| Back to Books build report for BioC 3.23 |
This page was generated on 2025-12-31 14:30 -0500 (Wed, 31 Dec 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | R Under development (unstable) (2025-12-22 r89219) -- "Unsuffered Consequences" | 4808 |
| lconway | macOS 12.7.6 Monterey | x86_64 | R Under development (unstable) (2025-10-21 r88958) -- "Unsuffered Consequences" | 4624 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences" | 4593 |
| 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 8/11 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | ||||||||
| OSCA.multisample 1.19.0 (landing page) Alan O'Callaghan
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | ERROR | ERROR | skipped | ||||||||
| lconway | macOS 12.7.6 Monterey / x86_64 | OK | ERROR | skipped | |||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | OK | |||||||||
|
To the developers/maintainers of the OSCA.multisample 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: OSCA.multisample |
| Version: 1.19.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD build --keep-empty-dirs --no-resave-data OSCA.multisample |
| StartedAt: 2025-12-31 06:47:09 -0500 (Wed, 31 Dec 2025) |
| EndedAt: 2025-12-31 07:53:35 -0500 (Wed, 31 Dec 2025) |
| EllapsedTime: 3986.4 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 OSCA.multisample
###
##############################################################################
##############################################################################
* checking for file ‘OSCA.multisample/DESCRIPTION’ ... OK
* preparing ‘OSCA.multisample’:
* checking DESCRIPTION meta-information ... OK
* installing the package (it is needed to build vignettes)
* creating vignettes ... ERROR
--- re-building ‘stub.Rmd’ using rmarkdown
[WARNING] This document format requires a nonempty <title> element.
Please specify either 'title' or 'pagetitle' in the metadata,
e.g. by using --metadata pagetitle="..." on the command line.
Falling back to 'stub.knit'
Could not fetch http://bioconductor.org/books/3.23/OSCA.multisample
HttpExceptionRequest Request {
host = "bioconductor.org"
port = 80
secure = False
requestHeaders = []
path = "/books/3.23/OSCA.multisample"
queryString = ""
method = "GET"
proxy = Nothing
rawBody = False
redirectCount = 10
responseTimeout = ResponseTimeoutDefault
requestVersion = HTTP/1.1
}
ResponseTimeout
Error: processing vignette 'stub.Rmd' failed with diagnostics:
pandoc document conversion failed with error 61
--- failed re-building ‘stub.Rmd’
"/Library/Frameworks/R.framework/Resources/bin/R" -e "work.dir <- rebook::bookCache('OSCA.multisample'); handle <- rebook::preCompileBook('../inst/book', work.dir=work.dir, desc='../DESCRIPTION'); old.dir <- setwd(work.dir); bookdown::render_book('index.Rmd'); setwd(old.dir); rebook::postCompileBook(work.dir=work.dir, final.dir='../inst/doc/book', handle=handle)"
R Under development (unstable) (2025-10-21 r88958) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
Natural language support but running in an English locale
