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### Running command:
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### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:BeadArrayUseCases.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings BeadArrayUseCases_1.42.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.19-data-experiment/meat/BeadArrayUseCases.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘BeadArrayUseCases/DESCRIPTION’ ... OK
* this is package ‘BeadArrayUseCases’ version ‘1.42.0’
* 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 ... NOTE
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
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: 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 2.54.0
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-3.19-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 19 file(s)
GSE5350-GPL1355_series_matrix.txt.gz
GSE5350-GPL1708_series_matrix.txt.gz
GSE5350-GPL2507_series_matrix.txt.gz
GSE5350-GPL2877_series_matrix.txt.gz
GSE5350-GPL2895_series_matrix.txt.gz
GSE5350-GPL2896_series_matrix.txt.gz
GSE5350-GPL2986_series_matrix.txt.gz
GSE5350-GPL2996_series_matrix.txt.gz
GSE5350-GPL4096_series_matrix.txt.gz
GSE5350-GPL4097_series_matrix.txt.gz
GSE5350-GPL4098_series_matrix.txt.gz
GSE5350-GPL4108_series_matrix.txt.gz
GSE5350-GPL4185_series_matrix.txt.gz
GSE5350-GPL4186_series_matrix.txt.gz
GSE5350-GPL4187_series_matrix.txt.gz
GSE5350-GPL4188_series_matrix.txt.gz
Error: processing vignette 'BeadArrayUseCases.rnw' failed with diagnostics:
chunk 48 (label = readFromGEO)
Error in curl::curl_download(url, destfile, mode = mode, quiet = quiet, :
Error in the HTTP2 framing layer
--- 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, 2 NOTEs
See
‘/home/biocbuild/bbs-3.19-data-experiment/meat/BeadArrayUseCases.Rcheck/00check.log’
for details.