Brad Nelms
| Snapshot Date: 2024-03-27 14:00:18 -0400 (Wed, 27 Mar 2024) |
| git_url: https://git.bioconductor.org/packages/CellMapper |
| git_branch: devel |
| git_last_commit: a37efb2 |
| git_last_commit_date: 2023-10-24 10:52:01 -0400 (Tue, 24 Oct 2023) |
| Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-03-28 11:40:25 -0400 (Thu, 28 Mar 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" | 4708 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-03-16 r86144 ucrt) -- "Unsuffered Consequences" | 4446 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" | 4471 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-03-19 r86153) -- "Unsuffered Consequences" | 4426 |
| 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 300/2270 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| CellMapper 1.29.0 (landing page) Brad Nelms
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | ERROR | skipped | |||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | TIMEOUT | skipped | skipped | |||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | ERROR | skipped | ||||||||||
|
To the developers/maintainers of the CellMapper package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/CellMapper.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: CellMapper |
| Version: 1.29.0 |
| Command: /home/biocbuild/R/R-4.4-devel-2024.03.20/bin/R CMD build --keep-empty-dirs --no-resave-data CellMapper |
| StartedAt: 2024-03-27 21:24:13 -0000 (Wed, 27 Mar 2024) |
| EndedAt: 2024-03-27 21:25:51 -0000 (Wed, 27 Mar 2024) |
| EllapsedTime: 98.1 seconds |
| RetCode: 1 |
| Status: ERROR |
| PackageFile: None |
| PackageFileSize: NA |
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### Running command:
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### /home/biocbuild/R/R-4.4-devel-2024.03.20/bin/R CMD build --keep-empty-dirs --no-resave-data CellMapper
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* checking for file ‘CellMapper/DESCRIPTION’ ... OK
* preparing ‘CellMapper’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘CellMapper.Rnw’ using Sweave
Loading required package: BiocGenerics
Attaching package: ‘BiocGenerics’
The following objects are masked from ‘package:stats’:
IQR, mad, sd, var, xtabs
The following objects are masked from ‘package:base’:
Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
as.data.frame, basename, cbind, colnames, dirname, do.call,
duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
pmin.int, rank, rbind, rownames, sapply, setdiff, table, tapply,
union, unique, unsplit, which.max, which.min
Loading required package: AnnotationHub
Loading required package: BiocFileCache
Loading required package: dbplyr
Warning: replacing previous import ‘stats::var’ by ‘S4Vectors::var’ when loading ‘CellMapper’
Warning: replacing previous import ‘stats::sd’ by ‘S4Vectors::sd’ when loading ‘CellMapper’
see ?CellMapperData and browseVignettes('CellMapperData') for documentation
loading from cache
see ?CellMapperData and browseVignettes('CellMapperData') for documentation
loading from cache
* Running CellMapper with query gene(s) '2571'...
see ?CellMapperData and browseVignettes('CellMapperData') for documentation
loading from cache
see ?CellMapperData and browseVignettes('CellMapperData') for documentation
loading from cache
see ?CellMapperData and browseVignettes('CellMapperData') for documentation
loading from cache
* Running CellMapper on 'Dataset 1' with query gene(s) '3856'...
* Running CellMapper on 'Dataset 2' with query gene(s) '3856'...
* Running CellMapper on 'Dataset 3' with query gene(s) '3856'...
* Pooling results...
Loading required package: Biobase
Welcome to Bioconductor
Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.
Attaching package: ‘Biobase’
The following object is masked from ‘package:ExperimentHub’:
cache
The following object is masked from ‘package:AnnotationHub’:
cache
* Scaling the data matrix...
* Computing the singular-value decomposition of the data matrix...
* Preparing data for CellMapper...
* Running CellMapper with query gene(s) '1000_at'...
see ?HumanAffyData and browseVignettes('HumanAffyData') for documentation
loading from cache
* Scaling the data matrix...
* Computing the singular-value decomposition of the data matrix...
* Preparing data for CellMapper...
see ?HumanAffyData and browseVignettes('HumanAffyData') for documentation
loading from cache
Warning in load(cache(getHub(x))) : lzma decoding result 10
Error: processing vignette 'CellMapper.Rnw' failed with diagnostics:
chunk 26
Error : failed to load resource
name: EH176
title: GEO accession data GSE64985 as an ExpressionSet
reason: error in evaluating the argument 'x' in selecting a method for function 'get': error reading from connection
--- failed re-building ‘CellMapper.Rnw’
SUMMARY: processing the following file failed:
‘CellMapper.Rnw’
Error: Vignette re-building failed.
Execution halted