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> work.dir <- rebook::bookCache('OSCA.multisample'); handle <- rebook::preCompileBook('../inst/book', work.dir=work.dir, desc='../DESCRIPTION'); old.dir <- setwd(work.dir); bookdown::render_book('index.Rmd'); setwd(old.dir); rebook::postCompileBook(work.dir=work.dir, final.dir='../inst/doc/book', handle=handle)
processing file: index.Rmd
1/4
2/4 [unnamed-chunk-1]
3/4
4/4 [unnamed-chunk-2]
output file: index.knit.md
processing file: batch-correction.Rmd
1/56
2/56 [setup]
3/56
4/56 [unnamed-chunk-1]
5/56
6/56 [unnamed-chunk-2]
7/56
8/56 [unnamed-chunk-3]
9/56
10/56 [quick-pbmc-corrected]
11/56
12/56 [unnamed-chunk-4]
13/56
14/56 [unnamed-chunk-5]
15/56
16/56 [unnamed-chunk-6]
17/56
18/56 [unnamed-chunk-7]
19/56
20/56 [unnamed-chunk-8]
21/56
22/56 [unnamed-chunk-9]
23/56
24/56 [tsne-pbmc-uncorrected]
25/56
26/56 [unnamed-chunk-10]
27/56
28/56 [unnamed-chunk-11]
29/56
30/56 [unnamed-chunk-12]
31/56
32/56 [tsne-pbmc-rescaled]
33/56
34/56 [unnamed-chunk-13]
35/56
36/56 [tsne-pbmc-residuals]
37/56
38/56 [mnn-pbmc]
39/56
40/56 [unnamed-chunk-14]
41/56
42/56 [unnamed-chunk-15]
43/56
44/56 [unnamed-chunk-16]
45/56
46/56 [mnn-clustering]
47/56
48/56 [unnamed-chunk-17]
49/56
50/56 [tsne-pbmc-corrected]
51/56
52/56 [unnamed-chunk-18]
53/56
54/56 [multi-pbmc-corrected]
55/56
56/56 [sessionInfo]
output file: batch-correction.knit.md
processing file: correction-diagnostics.Rmd
1/38
2/38 [setup]
3/38
4/38 [unnamed-chunk-1]
5/38
6/38 [unnamed-chunk-2]
7/38
8/38 [unnamed-chunk-3]
9/38
10/38 [unnamed-chunk-4]
11/38
12/38 [unnamed-chunk-5]
13/38
14/38 [unnamed-chunk-6]
15/38
16/38 [unnamed-chunk-7]
17/38
18/38 [unnamed-chunk-8]
19/38
20/38 [unnamed-chunk-9]
21/38
22/38 [heat-after-mnn]
23/38
24/38 [unnamed-chunk-10]
25/38
26/38 [unnamed-chunk-11]
27/38
28/38 [rand-after-mnn]
29/38
30/38 [unnamed-chunk-12]
31/38
32/38 [unnamed-chunk-13]
33/38
34/38 [mnn-delta-var-pbmc]
35/38
36/38 [unnamed-chunk-14]
37/38
38/38 [sessionInfo]
output file: correction-diagnostics.knit.md
processing file: using-corrected-values.Rmd
1/36
2/36 [setup]
3/36
4/36 [unnamed-chunk-1]
5/36
6/36 [unnamed-chunk-2]
7/36
8/36 [unnamed-chunk-3]
9/36
10/36 [unnamed-chunk-4]
11/36
12/36 [unnamed-chunk-5]
13/36
14/36 [pancreas-mnn-delta]
15/36
16/36 [unnamed-chunk-6]
17/36
18/36 [pancreas-mnn-delta2]
19/36
20/36 [unnamed-chunk-7]
21/36
22/36 [pbmc-marker-blocked]
23/36
24/36 [unnamed-chunk-8]
25/36
26/36 [unnamed-chunk-9]
27/36
28/36 [unnamed-chunk-10]
29/36
30/36 [seger-beta-ins-raw]
31/36
32/36 [seger-beta-ins-corrected]
33/36
34/36 [unnamed-chunk-11]
35/36
36/36 [sessionInfo]
output file: using-corrected-values.knit.md
processing file: pseudobulk-dge.Rmd
1/72
2/72 [setup]
3/72
4/72 [unnamed-chunk-1]
5/72
6/72 [unnamed-chunk-2]
7/72
8/72 [tsne-initial]
9/72
10/72 [unnamed-chunk-3]
11/72
12/72 [heat-cluster-label]
13/72
14/72 [unnamed-chunk-4]
15/72
16/72 [unnamed-chunk-5]
17/72
18/72 [unnamed-chunk-6]
19/72
20/72 [unnamed-chunk-7]
21/72
22/72 [unnamed-chunk-8]
23/72
