| Back to Build/check report for BioC 3.22: simplified long |
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This page was generated on 2026-03-17 11:57 -0400 (Tue, 17 Mar 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.2 (2025-10-31) -- "[Not] Part in a Rumble" | 4892 |
| 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 681/2361 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| EpiMix 1.12.0 (landing page) Yuanning Zheng
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | ERROR | skipped | |||||||||
| See other builds for EpiMix in R Universe. | ||||||||||||||
|
To the developers/maintainers of the EpiMix package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/EpiMix.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. |
| Package: EpiMix |
| Version: 1.12.0 |
| Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data --md5 EpiMix |
| StartedAt: 2026-03-16 17:25:22 -0400 (Mon, 16 Mar 2026) |
| EndedAt: 2026-03-16 17:30:58 -0400 (Mon, 16 Mar 2026) |
| EllapsedTime: 336.3 seconds |
| RetCode: 1 |
| Status: ERROR |
| PackageFile: None |
| PackageFileSize: NA |
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### Running command:
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### /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data --md5 EpiMix
###
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* checking for file ‘EpiMix/DESCRIPTION’ ... OK
* preparing ‘EpiMix’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘Methylation_Modeling.Rmd’ using rmarkdown
trying URL 'https://egg2.wustl.edu/roadmap/data/byFileType/chromhmmSegmentations/ChmmModels/core_K27ac/jointModel/final/E096_18_core_K27ac_hg38lift_mnemonics.bed.gz'
Content type 'application/x-gzip' length 3835377 bytes (3.7 MB)
==================================================
downloaded 3.7 MB
trying URL 'https://gdac.broadinstitute.org/runs/stddata__latest/data/OV/20160128/gdac.broadinstitute.org_OV.Merge_methylation__humanmethylation27__jhu_usc_edu__Level_3__within_bioassay_data_set_function__data.Level_3.2016012800.0.0.tar.gz'
Content type 'application/x-gzip' length 152968396 bytes (145.9 MB)
==================================================
downloaded 145.9 MB
trying URL 'https://gdac.broadinstitute.org/runs/stddata__latest/data/OV/20160128/gdac.broadinstitute.org_OV.Merge_methylation__humanmethylation450__jhu_usc_edu__Level_3__within_bioassay_data_set_function__data.Level_3.2016012800.0.0.tar.gz'
Content type 'application/x-gzip' length 51525820 bytes (49.1 MB)
==================================================
downloaded 49.1 MB
trying URL 'https://gdac.broadinstitute.org/runs/stddata__latest/data/OV/20160128/gdac.broadinstitute.org_OV.Merge_transcriptome__agilentg4502a_07_3__unc_edu__Level_3__unc_lowess_normalization_gene_level__data.Level_3.2016012800.0.0.tar.gz'
Content type 'application/x-gzip' length 36996192 bytes (35.3 MB)
==================================================
downloaded 35.3 MB
trying URL 'https://gdac.broadinstitute.org/runs/stddata__latest/data/OV/20160128/gdac.broadinstitute.org_OV.miRseq_Preprocess.Level_3.2016012800.0.0.tar.gz'
Content type 'application/x-gzip' length 2663096 bytes (2.5 MB)
==================================================
downloaded 2.5 MB
trying URL 'https://gdac.broadinstitute.org/runs/stddata__latest/data/LUAD/20160128/gdac.broadinstitute.org_LUAD.Merge_Clinical.Level_1.2016012800.0.0.tar.gz'
Content type 'application/x-gzip' length 1777018 bytes (1.7 MB)
==================================================
downloaded 1.7 MB
trying URL 'https://gdac.broadinstitute.org/runs/stddata__latest/data/LUAD/20160128/gdac.broadinstitute.org_LUAD.Merge_Clinical.Level_1.2016012800.0.0.tar.gz'
Content type 'application/x-gzip' length 1777018 bytes (1.7 MB)
==================================================
downloaded 1.7 MB
Quitting from Methylation_Modeling.Rmd:584-592 [unnamed-chunk-40]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/purrr_error_indexed>
Error in `map()`:
ℹ In index: 1.
ℹ With name: mirtarbase.
Caused by error:
! Malformed encoding found in chunked-encoding
---
Backtrace:
▆
1. ├─EpiMix::find_miRNA_targets(...)
2. │ └─multiMiR::get_multimir(...)
3. │ └─purrr::map(queries, query_multimir, org = org, add.link = add.link, use.tibble = use.tibble)
4. │ └─purrr:::map_("list", .x, .f, ..., .progress = .progress)
5. │ ├─purrr:::with_indexed_errors(...)
6. │ │ └─base::withCallingHandlers(...)
7. │ ├─purrr:::call_with_cleanup(...)
8. │ └─multiMiR (local) .f(.x[[i]], ...)
9. │ └─multiMiR::search_multimir(x$query)
10. │ └─multiMiR:::submit_request(...)
11. │ └─RCurl::postForm(url, query = query, ..., .opts = myOpts)
12. │ └─RCurl::.postForm(curl, .opts, .params, style)
13. └─RCurl (local) `<fn>`(56L, "Malformed encoding found in chunked-encoding", TRUE)
14. └─base (local) fun(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Error: processing vignette 'Methylation_Modeling.Rmd' failed with diagnostics:
ℹ In index: 1.
ℹ With name: mirtarbase.
Caused by error:
! Malformed encoding found in chunked-encoding
--- failed re-building ‘Methylation_Modeling.Rmd’
SUMMARY: processing the following file failed:
‘Methylation_Modeling.Rmd’
Error: Vignette re-building failed.
Execution halted