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This page was generated on 2025-02-10 11:42 -0500 (Mon, 10 Feb 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 24.04.1 LTS)x86_64R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences" 4719
palomino7Windows Server 2022 Datacenterx64R Under development (unstable) (2025-01-21 r87610 ucrt) -- "Unsuffered Consequences" 4480
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2025-01-22 r87618) -- "Unsuffered Consequences" 4491
kjohnson3macOS 13.7.1 Venturaarm64R 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

Package 2274/2295HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
wppi 1.15.0  (landing page)
Ana Galhoz
Snapshot Date: 2025-02-09 13:40 -0500 (Sun, 09 Feb 2025)
git_url: https://git.bioconductor.org/packages/wppi
git_branch: devel
git_last_commit: 321e17d
git_last_commit_date: 2024-10-29 10:58:10 -0500 (Tue, 29 Oct 2024)
nebbiolo1Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    ERROR  skipped
palomino7Windows Server 2022 Datacenter / x64  OK    ERROR  skippedskipped
lconwaymacOS 12.7.1 Monterey / x86_64  OK    ERROR  skippedskipped
kjohnson3macOS 13.7.1 Ventura / arm64  OK    ERROR  skippedskipped

BUILD results for wppi on palomino7

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: chmod a+r wppi -R && E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data wppi
StartedAt: 2025-02-09 22:19:13 -0500 (Sun, 09 Feb 2025)
EndedAt: 2025-02-09 22:19:53 -0500 (Sun, 09 Feb 2025)
EllapsedTime: 40.7 seconds
RetCode: 1
Status:   ERROR  
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   chmod a+r wppi -R && E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe 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
[2025-02-09 22:19:36] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-09 22:19:36] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-09 22:19:36] [INFO]    [OmnipathR] Initialized cache: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2025-02-09 22:19:36] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2025-02-09 22:19:36] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2025-02-09
[2025-02-09 22:19:36] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-02-09 20:50:19 UTC; windows
[2025-02-09 22:19:36] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.15.6
[2025-02-09 22:19:36] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.21
[2025-02-09 22:19:37] [INFO]    [OmnipathR] Session info: [version=R Under development (unstable) (2025-01-21 r87610 ucrt); os=Windows Server 2022 x64 (build 20348); system=x86_64, mingw32; ui=RTerm; language=(EN); collate=C; ctype=English_United States.utf8; tz=America/New_York; date=2025-02-09; pandoc=2.7.3 @ C:/PROGRA~1/Pandoc/ (via rmarkdown); quarto=NA]
[2025-02-09 22:19:37] [INFO]    [OmnipathR] External libraries: [cairo=1.18.2; cairoFT=; pango=; png=1.6.44; jpeg=9.6; tiff=LIBTIFF, Version 4.7.0; tcl=8.6.13; curl=8.10.1; zlib=1.3.1; bzlib=1.0.8, 13-Jul-2019; xz=5.6.3; deflate=1.22; PCRE=10.44 2024-06-07; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=win_iconv; readline=; BLAS=; lapack=; lapack_version=3.12.0]
[2025-02-09 22:19:37] [INFO]    [OmnipathR] CURL: version: 8.10.1; headers: 8.10.1; ssl_version: (OpenSSL/3.4.0) Schannel; libz_version: 1.3; libssh_version: libssh2/1.11.0; libidn_version: NA; host: x86_64-w64-mingw32; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, rtsp, scp, sftp, smb, smbs, smtp, smtps, telnet, tftp; ipv6: TRUE; http2: TRUE; idn: TRUE; url_parser: TRUE
[2025-02-09 22:19:37] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2025-02-09 22:19:37] [TRACE]   [OmnipathR] Cache is at `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2025-02-09 22:19:37] [TRACE]   [OmnipathR] Contains 1 files.
