| Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-10-18 20:42 -0400 (Fri, 18 Oct 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4763 |
| palomino7 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4500 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4530 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4480 |
| 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 1720/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| recount 1.30.2 (landing page) Leonardo Collado-Torres
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK |  | ||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | ERROR | skipped | skipped | |||||||||
|
To the developers/maintainers of the recount package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/recount.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: recount |
| Version: 1.30.2 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data recount |
| StartedAt: 2024-10-17 07:20:01 -0400 (Thu, 17 Oct 2024) |
| EndedAt: 2024-10-17 07:30:37 -0400 (Thu, 17 Oct 2024) |
| EllapsedTime: 636.4 seconds |
| RetCode: 1 |
| Status: ERROR |
| PackageFile: None |
| PackageFileSize: NA |
##############################################################################
##############################################################################
###
### 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
2024-10-17 07:22:48.540 R[89564:389935935] 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/SRP009615/bw/mean_SRP009615.bw'
Content type 'binary/octet-stream' length 1392034077 bytes (1327.5 MB)
==================================================
downloaded 1327.5 MB
trying URL 'http://duffel.rail.bio/recount/SRP009615/bw/SRR387777.bw'
Content type 'binary/octet-stream' length 94700336 bytes (90.3 MB)
==================================================
downloaded 90.3 MB
trying URL 'http://duffel.rail.bio/recount/SRP009615/bw/SRR387778.bw'
Content type 'binary/octet-stream' length 107837710 bytes (102.8 MB)
==================================================
downloaded 102.8 MB
trying URL 'http://duffel.rail.bio/recount/SRP009615/bw/SRR387779.bw'
Content type 'binary/octet-stream' length 97582496 bytes (93.1 MB)
==================================================
downloaded 93.1 MB
trying URL 'http://duffel.rail.bio/recount/SRP009615/bw/SRR387780.bw'
Content type 'binary/octet-stream' length 95744851 bytes (91.3 MB)
==================================================
downloaded 91.3 MB
trying URL 'http://duffel.rail.bio/recount/SRP009615/bw/SRR389077.bw'
Content type 'binary/octet-stream' length 66256981 bytes (63.2 MB)
==================================================
downloaded 63.2 MB
trying URL 'http://duffel.rail.bio/recount/SRP009615/bw/SRR389078.bw'
Content type 'binary/octet-stream' length 78183706 bytes (74.6 MB)
==================================================
downloaded 74.6 MB
trying URL 'http://duffel.rail.bio/recount/SRP009615/bw/SRR389079.bw'
Content type 'binary/octet-stream' length 127788534 bytes (121.9 MB)
==================================================
downloaded 121.9 MB
trying URL 'http://duffel.rail.bio/recount/SRP009615/bw/SRR389080.bw'
Content type 'binary/octet-stream' length 87858929 bytes (83.8 MB)
==================================================
downloaded 83.8 MB
trying URL 'http://duffel.rail.bio/recount/SRP009615/bw/SRR389081.bw'
Content type 'binary/octet-stream' length 79387326 bytes (75.7 MB)
==================================================
downloaded 75.7 MB
trying URL 'http://duffel.rail.bio/recount/SRP009615/bw/SRR389082.bw'
Content type 'binary/octet-stream' length 63161568 bytes (60.2 MB)
==================================================
downloaded 60.2 MB
trying URL 'http://duffel.rail.bio/recount/SRP009615/bw/SRR389083.bw'
Content type 'binary/octet-stream' length 69695346 bytes (66.5 MB)
==================================================
downloaded 66.5 MB
trying URL 'http://duffel.rail.bio/recount/SRP009615/bw/SRR389084.bw'
Content type 'binary/octet-stream' length 67003461 bytes (63.9 MB)
==================================================
downloaded 63.9 MB
trying URL 'http://duffel.rail.bio/recount/SRP009615/SRP009615.tsv'
Content type 'text/tab-separated-values' length 5016 bytes
==================================================
downloaded 5016 bytes
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
1/102
2/102 [vignetteSetup]
3/102
4/102 [installDer]
5/102
6/102 [citation]
7/102
8/102 [ultraQuick]
9/102
10/102 [er_analysis]
11/102
12/102 [install]
13/102
14/102 [start]
15/102
16/102 [search_abstract]
17/102
18/102 [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
19/102
20/102 [explore_rse]
21/102
22/102 [browse]
23/102
24/102 [sample_info]
25/102
26/102 [scale_counts]
27/102
28/102 [add_sample_info]
29/102
30/102 [de_analysis]
31/102
32/102 [maplot]
2024-10-17 07:27:15.876 R[95250:389949080] XType: Using static font registry.
33/102
34/102 [make_report]
35/102
36/102 [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="...".