24/72 [unnamed-chunk-9]
25/72
26/72 [md-embryo]
27/72
28/72 [mds-embryo]
29/72
30/72 [unnamed-chunk-10]
31/72
32/72 [bcvplot]
33/72
34/72 [qlplot]
35/72
36/72 [unnamed-chunk-11]
37/72
38/72 [unnamed-chunk-12]
39/72
40/72 [unnamed-chunk-13]
41/72
42/72 [allantois-dispersion]
43/72
44/72 [unnamed-chunk-14]
45/72
46/72 [unnamed-chunk-15]
47/72
48/72 [unnamed-chunk-16]
49/72
50/72 [unnamed-chunk-17]
51/72
52/72 [unnamed-chunk-18]
53/72
54/72 [unnamed-chunk-19]
55/72
56/72 [exprs-unique-de-allantois]
57/72
58/72 [unnamed-chunk-20]
59/72
60/72 [unnamed-chunk-21]
61/72
62/72 [exprs-unique-de-allantois-more]
63/72
64/72 [unnamed-chunk-22]
65/72
66/72 [unnamed-chunk-23]
67/72
68/72 [between-label-dge]
69/72
70/72 [unnamed-chunk-24]
71/72
72/72 [sessionInfo]
output file: pseudobulk-dge.knit.md
processing file: ambient-problems.Rmd
1/48
2/48 [setup]
3/48
4/48 [unnamed-chunk-1]
5/48
6/48 [unnamed-chunk-2]
7/48
8/48 [unnamed-chunk-3]
9/48
10/48 [unnamed-chunk-4]
11/48
12/48 [unnamed-chunk-5]
13/48
14/48 [unnamed-chunk-6]
15/48
16/48 [unnamed-chunk-7]
17/48
18/48 [unnamed-chunk-8]
19/48
20/48 [unnamed-chunk-9]
21/48
22/48 [unnamed-chunk-10]
23/48
24/48 [unnamed-chunk-11]
25/48
26/48 [unnamed-chunk-12]
27/48
28/48 [proxy-ambience]
29/48
30/48 [unnamed-chunk-13]
31/48
32/48 [unnamed-chunk-14]
33/48
34/48 [unnamed-chunk-15]
35/48
36/48 [unnamed-chunk-16]
37/48
38/48 [unnamed-chunk-17]
39/48
40/48 [unnamed-chunk-18]
41/48
42/48 [unnamed-chunk-19]
43/48
44/48 [unnamed-chunk-20]
45/48
46/48 [unnamed-chunk-21]
47/48
48/48 [sessionInfo]
output file: ambient-problems.knit.md
processing file: cluster-abundance.Rmd
1/32
2/32 [setup]
3/32
4/32 [cached]
5/32
6/32 [show-abundances]
7/32
8/32 [edger-init]
9/32
10/32 [filter-expr]
11/32
12/32 [model-mat]
13/32
14/32 [abplotbcv]
15/32
16/32 [abplotql]
17/32
18/32 [glmqlf]
19/32
20/32 [assert-abundances]
21/32
22/32 [norm]
23/32
24/32 [mode-glmqlf]
25/32
26/32 [assert-abundances-2]
27/32
28/32 [offending-labels]
29/32
30/32 [testing-logfc]
31/32
32/32 [sessionInfo]
output file: cluster-abundance.knit.md
processing file: tenx-filtered-pbmc3k-4k-8k.Rmd
1/38
2/38 [unref-setup]
3/38
4/38 [loading]
5/38
6/38 [unnamed-chunk-1]
7/38
8/38 [quality-control]
9/38
10/38 [unref-pbmc-filtered-var]
11/38
12/38 [unnamed-chunk-2]
13/38
14/38 [normalization]
15/38
16/38 [unnamed-chunk-3]
17/38
18/38 [variance-modelling]
19/38
20/38 [unref-filtered-pbmc-variance]
21/38
22/38 [dimensionality-reduction]
23/38
24/38 [clustering]
25/38
26/38 [unnamed-chunk-4]
27/38
28/38 [unref-filtered-pbmc-tsne]
29/38
30/38 [data-integration]
31/38
32/38 [unnamed-chunk-5]
33/38
34/38 [merged-clustering]
35/38
36/38 [unref-filtered-pbmc-merged-tsne]
37/38
38/38 [sessionInfo]
output file: tenx-filtered-pbmc3k-4k-8k.knit.md
processing file: merged-pancreas.Rmd
1/48
2/48 [unref-setup]
3/48
4/48 [grun-pancreas]
5/48
6/48 [print-sce-grun]
7/48
8/48 [muraro-pancreas]
9/48
10/48 [print-sce-muraro]
11/48
12/48 [subset-universe]
13/48
14/48 [tsne-pancreas-rescaled]
15/48
16/48 [tsne-pancreas-mnn]
17/48
18/48 [unnamed-chunk-1]