[2025-02-09 22:19:37] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2025-02-09 22:19:37] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-09 22:19:37] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-09 22:19:37] [SUCCESS] [OmnipathR] Removing all cache contents from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2025-02-09 22:19:37] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2025-02-09 22:19:37] [TRACE]   [OmnipathR] Reading JSON from `E:/biocbuild/bbs-3.21-bioc/R/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2025-02-09 22:19:37] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-09 22:19:37] [TRACE]   [OmnipathR] Reading JSON from `E:/biocbuild/bbs-3.21-bioc/R/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2025-02-09 22:19:37] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-09 22:19:37] [TRACE]   [OmnipathR] Reading JSON from `E:/biocbuild/bbs-3.21-bioc/R/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2025-02-09 22:19:37] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-09 22:19:37] [TRACE]   [OmnipathR] Reading JSON from `E:/biocbuild/bbs-3.21-bioc/R/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2025-02-09 22:19:37] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-09 22:19:37] [TRACE]   [OmnipathR] Cache locked: FALSE
[2025-02-09 22:19:38] [INFO]    [wppi] Executing WPPI workflow.
[2025-02-09 22:19:38] [INFO]    [wppi] Collecting database knowledge.
[2025-02-09 22:19:38] [TRACE]   [OmnipathR] Downloading by `generic_downloader`.
[2025-02-09 22:19:38] [TRACE]   [OmnipathR] Looking up in cache: `http://purl.obolibrary.org/obo/hp/hpoa/genes_to_phenotype.txt`.
[2025-02-09 22:19:38] [INFO]    [OmnipathR] Cache record does not exist: `http://purl.obolibrary.org/obo/hp/hpoa/genes_to_phenotype.txt`
[2025-02-09 22:19:38] [TRACE]   [OmnipathR] Could not find in cache, initiating download: `http://purl.obolibrary.org/obo/hp/hpoa/genes_to_phenotype.txt`.
[2025-02-09 22:19:38] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-09 22:19:38] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-09 22:19:38] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-09 22:19:38] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-09 22:19:38] [INFO]    [OmnipathR] Cache item `17e608c86c1284f1d80eb7aae56c9a652906c66e` version 1: status changed from `unknown` to `started`.
[2025-02-09 22:19:38] [TRACE]   [OmnipathR] Exporting object to RDS: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/17e608c86c1284f1d80eb7aae56c9a652906c66e-1.rds`.
[2025-02-09 22:19:38] [INFO]    [OmnipathR] Retrieving URL: `http://purl.obolibrary.org/obo/hp/hpoa/genes_to_phenotype.txt`
[2025-02-09 22:19:38] [TRACE]   [OmnipathR] Attempt 1/3: `http://purl.obolibrary.org/obo/hp/hpoa/genes_to_phenotype.txt`
[2025-02-09 22:19:38] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=13,tcp_keepidle=10,tcp_keepcnt=10,upkeep_interval_ms=30000,ssl_verifypeer=TRUE,ssl_verifyhost=TRUE]
[2025-02-09 22:19:39] [TRACE]   [OmnipathR] Downloaded 18.8 Mb in 1.205872s from purl.obolibrary.org (15.6 Mb/s); Redirect: 0.438676s, DNS look up: 0.237068s, Connection: 0.255041s, Pretransfer: 0.308709s, First byte at: 0.504154s
[2025-02-09 22:19:41] [TRACE]   [OmnipathR] Exported RDS to `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/17e608c86c1284f1d80eb7aae56c9a652906c66e-1.rds`.
[2025-02-09 22:19:41] [INFO]    [OmnipathR] Download ready [key=17e608c86c1284f1d80eb7aae56c9a652906c66e, version=1]
[2025-02-09 22:19:41] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-09 22:19:41] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-09 22:19:41] [INFO]    [OmnipathR] Cache item `17e608c86c1284f1d80eb7aae56c9a652906c66e` version 1: status changed from `started` to `ready`.
[2025-02-09 22:19:41] [SUCCESS] [OmnipathR] Human Phenotype Ontology (purl.obolibrary.org): downloaded 316589 records
[2025-02-09 22:19:41] [TRACE]   [OmnipathR] Downloading by `generic_downloader`.
[2025-02-09 22:19:41] [TRACE]   [OmnipathR] Looking up in cache: `http://current.geneontology.org/annotations/goa_human.gaf.gz`.
[2025-02-09 22:19:41] [INFO]    [OmnipathR] Cache record does not exist: `http://current.geneontology.org/annotations/goa_human.gaf.gz`
[2025-02-09 22:19:41] [TRACE]   [OmnipathR] Could not find in cache, initiating download: `http://current.geneontology.org/annotations/goa_human.gaf.gz`.