37/102
38/102 [geneSymbols]
39/102
40/102 [download_bigwigs]
trying URL 'http://duffel.rail.bio/recount/SRP009615/bw/mean_SRP009615.bw'
Content type 'binary/octet-stream' length 1392034077 bytes (1327.5 MB)
==================================================
downloaded 1327.5 MB
trying URL 'http://duffel.rail.bio/recount/SRP009615/bw/SRR387777.bw'
Content type 'binary/octet-stream' length 94700336 bytes (90.3 MB)
==================================================
downloaded 90.3 MB
trying URL 'http://duffel.rail.bio/recount/SRP009615/bw/SRR387778.bw'
Content type 'binary/octet-stream' length 107837710 bytes (102.8 MB)
==================================================
downloaded 102.8 MB
trying URL 'http://duffel.rail.bio/recount/SRP009615/bw/SRR387779.bw'
Content type 'binary/octet-stream' length 97582496 bytes (93.1 MB)
==================================================
downloaded 93.1 MB
trying URL 'http://duffel.rail.bio/recount/SRP009615/bw/SRR387780.bw'
Content type 'binary/octet-stream' length 95744851 bytes (91.3 MB)
==================================================
downloaded 91.3 MB
trying URL 'http://duffel.rail.bio/recount/SRP009615/bw/SRR389077.bw'
Content type 'binary/octet-stream' length 66256981 bytes (63.2 MB)
==================================================
downloaded 63.2 MB
trying URL 'http://duffel.rail.bio/recount/SRP009615/bw/SRR389078.bw'
Content type 'binary/octet-stream' length 78183706 bytes (74.6 MB)
==================================================
downloaded 74.6 MB
trying URL 'http://duffel.rail.bio/recount/SRP009615/bw/SRR389079.bw'
Content type 'binary/octet-stream' length 127788534 bytes (121.9 MB)
==================================================
downloaded 121.9 MB
trying URL 'http://duffel.rail.bio/recount/SRP009615/bw/SRR389080.bw'
Content type 'binary/octet-stream' length 87858929 bytes (83.8 MB)
==================================================
downloaded 83.8 MB
trying URL 'http://duffel.rail.bio/recount/SRP009615/bw/SRR389081.bw'
Content type 'binary/octet-stream' length 79387326 bytes (75.7 MB)
==================================================
downloaded 75.7 MB
trying URL 'http://duffel.rail.bio/recount/SRP009615/bw/SRR389082.bw'
Content type 'binary/octet-stream' length 63161568 bytes (60.2 MB)
==================================================
downloaded 60.2 MB
trying URL 'http://duffel.rail.bio/recount/SRP009615/bw/SRR389083.bw'
Content type 'binary/octet-stream' length 69695346 bytes (66.5 MB)
==================================================
downloaded 66.5 MB
trying URL 'http://duffel.rail.bio/recount/SRP009615/bw/SRR389084.bw'
Content type 'binary/octet-stream' length 67003461 bytes (63.9 MB)
==================================================
downloaded 63.9 MB
41/102
42/102 [define_ers]
43/102
44/102 [compute_covMat]
trying URL 'http://duffel.rail.bio/recount/SRP009615/SRP009615.tsv'
Content type 'text/tab-separated-values' length 5016 bytes
==================================================
downloaded 5016 bytes
45/102
46/102 [to_integer]
47/102
48/102 [phenoData]
49/102
50/102 [ers_dds]
51/102
52/102 [de_analysis_ers]
53/102
54/102 [maploters]
55/102
56/102 [report2]
57/102
58/102 [gene_annotation]
59/102
60/102 [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
61/102
62/102 [newer annotation]
63/102
64/102 [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
65/102
66/102 [snaptron]
67/102
68/102 [rse-fc example]
69/102
70/102 [recount-brain]
71/102
72/102 [downloadAll]
73/102
74/102 [actuallyDownload]
75/102
76/102 [Figure1]
77/102
78/102 [Figure2]
79/102
80/102 [Figure3]
81/102
82/102 [Figure4]
83/102
84/102 [Figure5]
85/102
86/102 [Figure6]
87/102
88/102 [ER-sciserver]
89/102
90/102 [createVignette]
91/102
92/102 [reproduce1]
93/102
94/102 [reproduce2]
95/102
96/102 [reproduce3]
97/102
98/102 [datasetup]
99/102
100/102 [cleanup]
101/102
102/102 [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/4.4-arm64/Resources/library/bookdown/rmarkdown/lua/custom-environment.lua --lua-filter /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /Library/Frameworks/R.framework/Versions/4.4-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/Rtmp0j4olL/BiocStyle/template.html --no-highlight --variable highlightjs=1 --number-sections --variable theme=bootstrap --css /Library/Frameworks/R.framework/Versions/4.4-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/Rtmp0j4olL/rmarkdown-str174123162ed3f.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