Ron Ammar
| Snapshot Date: 2025-11-11 13:45 -0500 (Tue, 11 Nov 2025) |
| git_url: https://git.bioconductor.org/packages/zFPKM |
| git_branch: RELEASE_3_22 |
| git_last_commit: 1b16803 |
| git_last_commit_date: 2025-10-29 10:40:03 -0500 (Wed, 29 Oct 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-11-12 11:58 -0500 (Wed, 12 Nov 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4902 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4668 |
| 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 2358/2361 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| zFPKM 1.32.0 (landing page) Ron Ammar
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | ERROR | skipped | ||||||||||
|
To the developers/maintainers of the zFPKM package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/zFPKM.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: zFPKM |
| Version: 1.32.0 |
| Command: /home/biocbuild/R/R/bin/R CMD build --keep-empty-dirs --no-resave-data zFPKM |
| StartedAt: 2025-11-11 06:16:33 -0000 (Tue, 11 Nov 2025) |
| EndedAt: 2025-11-11 06:17:37 -0000 (Tue, 11 Nov 2025) |
| EllapsedTime: 64.1 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 zFPKM
###
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* checking for file ‘zFPKM/DESCRIPTION’ ... OK
* preparing ‘zFPKM’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘zFPKM.Rmd’ using rmarkdown
trying URL 'ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE94nnn/GSE94802/suppl/GSE94802_Minkina_etal_normalized_FPKM.csv.gz'
Content type 'unknown' length 800733 bytes (781 KB)
==================================================
trying URL 'ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE94nnn/GSE94802/suppl/GSE94802_Minkina_etal_raw_counts.csv.gz'
Content type 'unknown' length 574041 bytes (560 KB)
==================================================
Quitting from zFPKM.Rmd:33-70 [unnamed-chunk-1]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `scan()`:
! error reading from the connection
---
Backtrace:
▆
1. ├─SummarizedExperiment::SummarizedExperiment(...)
2. │ └─SummarizedExperiment:::normarg_assays(assays, as.null.if.no.assay = TRUE)
3. ├─S4Vectors::SimpleList(...)
4. └─global getSpecificGEOSupp(gse94802_counts)
5. └─utils::read.csv(gzfile(temp), row.names = 1, check.names = FALSE)
6. └─utils::read.table(...)
7. └─base::scan(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'zFPKM.Rmd' failed with diagnostics:
error reading from the connection
--- failed re-building ‘zFPKM.Rmd’
SUMMARY: processing the following file failed:
‘zFPKM.Rmd’
Error: Vignette re-building failed.
Execution halted