[2025-02-09 22:19:41] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-09 22:19:41] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-09 22:19:41] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2025-02-09 22:19:41] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2025-02-09 22:19:41] [INFO]    [OmnipathR] Cache item `4dccec1f0141d8846ba49e6f0eada25ebf0253fa` version 1: status changed from `unknown` to `started`.
[2025-02-09 22:19:41] [TRACE]   [OmnipathR] Exporting object to RDS: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/4dccec1f0141d8846ba49e6f0eada25ebf0253fa-1.rds`.
[2025-02-09 22:19:41] [INFO]    [OmnipathR] Retrieving URL: `http://current.geneontology.org/annotations/goa_human.gaf.gz`
[2025-02-09 22:19:41] [TRACE]   [OmnipathR] Attempt 1/3: `http://current.geneontology.org/annotations/goa_human.gaf.gz`
[2025-02-09 22:19:41] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=13,tcp_keepidle=10,tcp_keepcnt=10,upkeep_interval_ms=30000,ssl_verifypeer=TRUE,ssl_verifyhost=TRUE]
[2025-02-09 22:19:41] [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&'
[2025-02-09 22:19:46] [TRACE]   [OmnipathR] Attempt 2/3: `http://current.geneontology.org/annotations/goa_human.gaf.gz`
[2025-02-09 22:19:46] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=13,tcp_keepidle=10,tcp_keepcnt=10,upkeep_interval_ms=30000,ssl_verifypeer=TRUE,ssl_verifyhost=TRUE]
[2025-02-09 22:19:46] [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&'
[2025-02-09 22:19:51] [TRACE]   [OmnipathR] Attempt 3/3: `http://current.geneontology.org/annotations/goa_human.gaf.gz`
[2025-02-09 22:19:51] [TRACE]   [OmnipathR] Curl options: [connecttimeout=10,timeout=300,debugfunction=<function>,verbose=FALSE,tcp_keepalive=TRUE,tcp_keepintvl=13,tcp_keepidle=10,tcp_keepcnt=10,upkeep_interval_ms=30000,ssl_verifypeer=TRUE,ssl_verifyhost=TRUE]
[2025-02-09 22:19:52] [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&'
[2025-02-09 22:19:52] [INFO]    [OmnipathR] Package `OmnipathR` packaged: NA
[2025-02-09 22:19:52] [INFO]    [OmnipathR] Package `OmnipathR` date/publication: 2025-02-09
[2025-02-09 22:19:52] [INFO]    [OmnipathR] Package `OmnipathR` built: R 4.5.0; ; 2025-02-09 20:50:19 UTC; windows
[2025-02-09 22:19:52] [INFO]    [OmnipathR] Package `OmnipathR` version: 3.15.6
[2025-02-09 22:19:52] [INFO]    [OmnipathR] Package `OmnipathR` repository: Bioconductor 3.21
[2025-02-09 22:19:52] [INFO]    [OmnipathR] Session info: [version=R Under development (unstable) (2025-01-21 r87610 ucrt); os=Windows Server 2022 x64 (build 20348); system=x86_64, mingw32; ui=RTerm; language=(EN); collate=C; ctype=English_United States.utf8; tz=America/New_York; date=2025-02-09; pandoc=2.7.3 @ C:/PROGRA~1/Pandoc/ (via rmarkdown); quarto=NA]
[2025-02-09 22:19:52] [INFO]    [OmnipathR] External libraries: [cairo=1.18.2; cairoFT=; pango=; png=1.6.44; jpeg=9.6; tiff=LIBTIFF, Version 4.7.0; tcl=8.6.13; curl=8.10.1; zlib=1.3.1; bzlib=1.0.8, 13-Jul-2019; xz=5.6.3; deflate=1.22; PCRE=10.44 2024-06-07; ICU=74.2; TRE=TRE 0.8.0 R_fixes (BSD); iconv=win_iconv; readline=; BLAS=; lapack=; lapack_version=3.12.0]
[2025-02-09 22:19:52] [INFO]    [OmnipathR] CURL: version: 8.10.1; headers: 8.10.1; ssl_version: (OpenSSL/3.4.0) Schannel; libz_version: 1.3; libssh_version: libssh2/1.11.0; libidn_version: NA; host: x86_64-w64-mingw32; protocols: dict, file, ftp, ftps, gopher, gophers, http, https, imap, imaps, ldap, ldaps, mqtt, pop3, pop3s, 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