRUE,ssl_verifyhost=TRUE]
[2025-02-10 19:55:24] [WARN]    [OmnipathR] Failed to download `http://current.geneontology.org/annotations/goa_human.gaf.gz` (attempt 1/3); error: embedded nul in string: '\037\x8b\b\b\x903)g\0\003goa_human.gaf\0ԝ[s\xdb8\xb2ǟ5\x9f\x82\xf3\xb6[u\xe8\020\027\x82\xa4\xab\u0383-ٱ\xe3K\024\xdbq./S\xb2L\xdb:#\x89^IΎ\xab\xf2\xe1\017H\xf0&'
[2025-02-10 19:55:29] [TRACE]   [OmnipathR] Attempt 2/3: `http://current.geneontology.org/annotations/goa_human.gaf.gz`
[2025-02-10 19:55:29] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-02-10 19:55:29] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=13,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=TRUE,ssl_verifyhost=TRUE]
[2025-02-10 19:55:29] [WARN]    [OmnipathR] Failed to download `http://current.geneontology.org/annotations/goa_human.gaf.gz` (attempt 2/3); error: embedded nul in string: '\037\x8b\b\b\x903)g\0\003goa_human.gaf\0ԝ[s\xdb8\xb2ǟ5\x9f\x82\xf3\xb6[u\xe8\020\027\x82\xa4\xab\u0383-ٱ\xe3K\024\xdbq./S\xb2L\xdb:#\x89^IΎ\xab\xf2\xe1\017H\xf0&'
[2025-02-10 19:55:34] [TRACE]   [OmnipathR] Attempt 3/3: `http://current.geneontology.org/annotations/goa_human.gaf.gz`
[2025-02-10 19:55:34] [TRACE]   [OmnipathR] The following curl options are not available: tcp_keepcnt
[2025-02-10 19:55:34] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=13,tcp_keepidle=10,upkeep_interval_ms=30000,ssl_verifypeer=TRUE,ssl_verifyhost=TRUE]
[2025-02-10 19:55:35] [ERROR]   [OmnipathR] Failed to download `http://current.geneontology.org/annotations/goa_human.gaf.gz` (attempt 3/3); error: embedded nul in string: '\037\x8b\b\b\x903)g\0\003goa_human.gaf\0ԝ[s\xdb8\xb2ǟ5\x9f\x82\xf3\xb6[u\xe8\020\027\x82\xa4\xab\u0383-ٱ\xe3K\024\xdbq./S\xb2L\xdb:#\x89^IΎ\xab\xf2\xe1\017H\xf0&'
[2025-02-10 19:55:35] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2025-02-10 19:55:35] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2025-02-10
[2025-02-10 19:55:35] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-02-10 20:17:41 UTC; unix
[2025-02-10 19:55:35] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.15.6
[2025-02-10 19:55:35] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.21
[2025-02-10 19:55:35] [INFO]    [OmnipathR] Session info: [version=R Under development (unstable) (2025-01-20 r87609); os=Ubuntu 24.04.1 LTS; system=x86_64, linux-gnu; ui=X11; language=(EN); collate=C; ctype=en_US.UTF-8; tz=America/New_York; date=2025-02-10; pandoc=2.7.3 @ /usr/bin/ (via rmarkdown); quarto=1.5.57 @ /usr/local/bin/quarto]
[2025-02-10 19:55:35] [INFO]    [OmnipathR] External libraries: [cairo=1.18.0; cairoFT=; pango=1.52.1; png=1.6.43; jpeg=8.0; tiff=LIBTIFF, Version 4.5.1; tcl=8.6.14; curl=8.5.0; zlib=1.3; bzlib=1.0.8, 13-Jul-2019; xz=5.4.5; deflate=1.19; PCRE=10.42 2022-12-11; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=glibc 2.39; readline=8.2; BLAS=/home/biocbuild/bbs-3.21-bioc/R/lib/libRblas.so; lapack=/usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0; lapack_version=3.12.0]
[2025-02-10 19:55:35] [INFO]    [OmnipathR] CURL: version: 8.5.0; headers: 8.5.0; ssl_version: OpenSSL/3.0.13; libz_version: 1.3; libssh_version: libssh/0.10.6/openssl/zlib; libidn_version: 2.3.7; host: x86_64-pc-linux-gnu; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtmp, rtmpe, rtmps, rtmpt, rtmpte, rtmpts, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE

Quitting from lines 80-102 [workflow] (wppi_workflow.Rmd)
Error: processing vignette 'wppi_workflow.Rmd' failed with diagnostics:
embedded nul in string: '\037\x8b\b\b\x903)g\0\003goa_human.gaf\0ԝ[s\xdb8\xb2ǟ5\x9f\x82\xf3\xb6[u\xe8\020\027\x82\xa4\xab\u0383-ٱ\xe3K\024\xdbq./S\xb2L\xdb:#\x89^IΎ\xab\xf2\xe1\017H\xf0&'
--- failed re-building ‘wppi_workflow.Rmd’

SUMMARY: processing the following file failed:
  ‘wppi_workflow.Rmd’

Error: Vignette re-building failed.
Execution halted