| Back to Mac ARM64 build report for BioC 3.18 |
|
This page was generated on 2024-03-28 11:32:29 -0400 (Thu, 28 Mar 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kjohnson1 | macOS 13.6.1 Ventura | arm64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4376 |
| 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 1700/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| recount 1.28.0 (landing page) Leonardo Collado-Torres
| kjohnson1 | macOS 13.6.1 Ventura / arm64 | OK | ERROR | skipped | skipped | ||||||||
|
To the developers/maintainers of the recount package: - 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: recount |
| Version: 1.28.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data recount |
| StartedAt: 2024-03-27 00:27:03 -0400 (Wed, 27 Mar 2024) |
| EndedAt: 2024-03-27 00:37:57 -0400 (Wed, 27 Mar 2024) |
| EllapsedTime: 654.1 seconds |
| RetCode: 1 |
| Status: ERROR |
| PackageFile: None |
| PackageFileSize: NA |
##############################################################################
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### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data recount
###
##############################################################################
##############################################################################
* checking for file ‘recount/DESCRIPTION’ ... OK
* preparing ‘recount’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘recount-quickstart.Rmd’ using rmarkdown
trying URL 'http://duffel.rail.bio/recount/v2/SRP009615/rse_gene.Rdata'
Content type 'binary/octet-stream' length 3130229 bytes (3.0 MB)
==================================================
downloaded 3.0 MB
2024-03-27 00:29:49.159 R[26143:394311115] XType: Using static font registry.
[WARNING] This document format requires a nonempty <title> element.
Defaulting to 'SRP009615-results.knit' as the title.
To specify a title, use 'title' in metadata or --metadata title="...".
trying URL 'http://duffel.rail.bio/recount/v2/SRP009615/rse_exon.Rdata'
Content type 'binary/octet-stream' length 15267923 bytes (14.6 MB)
==================================================
downloaded 14.6 MB
trying URL 'http://duffel.rail.bio/recount/SRP009615/rse_jx.Rdata'
Content type 'binary/octet-stream' length 8515523 bytes (8.1 MB)
==================================================
downloaded 8.1 MB
Error: processing vignette 'recount-quickstart.Rmd' failed with diagnostics:
pandoc document conversion failed with error 10
--- failed re-building ‘recount-quickstart.Rmd’
"/Library/Frameworks/R.framework/Resources/bin/Rscript" -e "library(rmarkdown); render('recount-quickstart.Rmd')"
Attaching package: ‘BiocStyle’
The following objects are masked from ‘package:rmarkdown’:
html_document, md_document, pdf_document
processing file: recount-quickstart.Rmd
1/100
2/100 [vignetteSetup]
3/100
4/100 [installDer]
5/100
6/100 [citation]
7/100
8/100 [ultraQuick]
9/100
10/100 [er_analysis]
11/100
12/100 [install]
13/100
14/100 [start]
15/100
16/100 [search_abstract]
17/100
18/100 [download]
trying URL 'http://duffel.rail.bio/recount/v2/SRP009615/rse_gene.Rdata'
Content type 'binary/octet-stream' length 3130229 bytes (3.0 MB)
==================================================
downloaded 3.0 MB
19/100
20/100 [explore_rse]
21/100
22/100 [browse]
23/100
24/100 [sample_info]
25/100
26/100 [scale_counts]
27/100
28/100 [add_sample_info]
29/100
30/100 [de_analysis]
31/100
32/100 [maplot]
2024-03-27 00:34:48.390 R[27872:394317095] XType: Using static font registry.
33/100
34/100 [make_report]
35/100
36/100 [make_report_real]
[WARNING] This document format requires a nonempty <title> element.
Defaulting to 'SRP009615-results.knit' as the title.
To specify a title, use 'title' in metadata or --metadata title="...".
37/100
38/100 [geneSymbols]
39/100
40/100 [define_ers]
41/100
42/100 [compute_covMat]
43/100
44/100 [to_integer]
45/100
46/100 [phenoData]
47/100
48/100 [ers_dds]
49/100
50/100 [de_analysis_ers]
51/100
52/100 [maploters]
53/100
54/100 [report2]
55/100
56/100 [gene_annotation]
57/100
58/100 [exon_annotation]
trying URL 'http://duffel.rail.bio/recount/v2/SRP009615/rse_exon.Rdata'
Content type 'binary/octet-stream' length 15267923 bytes (14.6 MB)
==================================================
downloaded 14.6 MB
59/100
60/100 [unnamed-chunk-1]
61/100
62/100 [gene_fusions]
trying URL 'http://duffel.rail.bio/recount/SRP009615/rse_jx.Rdata'
Content type 'binary/octet-stream' length 8515523 bytes (8.1 MB)
==================================================
downloaded 8.1 MB
63/100
64/100 [snaptron]
65/100
66/100 [rse-fc example]
67/100
68/100 [recount-brain]
69/100
70/100 [downloadAll]
71/100
72/100 [actuallyDownload]
73/100
74/100 [Figure1]
75/100
76/100 [Figure2]
77/100
78/100 [Figure3]
79/100
80/100 [Figure4]
81/100
82/100 [Figure5]
83/100
84/100 [Figure6]
85/100
86/100 [ER-sciserver]
87/100
88/100 [createVignette]
89/100
90/100 [reproduce1]
91/100
92/100 [reproduce2]
93/100
94/100 [reproduce3]
95/100
96/100 [datasetup]
97/100
98/100 [cleanup]
99/100
100/100 [vignetteBiblio]
output file: recount-quickstart.knit.md
/opt/homebrew/bin/pandoc +RTS -K512m -RTS recount-quickstart.knit.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output recount-quickstart.html --lua-filter /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/bookdown/rmarkdown/lua/custom-environment.lua --lua-filter /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/rmarkdown/rmarkdown/lua/latex-div.lua --embed-resources --standalone --wrap preserve --variable bs3=TRUE --section-divs --table-of-contents --toc-depth 2 --variable toc_float=1 --variable toc_selectors=h1,h2 --variable toc_collapsed=1 --variable toc_smooth_scroll=1 --variable toc_print=1 --template /tmp/Rtmp5uclI6/BiocStyle/template.html --no-highlight --variable highlightjs=1 --number-sections --variable theme=bootstrap --css /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/BiocStyle/resources/html/bioconductor.css --mathjax --variable 'mathjax-url=https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML' --include-in-header /tmp/Rtmp5uclI6/rmarkdown-str6ce0f73e5f5.html --variable code_folding=show --variable code_menu=1
Output created: recount-quickstart.html
cp fakeVignettes/*.Rmd .
SUMMARY: processing the following file failed:
‘recount-quickstart.Rmd’
Error: Vignette re-building failed.
Execution halted