Ben Bolstad
| Snapshot Date: 2025-03-06 13:00 -0500 (Thu, 06 Mar 2025) |
| git_url: https://git.bioconductor.org/packages/affyPLM |
| git_branch: RELEASE_3_20 |
| git_last_commit: 16d7387 |
| git_last_commit_date: 2024-10-29 09:22:04 -0500 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2025-03-10 12:12 -0400 (Mon, 10 Mar 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.3 (2025-02-28) -- "Trophy Case" | 4670 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.3 (2025-02-28 ucrt) -- "Trophy Case" | 4355 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.3 (2025-02-28) -- "Trophy Case" | 4446 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.3 (2025-02-28) -- "Trophy Case" | 4439 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.4.3 (2025-02-28) -- "Trophy Case" | 4306 |
| 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 31/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| affyPLM 1.82.0 (landing page) Ben Bolstad
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | | ||||||||
| merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | ERROR | skipped | ||||||||||
|
To the developers/maintainers of the affyPLM package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/affyPLM.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: affyPLM |
| Version: 1.82.0 |
| Command: /home/biocbuild/R/R/bin/R CMD build --keep-empty-dirs --no-resave-data affyPLM |
| StartedAt: 2025-03-06 23:26:44 -0000 (Thu, 06 Mar 2025) |
| EndedAt: 2025-03-06 23:27:16 -0000 (Thu, 06 Mar 2025) |
| EllapsedTime: 32.0 seconds |
| RetCode: 1 |
| Status: ERROR |
| PackageFile: None |
| PackageFileSize: NA |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/R/R/bin/R CMD build --keep-empty-dirs --no-resave-data affyPLM
###
##############################################################################
##############################################################################
* checking for file ‘affyPLM/DESCRIPTION’ ... OK
* preparing ‘affyPLM’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘AffyExtensions.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, saveRDS, setdiff, table,
tapply, union, unique, unsplit, which.max, which.min
Loading required package: affy
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")'.
Loading required package: gcrma
Loading required package: preprocessCore
Loading required package: affydata
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, :
there is no package called ‘affydata’
Warning in data(Dilution) : data set ‘Dilution’ not found
Error: processing vignette 'AffyExtensions.Rnw' failed with diagnostics:
chunk 1 (label = loadData)
Error in h(simpleError(msg, call)) :
error in evaluating the argument 'object' in selecting a method for function 'updateObject': object 'Dilution' not found
--- failed re-building ‘AffyExtensions.Rnw’
--- re-building ‘MAplots.Rnw’ using Sweave
Loading required package: affydata
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, :
there is no package called ‘affydata’
Warning in data(Dilution) : data set ‘Dilution’ not found
Error: processing vignette 'MAplots.Rnw' failed with diagnostics:
chunk 2 (label = makeExpressionSet)
Error in h(simpleError(msg, call)) :
error in evaluating the argument 'object' in selecting a method for function 'probeNames': object 'Dilution' not found
--- failed re-building ‘MAplots.Rnw’
--- re-building ‘QualityAssess.Rnw’ using Sweave
Loading required package: affydata
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, :
there is no package called ‘affydata’
Warning in data(Dilution) : data set ‘Dilution’ not found
Error: processing vignette 'QualityAssess.Rnw' failed with diagnostics:
chunk 2 (label = loadData)
Error in h(simpleError(msg, call)) :
error in evaluating the argument 'object' in selecting a method for function 'updateObject': object 'Dilution' not found
--- failed re-building ‘QualityAssess.Rnw’
--- re-building ‘ThreeStep.Rnw’ using Sweave
--- finished re-building ‘ThreeStep.Rnw’
SUMMARY: processing the following files failed:
‘AffyExtensions.Rnw’
‘MAplots.Rnw’ ‘QualityAssess.Rnw’
Error: Vignette re-building failed.
Execution halted