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This page was generated on 2024-07-04 14:51 -0400 (Thu, 04 Jul 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 22.04.3 LTS)x86_644.4.1 (2024-06-14) -- "Race for Your Life" 4591
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Package 186/425HostnameOS / ArchINSTALLBUILDCHECK
Hiiragi2013 1.41.0  (landing page)
Andrzej Oles
Snapshot Date: 2024-07-04 07:30 -0400 (Thu, 04 Jul 2024)
git_url: https://git.bioconductor.org/packages/Hiiragi2013
git_branch: devel
git_last_commit: 3911b68
git_last_commit_date: 2024-04-30 10:39:02 -0400 (Tue, 30 Apr 2024)
nebbiolo2Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    ERROR  skipped


BUILD results for Hiiragi2013 on nebbiolo2

To the developers/maintainers of the Hiiragi2013 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: Hiiragi2013
Version: 1.41.0
Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data Hiiragi2013
StartedAt: 2024-07-04 10:32:56 -0400 (Thu, 04 Jul 2024)
EndedAt: 2024-07-04 10:38:24 -0400 (Thu, 04 Jul 2024)
EllapsedTime: 328.3 seconds
RetCode: 1
Status:   ERROR  
PackageFile: None
PackageFileSize: NA

Command output

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### Running command:
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###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data Hiiragi2013
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* checking for file ‘Hiiragi2013/DESCRIPTION’ ... OK
* preparing ‘Hiiragi2013’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘Hiiragi2013.Rnw’ using Sweave
Loading required package: affy
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: boot
Loading required package: clue
Loading required package: cluster
Loading required package: genefilter
Loading required package: geneplotter
Loading required package: lattice

Attaching package: ‘lattice’

The following object is masked from ‘package:boot’:

    melanoma

Loading required package: annotate
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: XML
Loading required package: gplots

Attaching package: ‘gplots’

The following object is masked from ‘package:IRanges’:

    space

The following object is masked from ‘package:S4Vectors’:

    space

The following object is masked from ‘package:stats’:

    lowess

Loading required package: gtools

Attaching package: ‘gtools’

The following objects are masked from ‘package:boot’:

    inv.logit, logit

Loading required package: KEGGREST
Loading required package: MASS

Attaching package: ‘MASS’

The following object is masked from ‘package:AnnotationDbi’:

    select

The following object is masked from ‘package:genefilter’:

    area

Loading required package: mouse4302.db
Loading required package: org.Mm.eg.db


Loading required package: RColorBrewer
Loading required package: xtable
Warning: replacing previous import ‘AnnotationDbi::tail’ by ‘utils::tail’ when loading ‘mouse4302cdf’
Warning: replacing previous import ‘AnnotationDbi::head’ by ‘utils::head’ when loading ‘mouse4302cdf’

Error: processing vignette 'Hiiragi2013.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'Hiiragi2013.tex' failed.
LaTeX errors:
! Package xcolor Error: Undefined color `Gray'.

See the xcolor package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Emergency stop.
 ...                                              
                                                  
l.1 library("
             affy")
!  ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘Hiiragi2013.Rnw’

SUMMARY: processing the following file failed:
  ‘Hiiragi2013.Rnw’

Error: Vignette re-building failed.
Execution halted