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This page was generated on 2024-05-07 11:38:45 -0400 (Tue, 07 May 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4485
palomino3Windows Server 2022 Datacenterx644.4.0 (2024-04-24 ucrt) -- "Puppy Cup" 4258
lconwaymacOS 12.7.1 Montereyx86_644.4.0 (2024-04-24) -- "Puppy Cup" 4470
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" 4480
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 2246/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
VanillaICE 1.66.0  (landing page)
Robert Scharpf
Snapshot Date: 2024-05-06 14:00:20 -0400 (Mon, 06 May 2024)
git_url: https://git.bioconductor.org/packages/VanillaICE
git_branch: RELEASE_3_19
git_last_commit: 7ff0406
git_last_commit_date: 2024-04-30 10:17:20 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    ERROR  skippedskipped
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  
kjohnson3macOS 13.6.5 Ventura / arm64see weekly results here

BUILD results for VanillaICE on palomino3


To the developers/maintainers of the VanillaICE package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/VanillaICE.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.

raw results

Summary

Package: VanillaICE
Version: 1.66.0
Command: chmod a+r VanillaICE -R && F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data VanillaICE
StartedAt: 2024-05-06 22:06:34 -0400 (Mon, 06 May 2024)
EndedAt: 2024-05-06 22:08:03 -0400 (Mon, 06 May 2024)
EllapsedTime: 89.1 seconds
RetCode: 1
Status:   ERROR  
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   chmod a+r VanillaICE -R && F:\biocbuild\bbs-3.19-bioc\R\bin\R.exe CMD build --keep-empty-dirs --no-resave-data VanillaICE
###
##############################################################################
##############################################################################


* checking for file 'VanillaICE/DESCRIPTION' ... OK
* preparing 'VanillaICE':
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building 'VanillaICE.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: GenomicRanges
Loading required package: stats4
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: IRanges

Attaching package: 'IRanges'

The following object is masked from 'package:grDevices':

    windows

Loading required package: GenomeInfoDb
Loading required package: SummarizedExperiment
Loading required package: MatrixGenerics
Loading required package: matrixStats

Attaching package: 'MatrixGenerics'

The following objects are masked from 'package:matrixStats':

    colAlls, colAnyNAs, colAnys, colAvgsPerRowSet,
    colCollapse, colCounts, colCummaxs, colCummins,
    colCumprods, colCumsums, colDiffs, colIQRDiffs, colIQRs,
    colLogSumExps, colMadDiffs, colMads, colMaxs, colMeans2,
    colMedians, colMins, colOrderStats, colProds,
    colQuantiles, colRanges, colRanks, colSdDiffs, colSds,
    colSums2, colTabulates, colVarDiffs, colVars,
    colWeightedMads, colWeightedMeans, colWeightedMedians,
    colWeightedSds, colWeightedVars, rowAlls, rowAnyNAs,
    rowAnys, rowAvgsPerColSet, rowCollapse, rowCounts,
    rowCummaxs, rowCummins, rowCumprods, rowCumsums, rowDiffs,
    rowIQRDiffs, rowIQRs, rowLogSumExps, rowMadDiffs, rowMads,
    rowMaxs, rowMeans2, rowMedians, rowMins, rowOrderStats,
    rowProds, rowQuantiles, rowRanges, rowRanks, rowSdDiffs,
    rowSds, rowSums2, rowTabulates, rowVarDiffs, rowVars,
    rowWeightedMads, rowWeightedMeans, rowWeightedMedians,
    rowWeightedSds, rowWeightedVars

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")'.


