Yi Xiong
| Snapshot Date: 2026-04-17 13:40 -0400 (Fri, 17 Apr 2026) |
| git_url: https://git.bioconductor.org/packages/Aerith |
| git_branch: devel |
| git_last_commit: 4583495 |
| git_last_commit_date: 2025-11-12 04:06:43 -0400 (Wed, 12 Nov 2025) |
| Back to Multiple platform build/check report for BioC 3.23: simplified long |
|
This page was generated on 2026-04-18 11:37 -0400 (Sat, 18 Apr 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.4 LTS) | x86_64 | 4.6.0 alpha (2026-04-05 r89794) | 4957 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.6.0 alpha (2026-04-08 r89818) | 4686 |
| kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4627 |
| 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 22/2404 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| Aerith 0.99.11 (landing page) Yi Xiong
| nebbiolo1 | Linux (Ubuntu 24.04.4 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | WARNINGS | OK | | ||||||||
| kunpeng2 | Linux (openEuler 24.03 LTS) / aarch64 | OK | ERROR | skipped | ||||||||||
| See other builds for Aerith in R Universe. | ||||||||||||||
|
To the developers/maintainers of the Aerith package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/Aerith.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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: Aerith |
| Version: 0.99.11 |
| Command: /home/biocbuild/R/R/bin/R CMD build --keep-empty-dirs --no-resave-data Aerith |
| StartedAt: 2026-04-16 22:19:30 -0000 (Thu, 16 Apr 2026) |
| EndedAt: 2026-04-16 22:23:55 -0000 (Thu, 16 Apr 2026) |
| EllapsedTime: 265.1 seconds |
| RetCode: 1 |
| Status: ERROR |
| PackageFile: None |
| PackageFileSize: NA |
##############################################################################
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### Running command:
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### /home/biocbuild/R/R/bin/R CMD build --keep-empty-dirs --no-resave-data Aerith
###
##############################################################################
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* checking for file ‘Aerith/DESCRIPTION’ ... OK
* preparing ‘Aerith’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘Aerith.Rmd’ using rmarkdown
--- finished re-building ‘Aerith.Rmd’
--- re-building ‘Input-data-format.Rmd’ using rmarkdown
Quitting from Input-data-format.Rmd:206-225 [mzml-reading]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `dyn.load()`:
! unable to load shared object '/home/biocbuild/R/R-devel_2025-02-19/site-library/ncdf4/libs/ncdf4.so':
libnetcdf.so.19: cannot open shared object file: No such file or directory
---
Backtrace:
▆
1. ├─Aerith::readMzmlMS1(demo_file)
2. └─base::loadNamespace(x)
3. ├─base::namespaceImport(...)
4. └─base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
5. └─base::library.dynam(lib, package, package.lib)
6. └─base::dyn.load(file, DLLpath = DLLpath, ...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'Input-data-format.Rmd' failed with diagnostics:
unable to load shared object '/home/biocbuild/R/R-devel_2025-02-19/site-library/ncdf4/libs/ncdf4.so':
libnetcdf.so.19: cannot open shared object file: No such file or directory
--- failed re-building ‘Input-data-format.Rmd’
--- re-building ‘PSM-annotation-and-visualization.Rmd’ using rmarkdown
Warning in readLines(con, warn = FALSE) :
invalid input found on input connection '/home/biocbuild/tmp/RtmpLRqe79/Rbuild3778654ea88137/Aerith/vignettes/PSM-annotation-and-visualization.html'
--- finished re-building ‘PSM-annotation-and-visualization.Rmd’
--- re-building ‘Score-function-test-of-PSM.Rmd’ using rmarkdown
Warning in readLines(con, warn = FALSE) :
invalid input found on input connection 'Score-function-test-of-PSM.Rmd'
Warning in readLines(con, warn = FALSE) :
invalid input found on input connection 'Score-function-test-of-PSM.knit.md'
Warning in readLines(con, warn = FALSE) :
invalid input found on input connection 'Score-function-test-of-PSM.knit.md'
Warning in readLines(con, warn = FALSE) :
invalid input found on input connection '/home/biocbuild/tmp/RtmpLRqe79/Rbuild3778654ea88137/Aerith/vignettes/Score-function-test-of-PSM.html'
--- finished re-building ‘Score-function-test-of-PSM.Rmd’
--- re-building ‘Theoretic-spectra-generation-of-SIP-labeled-compound.Rmd’ using rmarkdown
Warning in readLines(con, warn = FALSE) :
invalid input found on input connection 'Theoretic-spectra-generation-of-SIP-labeled-compound.Rmd'
Warning: ggrepel: 13 unlabeled data points (too many overlaps). Consider increasing max.overlaps
Warning in readLines(con, warn = FALSE) :
invalid input found on input connection 'Theoretic-spectra-generation-of-SIP-labeled-compound.knit.md'
Warning in readLines(con, warn = FALSE) :
invalid input found on input connection 'Theoretic-spectra-generation-of-SIP-labeled-compound.knit.md'
Warning in readLines(con, warn = FALSE) :
invalid input found on input connection '/home/biocbuild/tmp/RtmpLRqe79/Rbuild3778654ea88137/Aerith/vignettes/Theoretic-spectra-generation-of-SIP-labeled-compound.html'
--- finished re-building ‘Theoretic-spectra-generation-of-SIP-labeled-compound.Rmd’
--- re-building ‘Theoretic-spectra-generation-of-SIP-labeled-peptide.Rmd’ using rmarkdown
Warning in readLines(con, warn = FALSE) :
invalid input found on input connection '/home/biocbuild/tmp/RtmpLRqe79/Rbuild3778654ea88137/Aerith/vignettes/Theoretic-spectra-generation-of-SIP-labeled-peptide.html'
--- finished re-building ‘Theoretic-spectra-generation-of-SIP-labeled-peptide.Rmd’
--- re-building ‘Visualization-of-SIP-proteomic-result.Rmd’ using rmarkdown
Warning in readLines(con, warn = FALSE) :
invalid input found on input connection 'Visualization-of-SIP-proteomic-result.Rmd'
Warning in readLines(con, warn = FALSE) :
invalid input found on input connection 'Visualization-of-SIP-proteomic-result.knit.md'
Warning in readLines(con, warn = FALSE) :
invalid input found on input connection 'Visualization-of-SIP-proteomic-result.knit.md'
Warning in readLines(con, warn = FALSE) :
invalid input found on input connection '/home/biocbuild/tmp/RtmpLRqe79/Rbuild3778654ea88137/Aerith/vignettes/Visualization-of-SIP-proteomic-result.html'
--- finished re-building ‘Visualization-of-SIP-proteomic-result.Rmd’
SUMMARY: processing the following file failed:
‘Input-data-format.Rmd’
Error: Vignette re-building failed.
Execution halted