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This page was generated on 2024-07-02 14:51 -0400 (Tue, 02 Jul 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4757
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Package 22/430HostnameOS / ArchINSTALLBUILDCHECK
BeadArrayUseCases 1.42.0  (landing page)
Mike Smith
Snapshot Date: 2024-07-02 07:30 -0400 (Tue, 02 Jul 2024)
git_url: https://git.bioconductor.org/packages/BeadArrayUseCases
git_branch: RELEASE_3_19
git_last_commit: 05c10b5
git_last_commit_date: 2024-04-30 10:31:05 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    ERROR  


CHECK results for BeadArrayUseCases on nebbiolo1

To the developers/maintainers of the BeadArrayUseCases 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.

raw results


Summary

Package: BeadArrayUseCases
Version: 1.42.0
Command: /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
StartedAt: 2024-07-02 11:00:55 -0400 (Tue, 02 Jul 2024)
EndedAt: 2024-07-02 11:07:20 -0400 (Tue, 02 Jul 2024)
EllapsedTime: 384.6 seconds
RetCode: 1
Status:   ERROR  
CheckDir: BeadArrayUseCases.Rcheck
Warnings: NA

Command output

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### Running command:
###
###   /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.


Installation output

BeadArrayUseCases.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL BeadArrayUseCases
###
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* installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-library’
* installing *source* package ‘BeadArrayUseCases’ ...
** using staged installation
** inst
** help
No man pages found in package  ‘BeadArrayUseCases’ 
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (BeadArrayUseCases)

Tests output


Example timings