Attaching package: 'Biobase'

The following object is masked from 'package:MatrixGenerics':

    rowMedians

The following objects are masked from 'package:matrixStats':

    anyMissing, rowMedians

No methods found in package 'oligoClasses' for request: 'mean' when loading 'crlmm'
Welcome to VanillaICE version 1.66.0
Loading required package: data.table

Attaching package: 'data.table'

The following object is masked from 'package:SummarizedExperiment':

    shift

The following object is masked from 'package:GenomicRanges':

    shift

The following object is masked from 'package:IRanges':

    shift

The following objects are masked from 'package:S4Vectors':

    first, second

Loading required package: BSgenome
Loading required package: Biostrings
Loading required package: XVector

Attaching package: 'Biostrings'

The following object is masked from 'package:VanillaICE':

    deletion

The following object is masked from 'package:base':

    strsplit

Loading required package: BiocIO
Loading required package: rtracklayer

Attaching package: 'rtracklayer'

The following object is masked from 'package:BiocIO':

    FileForFormat

Writing parsed files to F:\biocbuild\bbs-3.19-bioc\tmpdir\Rtmp8CRTRB
Warning in system(paste(shQuote(texi2dvi), "--version"), intern = TRUE) :
  running command '"C:\PROGRA~1\MiKTeX\miktex\bin\x64\texify.exe" --version' had status 1033
Warning in system(paste(shQuote(texi2dvi), if (quiet) "--quiet" else "",  :
  running command '"C:\PROGRA~1\MiKTeX\miktex\bin\x64\texify.exe" --quiet --pdf "VanillaICE.tex" ' had status 1033
Error: processing vignette 'VanillaICE.Rnw' failed with diagnostics:
Failed to locate 'texi2pdf' output file 'VanillaICE.pdf' for vignette with name 'VanillaICE' and engine 'utils::Sweave'. The following files exist in working directory 'F:\biocbuild\bbs-3.19-bioc\tmpdir\Rtmpy80IPM\Rbuild5e3011b31c41\VanillaICE\vignettes': 'VanillaICE-fig1.pdf' (4074 bytes), 'VanillaICE-fig2.pdf' (311727 bytes), 'VanillaICE-fig_reduced.pdf' (352521 bytes), 'VanillaICE.Rnw' (18702 bytes), 'VanillaICE.tex' (31250 bytes), 'crlmmDownstream.Rnw' (3582 bytes), 'ice.bib' (16372 bytes)
--- failed re-building 'VanillaICE.Rnw'

--- re-building 'crlmmDownstream.Rnw' using Sweave
Welcome to oligoClasses version 1.66.0
Loading required package: preprocessCore
Welcome to crlmm version 1.62.0

Attaching package: 'crlmm'

The following object is masked from 'package:VanillaICE':

    genotypes

Warning in system(paste(shQuote(texi2dvi), "--version"), intern = TRUE) :
  running command '"C:\PROGRA~1\MiKTeX\miktex\bin\x64\texify.exe" --version' had status 1033
Warning in system(paste(shQuote(texi2dvi), if (quiet) "--quiet" else "",  :
  running command '"C:\PROGRA~1\MiKTeX\miktex\bin\x64\texify.exe" --quiet --pdf "crlmmDownstream.tex" ' had status 1033
Error: processing vignette 'crlmmDownstream.Rnw' failed with diagnostics:
Failed to locate 'texi2pdf' output file 'crlmmDownstream.pdf' for vignette with name 'crlmmDownstream' and engine 'utils::Sweave'. The following files exist in working directory 'F:\biocbuild\bbs-3.19-bioc\tmpdir\Rtmpy80IPM\Rbuild5e3011b31c41\VanillaICE\vignettes': 'VanillaICE-fig1.pdf' (4074 bytes), 'VanillaICE-fig2.pdf' (311727 bytes), 'VanillaICE-fig_reduced.pdf' (352521 bytes), 'VanillaICE.R' (8875 bytes), 'VanillaICE.Rnw' (18702 bytes), 'VanillaICE.tex' (31250 bytes), 'crlmmDownstream.Rnw' (3582 bytes), 'crlmmDownstream.tex' (5888 bytes), 'ice.bib' (16372 bytes)
--- failed re-building 'crlmmDownstream.Rnw'

SUMMARY: processing the following files failed:
  'VanillaICE.Rnw' 'crlmmDownstream.Rnw'

Error: Vignette re-building failed.
Execution halted