Build/check report for BioC 3.22 - BUILD results for idpr on kjohnson3

Hostname	OS	Arch (*)	R version	Installed pkgs
kjohnson3	macOS 13.7.7 Ventura	arm64	4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root"	4637
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 idpr on kjohnson3

To the developers/maintainers of the idpr package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/idpr.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: idpr

Version: 1.19.0

Command: /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data idpr

StartedAt: 2025-10-26 16:53:37 -0400 (Sun, 26 Oct 2025)

EndedAt: 2025-10-26 16:54:26 -0400 (Sun, 26 Oct 2025)

EllapsedTime: 48.5 seconds

RetCode: 1

Status: ERROR

PackageFile: None

PackageFileSize: NA

Command output

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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data idpr
###
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* checking for file ‘idpr/DESCRIPTION’ ... OK
* preparing ‘idpr’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘chargeHydropathy-vignette.Rmd’ using rmarkdown
2025-10-26 16:53:40.775 R[37087:550296169] XType: Using static font registry.
--- finished re-building ‘chargeHydropathy-vignette.Rmd’

--- re-building ‘disorderedMatrices-vignette.Rmd’ using rmarkdown
--- finished re-building ‘disorderedMatrices-vignette.Rmd’

--- re-building ‘idpr-vignette.Rmd’ using rmarkdown

Quitting from idpr-vignette.Rmd:152-155 [unnamed-chunk-5]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `open.connection()`:
! cannot open the connection to 'https://iupred2a.elte.hu/iupred2a/long/P04637.json'
---
Backtrace:
    ▆
 1. └─idpr::idprofile(sequence = P53_HUMAN, uniprotAccession = P53_ID)
 2.   └─idpr::iupred(...)
 3.     └─jsonlite::fromJSON(iupredURL)
 4.       └─jsonlite:::parse_and_simplify(...)
 5.         └─jsonlite:::parseJSON(txt, bigint_as_char)
 6.           └─jsonlite:::parse_con(txt, bigint_as_char)
 7.             ├─base::open(con, "rb")
 8.             └─base::open.connection(con, "rb")
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'idpr-vignette.Rmd' failed with diagnostics:
cannot open the connection to 'https://iupred2a.elte.hu/iupred2a/long/P04637.json'
--- failed re-building ‘idpr-vignette.Rmd’

--- re-building ‘iupred-vignette.Rmd’ using rmarkdown

Quitting from iupred-vignette.Rmd:36-42 [unnamed-chunk-2]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `open.connection()`:
! cannot open the connection to 'https://iupred2a.elte.hu/iupred2a/long/P04637.json'
---
Backtrace:
    ▆
 1. └─idpr::iupred(p53_ID, proteinName = "HUMAN P53")
 2.   └─jsonlite::fromJSON(iupredURL)
 3.     └─jsonlite:::parse_and_simplify(...)
 4.       └─jsonlite:::parseJSON(txt, bigint_as_char)
 5.         └─jsonlite:::parse_con(txt, bigint_as_char)
 6.           ├─base::open(con, "rb")
 7.           └─base::open.connection(con, "rb")
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'iupred-vignette.Rmd' failed with diagnostics:
cannot open the connection to 'https://iupred2a.elte.hu/iupred2a/long/P04637.json'
--- failed re-building ‘iupred-vignette.Rmd’

--- re-building ‘sequenceMAP-vignette.Rmd’ using rmarkdown
--- finished re-building ‘sequenceMAP-vignette.Rmd’

--- re-building ‘structuralTendency-vignette.Rmd’ using rmarkdown
--- finished re-building ‘structuralTendency-vignette.Rmd’

SUMMARY: processing the following files failed:
  ‘idpr-vignette.Rmd’ ‘iupred-vignette.Rmd’

Error: Vignette re-building failed.
Execution halted