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### Running command:
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### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:BeadArrayUseCases.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings BeadArrayUseCases_1.46.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.21-data-experiment/meat/BeadArrayUseCases.Rcheck’
* using R version 4.5.1 (2025-06-13)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.2 LTS
* using session charset: UTF-8
* checking for file ‘BeadArrayUseCases/DESCRIPTION’ ... OK
* this is package ‘BeadArrayUseCases’ version ‘1.46.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘BeadArrayUseCases’ can be installed ... OK
* checking installed package size ... INFO
installed size is 249.8Mb
sub-directories of 1Mb or more:
extdata 249.7Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... NONE
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... ERROR
Error(s) in re-building vignettes:
--- re-building ‘BeadArrayUseCases.rnw’ using Sweave
Loading required package: BiocGenerics
Loading required package: generics
Attaching package: ‘generics’
The following objects are masked from ‘package:base’:
as.difftime, as.factor, as.ordered, intersect, is.element,
setdiff, setequal, union
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,
is.unsorted, lapply, mapply, match, mget, order, paste,
pmax, pmax.int, pmin, pmin.int, rank, rbind, rownames,
sapply, saveRDS, table, tapply, unique, unsplit,
which.max, which.min
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: hexbin
Welcome to beadarray version 2.58.0
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: IRanges
Loading required package: S4Vectors
Attaching package: ‘S4Vectors’
The following object is masked from ‘package:utils’:
findMatches
The following objects are masked from ‘package:base’:
I, expand.grid, unname
Loading required package: org.Hs.eg.db
Sample Sheet /home/biocbuild/bbs-3.21-bioc/R/site-library/BeadArrayUseCases/extdata/Chips/sampleSheet.csv will be used to read the data
Processing section 4613710017_B
Processing section 4613710052_B
Processing section 4613710054_B
Processing section 4616443079_B
Processing section 4616443093_B
Processing section 4616443115_B
Processing section 4616443081_B
Processing section 4616443081_H
Processing section 4616443092_B
Processing section 4616443107_A
Processing section 4616443136_A
Processing section 4616494005_A
HULKing section 4613710017_B
Calculating Neighbourhood
Using locs file to generate neighbours matrix
Loading required package: illuminaHumanv3.db
Annotating control probes using package illuminaHumanv3.db Version:1.26.0
Annotating control probes using package illuminaHumanv3.db Version:1.26.0
Annotating control probes using package illuminaHumanv3.db Version:1.26.0
Annotating control probes using package illuminaHumanv3.db Version:1.26.0
Annotating control probes using package illuminaHumanv3.db Version:1.26.0
Annotating control probes using package illuminaHumanv3.db Version:1.26.0
Loading required package: Biostrings
Loading required package: XVector
Loading required package: GenomeInfoDb
Attaching package: ‘Biostrings’
The following object is masked from ‘package:base’:
strsplit
Loading required package: GenomicRanges
Attaching package: ‘limma’
The following object is masked from ‘package:beadarray’:
imageplot
The following object is masked from ‘package:BiocGenerics’:
plotMA
Found 0 file(s)
NA
Error: processing vignette 'BeadArrayUseCases.rnw' failed with diagnostics:
chunk 48 (label = readFromGEO)
Error in httr2::req_perform(req) : HTTP 404 Not Found.
--- failed re-building ‘BeadArrayUseCases.rnw’
SUMMARY: processing the following file failed:
‘BeadArrayUseCases.rnw’
Error: Vignette re-building failed.
Execution halted
* checking PDF version of manual ... OK
* DONE
Status: 1 ERROR, 1 NOTE
See
‘/home/biocbuild/bbs-3.21-data-experiment/meat/BeadArrayUseCases.Rcheck/00check.log’
for details.