19/48
20/48 [lawlor-pancreas]
21/48
22/48 [print-sce-lawlor]
23/48
24/48 [segerstolpe-pancreas]
25/48
26/48 [print-sce-seger]
27/48
28/48 [all-sce]
29/48
30/48 [tsne-pancreas-mnn-many]
31/48
32/48 [assert-seger]
33/48
34/48 [tsne-pancreas-mnn-donor]
35/48
36/48 [merge-nocorrect]
37/48
38/48 [fastmnn]
39/48
40/48 [tsne-pancreas-mnn-donor-all]
41/48
42/48 [assert-seger2]
43/48
44/48 [identify-celltypes]
45/48
46/48 [assert-rand]
47/48
48/48 [sessionInfo]
output file: merged-pancreas.knit.md
processing file: merged-hsc.Rmd
1/44
2/44 [unref-setup]
3/44
4/44 [unnamed-chunk-1]
5/44
6/44 [unnamed-chunk-2]
7/44
8/44 [unnamed-chunk-3]
9/44
10/44 [unnamed-chunk-4]
11/44
12/44 [unnamed-chunk-5]
13/44
14/44 [unnamed-chunk-6]
15/44
16/44 [common-annotation]
17/44
18/44 [variance-modelling]
19/44
20/44 [normalization]
21/44
22/44 [batch-correction]
23/44
24/44 [unnamed-chunk-7]
25/44
26/44 [unnamed-chunk-8]
27/44
28/44 [clustering]
29/44
30/44 [unnamed-chunk-9]
31/44
32/44 [unref-umap-merged-hsc]
33/44
34/44 [trajectory]
35/44
36/44 [unref-umap-traj-hsc]
37/44
38/44 [unnamed-chunk-10]
39/44
40/44 [unref-umap-traj-hsc2]
41/44
42/44 [unnamed-chunk-11]
43/44
44/44 [sessionInfo]
output file: merged-hsc.knit.md
processing file: pijuan-embryo.Rmd
1/30
2/30 [unref-setup]
3/30
4/30 [loading]
5/30
6/30 [unnamed-chunk-1]
7/30
8/30 [feature-annotation]
9/30
10/30 [quality-control]
11/30
12/30 [normalization]
13/30
14/30 [variance-modelling]
15/30
16/30 [unref-pijuan-var]
17/30
18/30 [merging]
19/30
20/30 [unnamed-chunk-2]
21/30
22/30 [clustering]
23/30
24/30 [unnamed-chunk-3]
25/30
26/30 [dimensionality-reduction]
27/30
28/30 [unref-pijuan-tsne]
29/30
30/30 [sessionInfo]
output file: pijuan-embryo.knit.md
/usr/local/bin/pandoc +RTS -K512m -RTS OSCA.multisample.md --to html4 --from markdown+autolink_bare_uris+tex_math_single_backslash --output OSCA.multisample.html --lua-filter /Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/bookdown/rmarkdown/lua/custom-environment.lua --lua-filter /Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/rmarkdown/rmarkdown/lua/pagebreak.lua --lua-filter /Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/rmarkdown/rmarkdown/lua/latex-div.lua --lua-filter /Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/rmarkdown/rmarkdown/lua/anchor-sections.lua --metadata-file /tmp/RtmpIGk485/file161e2b115588 --wrap preserve --standalone --section-divs --table-of-contents --toc-depth 3 --template /Library/Frameworks/R.framework/Versions/4.6-x86_64/Resources/library/bookdown/templates/gitbook.html --highlight-style pygments --number-sections --css style.css --mathjax --include-in-header /tmp/RtmpIGk485/rmarkdown-str161e7f0669ce.html --filter /usr/local/bin/pandoc-citeproc
Output created: docs/index.html
[1] "/Users/biocbuild/Library/Caches/rebook/OSCA.multisample/1.19.0/docs/index.html"
Warning message:
The label(s) between-batch-comparisons not found
>
SUMMARY: processing the following file failed:
‘stub.Rmd’
Error: Vignette re-building failed.
Execution halted