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This page was generated on 2022-04-13 12:05:36 -0400 (Wed, 13 Apr 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.3 (2022-03-10) -- "One Push-Up" 4324
tokay2Windows Server 2012 R2 Standardx644.1.3 (2022-03-10) -- "One Push-Up" 4077
machv2macOS 10.14.6 Mojavex86_644.1.3 (2022-03-10) -- "One Push-Up" 4137
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

BUILD results for methylPipe on nebbiolo2


To the developers/maintainers of the methylPipe package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/methylPipe.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1125/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
methylPipe 1.28.0  (landing page)
Kamal Kishore
Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022)
git_url: https://git.bioconductor.org/packages/methylPipe
git_branch: RELEASE_3_14
git_last_commit: 34972d4
git_last_commit_date: 2021-10-26 12:15:34 -0400 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    ERROR  skipped
tokay2Windows Server 2012 R2 Standard / x64  OK    ERROR  skippedskipped
machv2macOS 10.14.6 Mojave / x86_64  OK    ERROR  skippedskipped

Summary

Package: methylPipe
Version: 1.28.0
Command: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data methylPipe
StartedAt: 2022-04-12 04:59:43 -0400 (Tue, 12 Apr 2022)
EndedAt: 2022-04-12 05:00:53 -0400 (Tue, 12 Apr 2022)
EllapsedTime: 69.6 seconds
RetCode: 1
Status:   ERROR  
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data methylPipe
###
##############################################################################
##############################################################################


* checking for file ‘methylPipe/DESCRIPTION’ ... OK
* preparing ‘methylPipe’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘methylPipe.rnw’ using knitr
Loading required package: GenomicRanges
Loading required package: stats4
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, 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, sort, table, tapply, union, unique,
    unsplit, which.max, which.min

Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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

    I, expand.grid, unname

Loading required package: IRanges
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

Loading required package: Rsamtools
Loading required package: Biostrings
Loading required package: XVector

Attaching package: 'Biostrings'

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

    strsplit

No methods found in package 'BiocGenerics' for requests: 'clusterApplyLB', 'clusterEvalQ' when loading 'methylPipe'
Loading required package: BSgenome
Loading required package: rtracklayer

Extracting methylation information from input SAM files and creating output files for each sample...

Creating temporary BAM files from input SAM files...

Creating uncovered regions objects for each sample from BAM files...

Removing all temporary BAM files...

Methylation info and Uncovered regions output files created for each sample in output_folder...

Processing done Successfully...

Warning in in_dir(input_dir(), expr) :
  You changed the working directory to /tmp/RtmpU3kKkt (probably via setwd()). It will be restored to /tmp/RtmpJf7ra9/Rbuild15a39a5193efdf/methylPipe/vignettes. See the Note section in ?knitr::knit
S4 Object of class BSdata

TABIX indexed file for this BSdata:
/tmp/RtmpJf7ra9/Rinst15a39a7d5f5fd7/methylPipe/extdata/H1_chr20_CG_10k_tabix_out.txt.gz

The first lines of the uncovered regions of this BSdata:
Associated organism genome:
Homo sapiens

Chromosomes available:
The first lines of the data:
Quitting from lines 170-174 (methylPipe.rnw) 
Error: processing vignette 'methylPipe.rnw' failed with diagnostics:
could not find function "clusterApplyLB"
--- failed re-building ‘methylPipe.rnw’

SUMMARY: processing the following file failed:
  ‘methylPipe.rnw’

Error: Vignette re-building failed.
Execution halted